==> Cloning r ... Cloning into 'r'... ==> Collecting packager identity from makepkg.conf -> name : Reproducible Arch Linux tests -> email : reproducible@archlinux.org -> gpg-key : undefined -> protocol: https ==> Configuring r :: Synchronizing package databases... % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 129k 100 129k 0 0 379k 0 --:--:-- --:--:-- --:--:-- 379k % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 8526k 0 45980 0 0 68379 0 0:02:07 --:--:-- 0:02:07 68320 26 8526k 26 2296k 0 0 1368k 0 0:00:06 0:00:01 0:00:05 1367k 88 8526k 88 7509k 0 0 2797k 0 0:00:03 0:00:02 0:00:01 2796k 100 8526k 100 8526k 0 0 3157k 0 0:00:02 0:00:02 --:--:-- 3156k % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 139k 100 139k 0 0 820k 0 --:--:-- --:--:-- --:--:-- 822k :: Starting full system upgrade... there is nothing to do ==> Making package: r 4.3.3-2 (Thu Apr 3 16:39:39 2025) ==> Checking runtime dependencies... ==> Installing missing dependencies... resolving dependencies... looking for conflicting packages... warning: dependency cycle detected: warning: harfbuzz will be installed before its freetype2 dependency Packages (35) fontconfig-2:2.15.0-2 freetype2-2.13.2-1 fribidi-1.0.13-2 graphite-1:1.3.14-3 harfbuzz-8.3.0-2 jbigkit-2.1-7 libdatrie-0.2.13-4 libice-1.1.1-2 libsm-1.2.4-1 libthai-0.1.29-3 libxau-1.0.11-2 libxcb-1.16-1 libxdmcp-1.1.4-2 libxext-1.3.6-1 libxft-2.3.8-1 libxrender-0.9.11-1 libxss-1.2.4-1 lzo-2.10-5 pixman-0.43.4-1 tcl-8.6.13-1 xcb-proto-1.16.0-1 xorgproto-2023.2-1 blas-3.12.0-3 cairo-1.18.0-1 lapack-3.12.0-3 libjpeg-turbo-3.0.2-2 libpng-1.6.43-1 libtiff-4.6.0-2 libx11-1.8.7-1 libxmu-1.1.4-1 libxt-1.3.0-1 pango-1:1.52.0-1 tk-8.6.13-2 unzip-6.0-20 zip-3.0-11 Total Download Size: 19.18 MiB Total Installed Size: 69.57 MiB :: Proceed with installation? [Y/n] :: Retrieving packages... % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 230k 100 230k 0 0 79.4M 0 --:--:-- --:--:-- --:--:-- 112M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 248k 100 248k 0 0 82.2M 0 --:--:-- --:--:-- --:--:-- 121M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 85987 100 85987 0 0 47.7M 0 --:--:-- --:--:-- --:--:-- 82.0M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 1008k 100 1008k 0 0 96.9M 0 --:--:-- --:--:-- --:--:-- 98.4M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 523k 100 523k 0 0 86.0M 0 --:--:-- --:--:-- --:--:-- 102M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 370k 100 370k 0 0 98.5M 0 --:--:-- --:--:-- --:--:-- 120M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 130k 100 130k 0 0 62.6M 0 --:--:-- --:--:-- --:--:-- 127M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 242k 100 242k 0 0 83.9M 0 --:--:-- --:--:-- --:--:-- 118M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 27477 100 27477 0 0 19.2M 0 --:--:-- --:--:-- --:--:-- 26.2M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 11204 100 11204 0 0 9631k 0 --:--:-- --:--:-- --:--:-- 10.6M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 1024k 100 1024k 0 0 94.8M 0 --:--:-- --:--:-- --:--:-- 100M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 2064k 100 2064k 0 0 103M 0 --:--:-- --:--:-- --:--:-- 106M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 106k 100 106k 0 0 52.5M 0 --:--:-- --:--:-- --:--:-- 103M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 29880 100 29880 0 0 20.8M 0 --:--:-- --:--:-- --:--:-- 28.4M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 89912 100 89912 0 0 50.7M 0 --:--:-- --:--:-- --:--:-- 85.7M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 277k 100 277k 0 0 89.6M 0 --:--:-- --:--:-- --:--:-- 135M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 614k 100 614k 0 0 88.3M 0 --:--:-- --:--:-- --:--:-- 100M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 2651k 100 2651k 0 0 103M 0 --:--:-- --:--:-- --:--:-- 107M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 539k 100 539k 0 0 86.4M 0 --:--:-- --:--:-- --:--:-- 87.7M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 52996 100 52996 0 0 33.0M 0 --:--:-- --:--:-- --:--:-- 50.5M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 961k 100 961k 0 0 95.3M 0 --:--:-- --:--:-- --:--:-- 104M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 80339 100 80339 0 0 43.2M 0 --:--:-- --:--:-- --:--:-- 76.6M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 47005 100 47005 0 0 32.2M 0 --:--:-- --:--:-- --:--:-- 44.8M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 535k 100 535k 0 0 86.1M 0 --:--:-- --:--:-- --:--:-- 87.1M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 78042 100 78042 0 0 47.3M 0 --:--:-- --:--:-- --:--:-- 74.4M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 72969 100 72969 0 0 42.8M 0 --:--:-- --:--:-- --:--:-- 69.5M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 114k 100 114k 0 0 56.2M 0 --:--:-- --:--:-- --:--:-- 111M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 275k 100 275k 0 0 82.5M 0 --:--:-- --:--:-- --:--:-- 89.6M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 61606 100 61606 0 0 40.2M 0 --:--:-- --:--:-- --:--:-- 58.7M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 402k 100 402k 0 0 97.2M 0 --:--:-- --:--:-- --:--:-- 131M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 2573k 100 2573k 0 0 104M 0 --:--:-- --:--:-- --:--:-- 109M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 14441 100 14441 0 0 10.9M 0 --:--:-- --:--:-- --:--:-- 13.7M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 3794k 100 3794k 0 0 107M 0 --:--:-- --:--:-- --:--:-- 108M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 142k 100 142k 0 0 60.9M 0 --:--:-- --:--:-- --:--:-- 69.4M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 169k 100 169k 0 0 69.6M 0 --:--:-- --:--:-- --:--:-- 82.9M checking keyring... checking package integrity... loading package files... checking for file conflicts... checking available disk space... :: Processing package changes... installing blas... installing libpng... installing graphite... Optional dependencies for graphite graphite-docs: Documentation installing harfbuzz... Optional dependencies for harfbuzz harfbuzz-utils: utilities installing freetype2... installing fontconfig... Creating fontconfig configuration... Rebuilding fontconfig cache... installing xcb-proto... installing xorgproto... installing libxdmcp... installing libxau... installing libxcb... installing libx11... installing libxext... installing libxrender... installing lzo... installing pixman... installing cairo... installing lapack... installing libjpeg-turbo... Optional dependencies for libjpeg-turbo java-runtime>11: for TurboJPEG Java wrapper installing jbigkit... installing libtiff... Optional dependencies for libtiff freeglut: for using tiffgt installing libice... installing libsm... installing libxt... installing libxmu... installing fribidi... installing libdatrie... installing libthai... installing libxft... installing pango... installing tcl... installing libxss... installing tk... installing unzip... installing zip... :: Running post-transaction hooks... (1/3) Arming ConditionNeedsUpdate... (2/3) Updating fontconfig configuration... (3/3) Updating fontconfig cache... ==> Checking buildtime dependencies... ==> Installing missing dependencies... resolving dependencies... looking for conflicting packages... Packages (50) aom-3.8.1-1 avahi-1:0.8+r194+g3f79789-1 dav1d-1.4.0-1 dvisvgm-3.2.1-1 ffcall-2.4-2 gd-2.3.3-7 gdk-pixbuf2-2.42.10-2 ghostscript-10.02.1-1 giflib-5.2.2-1 harfbuzz-icu-8.3.0-2 hicolor-icon-theme-0.17-3 ijs-0.35-6 java-environment-common-3-5 java-runtime-common-3-5 jbig2dec-0.20-1 lcms2-2.16-1 libavif-1.0.4-1 libcups-1:2.4.7-2 libdaemon-0.14-5 libde265-1.0.15-1 libheif-1.17.6-3 libidn-1.42-1 libnet-2:1.3-1 libpaper-2.1.3-1 libsigsegv-2.14-2 libsynctex-2023.66984-19 libwebp-1.3.2-1 libxaw-1.0.15-1 libxpm-3.5.17-1 libyuv-r2426+464c51a0-1 nspr-4.35-2 nss-3.98-1 openjpeg2-2.5.0-3 poppler-24.01.0-1 poppler-data-0.4.12-1 potrace-1.16-2 rav1e-0.7.1-1 shared-mime-info-2.4-1 svt-av1-1.8.0-1 t1lib-5.1.2-8 texlive-basic-2023.66594-20 texlive-bin-2023.66984-19 texlive-latex-2023.66594-20 woff2-1.0.2-4 x265-3.5-3 zziplib-0.13.73-1 gcc-fortran-13.2.1-5 jdk-openjdk-21.0.2.u13-3 texlive-fontsrecommended-2023.66594-20 texlive-latexrecommended-2023.66594-20 Total Download Size: 571.89 MiB Total Installed Size: 1336.13 MiB :: Proceed with installation? [Y/n] :: Retrieving packages... % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 12.0M 0 69061 0 0 45.3M 0 --:--:-- --:--:-- --:--:-- 32.9M 100 12.0M 100 12.0M 0 0 193M 0 --:--:-- --:--:-- --:--:-- 191M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 5077 100 5077 0 0 4599k 0 --:--:-- --:--:-- --:--:-- 4958k % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 197k 100 197k 0 0 116M 0 --:--:-- --:--:-- --:--:-- 193M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 1619k 100 1619k 0 0 172M 0 --:--:-- --:--:-- --:--:-- 175M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 220k 100 220k 0 0 116M 0 --:--:-- --:--:-- --:--:-- 214M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 294k 100 294k 0 0 139M 0 --:--:-- --:--:-- --:--:-- 144M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 2628 100 2628 0 0 2613k 0 --:--:-- --:--:-- --:--:-- 2566k % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 10021 100 10021 0 0 8614k 0 --:--:-- --:--:-- --:--:-- 9786k % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 78181 100 78181 0 0 64.4M 0 --:--:-- --:--:-- --:--:-- 74.5M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 406M 0 118k 0 0 138k 0 0:50:00 --:--:-- 0:50:00 138k 0 406M 0 3093k 0 0 1658k 0 0:04:11 0:00:01 0:04:10 1657k 2 406M 2 8573k 0 0 2978k 0 0:02:19 0:00:02 0:02:17 2978k 3 406M 3 15.5M 0 0 4092k 0 0:01:41 0:00:03 0:01:38 4091k 6 406M 6 25.1M 0 0 5255k 0 0:01:19 0:00:04 0:01:15 5255k 9 406M 9 38.0M 0 0 6586k 0 0:01:03 0:00:05 0:00:58 7674k 11 406M 11 48.1M 0 0 7107k 0 0:00:58 0:00:06 0:00:52 9113k 13 406M 13 55.3M 0 0 7137k 0 0:00:58 0:00:07 0:00:51 9501k 15 406M 15 61.3M 0 0 7134k 0 0:00:58 0:00:08 0:00:50 9539k 16 406M 16 67.6M 0 0 7064k 0 0:00:58 0:00:09 0:00:49 8870k 18 406M 18 74.3M 0 0 7038k 0 0:00:59 0:00:10 0:00:49 7584k 20 406M 20 81.4M 0 0 7051k 0 0:00:59 0:00:11 0:00:48 6971k 21 406M 21 88.6M 0 0 7071k 0 0:00:58 0:00:12 0:00:46 6964k 23 406M 23 95.9M 0 0 7092k 0 0:00:58 0:00:13 0:00:45 7020k 25 406M 25 103M 0 0 7111k 0 0:00:58 0:00:14 0:00:44 7203k 27 406M 27 110M 0 0 7127k 0 0:00:58 0:00:15 0:00:43 7317k 28 406M 28 117M 0 0 7141k 0 0:00:58 0:00:16 0:00:42 7350k 30 406M 30 125M 0 0 7156k 0 0:00:58 0:00:17 0:00:41 7371k 32 406M 32 132M 0 0 7175k 0 0:00:58 0:00:18 0:00:40 7402k 34 406M 34 140M 0 0 7200k 0 0:00:57 0:00:19 0:00:38 7463k 36 406M 36 147M 0 0 7236k 0 0:00:57 0:00:20 0:00:37 7579k 38 406M 38 155M 0 0 7311k 0 0:00:56 0:00:21 0:00:35 7894k 40 406M 40 163M 0 0 7354k 0 0:00:56 0:00:22 0:00:34 8075k 42 406M 42 172M 0 0 7427k 0 0:00:56 0:00:23 0:00:33 8400k 44 406M 44 182M 0 0 7539k 0 0:00:55 0:00:24 0:00:31 8918k 47 406M 47 193M 0 0 7682k 0 0:00:54 0:00:25 0:00:29 9588k 50 406M 50 206M 0 0 7860k 0 0:00:52 0:00:26 0:00:26 10.0M 54 406M 54 219M 0 0 8079k 0 0:00:51 0:00:27 0:00:24 11.0M 57 406M 57 234M 0 0 8302k 0 0:00:50 0:00:28 0:00:22 12.1M 59 406M 59 241M 0 0 8287k 0 0:00:50 0:00:29 0:00:21 11.6M 61 406M 61 250M 0 0 8297k 0 0:00:50 0:00:30 0:00:20 11.1M 63 406M 63 259M 0 0 8348k 0 0:00:49 0:00:31 0:00:18 10.7M 66 406M 66 268M 0 0 8382k 0 0:00:49 0:00:32 0:00:17 9.8M 68 406M 68 278M 0 0 8419k 0 0:00:49 0:00:33 0:00:16 9106k 70 406M 70 287M 0 0 8454k 0 0:00:49 0:00:34 0:00:15 9473k 72 406M 72 296M 0 0 8472k 0 0:00:49 0:00:35 0:00:14 9576k 75 406M 75 306M 0 0 8513k 0 0:00:48 0:00:36 0:00:12 9559k 77 406M 77 315M 0 0 8551k 0 0:00:48 0:00:37 0:00:11 9664k 80 406M 80 325M 0 0 8588k 0 0:00:48 0:00:38 0:00:10 9729k 82 406M 82 335M 0 0 8625k 0 0:00:48 0:00:39 0:00:09 9802k 84 406M 84 345M 0 0 8663k 0 0:00:48 0:00:40 0:00:08 9.7M 87 406M 87 355M 0 0 8717k 0 0:00:47 0:00:41 0:00:06 9.9M 90 406M 90 366M 0 0 8764k 0 0:00:47 0:00:42 0:00:05 10.1M 92 406M 92 377M 0 0 8820k 0 0:00:47 0:00:43 0:00:04 10.3M 95 406M 95 389M 0 0 8891k 0 0:00:46 0:00:44 0:00:02 10.7M 98 406M 98 401M 0 0 8971k 0 0:00:46 0:00:45 0:00:01 11.2M 100 406M 100 406M 0 0 9001k 0 0:00:46 0:00:46 --:--:-- 11.3M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 59458 100 59458 0 0 38.9M 0 --:--:-- --:--:-- --:--:-- 56.7M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 72558 100 72558 0 0 49.1M 0 --:--:-- --:--:-- --:--:-- 69.1M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 348k 100 348k 0 0 96.9M 0 --:--:-- --:--:-- --:--:-- 113M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 2815k 100 2815k 0 0 106M 0 --:--:-- --:--:-- --:--:-- 109M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 623k 100 623k 0 0 90.9M 0 --:--:-- --:--:-- --:--:-- 101M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 1595k 100 1595k 0 0 104M 0 --:--:-- --:--:-- --:--:-- 111M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 2065k 100 2065k 0 0 103M 0 --:--:-- --:--:-- --:--:-- 106M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 308k 100 308k 0 0 90.7M 0 --:--:-- --:--:-- --:--:-- 100M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 145k 100 145k 0 0 66.7M 0 --:--:-- --:--:-- --:--:-- 70.8M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 270k 100 270k 0 0 89.4M 0 --:--:-- --:--:-- --:--:-- 131M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 1727k 100 1727k 0 0 102M 0 --:--:-- --:--:-- --:--:-- 105M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 372k 100 372k 0 0 93.2M 0 --:--:-- --:--:-- --:--:-- 121M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 156k 100 156k 0 0 72.4M 0 --:--:-- --:--:-- --:--:-- 76.3M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 8215 100 8215 0 0 7049k 0 --:--:-- --:--:-- --:--:-- 8022k % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 33060 100 33060 0 0 22.9M 0 --:--:-- --:--:-- --:--:-- 31.5M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 10664 100 10664 0 0 8405k 0 --:--:-- --:--:-- --:--:-- 10.1M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 49923 100 49923 0 0 35.7M 0 --:--:-- --:--:-- --:--:-- 47.6M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 360k 100 360k 0 0 99.2M 0 --:--:-- --:--:-- --:--:-- 117M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 932k 100 932k 0 0 96.3M 0 --:--:-- --:--:-- --:--:-- 101M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 1618k 100 1618k 0 0 102M 0 --:--:-- --:--:-- --:--:-- 105M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 93258 100 93258 0 0 55.2M 0 --:--:-- --:--:-- --:--:-- 88.9M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 670k 100 670k 0 0 81.5M 0 --:--:-- --:--:-- --:--:-- 93.5M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 66211 100 66211 0 0 43.3M 0 --:--:-- --:--:-- --:--:-- 63.1M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 56 11.9M 56 6907k 0 0 108M 0 --:--:-- --:--:-- --:--:-- 108M 100 11.9M 100 11.9M 0 0 109M 0 --:--:-- --:--:-- --:--:-- 109M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 6757k 100 6757k 0 0 109M 0 --:--:-- --:--:-- --:--:-- 109M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 89.5M 100 89.5M 0 0 116M 0 --:--:-- --:--:-- --:--:-- 116M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 19643 100 19643 0 0 369k 0 --:--:-- --:--:-- --:--:-- 376k % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 434k 100 434k 0 0 106M 0 --:--:-- --:--:-- --:--:-- 141M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 27 276k 27 77437 0 0 51.3M 0 --:--:-- --:--:-- --:--:-- 36.9M 100 276k 100 276k 0 0 92.7M 0 --:--:-- --:--:-- --:--:-- 90.1M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 64323 100 64323 0 0 44.0M 0 --:--:-- --:--:-- --:--:-- 61.3M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 54345 100 54345 0 0 37.2M 0 --:--:-- --:--:-- --:--:-- 51.8M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 222k 100 222k 0 0 88.0M 0 --:--:-- --:--:-- --:--:-- 108M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 2014k 100 2014k 0 0 113M 0 --:--:-- --:--:-- --:--:-- 115M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 631k 100 631k 0 0 96.3M 0 --:--:-- --:--:-- --:--:-- 102M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 516k 100 516k 0 0 93.4M 0 --:--:-- --:--:-- --:--:-- 100M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 19.6M 100 19.6M 0 0 118M 0 --:--:-- --:--:-- --:--:-- 118M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 58680 100 58680 0 0 37.6M 0 --:--:-- --:--:-- --:--:-- 55.9M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 1028k 100 1028k 0 0 101M 0 --:--:-- --:--:-- --:--:-- 111M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 1254k 100 1254k 0 0 106M 0 --:--:-- --:--:-- --:--:-- 111M % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 2426k 100 2426k 0 0 113M 0 --:--:-- --:--:-- --:--:-- 118M checking keyring... checking package integrity... loading package files... checking for file conflicts... checking available disk space... :: Processing package changes... installing gcc-fortran... installing java-runtime-common... For the complete set of Java binaries to be available in your PATH, you need to re-login or source /etc/profile.d/jre.sh Please note that this package does not support forcing JAVA_HOME as former package java-common did installing nspr... installing nss... installing lcms2... installing libnet... installing java-environment-common... installing hicolor-icon-theme... installing giflib... installing jdk-openjdk... Optional dependencies for jdk-openjdk java-rhino: for some JavaScript support alsa-lib: for basic sound support gtk2: for the Gtk+ 2 look and feel - desktop usage gtk3: for the Gtk+ 3 look and feel - desktop usage installing ffcall... installing libxpm... installing libwebp... installing aom... installing dav1d... Optional dependencies for dav1d dav1d-doc: HTML documentation installing rav1e... installing svt-av1... installing libyuv... installing libavif... installing libde265... Optional dependencies for libde265 ffmpeg: for sherlock265 qt5-base: for sherlock265 sdl: dec265 YUV overlay output installing x265... installing libheif... Optional dependencies for libheif libjpeg: for heif-convert and heif-enc [installed] libpng: for heif-convert and heif-enc [installed] dav1d: dav1d encoder [installed] ffmpeg: hardware decode rav1e: rav1e encoder [installed] svt-av1: svt-av1 encoder [installed] installing gd... Optional dependencies for gd perl: bdftogd script [installed] installing harfbuzz-icu... installing libpaper... installing libsigsegv... installing libsynctex... installing libxaw... installing openjpeg2... installing poppler... Optional dependencies for poppler poppler-data: highly recommended encoding data to display PDF documents with certain encodings and characters [pending] installing potrace... installing t1lib... installing zziplib... installing texlive-bin... Optional dependencies for texlive-bin psutils: to manipulate the output of dvips installing texlive-basic... Optional dependencies for texlive-basic perl-tk: for the tlmgr GUI biber: for bibliography processing installing texlive-fontsrecommended... installing libdaemon... installing avahi... Optional dependencies for avahi gtk3: avahi-discover, avahi-discover-standalone, bshell, bssh, bvnc libevent: libevent bindings [installed] nss-mdns: NSS support for mDNS python-dbus: avahi-bookmarks, avahi-discover python-gobject: avahi-bookmarks, avahi-discover python-twisted: avahi-bookmarks qt5-base: qt5 bindings installing libcups... installing jbig2dec... installing ijs... installing libidn... installing poppler-data... installing shared-mime-info... installing gdk-pixbuf2... Optional dependencies for gdk-pixbuf2 libwmf: Load .wmf and .apm libopenraw: Load .dng, .cr2, .crw, .nef, .orf, .pef, .arw, .erf, .mrw, and .raf libavif: Load .avif [installed] libheif: Load .heif, .heic, and .avif [installed] libjxl: Load .jxl librsvg: Load .svg, .svgz, and .svg.gz webp-pixbuf-loader: Load .webp installing ghostscript... Optional dependencies for ghostscript gtk3: needed for gsx installing woff2... installing dvisvgm... Optional dependencies for dvisvgm mupdf-tools: to process PDF files installing texlive-latex... installing texlive-latexrecommended... :: Running post-transaction hooks... ( 1/11) Creating system user accounts... Suggested group ID 8 for mem already used. Creating group 'mem' with GID 997. Creating group 'ftp' with GID 11. Creating group 'log' with GID 19. Suggested group ID 25 for smmsp already used. Creating group 'smmsp' with GID 996. Suggested group ID 26 for proc already used. Creating group 'proc' with GID 995. Creating group 'lock' with GID 54. Creating group 'network' with GID 90. Creating group 'scanner' with GID 96. Creating group 'power' with GID 98. Suggested group ID 65534 for nobody already used. Creating group 'nobody' with GID 994. Creating group 'wheel' with GID 993. Creating group 'optical' with GID 992. Creating group 'storage' with GID 991. Creating group 'groups' with GID 990. Creating group 'rfkill' with GID 989. Creating user 'ftp' (n/a) with UID 14 and GID 11. Creating group 'http' with GID 988. Suggested user ID 33 for http already used. Creating user 'http' (n/a) with UID 988 and GID 988. Creating group 'avahi' with GID 987. Creating user 'avahi' (Avahi mDNS/DNS-SD daemon) with UID 987 and GID 987. Creating group 'dbus' with GID 81. Creating user 'dbus' (System Message Bus) with UID 81 and GID 81. Creating group 'git' with GID 986. Creating user 'git' (git daemon user) with UID 986 and GID 986. Creating group 'systemd-journal-remote' with GID 985. Creating user 'systemd-journal-remote' (systemd Journal Remote) with UID 985 and GID 985. Creating group 'tss' with GID 984. Creating user 'tss' (tss user for tpm2) with UID 984 and GID 984. Creating group 'uuidd' with GID 68. Creating user 'uuidd' (n/a) with UID 68 and GID 68. ( 2/11) Reloading system manager configuration... Skipped: Running in chroot. ( 3/11) Arming ConditionNeedsUpdate... ( 4/11) Updating the MIME type database... ( 5/11) Updating TeXLive filename database... ( 6/11) Updating TeXLive format files... ( 7/11) Updating TeXLive font maps... ( 8/11) Reloading system bus configuration... Skipped: Running in chroot. ( 9/11) Updating fontconfig cache... (10/11) Probing GDK-Pixbuf loader modules... (11/11) Updating the info directory file... ==> Retrieving sources... -> Downloading R-4.3.3.tar.gz... % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 1 34.1M 1 432k 0 0 303k 0 0:01:55 0:00:01 0:01:54 303k 36 34.1M 36 12.3M 0 0 5303k 0 0:00:06 0:00:02 0:00:04 5301k 87 34.1M 87 29.9M 0 0 9198k 0 0:00:03 0:00:03 --:--:-- 9197k 100 34.1M 100 34.1M 0 0 9931k 0 0:00:03 0:00:03 --:--:-- 9929k -> Found r.desktop -> Found r.png -> Found R.conf ==> WARNING: Skipping verification of source file PGP signatures. ==> Validating source files with sha256sums... R-4.3.3.tar.gz ... Passed r.desktop ... Passed r.png ... Passed R.conf ... Passed ==> Extracting sources... -> Extracting R-4.3.3.tar.gz with bsdtar ==> Starting prepare()... ==> Starting build()... checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu loading site script './config.site' loading build-specific script './config.site' checking for pwd... /usr/sbin/pwd checking whether builddir is srcdir... yes checking whether ln -s works... yes checking for ar... ar checking for a BSD-compatible install... /usr/bin/install -c checking for sed... /usr/sbin/sed checking for which... /usr/sbin/which checking for less... no checking for more... /usr/sbin/more checking for gtar... no checking for gnutar... no checking for tar... /usr/sbin/tar checking for tex... /usr/sbin/tex checking for pdftex... /usr/sbin/pdftex checking for pdflatex... /usr/sbin/pdflatex checking for makeindex... /usr/sbin/makeindex checking for texi2any... /usr/sbin/texi2any checking whether texi2any version is at least 5.1... yes checking for ginstall-info... no checking for install-info... /usr/sbin/install-info checking for texi2dvi... /usr/sbin/texi2dvi checking for kpsewhich... /usr/sbin/kpsewhich checking for latex inconsolata package... missing configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally checking for unzip... /usr/sbin/unzip checking for zip... /usr/sbin/zip checking for gzip... /usr/sbin/gzip checking for bzip2... /usr/sbin/bzip2 checking for xdg-open... no checking for firefox... no checking for mozilla... no checking for epiphany... no checking for galeon... no checking for opera... no checking for kfmclient... no checking for gnome-moz-remote... no checking for open... no checking for lynx... no checking for links... no configure: WARNING: I could not determine a browser checking for xdg-open... no checking for acroread... no checking for acroread4... no checking for evince... no checking for atril... no checking for xpdf... no checking for gv... no checking for gnome-gv... no checking for ggv... no checking for okular... no checking for kpdf... no checking for open... no checking for gpdf... no checking for kghostview... no configure: WARNING: I could not determine a PDF viewer checking for working aclocal... found checking for working autoconf... found checking for working autoheader... found checking for bison... bison -y checking for notangle... false checking for realpath... /usr/sbin/realpath checking for pkg-config... /usr/sbin/pkg-config checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for wchar.h... yes checking for minix/config.h... no checking for sys/time.h... yes checking for sys/param.h... yes checking whether it is safe to define __EXTENSIONS__... yes checking whether _XOPEN_SOURCE should be defined... no checking how to run the C preprocessor... gcc -E looking for a modern Fortran compiler checking for gfortran... gfortran checking whether the compiler supports GNU Fortran... yes checking whether gfortran accepts -g... yes checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether g++ -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -ffat-lto-objects can compile C++ code... yes checking how to run the C++ preprocessor... g++ -E checking whether __attribute__((visibility())) is supported... yes checking whether gcc accepts -fvisibility... yes checking whether g++ accepts -fvisibility... yes checking whether gfortran accepts -fvisibility... yes checking for gcc... gcc checking whether the compiler supports GNU Objective C... no checking whether gcc accepts -g... no checking whether g++ can compile ObjC++... no checking whether can compile ObjC++... no checking for Objective C++ compiler... no working ObjC++ compiler found checking whether gcc -std=gnu17 is a C17 compiler... yes checking whether gcc -std=gnu23 is a C23 compiler... no checking whether gcc -std=gnu2x is a C23 compiler... yes checking whether gcc -std=gnu90 is a C90 compiler... yes checking whether gcc -std=gnu99 is a C99 compiler... yes checking how to print strings... printf checking for a sed that does not truncate output... (cached) /usr/sbin/sed checking for grep that handles long lines and -e... /usr/sbin/grep checking for egrep... /usr/sbin/grep -E checking for fgrep... /usr/sbin/grep -F checking for ld used by gcc... /usr/sbin/ld checking if the linker (/usr/sbin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/sbin/nm -B checking the name lister (/usr/sbin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/sbin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking for gawk... gawk checking command to parse /usr/sbin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/sbin/dd checking how to truncate binary pipes... /usr/sbin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/sbin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/sbin/ld -m elf_x86_64 checking if the linker (/usr/sbin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/sbin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/sbin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking for gfortran option to produce PIC... -fPIC checking if gfortran PIC flag -fPIC works... yes checking if gfortran static flag -static works... no checking if gfortran supports -c -o file.o... yes checking if gfortran supports -c -o file.o... (cached) yes checking whether the gfortran linker (/usr/sbin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for cos in -lm... yes checking for sin in -lm... yes checking for dlopen in -ldl... yes checking for readline/history.h... yes checking for readline/readline.h... yes checking for rl_callback_read_char in -lreadline... yes checking for history_truncate_file... yes checking for tilde_expand_word... yes checking whether rl_completion_matches exists and is declared... yes checking whether rl_resize_terminal exists and is declared... yes checking whether rl_sort_completion_matches exists and is declared... yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for sys/wait.h that is POSIX.1 compatible... yes checking for dlfcn.h... (cached) yes checking for fcntl.h... yes checking for glob.h... yes checking for grp.h... yes checking for pwd.h... yes checking for sched.h... yes checking for strings.h... (cached) yes checking for sys/resource.h... yes checking for sys/select.h... yes checking for sys/socket.h... yes checking for sys/stat.h... (cached) yes checking for sys/time.h... (cached) yes checking for sys/times.h... yes checking for sys/utsname.h... yes checking for unistd.h... (cached) yes checking for utime.h... yes checking for arpa/inet.h... yes checking for elf.h... yes checking for features.h... yes checking for floatingpoint.h... no checking for langinfo.h... yes checking for netdb.h... yes checking for netinet/in.h... yes checking for sys/param.h... (cached) yes checking for stdalign.h... yes checking for errno.h... yes checking for inttypes.h... (cached) yes checking for limits.h... yes checking for locale.h... yes checking for stdarg.h... yes checking for stdbool.h... yes checking for stdint.h... (cached) yes checking for string.h... (cached) yes checking for gcc options needed to detect all undeclared functions... none needed checking whether setjmp.h is POSIX.1 compatible... yes checking whether sigsetjmp is declared... yes checking whether siglongjmp is declared... yes checking for GNU C library with version >= 2... yes checking for uint64_t... yes checking for int64_t... yes checking for int_fast64_t... yes checking for pid_t... yes checking for size_t... yes checking whether SIZE_MAX is declared... yes checking for blkcnt_t... yes checking for type of socket length... socklen_t * checking for stack_t... yes checking for intptr_t... yes checking for uintptr_t... yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for inline... inline checking size of int... 4 checking size of long... 8 checking size of long long... 8 checking size of double... 8 checking size of size_t... 8 checking for C stack direction... down checking size of long double... 16 checking whether we can compute C Make dependencies... yes, using $(CC) -MM checking whether gcc supports -c -o FILE.lo... yes checking for gcc option to support OpenMP... -fopenmp checking how to get verbose linking output from gfortran... -v checking for Fortran libraries of gfortran... -L/usr/lib/gcc/x86_64-pc-linux-gnu/13.2.1 -L/usr/lib/gcc/x86_64-pc-linux-gnu/13.2.1/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/13.2.1/../../.. -lgfortran -lm -lquadmath checking how to get verbose linking output from gcc... -v checking for C libraries of gcc... -L/usr/lib/gcc/x86_64-pc-linux-gnu/13.2.1 -L/usr/lib/gcc/x86_64-pc-linux-gnu/13.2.1/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/13.2.1/../../.. -lgcc_s checking for dummy main to link with Fortran libraries... none checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore checking whether gfortran appends underscores to external names... yes checking whether gfortran appends extra underscores to external names... no checking whether mixed C/Fortran code can be run... yes checking whether gfortran and gcc agree on int and double... yes checking whether gfortran and gcc agree on double complex... yes checking for gfortran option to support OpenMP... -fopenmp checking whether g++ accepts -M for generating dependencies... yes checking whether we can compute ObjC Make dependencies... no checking for type of 'hidden' Fortran character lengths... size_t checking for xmkmf... no checking whether g++ supports C++11 features with -std=gnu++11... yes checking whether g++ supports C++14 features with -std=gnu++14... yes checking whether g++ supports C++17 features with -std=gnu++17... yes checking whether g++ supports C++20 features with -std=gnu++20... yes checking whether g++ supports C++23 features with -std=gnu++23... yes checking for g++ -std=gnu++17 option to support OpenMP... -fopenmp checking for option providing pthread_kill... none required checking whether POSIX threads are supported... yes checking for off_t... yes checking for working alloca.h... yes checking for alloca... yes checking whether alloca is declared... yes checking whether expm1 exists and is declared... yes checking whether hypot exists and is declared... yes checking whether log1p exists and is declared... yes checking whether log1pl exists and is declared... yes checking whether log2 exists and is declared... yes checking whether log10 exists and is declared... yes checking whether nearbyint exists and is declared... yes checking whether nearbyintl exists and is declared... yes checking whether powl exists and is declared... yes checking whether rintl exists and is declared... yes checking whether va_copy exists and is declared... yes checking for isblank... yes checking for sunmath.h... no checking for cospi in -lsunmath... no checking for atanpi... no checking for atan2pi... no checking for cospi... no checking for exp10... yes checking for pown... no checking for sinpi... no checking for tanpi... no checking for __cospi... no checking for __sinpi... no checking for __tanpi... no checking for fseeko... yes checking for ftello... yes checking for matherr... no checking whether fcntl exists and is declared... yes checking whether getgrgid exists and is declared... yes checking whether getpwnam exists and is declared... yes checking whether getpwuid exists and is declared... yes checking whether kill exists and is declared... yes checking whether sigaction exists and is declared... yes checking whether sigaltstack exists and is declared... yes checking whether sigemptyset exists and is declared... yes checking whether fdopen exists and is declared... yes checking whether popen exists and is declared... yes checking whether getline exists and is declared... yes checking whether select exists and is declared... yes checking whether setenv exists and is declared... yes checking whether unsetenv exists and is declared... yes checking whether getrlimit exists and is declared... yes checking whether setrlimit exists and is declared... yes checking whether getrusage exists and is declared... yes checking whether getpriority exists and is declared... yes checking whether chmod exists and is declared... yes checking whether mkfifo exists and is declared... yes checking whether stat exists and is declared... yes checking whether umask exists and is declared... yes checking whether gettimeofday exists and is declared... yes checking whether utimes exists and is declared... yes checking whether times exists and is declared... yes checking whether gmtime_r exists and is declared... yes checking whether localtime_r exists and is declared... yes checking whether nl_langinfo exists and is declared... yes checking whether access exists and is declared... yes checking whether chdir exists and is declared... yes checking whether execv exists and is declared... yes checking whether ftruncate exists and is declared... yes checking whether getcwd exists and is declared... yes checking whether geteuid exists and is declared... yes checking whether getuid exists and is declared... yes checking whether link exists and is declared... yes checking whether readlink exists and is declared... yes checking whether symlink exists and is declared... yes checking whether sysconf exists and is declared... yes checking whether sched_setaffinity exists and is declared... yes checking whether sched_getaffinity exists and is declared... yes checking whether utime exists and is declared... yes checking whether utimensat exists and is declared... yes checking for clock_gettime in -lrt... yes checking whether clock_gettime exists and is declared... yes checking whether timespec_get exists and is declared... yes checking for putenv... yes checking whether putenv is declared... yes checking for vasprintf... yes checking whether vasprintf is declared... yes checking for mempcpy... yes checking for realpath... yes checking whether realpath is declared... yes checking whether glob exists and is declared... yes checking for dladdr... yes checking for dlsym... yes checking whether dladdr is declared... yes checking whether dlsym is declared... yes checking whether RTLD_DEFAULT is declared... yes checking whether RTLD_NEXT is declared... yes checking for thread.h... no checking whether thr_stksegment exists and is declared... no checking for isnan... yes checking whether isfinite is declared... yes checking whether isnan is declared... yes checking whether you have IEEE 754 floating-point arithmetic... yes checking whether putenv("FOO") can unset an environment variable... yes checking whether putenv("FOO=") can unset an environment variable... no checking for nl_langinfo and CODESET... yes checking for mkdtemp... yes checking for strdup... yes checking for strncasecmp... yes checking whether mkdtemp is declared... yes checking whether strdup is declared... yes checking whether 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(cached) no checking whether included gettext is requested... no checking for GNU gettext in libc... yes checking whether to use NLS... yes checking where the gettext function comes from... libc Finished configuring src/extra/intl directory checking whether OpenMP SIMD reduction is supported... yes using as R_SHELL for scripts ... /bin/sh configure: creating ./config.status config.status: creating Makeconf config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/html/Makefile config.status: creating doc/manual/Makefile config.status: creating etc/Makefile config.status: creating etc/Makeconf config.status: creating etc/Renviron config.status: creating etc/javaconf config.status: creating etc/ldpaths config.status: creating m4/Makefile config.status: creating po/Makefile config.status: creating share/Makefile config.status: creating src/Makefile config.status: creating src/appl/Makefile config.status: creating src/extra/Makefile config.status: creating src/extra/blas/Makefile config.status: creating src/extra/intl/Makefile config.status: creating src/extra/tre/Makefile config.status: creating src/extra/tzone/Makefile config.status: creating src/extra/xdr/Makefile config.status: creating src/include/Makefile config.status: creating src/include/Rmath.h0 config.status: creating src/include/R_ext/Makefile config.status: creating src/library/Recommended/Makefile config.status: creating src/library/Makefile config.status: creating src/library/base/DESCRIPTION config.status: creating src/library/base/Makefile config.status: creating src/library/compiler/DESCRIPTION config.status: creating src/library/compiler/Makefile config.status: creating src/library/datasets/DESCRIPTION config.status: creating src/library/datasets/Makefile config.status: creating src/library/graphics/DESCRIPTION config.status: creating src/library/graphics/Makefile config.status: creating src/library/graphics/src/Makefile config.status: creating src/library/grDevices/DESCRIPTION config.status: creating src/library/grDevices/Makefile config.status: creating src/library/grDevices/src/Makefile config.status: creating src/library/grDevices/src/cairo/Makefile config.status: creating src/library/grid/DESCRIPTION config.status: creating src/library/grid/Makefile config.status: creating src/library/grid/src/Makefile config.status: creating src/library/methods/DESCRIPTION config.status: creating src/library/methods/Makefile config.status: creating src/library/methods/src/Makefile config.status: creating src/library/parallel/DESCRIPTION config.status: creating src/library/parallel/Makefile config.status: creating src/library/parallel/src/Makefile config.status: creating src/library/profile/Makefile config.status: creating src/library/stats/DESCRIPTION config.status: creating src/library/stats/Makefile config.status: creating src/library/stats/src/Makefile config.status: creating src/library/stats4/DESCRIPTION config.status: creating src/library/stats4/Makefile config.status: creating src/library/splines/DESCRIPTION config.status: creating src/library/splines/Makefile config.status: creating src/library/splines/src/Makefile config.status: creating src/library/tcltk/DESCRIPTION config.status: creating src/library/tcltk/Makefile config.status: creating src/library/tcltk/src/Makefile config.status: creating src/library/tools/DESCRIPTION config.status: creating src/library/tools/Makefile config.status: creating src/library/tools/src/Makefile config.status: creating src/library/translations/DESCRIPTION config.status: creating src/library/translations/Makefile config.status: creating src/library/utils/DESCRIPTION config.status: creating src/library/utils/Makefile config.status: creating src/library/utils/src/Makefile config.status: creating src/main/Makefile config.status: creating src/modules/Makefile config.status: creating src/modules/X11/Makefile config.status: creating src/modules/internet/Makefile config.status: creating src/modules/lapack/Makefile config.status: creating src/nmath/Makefile config.status: creating src/nmath/standalone/Makefile config.status: creating src/scripts/Makefile config.status: creating src/scripts/R.sh config.status: creating src/scripts/Rcmd config.status: creating src/scripts/javareconf config.status: creating src/scripts/mkinstalldirs config.status: creating src/scripts/pager config.status: creating src/scripts/rtags config.status: creating src/unix/Makefile config.status: creating tests/Makefile config.status: creating tests/Embedding/Makefile config.status: creating tests/Examples/Makefile config.status: creating tools/Makefile config.status: creating src/include/config.h config.status: executing libtool commands config.status: executing stamp-h commands R is now configured for x86_64-pc-linux-gnu Source directory: . Installation directory: /usr C compiler: gcc -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects Fortran fixed-form compiler: gfortran -g -O2 Default C++ compiler: g++ -std=gnu++17 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -ffat-lto-objects C++11 compiler: g++ -std=gnu++11 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -ffat-lto-objects C++14 compiler: g++ -std=gnu++14 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -ffat-lto-objects C++17 compiler: g++ -std=gnu++17 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -ffat-lto-objects C++20 compiler: g++ -std=gnu++20 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -ffat-lto-objects C++23 compiler: g++ -std=gnu++23 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -ffat-lto-objects Fortran free-form compiler: gfortran -g -O2 Obj-C compiler: Interfaces supported: X11, tcltk External libraries: pcre2, readline, BLAS(generic), LAPACK(generic), curl Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU Options enabled: shared R library, R profiling, memory profiling Capabilities skipped: Options not enabled: shared BLAS Recommended packages: yes configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally configure: WARNING: I could not determine a browser configure: WARNING: I could not determine a PDF viewer make[1]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/m4' make[1]: Nothing to be done for 'R'. make[1]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/m4' make[1]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/tools' make[1]: Nothing to be done for 'R'. make[1]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/tools' make[1]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/doc' make[2]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/doc/html' make[2]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/doc/html' make[2]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/doc/manual' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/doc/manual' make[1]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/doc' make[1]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/etc' make[1]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/etc' make[1]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/share' make[1]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/share' make[1]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src' make[2]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/scripts' creating src/scripts/R.fe make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/scripts' mkdir -p -- ../../bin make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/scripts' make[2]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/scripts' make[2]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/include' mkdir -p -- ../../include make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/include/R_ext' mkdir -p -- ../../../include/R_ext make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/include/R_ext' make[2]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/include' make[2]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/extra' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/extra/tre' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/extra/tre' making regcomp.d from regcomp.c making regerror.d from regerror.c making regexec.d from regexec.c making tre-ast.d from tre-ast.c making tre-compile.d from tre-compile.c making tre-match-approx.d from tre-match-approx.c making tre-match-backtrack.d from tre-match-backtrack.c making tre-match-parallel.d from tre-match-parallel.c making tre-mem.d from tre-mem.c making tre-parse.d from tre-parse.c making tre-stack.d from tre-stack.c make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/extra/tre' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/extra/tre' gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -fvisibility=hidden -c regcomp.c -o regcomp.o gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -fvisibility=hidden -c regerror.c -o regerror.o gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -fvisibility=hidden -c regexec.c -o regexec.o gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -fvisibility=hidden -c tre-ast.c -o tre-ast.o gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -fvisibility=hidden -c tre-compile.c -o tre-compile.o gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -fvisibility=hidden -c tre-match-approx.c -o tre-match-approx.o gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -fvisibility=hidden -c tre-match-backtrack.c -o tre-match-backtrack.o gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -fvisibility=hidden -c tre-match-parallel.c -o tre-match-parallel.o gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -fvisibility=hidden -c tre-mem.c -o tre-mem.o gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -fvisibility=hidden -c tre-parse.c -o tre-parse.o gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -fvisibility=hidden -c tre-stack.c -o tre-stack.o ar -cr libtre.a regcomp.o regerror.o regexec.o tre-ast.o tre-compile.o tre-match-approx.o tre-match-backtrack.o tre-match-parallel.o tre-mem.o tre-parse.o tre-stack.o ranlib libtre.a make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/extra/tre' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/extra/tre' make[2]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/extra' make[2]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/appl' making integrate.d from integrate.c making interv.d from interv.c making maxcol.d from maxcol.c making optim.d from optim.c making pretty.d from pretty.c making uncmin.d from uncmin.c make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/appl' gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c integrate.c -o integrate.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c interv.c -o interv.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c maxcol.c -o maxcol.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c optim.c -o optim.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pretty.c -o pretty.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c uncmin.c -o uncmin.o gfortran -fpic -g -O2 -c dchdc.f -o dchdc.o gfortran -fpic -g -O2 -c dpbfa.f -o dpbfa.o gfortran -fpic -g -O2 -c dpbsl.f -o dpbsl.o gfortran -fpic -g -O2 -c dpoco.f -o dpoco.o gfortran -fpic -g -O2 -c dpodi.f -o dpodi.o gfortran -fpic -g -O2 -c dpofa.f -o dpofa.o gfortran -fpic -g -O2 -c dposl.f -o dposl.o gfortran -fpic -g -O2 -c dqrdc.f -o dqrdc.o gfortran -fpic -g -O2 -c dqrdc2.f -o dqrdc2.o gfortran -fpic -g -O2 -c dqrls.f -o dqrls.o gfortran -fpic -g -O2 -c dqrsl.f -o dqrsl.o gfortran -fpic -g -O2 -c dqrutl.f -o dqrutl.o gfortran -fpic -g -O2 -c dsvdc.f -o dsvdc.o gfortran -fpic -g -O2 -c dtrco.f -o dtrco.o gfortran -fpic -g -O2 -c dtrsl.f -o dtrsl.o ar -cr libappl.a integrate.o interv.o maxcol.o optim.o pretty.o uncmin.o dchdc.o dpbfa.o dpbsl.o dpoco.o dpodi.o dpofa.o dposl.o dqrdc.o dqrdc2.o dqrls.o dqrsl.o dqrutl.o dsvdc.o dtrco.o dtrsl.o ranlib libappl.a make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/appl' #@make install-Linpack make[2]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/appl' make[2]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/nmath' making mlutils.d from mlutils.c making i1mach.d from i1mach.c making d1mach.d from d1mach.c making fmax2.d from fmax2.c making fmin2.d from fmin2.c making fprec.d from fprec.c making fround.d from fround.c making sign.d from sign.c making ftrunc.d from ftrunc.c making imax2.d from imax2.c making fsign.d from fsign.c making chebyshev.d from chebyshev.c making imin2.d from imin2.c making log1p.d from log1p.c making lgammacor.d from lgammacor.c making gammalims.d from gammalims.c making bd0.d from bd0.c making stirlerr.d from stirlerr.c making gamma.d from gamma.c making lgamma.d from lgamma.c making gamma_cody.d from gamma_cody.c making beta.d from beta.c making lbeta.d from lbeta.c making polygamma.d from polygamma.c making cospi.d from cospi.c making bessel_i.d from bessel_i.c making bessel_j.d from bessel_j.c making bessel_k.d from bessel_k.c making bessel_y.d from bessel_y.c making choose.d from choose.c making snorm.d from snorm.c making sexp.d from sexp.c making dgamma.d from dgamma.c making pgamma.d from pgamma.c making qgamma.d from qgamma.c making rgamma.d from rgamma.c making dbeta.d from dbeta.c making pbeta.d from pbeta.c making qbeta.d from qbeta.c making rbeta.d from rbeta.c making dunif.d from dunif.c making punif.d from punif.c making qunif.d from qunif.c making runif.d from runif.c making dnorm.d from dnorm.c making pnorm.d from pnorm.c making qnorm.d from qnorm.c making rnorm.d from rnorm.c making dlnorm.d from dlnorm.c making plnorm.d from plnorm.c making qlnorm.d from qlnorm.c making rlnorm.d from rlnorm.c making df.d from df.c making pf.d from pf.c making rf.d from rf.c making qf.d from qf.c making dnf.d from dnf.c making dt.d from dt.c making pt.d from pt.c making qt.d from qt.c making rt.d from rt.c making dnt.d from dnt.c making dchisq.d from dchisq.c making pchisq.d from pchisq.c making qchisq.d from qchisq.c making rchisq.d from rchisq.c making rnchisq.d from rnchisq.c making dbinom.d from dbinom.c making pbinom.d from pbinom.c making qbinom.d from qbinom.c making rmultinom.d from rmultinom.c making rbinom.d from rbinom.c making dcauchy.d from dcauchy.c making pcauchy.d from pcauchy.c making rcauchy.d from rcauchy.c making qcauchy.d from qcauchy.c making dexp.d from dexp.c making pexp.d from pexp.c making qexp.d from qexp.c making rexp.d from rexp.c making dgeom.d from dgeom.c making pgeom.d from pgeom.c making qgeom.d from qgeom.c making rgeom.d from rgeom.c making phyper.d from phyper.c making dhyper.d from dhyper.c making qhyper.d from qhyper.c making rhyper.d from rhyper.c making dnbinom.d from dnbinom.c making qnbinom.d from qnbinom.c making pnbinom.d from pnbinom.c making qnbinom_mu.d from qnbinom_mu.c making rnbinom.d from rnbinom.c making dpois.d from dpois.c making ppois.d from ppois.c making qpois.d from qpois.c making rpois.d from rpois.c making dweibull.d from dweibull.c making pweibull.d from pweibull.c making qweibull.d from qweibull.c making dlogis.d from dlogis.c making rweibull.d from rweibull.c making plogis.d from plogis.c making qlogis.d from qlogis.c making rlogis.d from rlogis.c making dnchisq.d from dnchisq.c making pnchisq.d from pnchisq.c making qnchisq.d from qnchisq.c making dnbeta.d from dnbeta.c making pnbeta.d from pnbeta.c making pnf.d from pnf.c making qnbeta.d from qnbeta.c making pnt.d from pnt.c making qnf.d from qnf.c making qnt.d from qnt.c making ptukey.d from ptukey.c making qtukey.d from qtukey.c making toms708.d from toms708.c making wilcox.d from wilcox.c making signrank.d from signrank.c make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/nmath' gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c mlutils.c -o mlutils.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c d1mach.c -o d1mach.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c i1mach.c -o i1mach.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c fmax2.c -o fmax2.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c fmin2.c -o fmin2.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c fprec.c -o fprec.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c fround.c -o fround.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ftrunc.c -o ftrunc.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c sign.c -o sign.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c fsign.c -o fsign.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c imax2.c -o imax2.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c imin2.c -o imin2.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c chebyshev.c -o chebyshev.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c log1p.c -o log1p.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c lgammacor.c -o lgammacor.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c gammalims.c -o gammalims.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c stirlerr.c -o stirlerr.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c bd0.c -o bd0.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c gamma.c -o gamma.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c lgamma.c -o lgamma.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c gamma_cody.c -o gamma_cody.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c beta.c -o beta.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c lbeta.c -o lbeta.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c polygamma.c -o polygamma.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c cospi.c -o cospi.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c bessel_i.c -o bessel_i.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c bessel_j.c -o bessel_j.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c bessel_k.c -o bessel_k.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c bessel_y.c -o bessel_y.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c choose.c -o choose.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c snorm.c -o snorm.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c sexp.c -o sexp.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dgamma.c -o dgamma.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pgamma.c -o pgamma.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qgamma.c -o qgamma.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rgamma.c -o rgamma.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dbeta.c -o dbeta.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pbeta.c -o pbeta.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qbeta.c -o qbeta.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rbeta.c -o rbeta.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dunif.c -o dunif.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c punif.c -o punif.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qunif.c -o qunif.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c runif.c -o runif.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dnorm.c -o dnorm.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pnorm.c -o pnorm.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qnorm.c -o qnorm.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rnorm.c -o rnorm.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dlnorm.c -o dlnorm.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c plnorm.c -o plnorm.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qlnorm.c -o qlnorm.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rlnorm.c -o rlnorm.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c df.c -o df.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pf.c -o pf.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qf.c -o qf.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rf.c -o rf.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dnf.c -o dnf.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dt.c -o dt.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pt.c -o pt.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qt.c -o qt.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rt.c -o rt.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dnt.c -o dnt.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dchisq.c -o dchisq.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pchisq.c -o pchisq.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qchisq.c -o qchisq.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rchisq.c -o rchisq.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rnchisq.c -o rnchisq.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dbinom.c -o dbinom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pbinom.c -o pbinom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qbinom.c -o qbinom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rbinom.c -o rbinom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rmultinom.c -o rmultinom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dcauchy.c -o dcauchy.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pcauchy.c -o pcauchy.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qcauchy.c -o qcauchy.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rcauchy.c -o rcauchy.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dexp.c -o dexp.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pexp.c -o pexp.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qexp.c -o qexp.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rexp.c -o rexp.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dgeom.c -o dgeom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pgeom.c -o pgeom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qgeom.c -o qgeom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rgeom.c -o rgeom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dhyper.c -o dhyper.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c phyper.c -o phyper.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qhyper.c -o qhyper.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rhyper.c -o rhyper.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dnbinom.c -o dnbinom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pnbinom.c -o pnbinom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qnbinom.c -o qnbinom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qnbinom_mu.c -o qnbinom_mu.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rnbinom.c -o rnbinom.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dpois.c -o dpois.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ppois.c -o ppois.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qpois.c -o qpois.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rpois.c -o rpois.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dweibull.c -o dweibull.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pweibull.c -o pweibull.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qweibull.c -o qweibull.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rweibull.c -o rweibull.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dlogis.c -o dlogis.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c plogis.c -o plogis.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qlogis.c -o qlogis.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rlogis.c -o rlogis.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dnchisq.c -o dnchisq.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pnchisq.c -o pnchisq.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qnchisq.c -o qnchisq.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dnbeta.c -o dnbeta.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pnbeta.c -o pnbeta.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qnbeta.c -o qnbeta.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pnf.c -o pnf.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pnt.c -o pnt.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qnf.c -o qnf.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qnt.c -o qnt.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ptukey.c -o ptukey.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qtukey.c -o qtukey.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c toms708.c -o toms708.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c wilcox.c -o wilcox.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c signrank.c -o signrank.o ar -cr libnmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o qnbinom_mu.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o ranlib libnmath.a make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/nmath' make[2]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/nmath' make[2]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/unix' config.status: creating src/unix/Makefile making Rembedded.d from Rembedded.c making dynload.d from dynload.c making system.d from system.c making sys-unix.d from sys-unix.c making sys-std.d from sys-std.c making X11.d from X11.c make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/unix' gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c Rembedded.c -o Rembedded.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dynload.c -o dynload.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c system.c -o system.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c sys-unix.c -o sys-unix.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c sys-std.c -o sys-std.o gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c X11.c -o X11.o ar -cr libunix.a Rembedded.o dynload.o system.o sys-unix.o sys-std.o X11.o ranlib libunix.a make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/unix' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/unix' gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -DR_HOME='"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3"' \ -o Rscript ./Rscript.c make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/unix' make[2]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/unix' make[2]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/main' config.status: creating src/main/Makefile making CommandLineArgs.d from CommandLineArgs.c making Rdynload.d from Rdynload.c making Renviron.d from Renviron.c making RNG.d from RNG.c making agrep.d from agrep.c making altclasses.d from altclasses.c making altrep.d from altrep.c making apply.d from apply.c making arithmetic.d from arithmetic.c making array.d from array.c making attrib.d from attrib.c making bind.d from bind.c making builtin.d from builtin.c making character.d from character.c making clippath.d from clippath.c making coerce.d from coerce.c making colors.d from colors.c making complex.d from complex.c making connections.d from connections.c making context.d from context.c making cum.d from cum.c making dcf.d from dcf.c making datetime.d from datetime.c making debug.d from debug.c making deparse.d from deparse.c making devices.d from devices.c making dotcode.d from dotcode.c making dounzip.d from dounzip.c making dstruct.d from dstruct.c making duplicate.d from duplicate.c making edit.d from edit.c making engine.d from engine.c making envir.d from envir.c making errors.d from errors.c making eval.d from eval.c making flexiblas.d from flexiblas.c making format.d from format.c making gevents.d from gevents.c making gram.d from gram.c making gram-ex.d from gram-ex.c making graphics.d from graphics.c making grep.d from grep.c making identical.d from identical.c making inlined.d from inlined.c making inspect.d from inspect.c making internet.d from internet.c making iosupport.d from iosupport.c making lapack.d from lapack.c making list.d from list.c making localecharset.d from localecharset.c making logic.d from logic.c making machine.d from machine.c making main.d from main.c making mapply.d from mapply.c making mask.d from mask.c making match.d from match.c making memory.d from memory.c making names.d from names.c making objects.d from objects.c making options.d from options.c making paste.d from paste.c making patterns.d from patterns.c making platform.d from platform.c making plot.d from plot.c making plot3d.d from plot3d.c making plotmath.d from plotmath.c making print.d from print.c making printarray.d from printarray.c making printvector.d from printvector.c making printutils.d from printutils.c making qsort.d from qsort.c making radixsort.d from radixsort.c making random.d from random.c making raw.d from raw.c making registration.d from registration.c making relop.d from relop.c making rlocale.d from rlocale.c making saveload.d from saveload.c making scan.d from scan.c making seq.d from seq.c making serialize.d from serialize.c making sort.d from sort.c making source.d from source.c making split.d from split.c making sprintf.d from sprintf.c making startup.d from startup.c making subassign.d from subassign.c making subscript.d from subscript.c making subset.d from subset.c making summary.d from summary.c making sysutils.d from sysutils.c making times.d from times.c making unique.d from unique.c making util.d from util.c making version.d from version.c making g_alab_her.d from g_alab_her.c making g_cntrlify.d from g_cntrlify.c making g_fontdb.d from g_fontdb.c making g_her_glyph.d from g_her_glyph.c making Rmain.d from Rmain.c making alloca.d from alloca.c making mkdtemp.d from mkdtemp.c making strdup.d from strdup.c making strncasecmp.d from strncasecmp.c make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/main' gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c CommandLineArgs.c -o CommandLineArgs.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c Rdynload.c -o Rdynload.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c Renviron.c -o Renviron.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c RNG.c -o RNG.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c agrep.c -o agrep.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c altclasses.c -o altclasses.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c altrep.c -o altrep.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c apply.c -o apply.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c arithmetic.c -o arithmetic.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c array.c -o array.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c attrib.c -o attrib.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c bind.c -o bind.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c builtin.c -o builtin.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c character.c -o character.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c clippath.c -o clippath.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c coerce.c -o coerce.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c colors.c -o colors.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c complex.c -o complex.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c connections.c -o connections.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c context.c -o context.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c cum.c -o cum.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dcf.c -o dcf.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c datetime.c -o datetime.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c debug.c -o debug.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c deparse.c -o deparse.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c devices.c -o devices.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dotcode.c -o dotcode.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dounzip.c -o dounzip.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dstruct.c -o dstruct.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c duplicate.c -o duplicate.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c edit.c -o edit.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c engine.c -o engine.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c envir.c -o envir.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c errors.c -o errors.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c eval.c -o eval.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c flexiblas.c -o flexiblas.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c format.c -o format.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c gevents.c -o gevents.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c gram.c -o gram.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c gram-ex.c -o gram-ex.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c graphics.c -o graphics.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c grep.c -o grep.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c identical.c -o identical.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c inlined.c -o inlined.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c inspect.c -o inspect.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c internet.c -o internet.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c iosupport.c -o iosupport.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c lapack.c -o lapack.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c list.c -o list.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c localecharset.c -o localecharset.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c logic.c -o logic.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c machine.c -o machine.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c main.c -o main.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c mapply.c -o mapply.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c mask.c -o mask.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c match.c -o match.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c memory.c -o memory.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c names.c -o names.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c objects.c -o objects.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c options.c -o options.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c paste.c -o paste.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c patterns.c -o patterns.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c platform.c -o platform.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c plot.c -o plot.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c plot3d.c -o plot3d.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c plotmath.c -o plotmath.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c print.c -o print.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c printarray.c -o printarray.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c printvector.c -o printvector.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c printutils.c -o printutils.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qsort.c -o qsort.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c radixsort.c -o radixsort.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c random.c -o random.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c raw.c -o raw.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c registration.c -o registration.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c relop.c -o relop.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rlocale.c -o rlocale.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c saveload.c -o saveload.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c scan.c -o scan.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c seq.c -o seq.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c serialize.c -o serialize.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c sort.c -o sort.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c source.c -o source.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c split.c -o split.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c sprintf.c -o sprintf.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c startup.c -o startup.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c subassign.c -o subassign.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c subscript.c -o subscript.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c subset.c -o subset.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c summary.c -o summary.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c sysutils.c -o sysutils.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c times.c -o times.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c unique.c -o unique.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c util.c -o util.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c version.c -o version.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c g_alab_her.c -o g_alab_her.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c g_cntrlify.c -o g_cntrlify.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c g_fontdb.c -o g_fontdb.o gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c g_her_glyph.c -o g_her_glyph.o gfortran -fpic -g -O2 -c xxxpr.f -o xxxpr.o gcc -shared -fopenmp -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o altclasses.o altrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o clippath.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o flexiblas.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o machine.o main.o mapply.o mask.o match.o memory.o names.o objects.o options.o paste.o patterns.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o radixsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o xxxpr.o `ls ../unix/*.o ../appl/*.o ../nmath/*.o` ../extra/tre/libtre.a -lblas -lgfortran -lm -lquadmath -lreadline -lpcre2-8 -llzma -lbz2 -lz -ltirpc -lrt -ldl -lm -licuuc -licui18n make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/main' mkdir -p -- /tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/bin/exec mkdir -p -- /tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/main' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/main' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/main' gcc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c Rmain.c -o Rmain.o gcc -Wl,--export-dynamic -fopenmp -L"../../lib" -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o R.bin Rmain.o -lR make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/main' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/main' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/main' make[2]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/main' make[2]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/modules' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/modules/internet' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/modules/lapack' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/modules/X11' making Rhttpd.d from Rhttpd.c making Lapack.d from Lapack.c making devX11.d from devX11.c making internet.d from internet.c making Rsock.d from Rsock.c making rotated.d from rotated.c making rbitmap.d from rbitmap.c making libcurl.d from libcurl.c making sock.d from sock.c making sockconn.d from sockconn.c make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/modules/lapack' gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c Lapack.c -o Lapack.o gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../../main/flexiblas.c -o flexiblas.o make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/modules/internet' gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -fvisibility=hidden -c Rsock.c -o Rsock.o gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -fvisibility=hidden -c internet.c -o internet.o gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -fvisibility=hidden -c libcurl.c -o libcurl.o gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -fvisibility=hidden -c sock.c -o sock.o gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -fvisibility=hidden -c sockconn.c -o sockconn.o make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/modules/X11' gcc -I/usr/include/libpng16 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi -I/usr/include/sysprof-6 -pthread -I/usr/include/pixman-1 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c devX11.c -o devX11.o gcc -I/usr/include/libpng16 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi -I/usr/include/sysprof-6 -pthread -I/usr/include/pixman-1 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rotated.c -o rotated.o gcc -I/usr/include/libpng16 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi -I/usr/include/sysprof-6 -pthread -I/usr/include/pixman-1 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rbitmap.c -o rbitmap.o gcc -I/usr/include/libpng16 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi -I/usr/include/sysprof-6 -pthread -I/usr/include/pixman-1 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dataentry.c -o dataentry.o gcc -shared -L"../../../lib" -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o internet.so Rhttpd.o Rsock.o internet.o libcurl.o sock.o sockconn.o -lcurl -lR make[5]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/modules/internet' mkdir -p -- /tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/modules make[5]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/modules/internet' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/modules/internet' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/modules/internet' gcc -shared -L"../../../lib" -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o R_de.so dataentry.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lz -lpng16 -lcairo -lX11 -lXext -lX11 -lXt -lXmu -lR -lm gcc -shared -L"../../../lib" -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o lapack.so Lapack.o flexiblas.o -lR -llapack -lblas -lgfortran -lm -lquadmath make[5]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/modules/lapack' make[5]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/modules/lapack' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/modules/lapack' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/modules/lapack' gcc -shared -L"../../../lib" -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o R_X11.so devX11.o rotated.o rbitmap.o -ltiff -ljpeg -lpng16 -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lz -lpng16 -lcairo -lX11 -lXext -lX11 -lXt -lXmu -lR -lm make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/modules/X11' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/modules/X11' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/modules/X11' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/modules/X11' make[2]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/modules' make[2]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library' mkdir -p -- ../../library make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/profile' building system startup profile mkdir -p -- ../../../library/base/R make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/profile' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/translations' building package 'translations' mkdir -p -- ../../../library/translations make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/translations' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/translations' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/translations' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/base' building package 'base' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/base' mkdir -p -- ../../../library/base/demo make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/base' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/base' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/tools' building package 'tools' mkdir -p -- ../../../library/tools make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/tools' mkdir -p -- ../../../library/tools/R make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/tools' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/tools' make[5]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/tools/src' making text.d from text.c making init.d from init.c making Rmd5.d from Rmd5.c making md5.d from md5.c making signals.d from signals.c making install.d from install.c making getfmts.d from getfmts.c making http.d from http.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c text.c -o text.o making gramLatex.d from gramLatex.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c init.c -o init.o making gramRd.d from gramRd.c making pdscan.d from pdscan.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c Rmd5.c -o Rmd5.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c md5.c -o md5.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c signals.c -o signals.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c install.c -o install.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c getfmts.c -o getfmts.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c http.c -o http.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c gramLatex.c -o gramLatex.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c gramRd.c -o gramRd.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pdscan.c -o pdscan.o gcc -shared -L../../../../lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o tools.so text.o init.o Rmd5.o md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o pdscan.o -L../../../../lib -lR make[6]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/tools/src' mkdir -p -- ../../../../library/tools/libs make[6]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/tools/src' make[5]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/tools/src' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/tools' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/tools' installing 'sysdata.rda' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/tools' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/tools' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/compiler' building package 'compiler' mkdir -p -- ../../../library/compiler make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/compiler' mkdir -p -- ../../../library/compiler/R make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/compiler' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/compiler' byte-compiling package 'compiler' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/compiler' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/compiler' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/base' byte-compiling package 'base' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/base' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/tools' byte-compiling package 'tools' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/tools' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/utils' building package 'utils' mkdir -p -- ../../../library/utils mkdir -p -- ../../../library/utils/doc make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/utils' mkdir -p -- ../../../library/utils/R mkdir -p -- ../../../library/utils/Sweave mkdir -p -- ../../../library/utils/misc make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/utils' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/utils' make[5]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/utils/src' making init.d from init.c making io.d from io.c making size.d from size.c making sock.d from sock.c making stubs.d from stubs.c making utils.d from utils.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c init.c -o init.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c io.c -o io.o making hashtab.d from hashtab.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c size.c -o size.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c sock.c -o sock.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c stubs.c -o stubs.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c utils.c -o utils.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c hashtab.c -o hashtab.o gcc -shared -L../../../../lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o utils.so init.o io.o size.o sock.o stubs.o utils.o hashtab.o -L../../../../lib -lR make[6]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/utils/src' mkdir -p -- ../../../../library/utils/libs make[6]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/utils/src' make[5]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/utils/src' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/utils' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/utils' installing 'sysdata.rda' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/utils' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/utils' byte-compiling package 'utils' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/utils' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/utils' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grDevices' building package 'grDevices' mkdir -p -- ../../../library/grDevices make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grDevices' mkdir -p -- ../../../library/grDevices/R mkdir -p -- ../../../library/grDevices/afm mkdir -p -- ../../../library/grDevices/enc mkdir -p -- ../../../library/grDevices/fonts/Roboto mkdir -p -- ../../../library/grDevices/fonts/Montserrat/static mkdir -p -- ../../../library/grDevices/icc make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grDevices' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grDevices' make[5]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grDevices/src' making axis_scales.d from axis_scales.c making devices.d from devices.c making chull.d from chull.c making init.d from init.c making stubs.d from stubs.c making colors.d from colors.c making clippath.d from clippath.c making patterns.d from patterns.c making mask.d from mask.c making devCairo.d from devCairo.c making group.d from group.c making devPicTeX.d from devPicTeX.c making devPS.d from devPS.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c axis_scales.c -o axis_scales.o making devQuartz.d from devQuartz.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c chull.c -o chull.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c devices.c -o devices.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c init.c -o init.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c stubs.c -o stubs.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c colors.c -o colors.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c clippath.c -o clippath.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c patterns.c -o patterns.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c mask.c -o mask.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c group.c -o group.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c devCairo.c -o devCairo.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c devPicTeX.c -o devPicTeX.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c devPS.c -o devPS.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c devQuartz.c -o devQuartz.o gcc -shared -L../../../../lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o clippath.o patterns.o mask.o group.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR make[6]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grDevices/src' mkdir -p -- ../../../../library/grDevices/libs make[7]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grDevices/src/cairo' making cairoBM.d from cairoBM.c make[8]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grDevices/src/cairo' make[9]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grDevices/src/cairo' gcc -I. -I../../../../../src/include -I../../../../../src/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi -I/usr/include/sysprof-6 -pthread -I/usr/include/pixman-1 -I../../../../../src/modules/X11 -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c cairoBM.c -o cairoBM.o gcc -shared -L"../../../../../lib" -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -ltiff -ljpeg -lpng16 -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lz -lcairo -lpng16 -L"../../../../../lib" -lR -lm make[9]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grDevices/src/cairo' make[8]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grDevices/src/cairo' make[7]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grDevices/src/cairo' make[6]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grDevices/src' make[5]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grDevices/src' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grDevices' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grDevices' byte-compiling package 'grDevices' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grDevices' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grDevices' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/graphics' building package 'graphics' mkdir -p -- ../../../library/graphics make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/graphics' mkdir -p -- ../../../library/graphics/R make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/graphics' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/graphics' make[5]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/graphics/src' making init.d from init.c making base.d from base.c making graphics.d from graphics.c making par.d from par.c making plot.d from plot.c making plot3d.d from plot3d.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c init.c -o init.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c base.c -o base.o making stem.d from stem.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c graphics.c -o graphics.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c par.c -o par.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c plot.c -o plot.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c plot3d.c -o plot3d.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c stem.c -o stem.o gcc -shared -L../../../../lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o graphics.so init.o base.o graphics.o par.o plot.o plot3d.o stem.o -L../../../../lib -lR make[6]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/graphics/src' mkdir -p -- ../../../../library/graphics/libs make[6]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/graphics/src' make[5]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/graphics/src' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/graphics' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/graphics' byte-compiling package 'graphics' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/graphics' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/graphics' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/stats' building package 'stats' mkdir -p -- ../../../library/stats make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/stats' mkdir -p -- ../../../library/stats/R make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/stats' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/stats' make[5]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/stats/src' making init.d from init.c making ansari.d from ansari.c making kmeans.d from kmeans.c making chisqsim.d from chisqsim.c making bandwidths.d from bandwidths.c making fexact.d from fexact.c making d2x2xk.d from d2x2xk.c making kendall.d from kendall.c making ks.d from ks.c making line.d from line.c making smooth.d from smooth.c making swilk.d from swilk.c making prho.d from prho.c making ksmooth.d from ksmooth.c making loessc.d from loessc.c making monoSpl.d from monoSpl.c making isoreg.d from isoreg.c making Srunmed.d from Srunmed.c making dblcen.d from dblcen.c making distance.d from distance.c making hclust-utils.d from hclust-utils.c making nls.d from nls.c making rWishart.d from rWishart.c making HoltWinters.d from HoltWinters.c making PPsum.d from PPsum.c making arima.d from arima.c making filter.d from filter.c making burg.d from burg.c making mAR.d from mAR.c making pacf.d from pacf.c making starma.d from starma.c making port.d from port.c making family.d from family.c making sbart.d from sbart.c making approx.d from approx.c making loglin.d from loglin.c making lowess.d from lowess.c making massdist.d from massdist.c making splines.d from splines.c making lm.d from lm.c making complete_cases.d from complete_cases.c making cov.d from cov.c making deriv.d from deriv.c making fft.d from fft.c making fourier.d from fourier.c making model.d from model.c making optim.d from optim.c making optimize.d from optimize.c making integrate.d from integrate.c making random.d from random.c making distn.d from distn.c making zeroin.d from zeroin.c making influence.d from influence.c making rcont.d from rcont.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c init.c -o init.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c kmeans.c -o kmeans.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ansari.c -o ansari.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c bandwidths.c -o bandwidths.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c chisqsim.c -o chisqsim.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c d2x2xk.c -o d2x2xk.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c fexact.c -o fexact.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c kendall.c -o kendall.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ks.c -o ks.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c line.c -o line.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c smooth.c -o smooth.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c prho.c -o prho.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c swilk.c -o swilk.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ksmooth.c -o ksmooth.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c loessc.c -o loessc.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c monoSpl.c -o monoSpl.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c isoreg.c -o isoreg.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c Srunmed.c -o Srunmed.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dblcen.c -o dblcen.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c distance.c -o distance.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c hclust-utils.c -o hclust-utils.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c nls.c -o nls.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rWishart.c -o rWishart.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c HoltWinters.c -o HoltWinters.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c PPsum.c -o PPsum.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c arima.c -o arima.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c burg.c -o burg.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c filter.c -o filter.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c mAR.c -o mAR.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pacf.c -o pacf.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c starma.c -o starma.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c port.c -o port.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c family.c -o family.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c sbart.c -o sbart.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c approx.c -o approx.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c loglin.c -o loglin.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c lowess.c -o lowess.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c massdist.c -o massdist.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c splines.c -o splines.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c lm.c -o lm.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c complete_cases.c -o complete_cases.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c cov.c -o cov.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c deriv.c -o deriv.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c fft.c -o fft.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c fourier.c -o fourier.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c model.c -o model.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c optim.c -o optim.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c optimize.c -o optimize.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c integrate.c -o integrate.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c random.c -o random.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c distn.c -o distn.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c zeroin.c -o zeroin.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rcont.c -o rcont.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c influence.c -o influence.o gfortran -fvisibility=hidden -fpic -g -O2 -c bsplvd.f -o bsplvd.o gfortran -fvisibility=hidden -fpic -g -O2 -c bvalue.f -o bvalue.o gfortran -fvisibility=hidden -fpic -g -O2 -c bvalus.f -o bvalus.o gfortran -fvisibility=hidden -fpic -g -O2 -c loessf.f -o loessf.o gfortran -fvisibility=hidden -fpic -g -O2 -c ppr.f -o ppr.o gfortran -fvisibility=hidden -fpic -g -O2 -c qsbart.f -o qsbart.o gfortran -fvisibility=hidden -fpic -g -O2 -c sgram.f -o sgram.o gfortran -fvisibility=hidden -fpic -g -O2 -c sinerp.f -o sinerp.o gfortran -fvisibility=hidden -fpic -g -O2 -c sslvrg.f -o sslvrg.o gfortran -fvisibility=hidden -fpic -g -O2 -c stxwx.f -o stxwx.o gfortran -fvisibility=hidden -fpic -g -O2 -c hclust.f -o hclust.o gfortran -fvisibility=hidden -fpic -g -O2 -c kmns.f -o kmns.o gfortran -fvisibility=hidden -fpic -g -O2 -c eureka.f -o eureka.o gfortran -fvisibility=hidden -fpic -g -O2 -c stl.f -o stl.o gfortran -fpic -g -O2 -msse2 -mfpmath=sse -c portsrc.f -o portsrc.o gfortran -fvisibility=hidden -fpic -g -O2 -c lminfl.f -o lminfl.o gcc -shared -L../../../../lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o monoSpl.o isoreg.o Srunmed.o dblcen.o distance.o hclust-utils.o nls.o rWishart.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o sbart.o approx.o loglin.o lowess.o massdist.o splines.o lm.o complete_cases.o cov.o deriv.o fft.o fourier.o model.o optim.o optimize.o integrate.o random.o distn.o zeroin.o rcont.o influence.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o lminfl.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L../../../../lib -lR make[6]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/stats/src' mkdir -p -- ../../../../library/stats/libs make[6]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/stats/src' make[5]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/stats/src' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/stats' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/stats' byte-compiling package 'stats' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/stats' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/stats' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/datasets' building package 'datasets' mkdir -p -- ../../../library/datasets make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/datasets' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/datasets' mkdir -p -- ../../../library/datasets/data make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/datasets' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/methods' building package 'methods' mkdir -p -- ../../../library/methods make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/methods' mkdir -p -- ../../../library/methods/R make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/methods' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/methods' make[5]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/methods/src' making init.d from init.c making do_substitute_direct.d from do_substitute_direct.c making slot.d from slot.c making methods_list_dispatch.d from methods_list_dispatch.c making tests.d from tests.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c do_substitute_direct.c -o do_substitute_direct.o making class_support.d from class_support.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c init.c -o init.o making utils.d from utils.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c methods_list_dispatch.c -o methods_list_dispatch.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c slot.c -o slot.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c class_support.c -o class_support.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c tests.c -o tests.o gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c utils.c -o utils.o gcc -shared -L../../../../lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o methods.so do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o utils.o -L../../../../lib -lR make[6]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/methods/src' mkdir -p -- ../../../../library/methods/libs make[6]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/methods/src' make[5]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/methods/src' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/methods' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/methods' byte-compiling package 'methods' initializing class and method definitions ... done make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/methods' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/methods' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grid' building package 'grid' mkdir -p -- ../../../library/grid mkdir -p -- ../../../library/grid/doc make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grid' mkdir -p -- ../../../library/grid/R make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grid' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grid' make[5]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grid/src' making clippath.d from clippath.c making grid.d from grid.c making gpar.d from gpar.c making just.d from just.c making layout.d from layout.c making matrix.d from matrix.c making mask.d from mask.c making register.d from register.c making path.d from path.c making state.d from state.c making typeset.d from typeset.c gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c clippath.c -o clippath.o making unit.d from unit.c making util.d from util.c making viewport.d from viewport.c gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c gpar.c -o gpar.o gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c grid.c -o grid.o gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c just.c -o just.o gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c layout.c -o layout.o gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c mask.c -o mask.o gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c matrix.c -o matrix.o gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c path.c -o path.o gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c register.c -o register.o gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c state.c -o state.o gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c typeset.c -o typeset.o gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c unit.c -o unit.o gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c util.c -o util.o gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c viewport.c -o viewport.o gcc -shared -L../../../../lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o grid.so clippath.o gpar.o grid.o just.o layout.o mask.o matrix.o path.o register.o state.o typeset.o unit.o util.o viewport.o -L../../../../lib -lR make[6]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grid/src' mkdir -p -- ../../../../library/grid/libs make[6]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grid/src' make[5]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grid/src' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grid' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grid' byte-compiling package 'grid' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grid' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/grid' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/splines' building package 'splines' mkdir -p -- ../../../library/splines make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/splines' mkdir -p -- ../../../library/splines/R make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/splines' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/splines' make[5]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/splines/src' gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c splines.c -o splines.o making splines.d from splines.c gcc -shared -L../../../../lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o splines.so splines.o -L../../../../lib -lR make[6]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/splines/src' mkdir -p -- ../../../../library/splines/libs make[6]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/splines/src' make[5]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/splines/src' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/splines' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/splines' byte-compiling package 'splines' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/splines' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/splines' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/stats4' building package 'stats4' mkdir -p -- ../../../library/stats4 make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/stats4' mkdir -p -- ../../../library/stats4/R make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/stats4' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/stats4' byte-compiling package 'stats4' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/stats4' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/stats4' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/tcltk' building package 'tcltk' mkdir -p -- ../../../library/tcltk/R make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/tcltk' mkdir -p -- ../../../library/tcltk/exec make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/tcltk' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/tcltk/src' gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/include -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c init.c -o init.o making init.d from init.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/include -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c tcltk.c -o tcltk.o making tcltk_unix.d from tcltk_unix.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/include -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c tcltk_unix.c -o tcltk_unix.o making tcltk.d from tcltk.c gcc -shared -L../../../../lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/lib -ltcl8.6 -L/usr/lib -ltk8.6 -lX11 -lXss -lXext -lm -L../../../../lib -lR make[5]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/tcltk/src' mkdir -p -- ../../../../library/tcltk/libs make[5]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/tcltk/src' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/tcltk/src' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/tcltk' byte-compiling package 'tcltk' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/tcltk' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/tcltk' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/parallel' building package 'parallel' mkdir -p -- ../../../library/parallel mkdir -p -- ../../../library/parallel/doc make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/parallel' mkdir -p -- ../../../library/parallel/R make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/parallel' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/parallel' make[5]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/parallel/src' gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c init.c -o init.o making init.d from init.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rngstream.c -o rngstream.o making fork.d from fork.c making rngstream.d from rngstream.c gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c fork.c -o fork.o gcc -shared -L../../../../lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o parallel.so init.o rngstream.o fork.o -L../../../../lib -lR make[6]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/parallel/src' mkdir -p -- ../../../../library/parallel/libs make[6]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/parallel/src' make[5]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/parallel/src' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/parallel' make[4]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/parallel' byte-compiling package 'parallel' make[4]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/parallel' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/parallel' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/base' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/base' installing parsed NAMESPACE files make[2]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library' make[1]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src' make[1]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/tests' make[1]: Nothing to be done for 'R'. make[1]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/tests' you should 'make docs' now ... make[1]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3' make[1]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/doc' make[1]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library' configuring Java ... building/updating vignettes for package 'grid' ... Java interpreter : /usr/sbin/java Java version : 21.0.2 Java home path : /usr/lib/jvm/java-21-openjdk Java compiler : /usr/sbin/javac Java headers gen.: Java archive tool: /usr/sbin/jar trying to compile and link a JNI program detected JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm using C compiler: 'gcc (GCC) 13.2.1 20230801' make[2]: Entering directory '/tmp/archlinux-ci/Rjavareconf.C7MN2j' gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/lib/jvm/java-21-openjdk/include -I/usr/lib/jvm/java-21-openjdk/include/linux -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c conftest.c -o conftest.o creating doc/NEWS creating doc/NEWS.pdf gcc -shared -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o conftest.so conftest.o -L/usr/lib/jvm/java-21-openjdk/lib/server -ljvm -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -lR make[2]: Leaving directory '/tmp/archlinux-ci/Rjavareconf.C7MN2j' JAVA_HOME : /usr/lib/jvm/java-21-openjdk Java library path: $(JAVA_HOME)/lib/server JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm Updating Java configuration in /tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3 Done. make[1]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3' building/updating vignettes for package 'parallel' ... building/updating vignettes for package 'utils' ... building/updating vignettes for package 'stats' ... processing 'reshape.Rnw' make[2]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/doc/manual' creating doc/manual/R-FAQ.html creating doc/manual/version.texi creating doc/manual/R-data.html creating doc/manual/R-admin.html creating doc/manual/R-intro.html creating doc/manual/R-exts.html creating doc/manual/R-lang.html creating doc/manual/R-ints.html make[1]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/doc/html' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/doc/html' make[2]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/doc/manual' make[1]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/doc' make[1]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library' make[2]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library' installing parsed Rd make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library' compiler stats4 splines parallel tcltk datasets tools graphics grid grDevices methods utils stats base make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library' make[2]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library' make[2]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library' building/updating package metadata ... make[2]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library' make[2]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library' writing package indices make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library' make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library' make[2]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library' make[1]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library' make[1]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/Recommended' make[2]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/Recommended' begin installing recommended package MASS begin installing recommended package lattice begin installing recommended package codetools begin installing recommended package rpart begin installing recommended package foreign begin installing recommended package KernSmooth begin installing recommended package nnet begin installing recommended package spatial * installing *source* package 'codetools' ... ** package 'codetools' successfully unpacked and MD5 sums checked ** using non-staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (codetools) * installing *source* package 'KernSmooth' ... ** package 'KernSmooth' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: 'gcc (GCC) 13.2.1 20230801' using Fortran compiler: 'GNU Fortran (GCC) 13.2.1 20230801' make[3]: Entering directory '/tmp/archlinux-ci/RtmpB7PrSK/R.INSTALL107c18782432c5/KernSmooth/src' gfortran -fpic -g -O2 -c blkest.f -o blkest.o gfortran -fpic -g -O2 -c cp.f -o cp.o gfortran -fpic -g -O2 -c dgedi.f -o dgedi.o gfortran -fpic -g -O2 -c dgefa.f -o dgefa.o gfortran -fpic -g -O2 -c dgesl.f -o dgesl.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c init.c -o init.o gfortran -fpic -g -O2 -c linbin.f -o linbin.o gfortran -fpic -g -O2 -c linbin2D.f -o linbin2D.o gfortran -fpic -g -O2 -c locpoly.f -o locpoly.o gfortran -fpic -g -O2 -c rlbin.f -o rlbin.o gfortran -fpic -g -O2 -c sdiag.f -o sdiag.o gfortran -fpic -g -O2 -c sstdiag.f -o sstdiag.o gcc -shared -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o KernSmooth.so blkest.o cp.o dgedi.o dgefa.o dgesl.o init.o linbin.o linbin2D.o locpoly.o rlbin.o sdiag.o sstdiag.o -lblas -lgfortran -lm -lquadmath -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -lR make[3]: Leaving directory '/tmp/archlinux-ci/RtmpB7PrSK/R.INSTALL107c18782432c5/KernSmooth/src' installing to /tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/library/KernSmooth/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (KernSmooth) * installing *source* package 'spatial' ... ** package 'spatial' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: 'gcc (GCC) 13.2.1 20230801' make[3]: Entering directory '/tmp/archlinux-ci/Rtmpan1oAd/R.INSTALL107c1c61ce96fa/spatial/src' gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c init.c -o init.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c krc.c -o krc.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pps.c -o pps.o gcc -shared -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o spatial.so init.o krc.o pps.o -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -lR make[3]: Leaving directory '/tmp/archlinux-ci/Rtmpan1oAd/R.INSTALL107c1c61ce96fa/spatial/src' installing to /tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/library/spatial/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (spatial) * installing *source* package 'nnet' ... ** package 'nnet' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: 'gcc (GCC) 13.2.1 20230801' make[3]: Entering directory '/tmp/archlinux-ci/RtmpPZXV3u/R.INSTALL107c14ea18c9f/nnet/src' gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c nnet.c -o nnet.o gcc -shared -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o nnet.so nnet.o -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -lR make[3]: Leaving directory '/tmp/archlinux-ci/RtmpPZXV3u/R.INSTALL107c14ea18c9f/nnet/src' installing to /tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/library/nnet/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (nnet) * installing *source* package 'foreign' ... ** package 'foreign' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: 'gcc (GCC) 13.2.1 20230801' make[3]: Entering directory '/tmp/archlinux-ci/Rtmpoga6vh/R.INSTALL107c0d37f48f44/foreign/src' gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c R_systat.c -o R_systat.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c Rdbfread.c -o Rdbfread.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c Rdbfwrite.c -o Rdbfwrite.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c SASxport.c -o SASxport.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c avl.c -o avl.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dbfopen.c -o dbfopen.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c file-handle.c -o file-handle.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c format.c -o format.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c init.c -o init.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c minitab.c -o minitab.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pfm-read.c -o pfm-read.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c sfm-read.c -o sfm-read.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c spss.c -o spss.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c stataread.c -o stataread.o gcc -shared -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o foreign.so R_systat.o Rdbfread.o Rdbfwrite.o SASxport.o avl.o dbfopen.o file-handle.o format.o init.o minitab.o pfm-read.o sfm-read.o spss.o stataread.o -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -lR make[3]: Leaving directory '/tmp/archlinux-ci/Rtmpoga6vh/R.INSTALL107c0d37f48f44/foreign/src' installing to /tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/library/foreign/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (foreign) * installing *source* package 'rpart' ... ** package 'rpart' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: 'gcc (GCC) 13.2.1 20230801' make[3]: Entering directory '/tmp/archlinux-ci/RtmpDPzM4T/R.INSTALL107c1a4d16e0fe/rpart/src' gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c anova.c -o anova.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c anovapred.c -o anovapred.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c branch.c -o branch.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c bsplit.c -o bsplit.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c choose_surg.c -o choose_surg.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c fix_cp.c -o fix_cp.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c free_tree.c -o free_tree.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c gini.c -o gini.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c graycode.c -o graycode.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c init.c -o init.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c insert_split.c -o insert_split.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c make_cp_list.c -o make_cp_list.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c make_cp_table.c -o make_cp_table.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c mysort.c -o mysort.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c nodesplit.c -o nodesplit.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c partition.c -o partition.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c poisson.c -o poisson.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pred_rpart.c -o pred_rpart.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c print_tree.c -o print_tree.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rpart.c -o rpart.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rpart_callback.c -o rpart_callback.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rpartexp.c -o rpartexp.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rpartexp2.c -o rpartexp2.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rpcountup.c -o rpcountup.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rpmatrix.c -o rpmatrix.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rundown.c -o rundown.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rundown2.c -o rundown2.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c surrogate.c -o surrogate.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c usersplit.c -o usersplit.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c xpred.c -o xpred.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c xval.c -o xval.o gcc -shared -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o rpart.so anova.o anovapred.o branch.o bsplit.o choose_surg.o fix_cp.o free_tree.o gini.o graycode.o init.o insert_split.o make_cp_list.o make_cp_table.o mysort.o nodesplit.o partition.o poisson.o pred_rpart.o print_tree.o rpart.o rpart_callback.o rpartexp.o rpartexp2.o rpcountup.o rpmatrix.o rundown.o rundown2.o surrogate.o usersplit.o xpred.o xval.o -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -lR make[3]: Leaving directory '/tmp/archlinux-ci/RtmpDPzM4T/R.INSTALL107c1a4d16e0fe/rpart/src' installing to /tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/library/rpart/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (rpart) * installing *source* package 'MASS' ... ** package 'MASS' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: 'gcc (GCC) 13.2.1 20230801' make[3]: Entering directory '/tmp/archlinux-ci/RtmpQ0n7Yi/R.INSTALL107c076427f992/MASS/src' gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c MASS.c -o MASS.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c lqs.c -o lqs.o gcc -shared -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o MASS.so MASS.o lqs.o -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -lR make[3]: Leaving directory '/tmp/archlinux-ci/RtmpQ0n7Yi/R.INSTALL107c076427f992/MASS/src' installing to /tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/library/MASS/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (MASS) begin installing recommended package cluster begin installing recommended package class * installing *source* package 'class' ... ** package 'class' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: 'gcc (GCC) 13.2.1 20230801' make[3]: Entering directory '/tmp/archlinux-ci/Rtmp9ujKeB/R.INSTALL107deec591274/class/src' gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c class.c -o class.o gcc -shared -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o class.so class.o -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -lR make[3]: Leaving directory '/tmp/archlinux-ci/Rtmp9ujKeB/R.INSTALL107deec591274/class/src' installing to /tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/library/class/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (class) * installing *source* package 'lattice' ... ** package 'lattice' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: 'gcc (GCC) 13.2.1 20230801' make[3]: Entering directory '/tmp/archlinux-ci/RtmpKRazbi/R.INSTALL107c113c53dacf/lattice/src' gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c init.c -o init.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c threeDplot.c -o threeDplot.o gcc -shared -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o lattice.so init.o threeDplot.o -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -lR make[3]: Leaving directory '/tmp/archlinux-ci/RtmpKRazbi/R.INSTALL107c113c53dacf/lattice/src' installing to /tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/library/lattice/libs ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (lattice) begin installing recommended package Matrix begin installing recommended package nlme * installing *source* package 'cluster' ... ** package 'cluster' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: 'gcc (GCC) 13.2.1 20230801' using Fortran compiler: 'GNU Fortran (GCC) 13.2.1 20230801' make[3]: Entering directory '/tmp/archlinux-ci/RtmpWxuKrc/R.INSTALL107df0634d2f15/cluster/src' gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c clara.c -o clara.o gfortran -fpic -g -O2 -c daisy.f -o daisy.o gfortran -fpic -g -O2 -c dysta.f -o dysta.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c fanny.c -o fanny.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c init.c -o init.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c mona.c -o mona.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pam.c -o pam.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c sildist.c -o sildist.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c spannel.c -o spannel.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c twins.c -o twins.o gcc -shared -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o cluster.so clara.o daisy.o dysta.o fanny.o init.o mona.o pam.o sildist.o spannel.o twins.o -lgfortran -lm -lquadmath -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -lR make[3]: Leaving directory '/tmp/archlinux-ci/RtmpWxuKrc/R.INSTALL107df0634d2f15/cluster/src' installing to /tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/library/cluster/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (cluster) * installing *source* package 'nlme' ... ** package 'nlme' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: 'gcc (GCC) 13.2.1 20230801' using Fortran compiler: 'GNU Fortran (GCC) 13.2.1 20230801' make[3]: Entering directory '/tmp/archlinux-ci/RtmpFzhitF/R.INSTALL107e6841eb0c3/nlme/src' gfortran -fpic -g -O2 -c chol.f -o chol.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c corStruct.c -o corStruct.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c gnls.c -o gnls.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c init.c -o init.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c matrix.c -o matrix.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c nlOptimizer.c -o nlOptimizer.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c nlme.c -o nlme.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c nlmefit.c -o nlmefit.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pdMat.c -o pdMat.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pythag.c -o pythag.o gfortran -fpic -g -O2 -c rs.f -o rs.o gcc -shared -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o pdMat.o pythag.o rs.o -lgfortran -lm -lquadmath -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -lR make[3]: Leaving directory '/tmp/archlinux-ci/RtmpFzhitF/R.INSTALL107e6841eb0c3/nlme/src' installing to /tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/library/nlme/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (nlme) * installing *source* package 'Matrix' ... ** package 'Matrix' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: 'gcc (GCC) 13.2.1 20230801' make[3]: Entering directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src' gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c Csparse.c -o Csparse.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c abIndex.c -o abIndex.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c attrib.c -o attrib.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c bind.c -o bind.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c chm_common.c -o chm_common.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c cholmod-etc.c -o cholmod-etc.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c coerce.c -o coerce.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c cs.c -o cs.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c cs-etc.c -o cs-etc.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dense.c -o dense.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c determinant.c -o determinant.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dgCMatrix.c -o dgCMatrix.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dgeMatrix.c -o dgeMatrix.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c factorizations.c -o factorizations.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c idz.c -o idz.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c init.c -o init.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c kappa.c -o kappa.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c objects.c -o objects.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c perm.c -o perm.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c products.c -o products.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c solve.c -o solve.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c sparse.c -o sparse.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c sparseVector.c -o sparseVector.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c subscript.c -o subscript.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c utils-R.c -o utils-R.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c utils.c -o utils.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I./SuiteSparse_config -DNTIMER -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c validity.c -o validity.o make[4]: Entering directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/CHOLMOD' ( cd Lib ; make clean ) make[5]: Entering directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/CHOLMOD/Lib' make[5]: Leaving directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/CHOLMOD/Lib' make[4]: Leaving directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/CHOLMOD' make[4]: Entering directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/COLAMD' ( cd Source ; make clean ) make[5]: Entering directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/COLAMD/Source' make[5]: Leaving directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/COLAMD/Source' make[4]: Leaving directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/COLAMD' make[4]: Entering directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/AMD' ( cd Source ; make clean ) make[5]: Entering directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/AMD/Source' make[5]: Leaving directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/AMD/Source' make[4]: Leaving directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/AMD' make[4]: Entering directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/SuiteSparse_config' make[4]: Leaving directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/SuiteSparse_config' make[4]: Entering directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/CHOLMOD' ( cd Lib ; make -f "/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/etc/Makeconf" -f Makefile ) make[5]: Entering directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/CHOLMOD/Lib' gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Core/cholmod_aat.c -o cholmod_aat.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Core/cholmod_add.c -o cholmod_add.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Core/cholmod_band.c -o cholmod_band.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Core/cholmod_change_factor.c -o cholmod_change_factor.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Core/cholmod_common.c -o cholmod_common.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Core/cholmod_complex.c -o cholmod_complex.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Core/cholmod_copy.c -o cholmod_copy.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Core/cholmod_dense.c -o cholmod_dense.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Core/cholmod_error.c -o cholmod_error.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Core/cholmod_factor.c -o cholmod_factor.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Core/cholmod_memory.c -o cholmod_memory.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Core/cholmod_sparse.c -o cholmod_sparse.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Core/cholmod_transpose.c -o cholmod_transpose.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Core/cholmod_triplet.c -o cholmod_triplet.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Core/cholmod_version.c -o cholmod_version.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Check/cholmod_check.c -o cholmod_check.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Check/cholmod_read.c -o cholmod_read.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Check/cholmod_write.c -o cholmod_write.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Cholesky/cholmod_analyze.c -o cholmod_analyze.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Cholesky/cholmod_factorize.c -o cholmod_factorize.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Cholesky/cholmod_rowfac.c -o cholmod_rowfac.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Cholesky/cholmod_solve.c -o cholmod_solve.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../MatrixOps/cholmod_sdmult.c -o cholmod_sdmult.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Modify/cholmod_updown.c -o cholmod_updown.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Supernodal/cholmod_super_numeric.c -o cholmod_super_numeric.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Supernodal/cholmod_super_solve.c -o cholmod_super_solve.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_super_symbolic.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Core/cholmod_aat.c -o cholmod_l_aat.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Core/cholmod_add.c -o cholmod_l_add.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Core/cholmod_band.c -o cholmod_l_band.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Core/cholmod_change_factor.c -o cholmod_l_change_factor.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Core/cholmod_common.c -o cholmod_l_common.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Core/cholmod_complex.c -o cholmod_l_complex.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Core/cholmod_copy.c -o cholmod_l_copy.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Core/cholmod_dense.c -o cholmod_l_dense.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Core/cholmod_error.c -o cholmod_l_error.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Core/cholmod_factor.c -o cholmod_l_factor.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Core/cholmod_memory.c -o cholmod_l_memory.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Core/cholmod_sparse.c -o cholmod_l_sparse.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Core/cholmod_transpose.c -o cholmod_l_transpose.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Core/cholmod_triplet.c -o cholmod_l_triplet.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Core/cholmod_version.c -o cholmod_l_version.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Check/cholmod_check.c -o cholmod_l_check.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Check/cholmod_read.c -o cholmod_l_read.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Check/cholmod_write.c -o cholmod_l_write.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Cholesky/cholmod_analyze.c -o cholmod_l_analyze.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Cholesky/cholmod_factorize.c -o cholmod_l_factorize.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Modify/cholmod_updown.c -o cholmod_l_updown.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Supernodal/cholmod_super_numeric.c -o cholmod_l_super_numeric.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Supernodal/cholmod_super_solve.c -o cholmod_l_super_solve.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -DDLONG -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_l_super_symbolic.o ar -rucs ../../CHOLMOD.a cholmod_aat.o cholmod_add.o cholmod_band.o cholmod_change_factor.o cholmod_common.o cholmod_complex.o cholmod_copy.o cholmod_dense.o cholmod_error.o cholmod_factor.o cholmod_memory.o cholmod_sparse.o cholmod_transpose.o cholmod_triplet.o cholmod_version.o cholmod_check.o cholmod_read.o cholmod_write.o cholmod_amd.o cholmod_analyze.o cholmod_colamd.o cholmod_etree.o cholmod_factorize.o cholmod_postorder.o cholmod_rcond.o cholmod_resymbol.o cholmod_rowcolcounts.o cholmod_rowfac.o cholmod_solve.o cholmod_spsolve.o cholmod_drop.o cholmod_horzcat.o cholmod_norm.o cholmod_scale.o cholmod_sdmult.o cholmod_ssmult.o cholmod_submatrix.o cholmod_vertcat.o cholmod_symmetry.o cholmod_rowadd.o cholmod_rowdel.o cholmod_updown.o cholmod_super_numeric.o cholmod_super_solve.o cholmod_super_symbolic.o cholmod_l_aat.o cholmod_l_add.o cholmod_l_band.o cholmod_l_change_factor.o cholmod_l_common.o cholmod_l_complex.o cholmod_l_copy.o cholmod_l_dense.o cholmod_l_error.o cholmod_l_factor.o cholmod_l_memory.o cholmod_l_sparse.o cholmod_l_transpose.o cholmod_l_triplet.o cholmod_l_version.o cholmod_l_check.o cholmod_l_read.o cholmod_l_write.o cholmod_l_amd.o cholmod_l_analyze.o cholmod_l_colamd.o cholmod_l_etree.o cholmod_l_factorize.o cholmod_l_postorder.o cholmod_l_rcond.o cholmod_l_resymbol.o cholmod_l_rowcolcounts.o cholmod_l_rowfac.o cholmod_l_solve.o cholmod_l_spsolve.o cholmod_l_drop.o cholmod_l_horzcat.o cholmod_l_norm.o cholmod_l_scale.o cholmod_l_sdmult.o cholmod_l_ssmult.o cholmod_l_submatrix.o cholmod_l_vertcat.o cholmod_l_symmetry.o cholmod_l_rowadd.o cholmod_l_rowdel.o cholmod_l_updown.o cholmod_l_super_numeric.o cholmod_l_super_solve.o cholmod_l_super_symbolic.o ar: `u' modifier ignored since `D' is the default (see `U') make[5]: Leaving directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/CHOLMOD/Lib' make[4]: Leaving directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/CHOLMOD' make[4]: Entering directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/COLAMD' ( cd Source ; make -f "/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/etc/Makeconf" -f Makefile lib ) make[5]: Entering directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/COLAMD/Source' gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c colamd.c -o colamd.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDLONG -c colamd.c -o colamd_l.o ar -rucs ../../COLAMD.a colamd.o colamd_l.o ar: `u' modifier ignored since `D' is the default (see `U') make[5]: Leaving directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/COLAMD/Source' make[4]: Leaving directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/COLAMD' make[4]: Entering directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/AMD' ( cd Source ; make -f "/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/etc/Makeconf" -f Makefile lib ) make[5]: Entering directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/AMD/Source' gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDINT -c amd_1.c -o amd_i_1.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDLONG -c amd_1.c -o amd_l_1.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDINT -c amd_2.c -o amd_i_2.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDLONG -c amd_2.c -o amd_l_2.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDINT -c amd_order.c -o amd_i_order.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDLONG -c amd_order.c -o amd_l_order.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDINT -c amd_control.c -o amd_i_control.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDLONG -c amd_control.c -o amd_l_control.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDINT -c amd_info.c -o amd_i_info.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDLONG -c amd_info.c -o amd_l_info.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o ar -rucs ../../AMD.a amd_i_aat.o amd_l_aat.o amd_i_1.o amd_l_1.o amd_i_2.o amd_l_2.o amd_i_postorder.o amd_l_postorder.o amd_i_post_tree.o amd_l_post_tree.o amd_i_defaults.o amd_l_defaults.o amd_i_order.o amd_l_order.o amd_i_control.o amd_l_control.o amd_i_info.o amd_l_info.o amd_i_valid.o amd_l_valid.o amd_i_preprocess.o amd_l_preprocess.o amd_i_dump.o amd_l_dump.o ar: `u' modifier ignored since `D' is the default (see `U') make[5]: Leaving directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/AMD/Source' make[4]: Leaving directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/AMD' make[4]: Entering directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/SuiteSparse_config' gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -DNTIMER -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c SuiteSparse_config.c -o SuiteSparse_config.o ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Leaving directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src/SuiteSparse_config' gcc -shared -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o Matrix.so Csparse.o abIndex.o attrib.o bind.o chm_common.o cholmod-etc.o coerce.o cs.o cs-etc.o dense.o determinant.o dgCMatrix.o dgeMatrix.o factorizations.o idz.o init.o kappa.o objects.o perm.o products.o solve.o sparse.o sparseVector.o subscript.o utils-R.o utils.o validity.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -llapack -lblas -lgfortran -lm -lquadmath -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -lR make[3]: Leaving directory '/tmp/archlinux-ci/RtmpQkdrbc/R.INSTALL107e6749bfa544/Matrix/src' installing to /tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/library/Matrix/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for 'zapsmall' from package 'base' in package 'Matrix' in method for 'coerce' with signature '"matrix.csc","dgCMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csr","dgRMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","dgTMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csr","dgCMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","dgCMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csc","CsparseMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csc","RsparseMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csc","TsparseMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csr","CsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csr","RsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csr","TsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","CsparseMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.coo","RsparseMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.coo","TsparseMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csc","sparseMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csr","sparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","sparseMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csc","Matrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csr","Matrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","Matrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"dgCMatrix","matrix.csc"': no definition for class "matrix.csc" in method for 'coerce' with signature '"dgRMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"dgTMatrix","matrix.coo"': no definition for class "matrix.coo" in method for 'coerce' with signature '"Matrix","matrix.csc"': no definition for class "matrix.csc" in method for 'coerce' with signature '"Matrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"Matrix","matrix.coo"': no definition for class "matrix.coo" Creating a generic function for 'drop' from package 'base' in package 'Matrix' Creating a generic function for 'chol2inv' from 'base' in package 'Matrix' (from the saved implicit definition) Creating a generic function for 'chol2inv' from package 'base' in package 'Matrix' Creating a generic function for 'diag' from package 'base' in package 'Matrix' Creating a generic function for 'colSums' from package 'base' in package 'Matrix' Creating a generic function for 'colMeans' from package 'base' in package 'Matrix' Creating a generic function for 'rowSums' from package 'base' in package 'Matrix' Creating a generic function for 'rowMeans' from package 'base' in package 'Matrix' Creating a generic function for 'diag<-' from package 'base' in package 'Matrix' Creating a generic function for 'unname' from package 'base' in package 'Matrix' in method for 'coerce' with signature '"graphAM","TsparseMatrix"': no definition for class "graphAM" in method for 'coerce' with signature '"graphNEL","TsparseMatrix"': no definition for class "graphNEL" in method for 'coerce' with signature '"graph","CsparseMatrix"': no definition for class "graph" in method for 'coerce' with signature '"graph","RsparseMatrix"': no definition for class "graph" in method for 'coerce' with signature '"graph","TsparseMatrix"': no definition for class "graph" in method for 'coerce' with signature '"graph","sparseMatrix"': no definition for class "graph" in method for 'coerce' with signature '"graph","Matrix"': no definition for class "graph" in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no definition for class "graphNEL" in method for 'coerce' with signature '"Matrix","graphNEL"': no definition for class "graphNEL" in method for 'coerce' with signature '"Matrix","graph"': no definition for class "graph" Creating a generic function for 'norm' from package 'base' in package 'Matrix' Creating a generic function for 'rcond' from 'base' in package 'Matrix' (from the saved implicit definition) Creating a generic function for 'rcond' from package 'base' in package 'Matrix' Creating a generic function for 'cov2cor' from package 'stats' in package 'Matrix' Creating a generic function for 'crossprod' from package 'base' in package 'Matrix' Creating a generic function for 'tcrossprod' from package 'base' in package 'Matrix' Creating a generic function for 'qr.Q' from package 'base' in package 'Matrix' Creating a generic function for 'qr.R' from package 'base' in package 'Matrix' Creating a generic function for 'qr.X' from package 'base' in package 'Matrix' Creating a generic function for 'qr.coef' from package 'base' in package 'Matrix' Creating a generic function for 'qr.fitted' from package 'base' in package 'Matrix' Creating a generic function for 'qr.resid' from package 'base' in package 'Matrix' Creating a generic function for 'qr.qty' from package 'base' in package 'Matrix' Creating a generic function for 'qr.qy' from package 'base' in package 'Matrix' Creating a generic function for 'toeplitz' from 'stats' in package 'Matrix' (from the saved implicit definition) Creating a generic function for 'toeplitz' from package 'stats' in package 'Matrix' Creating a generic function for 'which' from package 'base' in package 'Matrix' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (Matrix) begin installing recommended package survival begin installing recommended package mgcv * installing *source* package 'survival' ... ** package 'survival' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: 'gcc (GCC) 13.2.1 20230801' make[3]: Entering directory '/tmp/archlinux-ci/RtmpajYBlX/R.INSTALL1080ce778c1c70/survival/src' gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c agexact.c -o agexact.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c agfit4.c -o agfit4.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c agfit5.c -o agfit5.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c agmart.c -o agmart.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c agmart3.c -o agmart3.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c agscore2.c -o agscore2.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c agscore3.c -o agscore3.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c agsurv4.c -o agsurv4.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c agsurv5.c -o agsurv5.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c cdecomp.c -o cdecomp.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c chinv2.c -o chinv2.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c chinv3.c -o chinv3.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c cholesky2.c -o cholesky2.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c cholesky3.c -o cholesky3.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c cholesky5.c -o cholesky5.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c chsolve2.c -o chsolve2.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c chsolve3.c -o chsolve3.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c chsolve5.c -o chsolve5.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c collapse.c -o collapse.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c concordance1.c -o concordance1.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c concordance3.c -o concordance3.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c concordance5.c -o concordance5.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c cox_Rcallback.c -o cox_Rcallback.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c coxcount1.c -o coxcount1.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c coxdetail.c -o coxdetail.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c coxexact.c -o coxexact.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c coxfit5.c -o coxfit5.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c coxfit6.c -o coxfit6.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c coxfit7.c -o coxfit7.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c coxmart.c -o coxmart.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c coxmart2.c -o coxmart2.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c coxph_wtest.c -o coxph_wtest.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c coxsafe.c -o coxsafe.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c coxscho.c -o coxscho.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c coxscore2.c -o coxscore2.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c coxsurv1.c -o coxsurv1.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c coxsurv2.c -o coxsurv2.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c coxsurv3.c -o coxsurv3.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c coxsurv4.c -o coxsurv4.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dmatrix.c -o dmatrix.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c doloop.c -o doloop.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c fastkm.c -o fastkm.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c finegray.c -o finegray.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c gchol.c -o gchol.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c init.c -o init.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c multicheck.c -o multicheck.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c norisk.c -o norisk.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pyears1.c -o pyears1.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pyears2.c -o pyears2.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pyears3b.c -o pyears3b.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pystep.c -o pystep.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c residcsum.c -o residcsum.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c survConcordance.c -o survConcordance.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c survdiff2.c -o survdiff2.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c survfit4.c -o survfit4.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c survfitci.c -o survfitci.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c survfitkm.c -o survfitkm.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c survfitresid.c -o survfitresid.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c survpenal.c -o survpenal.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c survreg6.c -o survreg6.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c survreg7.c -o survreg7.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c survregc1.c -o survregc1.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c survregc2.c -o survregc2.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c survsplit.c -o survsplit.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c tmerge.c -o tmerge.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c zph1.c -o zph1.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c zph2.c -o zph2.o gcc -shared -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o survival.so agexact.o agfit4.o agfit5.o agmart.o agmart3.o agscore2.o agscore3.o agsurv4.o agsurv5.o cdecomp.o chinv2.o chinv3.o cholesky2.o cholesky3.o cholesky5.o chsolve2.o chsolve3.o chsolve5.o collapse.o concordance1.o concordance3.o concordance5.o cox_Rcallback.o coxcount1.o coxdetail.o coxexact.o coxfit5.o coxfit6.o coxfit7.o coxmart.o coxmart2.o coxph_wtest.o coxsafe.o coxscho.o coxscore2.o coxsurv1.o coxsurv2.o coxsurv3.o coxsurv4.o dmatrix.o doloop.o fastkm.o finegray.o gchol.o init.o multicheck.o norisk.o pyears1.o pyears2.o pyears3b.o pystep.o residcsum.o survConcordance.o survdiff2.o survfit4.o survfitci.o survfitkm.o survfitresid.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o survsplit.o tmerge.o zph1.o zph2.o -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -lR make[3]: Leaving directory '/tmp/archlinux-ci/RtmpajYBlX/R.INSTALL1080ce778c1c70/survival/src' installing to /tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/library/survival/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (survival) begin installing recommended package boot * installing *source* package 'boot' ... ** package 'boot' successfully unpacked and MD5 sums checked ** using non-staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (boot) * installing *source* package 'mgcv' ... ** package 'mgcv' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: 'gcc (GCC) 13.2.1 20230801' make[3]: Entering directory '/tmp/archlinux-ci/RtmpMlhTb5/R.INSTALL1080cb531f33d5/mgcv/src' gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c coxph.c -o coxph.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c davies.c -o davies.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c discrete.c -o discrete.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c gdi.c -o gdi.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c init.c -o init.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c magic.c -o magic.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c mat.c -o mat.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c matrix.c -o matrix.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c mgcv.c -o mgcv.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c misc.c -o misc.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c mvn.c -o mvn.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ncv.c -o ncv.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qp.c -o qp.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c soap.c -o soap.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c sparse-smooth.c -o sparse-smooth.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c sparse.c -o sparse.o gcc -I"/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c tprs.c -o tprs.o gcc -shared -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o mgcv.so coxph.o davies.o discrete.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o ncv.o qp.o soap.o sparse-smooth.o sparse.o tprs.o -llapack -lblas -lgfortran -lm -lquadmath -fopenmp -L/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/lib -lR make[3]: Leaving directory '/tmp/archlinux-ci/RtmpMlhTb5/R.INSTALL1080cb531f33d5/mgcv/src' installing to /tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/library/mgcv/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (mgcv) make[2]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/Recommended' make[1]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library/Recommended' make[1]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/doc' make[1]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/doc' make[2]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/doc/manual' creating 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R-FAQ.texi collecting LaTeX docs for package 'methods' ... collecting LaTeX docs for package 'tcltk' ... collecting LaTeX docs for package 'base' ... collecting LaTeX docs for package 'graphics' ... collecting LaTeX docs for package 'parallel' ... collecting LaTeX docs for package 'stats4' ... collecting LaTeX docs for package 'stats' ... collecting LaTeX docs for package 'grid' ... collecting LaTeX docs for package 'utils' ... collecting LaTeX docs for package 'grDevices' ... collecting LaTeX docs for package 'splines' ... collecting LaTeX docs for package 'datasets' ... collecting LaTeX docs for package 'tools' ... collecting LaTeX docs for package 'compiler' ... Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX . collecting LaTeX docs for package 'MASS' ... collecting LaTeX docs for package 'lattice' ... ..... collecting LaTeX docs for package 'Matrix' ... . collecting LaTeX docs for package 'nlme' ... collecting LaTeX docs for package 'survival' ... ....Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX .....Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX ..Converting parsed Rd's to LaTeX .............../usr/sbin/texi2any --enable-encoding -D UseExternalXrefs -I. R-admin.texi ......... collecting LaTeX docs for package 'boot' ... ...... ...collecting LaTeX docs for package 'cluster' ... ..Converting parsed Rd's to LaTeX ............Converting parsed Rd's to LaTeX .... .collecting LaTeX docs for package 'codetools' ... .............Converting parsed Rd's to LaTeX ...... ...collecting LaTeX docs for package 'foreign' ... ............Converting parsed Rd's to LaTeX ......... .collecting LaTeX docs for package 'KernSmooth' ... ...... collecting LaTeX docs for package 'rpart' ... .... ..collecting LaTeX docs for package 'class' ... ..Converting parsed Rd's to LaTeX ..collecting LaTeX docs for package 'nnet' ... Converting parsed Rd's to LaTeX ...... Converting parsed Rd's to LaTeX collecting LaTeX docs for package 'spatial' ... collecting LaTeX docs for package 'mgcv' ... ... ..TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/sbin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-FAQ.texi TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/sbin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-admin.texi Converting parsed Rd's to LaTeX ..../usr/sbin/texi2any --enable-encoding -D UseExternalXrefs -I. R-data.texi Converting parsed Rd's to LaTeX TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/sbin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-data.texi Converting parsed Rd's to LaTeX ...TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/sbin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-exts.texi /usr/sbin/texi2dvi: texinfo.tex appears to be broken. This may be due to the environment variable TEX set to something other than (plain) tex, a corrupt texinfo.tex file, or to tex itself simply not working. This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Arch Linux) (preloaded format=etex) restricted \write18 enabled. entering extended mode (./txiversion.tex ! I can't find file `texinfo.tex'. l.1 \input texinfo.tex @bye (Press Enter to retry, or Control-D to exit) Please type another input file name: ! Emergency stop. l.1 No pages of output. Transcript written on txiversion.log. /usr/sbin/texi2dvi: texinfo.tex appears to be broken. This may be due to the environment variable TEX set to something other than (plain) tex, a corrupt texinfo.tex file, or to tex itself simply not working. /usr/sbin/texi2dvi: quitting. This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Arch Linux) (preloaded format=etex) restricted \write18 enabled. entering extended mode (./txiversion.tex ! I can't find file `texinfo.tex'. l.1 \input texinfo.tex @bye (Press Enter to retry, or Control-D to exit) Please type another input file name: ! Emergency stop. l.1 No pages of output. 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I can't find file `texinfo.tex'. l.1 \input texinfo.tex @bye (Press Enter to retry, or Control-D to exit) Please type another input file name: ! Emergency stop. l.1 No pages of output. Transcript written on txiversion.log. /usr/sbin/texi2dvi: quitting. make[2]: *** [Makefile:109: R-data.pdf] Error 1 .../usr/sbin/texi2dvi: texinfo.tex appears to be broken. This may be due to the environment variable TEX set to something other than (plain) tex, a corrupt texinfo.tex file, or to tex itself simply not working. This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Arch Linux) (preloaded format=etex) restricted \write18 enabled. entering extended mode (./txiversion.tex ! I can't find file `texinfo.tex'. l.1 \input texinfo.tex @bye (Press Enter to retry, or Control-D to exit) Please type another input file name: ! Emergency stop. l.1 No pages of output. Transcript written on txiversion.log. /usr/sbin/texi2dvi: quitting. make[2]: *** [Makefile:109: R-exts.pdf] Error 1 . ............ ...................... ....................... ........... ............. ...make[2]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/doc/manual' make[1]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/doc' ........... make[2]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/doc/manual' make[1]: *** [Makefile:174: pdf] Error 2 make[1]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/doc' make: [Makefile:292: pdf] Error 2 (ignored) (cd ../../include; make Rmath.h) Copying source files make[1]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/include' make[1]: 'Rmath.h' is up to date. make[1]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/include' make[1]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/nmath/standalone' making d1mach.d from d1mach.c making mlutils.d from mlutils.c making fmax2.d from fmax2.c making i1mach.d from i1mach.c making fprec.d from fprec.c making fmin2.d from fmin2.c making fround.d from fround.c making ftrunc.d from ftrunc.c making sign.d from sign.c making fsign.d from fsign.c making imax2.d from imax2.c making imin2.d from imin2.c making chebyshev.d from chebyshev.c making log1p.d from log1p.c making lgammacor.d from lgammacor.c making gammalims.d from gammalims.c making stirlerr.d from stirlerr.c making bd0.d from bd0.c making gamma.d from gamma.c making lgamma.d from lgamma.c making gamma_cody.d from gamma_cody.c making beta.d from beta.c making lbeta.d from lbeta.c making polygamma.d from polygamma.c making cospi.d from cospi.c making bessel_i.d from bessel_i.c making bessel_j.d from bessel_j.c making bessel_k.d from bessel_k.c making bessel_y.d from bessel_y.c making choose.d from choose.c making snorm.d from snorm.c making sexp.d from sexp.c making dgamma.d from dgamma.c making pgamma.d from pgamma.c making qgamma.d from qgamma.c making rgamma.d from rgamma.c making dbeta.d from dbeta.c making pbeta.d from pbeta.c making qbeta.d from qbeta.c making rbeta.d from rbeta.c making dunif.d from dunif.c making punif.d from punif.c making qunif.d from qunif.c making runif.d from runif.c making dnorm.d from dnorm.c making pnorm.d from pnorm.c making qnorm.d from qnorm.c making rnorm.d from rnorm.c making dlnorm.d from dlnorm.c making plnorm.d from plnorm.c making qlnorm.d from qlnorm.c making rlnorm.d from rlnorm.c making df.d from df.c making pf.d from pf.c making qf.d from qf.c making rf.d from rf.c making dnf.d from dnf.c making dt.d from dt.c making pt.d from pt.c making qt.d from qt.c making rt.d from rt.c making dnt.d from dnt.c making dchisq.d from dchisq.c making pchisq.d from pchisq.c making qchisq.d from qchisq.c making rchisq.d from rchisq.c making rnchisq.d from rnchisq.c making dbinom.d from dbinom.c making pbinom.d from pbinom.c making qbinom.d from qbinom.c making rbinom.d from rbinom.c making rmultinom.d from rmultinom.c making dcauchy.d from dcauchy.c making pcauchy.d from pcauchy.c making qcauchy.d from qcauchy.c making rcauchy.d from rcauchy.c making dexp.d from dexp.c making pexp.d from pexp.c making qexp.d from qexp.c making rexp.d from rexp.c making dgeom.d from dgeom.c making pgeom.d from pgeom.c making qgeom.d from qgeom.c making rgeom.d from rgeom.c making dhyper.d from dhyper.c making phyper.d from phyper.c making qhyper.d from qhyper.c making rhyper.d from rhyper.c making dnbinom.d from dnbinom.c making pnbinom.d from pnbinom.c making qnbinom.d from qnbinom.c making qnbinom_mu.d from qnbinom_mu.c making rnbinom.d from rnbinom.c making dpois.d from dpois.c making ppois.d from ppois.c making qpois.d from qpois.c making rpois.d from rpois.c making dweibull.d from dweibull.c making pweibull.d from pweibull.c making qweibull.d from qweibull.c making rweibull.d from rweibull.c making dlogis.d from dlogis.c making plogis.d from plogis.c making qlogis.d from qlogis.c making rlogis.d from rlogis.c making dnchisq.d from dnchisq.c making pnchisq.d from pnchisq.c making qnchisq.d from qnchisq.c making dnbeta.d from dnbeta.c making pnbeta.d from pnbeta.c making qnbeta.d from qnbeta.c making pnf.d from pnf.c making pnt.d from pnt.c making qnf.d from qnf.c making qnt.d from qnt.c making ptukey.d from ptukey.c making qtukey.d from qtukey.c making toms708.d from toms708.c making wilcox.d from wilcox.c making signrank.d from signrank.c making std_unif.d from std_unif.c make[1]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/nmath/standalone' make[1]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/nmath/standalone' gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c mlutils.c -o mlutils.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c d1mach.c -o d1mach.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c i1mach.c -o i1mach.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c fmax2.c -o fmax2.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c fmin2.c -o fmin2.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c fprec.c -o fprec.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c fround.c -o fround.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ftrunc.c -o ftrunc.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c sign.c -o sign.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c fsign.c -o fsign.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c imax2.c -o imax2.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c imin2.c -o imin2.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c chebyshev.c -o chebyshev.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c log1p.c -o log1p.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c lgammacor.c -o lgammacor.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c gammalims.c -o gammalims.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c stirlerr.c -o stirlerr.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c bd0.c -o bd0.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c gamma.c -o gamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c lgamma.c -o lgamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c gamma_cody.c -o gamma_cody.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c beta.c -o beta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c lbeta.c -o lbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c polygamma.c -o polygamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c cospi.c -o cospi.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c bessel_i.c -o bessel_i.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c bessel_j.c -o bessel_j.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c bessel_k.c -o bessel_k.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c bessel_y.c -o bessel_y.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c choose.c -o choose.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c snorm.c -o snorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c sexp.c -o sexp.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dgamma.c -o dgamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pgamma.c -o pgamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qgamma.c -o qgamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rgamma.c -o rgamma.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dbeta.c -o dbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pbeta.c -o pbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qbeta.c -o qbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rbeta.c -o rbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dunif.c -o dunif.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c punif.c -o punif.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qunif.c -o qunif.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c runif.c -o runif.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dnorm.c -o dnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pnorm.c -o pnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qnorm.c -o qnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rnorm.c -o rnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dlnorm.c -o dlnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c plnorm.c -o plnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qlnorm.c -o qlnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rlnorm.c -o rlnorm.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c df.c -o df.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pf.c -o pf.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qf.c -o qf.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rf.c -o rf.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dnf.c -o dnf.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dt.c -o dt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pt.c -o pt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qt.c -o qt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rt.c -o rt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dnt.c -o dnt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dchisq.c -o dchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pchisq.c -o pchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qchisq.c -o qchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rchisq.c -o rchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rnchisq.c -o rnchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dbinom.c -o dbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pbinom.c -o pbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qbinom.c -o qbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rbinom.c -o rbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rmultinom.c -o rmultinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dcauchy.c -o dcauchy.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pcauchy.c -o pcauchy.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qcauchy.c -o qcauchy.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rcauchy.c -o rcauchy.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dexp.c -o dexp.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pexp.c -o pexp.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qexp.c -o qexp.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rexp.c -o rexp.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dgeom.c -o dgeom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pgeom.c -o pgeom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qgeom.c -o qgeom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rgeom.c -o rgeom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dhyper.c -o dhyper.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c phyper.c -o phyper.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qhyper.c -o qhyper.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rhyper.c -o rhyper.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dnbinom.c -o dnbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pnbinom.c -o pnbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qnbinom.c -o qnbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qnbinom_mu.c -o qnbinom_mu.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rnbinom.c -o rnbinom.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dpois.c -o dpois.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ppois.c -o ppois.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qpois.c -o qpois.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rpois.c -o rpois.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dweibull.c -o dweibull.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pweibull.c -o pweibull.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qweibull.c -o qweibull.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rweibull.c -o rweibull.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dlogis.c -o dlogis.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c plogis.c -o plogis.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qlogis.c -o qlogis.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c rlogis.c -o rlogis.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dnchisq.c -o dnchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pnchisq.c -o pnchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qnchisq.c -o qnchisq.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c dnbeta.c -o dnbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pnbeta.c -o pnbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qnbeta.c -o qnbeta.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pnf.c -o pnf.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c pnt.c -o pnt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qnf.c -o qnf.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qnt.c -o qnt.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c ptukey.c -o ptukey.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c qtukey.c -o qtukey.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c toms708.c -o toms708.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c wilcox.c -o wilcox.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c signrank.c -o signrank.lo gcc -I. -I../../../src/include -I../../../src/include -I./.. -I/usr/local/include -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -c std_unif.c -o std_unif.lo gcc -shared -fopenmp -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o libRmath.so mlutils.lo d1mach.lo i1mach.lo fmax2.lo fmin2.lo fprec.lo fround.lo ftrunc.lo sign.lo fsign.lo imax2.lo imin2.lo chebyshev.lo log1p.lo lgammacor.lo gammalims.lo stirlerr.lo bd0.lo gamma.lo lgamma.lo gamma_cody.lo beta.lo lbeta.lo polygamma.lo cospi.lo bessel_i.lo bessel_j.lo bessel_k.lo bessel_y.lo choose.lo snorm.lo sexp.lo dgamma.lo pgamma.lo qgamma.lo rgamma.lo dbeta.lo pbeta.lo qbeta.lo rbeta.lo dunif.lo punif.lo qunif.lo runif.lo dnorm.lo pnorm.lo qnorm.lo rnorm.lo dlnorm.lo plnorm.lo qlnorm.lo rlnorm.lo df.lo pf.lo qf.lo rf.lo dnf.lo dt.lo pt.lo qt.lo rt.lo dnt.lo dchisq.lo pchisq.lo qchisq.lo rchisq.lo rnchisq.lo dbinom.lo pbinom.lo qbinom.lo rbinom.lo rmultinom.lo dcauchy.lo pcauchy.lo qcauchy.lo rcauchy.lo dexp.lo pexp.lo qexp.lo rexp.lo dgeom.lo pgeom.lo qgeom.lo rgeom.lo dhyper.lo phyper.lo qhyper.lo rhyper.lo dnbinom.lo pnbinom.lo qnbinom.lo qnbinom_mu.lo rnbinom.lo dpois.lo ppois.lo qpois.lo rpois.lo dweibull.lo pweibull.lo qweibull.lo rweibull.lo dlogis.lo plogis.lo qlogis.lo rlogis.lo dnchisq.lo pnchisq.lo qnchisq.lo dnbeta.lo pnbeta.lo qnbeta.lo pnf.lo pnt.lo qnf.lo qnt.lo ptukey.lo qtukey.lo toms708.lo wilcox.lo signrank.lo std_unif.lo -lm make[1]: Leaving directory 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I can't find file `texinfo.tex'. l.1 \input texinfo.tex @bye (Press Enter to retry, or Control-D to exit) Please type another input file name: ! Emergency stop. l.1 No pages of output. Transcript written on txiversion.log. This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Arch Linux) (preloaded format=etex) restricted \write18 enabled. entering extended mode (./txiversion.tex ! I can't find file `texinfo.tex'. l.1 \input texinfo.tex @bye (Press Enter to retry, or Control-D to exit) Please type another input file name: ! Emergency stop. l.1 No pages of output. Transcript written on txiversion.log. make[1]: *** [Makefile:109: R-FAQ.pdf] Error 1 make[1]: *** Waiting for unfinished jobs.... This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Arch Linux) (preloaded format=etex) restricted \write18 enabled. entering extended mode (./txiversion.tex ! I can't find file `texinfo.tex'. l.1 \input texinfo.tex @bye (Press Enter to retry, or Control-D to exit) Please type another input file name: ! Emergency stop. l.1 No pages of output. Transcript written on txiversion.log. make[1]: *** [Makefile:109: R-data.pdf] Error 1 /usr/sbin/texi2dvi: quitting. /usr/sbin/texi2dvi: quitting. /usr/sbin/texi2dvi: quitting. make[1]: *** [Makefile:109: R-admin.pdf] Error 1 make[1]: *** [Makefile:109: R-exts.pdf] Error 1 /usr/sbin/texi2dvi: texinfo.tex appears to be broken. This may be due to the environment variable TEX set to something other than (plain) tex, a corrupt texinfo.tex file, or to tex itself simply not working. /usr/sbin/texi2dvi: texinfo.tex appears to be broken. This may be due to the environment variable TEX set to something other than (plain) tex, a corrupt texinfo.tex file, or to tex itself simply not working. make[1]: *** [Makefile:109: R-ints.pdf] Error 1 This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Arch Linux) (preloaded format=etex) restricted \write18 enabled. entering extended mode (./txiversion.tex ! I can't find file `texinfo.tex'. l.1 \input texinfo.tex @bye (Press Enter to retry, or Control-D to exit) Please type another input file name: ! Emergency stop. l.1 No pages of output. Transcript written on txiversion.log. This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Arch Linux) (preloaded format=etex) restricted \write18 enabled. entering extended mode (./txiversion.tex ! I can't find file `texinfo.tex'. l.1 \input texinfo.tex @bye (Press Enter to retry, or Control-D to exit) Please type another input file name: ! Emergency stop. l.1 No pages of output. Transcript written on txiversion.log. /usr/sbin/texi2dvi: quitting. /usr/sbin/texi2dvi: quitting. make[1]: *** [Makefile:109: R-intro.pdf] Error 1 make[1]: *** [Makefile:109: R-lang.pdf] Error 1 make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/include/R_ext' make[2]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/include' make[2]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/extra' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/extra/blas' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/extra/blas' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/extra/tre' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/extra/tre' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/extra/tzone' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/extra/tzone' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/extra/xdr' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/extra/xdr' make[3]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/extra/intl' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/extra/intl' make[2]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/extra' make[2]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/appl' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/appl' entering extended mode (./fullrefman.tex LaTeX2e <2022-11-01> patch level 1 L3 programming layer <2023-02-22>make[2]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/nmath' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/nmath' (/usr/share/texmf-dist/tex/latex/base/book.cls Document Class: book 2022/07/02 v1.4n Standard LaTeX document class (/usr/share/texmf-dist/tex/latex/base/bk10.clo)make[2]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/unix' gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -ffat-lto-objects -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -DR_HOME='"/usr/lib/R"' \ -o Rscript ./Rscript.c ) (../../share/texmf/tex/latex/Rd.stymkdir -p -- /tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/pkg/r/usr/lib/pkgconfig (/usr/share/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texmf-dist/tex/latex/tools/bm.sty) (/usr/share/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texmf-dist/tex/latex/url/url.sty) (/usr/share/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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[1] [2]make[3]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/modules/X11' (./base-pkg.texmake[2]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/modules' Chapter 1. (/usr/share/texmf-dist/tex/latex/psnfss/t1pcr.fd)make[2]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library' (/usr/share/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texmf-dist/tex/latex/amsfonts/umsb.fd)mkdir -p -- /tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/pkg/r/usr/lib/R/library (/usr/share/texmf-dist/tex/latex/jknapltx/ursfs.fd)installing packages ... [3] [4] Underfull \hbox (badness 6741) in paragraph at lines 137--143 []\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber []\T1/pcr/m/n/ 10 x []\T1/ptm/m/n/10 such that []\T1/pcr/m/n/10 1 + x != 1[]\T1/ptm/m/n/10 . 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It Underfull \hbox (badness 1028) in paragraph at lines 143--151 \T1/ptm/m/n/10 equals []\T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits []\T 1/ptm/m/n/10 if []\T1/pcr/m/n/10 double.base Underfull \hbox (badness 2980) in paragraph at lines 143--151 []\T1/ptm/m/n/10 is 2 or []\T1/pcr/m/n/10 double.rounding []\T1/ptm/m/n/10 is 0 ; oth-er-wise, it is []\T1/pcr/m/n/10 (double.base Underfull \hbox (badness 1394) in paragraph at lines 143--151 \T1/pcr/m/n/10 ^ double.neg.ulp.digits) / 2[]\T1/ptm/m/n/10 . Nor-mally []\T1/p cr/m/n/10 1.110223e-16[]\T1/ptm/m/n/10 . As [5] Underfull \hbox (badness 1142) in paragraph at lines 215--220 []\T1/ptm/m/n/10 the num-ber of \T1/ptm/m/it/10 bytes \T1/ptm/m/n/10 in the C [ ]\T1/pcr/m/n/10 time_t []\T1/ptm/m/n/10 type: a 64-bit []\T1/pcr/m/n/10 time_t []\T1/ptm/m/n/10 (value Underfull \hbox (badness 1478) in paragraph at lines 215--220 []\T1/pcr/m/n/10 8[]\T1/ptm/m/n/10 ) is much pre-ferred these days. Note that t his is the type used by Underfull \hbox (badness 3009) in paragraph at lines 231--243 []\T1/pcr/m/n/10 *.exponent[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 *.min.exp[]\T1/p tm/m/n/10 , and []\T1/pcr/m/n/10 *.max.exp[]\T1/ptm/m/n/10 , com-puted en-tirel y anal-o-gously to their [6] [7] Underfull \hbox (badness 10000) in paragraph at lines 374--378 [][][]\T1/pcr/m/n/10 R.version[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 Sys.info[][][] []\T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-l ar, [8] [9] [10] Underfull \hbox (badness 1072) in paragraph at lines 571--577 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[] \T1/pcr/m/n/10 insertions[]\T1/ptm/m/n/10 ', [11] Overfull \hbox (4.38043pt too wide) in paragraph at lines 639--639 []\T1/pcr/m/n/9 agrep("laysy", c("1 lazy", "1", "1 LAZY"), max.distance = 2, v alue = TRUE)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 640--640 []\T1/pcr/m/n/9 agrep("laysy", c("1 lazy", "1", "1 LAZY"), max.distance = 2, i gnore.case = TRUE)[] [12] [13] (/usr/share/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [14] [15] Overfull \hbox (4.38043pt too wide) in paragraph at lines 920--920 []\T1/pcr/m/n/9 all.equal(tan(d45), one, tolerance = 0, scale = 1+(-2:2)/1e9) # "absolute"[] [16] Overfull \hbox (4.38043pt too wide) in paragraph at lines 941--941 []\T1/pcr/m/n/9 mtext(paste("mean(all.equal(x1, x2*(1 + eps_k))) {100 x} Mean rel.diff.=",[] [17] Overfull \hbox (0.78088pt too wide) in paragraph at lines 990--990 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE) [18] [19] [20] building HTML index ... [21] [22] [23] [24] (/usr/share/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texmf-dist/tex/latex/base/ts1cmtt.fd) [25{/usr/share/texmf-dist/fon ts/enc/dvips/cm-super/cm-super-ts1.enc}] Underfull \hbox (badness 1221) in paragraph at lines 1523--1529 []\T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion, where \T1/phv/m/n/10 R \T1/p tm/m/n/10 uses ``floored'' in-te-ger di-vi-sion, i.e., []\T1/pcr/m/n/10 q <- x %/% y := [26] Underfull \hbox (badness 10000) in paragraph at lines 1611--1617 Underfull \hbox (badness 10000) in paragraph at lines 1624--1626 []\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac le . com / cd / E19957-[]01 / 806-[]3568 / ncg _ [27] [28] [29] [30] Underfull \vbox (badness 10000) has occurred while \output is active [31]make[2]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/library' make[1]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src' make[1]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/tests' make[1]: Nothing to be done for 'install'. make[1]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/tests' Overfull \hbox (72.78088pt too wide) in paragraph at lines 1966--1966 [] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em pty.names = TRUE,[] Underfull \hbox (badness 1303) in paragraph at lines 1998--2001 []\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more than 256 (or [32] Underfull \hbox (badness 1325) in paragraph at lines 2027--2031 []\T1/ptm/m/n/10 Direct calls to []\T1/pcr/m/n/10 as.data.frame.() []\T1 /ptm/m/n/10 are still pos-si-ble (base pack-age!), for 12 Underfull \hbox (badness 3568) in paragraph at lines 2027--2031 \T1/ptm/m/n/10 atomic base classes, but will dep-re-cated (al-ready vis-i-bly b y set-ting en-vi-ron-ment vari- Underfull \hbox (badness 4144) in paragraph at lines 2027--2031 \T1/ptm/m/n/10 able []\T1/pcr/m/n/10 _R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_ [] \T1/ptm/m/n/10 to non-empty) where call-ing [33] [34] [35] Overfull \hbox (112.38031pt too wide) in paragraph at lines 2267--2267 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [36] Underfull \hbox (badness 10000) in paragraph at lines 2305--2307 []\T1/ptm/m/n/10 If [][][]\T1/pcr/m/n/10 is.object[][][](x) []\T1/ptm/m/n/10 is true and it has a [][][]\T1/pcr/m/n/10 class[][][] []\T1/ptm/m/n/10 for which an [37] [38] [39] [40] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2579--2579 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla ss "POSIXlt"[] [41] [42] [43] Underfull \hbox (badness 1107) in paragraph at lines 2783--2785 []\T1/ptm/m/n/10 There are no re-stric-tions on the name given as []\T1/pcr/m/n /10 x[]\T1/ptm/m/n/10 : it can be a non-syntactic name (see [44] [45] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2950--2950 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse1(substitute(what), back tick=FALSE), [46] [47] [48] [49] [50] [51] [52] Underfull \hbox (badness 10000) in paragraph at lines 3413--3416 []\T1/pcr/m/n/10 unCfillPOSIXlt(x) []\T1/ptm/m/n/10 is a fast [][]prim-i-tive[] [][] ver-sion of []\T1/pcr/m/n/10 balancePOSIXlt(x, [53] [54] [55] [56] Overfull \hbox (31.3804pt too wide) in paragraph at lines 3718--3718 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2, lwd = 1, bty="n")[] [57] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3749--3749 []\T1/pcr/m/n/9 plot(range(x0), c(1e-40, 1), log = "xy", xlab = "x", ylab = "" , type = "n",[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3750--3750 [] \T1/pcr/m/n/9 main = "Bessel Functions J_nu(x) near 0\n log - log sc ale") ; axis(2, at=1)[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3757--3757 []\T1/pcr/m/n/9 plot(range(x0), 10^c(-100, 80), log = "xy", xlab = "x", ylab = "", type = "n",[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3758--3758 [] \T1/pcr/m/n/9 main = "Bessel Functions K_nu(x) near 0\n log - log sc ale") ; axis(2, at=1)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3761--3761 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5, sep = ", ")),[] Underfull \vbox (badness 10000) has occurred while \output is active [58] [59] [60] [61] [62] [63] [64] Underfull \hbox (badness 10000) in paragraph at lines 4209--4211 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [65] [66] [67] [68] [69] [70] [71] Underfull \hbox (badness 4927) in paragraph at lines 4714--4718 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an ob-ject Underfull \hbox (badness 2012) in paragraph at lines 4714--4718 \T1/ptm/m/n/10 of class []\T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"[]\T1/ptm/ m/n/10 , []\T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" []\T1/ptm/m/n/10 o r [72] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4798--4798 [] \T1/pcr/m/n/10 Xchk = any(nas %in% c("X11", "jpeg", "png", "tif f")))[] [73] Underfull \hbox (badness 4595) in paragraph at lines 4872--4875 []\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par -i-son[][][] and [74] [75] [76] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5035--5035 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{ ", 1:10, "}:"))[] Underfull \hbox (badness 1199) in paragraph at lines 5064--5070 []\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na med ar-gu- Underfull \hbox (badness 2573) in paragraph at lines 5076--5079 []\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu e and valid [77] [78] [79] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5249--5249 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna mes (default)[] [80] [81] [82] Underfull \hbox (badness 2521) in paragraph at lines 5506--5508 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [83] [84] [85] [86] [87] [88] [89] [90] Underfull \hbox (badness 1270) in paragraph at lines 5998--6006 []\T1/ptm/m/n/10 When a generic func-tion []\T1/pcr/m/n/10 fun []\T1/ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute []\T1/pcr/m/n/10 c("first", [91] [92] [93] [94] [95] [96] [97] [98] Underfull \hbox (badness 1796) in paragraph at lines 6572--6580 []\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i n-tro-duc-tion see [][]$\T1/pcr/m/n/10 https : / / [99] [100] [101] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6769--6769 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile r, math-library:[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 6771--6771 []\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6772--6772 []\T1/pcr/m/n/9 showC(NpNA)# but not always is {shows \TS1/pcr/m/n/9 '\T1/pcr /m/n/9 (R = NaN, I = NA)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 on some platforms}[] [102] [103] Underfull \hbox (badness 1635) in paragraph at lines 6974--6977 []\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class []\T1/pcr/m/n /10 interrupt []\T1/ptm/m/n/10 that in-her-its di-rectly from class Underfull \hbox (badness 3009) in paragraph at lines 6978--6981 []\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols. They can be es-tab-lished us-ing [104] Underfull \hbox (badness 1308) in paragraph at lines 7021--7029 []\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i s []\T1/pcr/m/n/10 interactive[]\T1/ptm/m/n/10 . This should [105] [106] Overfull \hbox (30.78088pt too wide) in paragraph at lines 7185--7185 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e ncoding"))[] [107] Underfull \hbox (badness 4505) in paragraph at lines 7237--7240 []\T1/ptm/m/n/10 character string, par-tially matched to []\T1/pcr/m/n/10 c("de fault", "internal", [108] [109] Underfull \hbox (badness 1997) in paragraph at lines 7374--7379 []\T1/pcr/m/n/10 file[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pipe[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 fifo[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 url[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 gzfile[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 bzfile[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 xzfile[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 unz[]\T1/ptm/m /n/10 , []\T1/pcr/m/n/10 socketConnection[]\T1/ptm/m/n/10 , [110] [111] [112] Underfull \hbox (badness 10000) in paragraph at lines 7622--7624 []\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in g from Underfull \hbox (badness 3302) in paragraph at lines 7664--7671 []\T1/pcr/m/n/10 file []\T1/ptm/m/n/10 can be used with []\T1/pcr/m/n/10 descri ption = "clipboard" []\T1/ptm/m/n/10 in mode []\T1/pcr/m/n/10 "r" []\T1/ptm/m/n /10 only. This Underfull \hbox (badness 6592) in paragraph at lines 7664--7671 \T1/ptm/m/n/10 reads the X11 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http s : / / specifications . freedesktop . Underfull \hbox (badness 1735) in paragraph at lines 7664--7671 []\T1/pcr/m/n/10 "X11_primary" []\T1/ptm/m/n/10 and the sec-ondary se-lec-tion as []\T1/pcr/m/n/10 "X11_secondary"[]\T1/ptm/m/n/10 . On most sys- [113] [114] [115] Underfull \vbox (badness 10000) has occurred while \output is active [116] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7879--7879 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE")) ; close(con)[] [117] [118] [119] [120] Underfull \hbox (badness 10000) in paragraph at lines 8212--8214 []\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th e call to [121] [122] [123] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8370--8370 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect s to https://[] [124] [125] [126] [127] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8604--8604 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng th.out = 24)[] [128] Underfull \hbox (badness 10000) in paragraph at lines 8720--8730 []\T1/pcr/m/n/10 data.frame []\T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing Underfull \hbox (badness 1975) in paragraph at lines 8720--8730 [][][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)[]\T1/ptm/m/n/10 . As that is a generic func-tion, meth-ods can be [129] [130] [131] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8888--8888 [] \T1/pcr/m/n/9 c = seq(as.Date("2004-01-01"), by = "week", l ength.out = 3),[] [132] [133] [134] [135] Underfull \hbox (badness 10000) in paragraph at lines 9216--9228 \T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") []\T1/ptm/m /n/10 may give []\T1/pcr/m/n/10 NA[]\T1/ptm/m/n/10 , and [136] [137] [138] [139] [140] [141] [142] Underfull \hbox (badness 10000) in paragraph at lines 9760--9764 []\T1/pcr/m/n/10 .Defunct []\T1/ptm/m/n/10 is called from de-funct func-tions. Func-tions should be listed in [143] [144] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9851--9851 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: -------- -------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9853--9853 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO !\n"); pi+2})[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9881--9881 [] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "( ", "function"),[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9882--9882 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh owAttributes"),[] [145] [146] Underfull \hbox (badness 5403) in paragraph at lines 10013--10015 []\T1/pcr/m/n/10 ..deparseOpts []\T1/ptm/m/n/10 is the [][][]\T1/pcr/m/n/10 cha racter[][][] []\T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used b y Underfull \hbox (badness 6063) in paragraph at lines 10032--10034 []\T1/ptm/m/n/10 Surround un-eval-u-ated ex-pres-sions, but not [][][]\T1/pcr/m /n/10 formula[][][][]\T1/ptm/m/n/10 s, with [147] [148] [149] Underfull \hbox (badness 1603) in paragraph at lines 10263--10266 []\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t er-mi-nant if [150] [151] [152] [153] [154] [155] [156] Overfull \hbox (12.78088pt too wide) in paragraph at lines 10728--10728 [] \T1/pcr/m/n/10 z <- as.POSIXct(c("2016-12-31 23:59:59", "2017-01-01 00:0 0:01"))[] [157] [158] Underfull \hbox (badness 1917) in paragraph at lines 10892--10897 []\T1/pcr/m/n/10 provideDimnames(x) []\T1/ptm/m/n/10 pro-vides []\T1/pcr/m/n/10 dimnames []\T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has [159] Overfull \hbox (36.7804pt too wide) in paragraph at lines 10947--10947 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE RS)))) # recycling[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10948--10948 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling on both levels[] [160] [161] Underfull \hbox (badness 1168) in paragraph at lines 11050--11055 []\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of []\ T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . Cur-rently this is only used by [162] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11152--11152 []\T1/pcr/m/n/9 ## From R 4.1.0 to 4.1.2, ...names() sometimes did not match n ames(list(...));[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 11154--11154 []\T1/pcr/m/n/9 chk.n2 <- function(...) stopifnot(identical(print(...names()), names(list(...))))[] [163] [164] Underfull \hbox (badness 2828) in paragraph at lines 11273--11278 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19 85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Underfull \hbox (badness 10000) in paragraph at lines 11273--11278 \T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr /m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ Underfull \hbox (badness 10000) in paragraph at lines 11273--11278 \T1/pcr/m/n/10 754-[]2019$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ pcr/m/n/10 https : Overfull \hbox (42.78088pt too wide) in paragraph at lines 11304--11304 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA ttributes"))[] [165] Overfull \hbox (15.18042pt too wide) in paragraph at lines 11378--11378 []\T1/pcr/m/n/9 ## Write an ASCII version of the \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 base\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 function mean() to our temp file, ..[] [166] [167] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11527--11527 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon th.abb[5:9])) [168] [169] [170] Underfull \hbox (badness 6396) in paragraph at lines 11725--11733 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for Underfull \hbox (badness 10000) in paragraph at lines 11734--11736 []\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) []\T1/ptm/m/n/10 is equiv-a-len t to but faster than [171] [172] [173] Underfull \hbox (badness 10000) in paragraph at lines 11951--11954 []\T1/ptm/m/n/10 Do not use []\T1/pcr/m/n/10 dyn.unload []\T1/ptm/m/n/10 on a D LL loaded by [][][]\T1/pcr/m/n/10 library.dynam[][][][]\T1/ptm/m/n/10 : use [174] [175] [176] [177] [178] [179] Underfull \hbox (badness 2744) in paragraph at lines 12398--12400 []\T1/ptm/m/n/10 Changing the cur-rent en-cod-ing from a run-ning R ses-sion ma y lead to con-fu-sion (see [180] Overfull \hbox (20.58041pt too wide) in paragraph at lines 12421--12421 []\T1/pcr/m/n/9 Encoding(x.) # "unknown" (UTF-8 loc.) | "latin1" (8859-1/CP-12 52 loc.) | ....[] [181] [182] [183] Underfull \hbox (badness 5288) in paragraph at lines 12673--12675 []\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val ue of Underfull \hbox (badness 3039) in paragraph at lines 12683--12688 []\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][][]\T1/pcr/m/n/1 0 dev2bitmap[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 bitmap[][][] []\T1/pt m/m/n/10 and [184] Underfull \hbox (badness 10000) in paragraph at lines 12740--12743 []\T1/ptm/m/n/10 The path to HTML []\T1/pcr/m/n/10 tidy[]\T1/ptm/m/n/10 . Used by []\T1/pcr/m/n/10 R CMD check []\T1/ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 12758--12760 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [185] [186] [187] [188] Underfull \hbox (badness 10000) in paragraph at lines 13008--13010 []\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing []\T1/pc r/m/n/10 where []\T1/ptm/m/n/10 as Underfull \hbox (badness 5970) in paragraph at lines 13051--13053 []\T1/pcr/m/n/10 get0(): []\T1/ptm/m/n/10 The object---as from [][][]\T1/pcr/m/ n/10 get[][][](x, *)[]\T1/ptm/m/n/10 --- if []\T1/pcr/m/n/10 exists(x, *) []\T1 /ptm/m/n/10 is true, oth-er-wise [189] [190] [191] [192] [193] [194] [195] [196] [197] [198] [199] [200] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13874--13874 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide a constructor[] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] Underfull \hbox (badness 2253) in paragraph at lines 14602--14604 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see Underfull \hbox (badness 1490) in paragraph at lines 14637--14640 []\T1/ptm/m/n/10 Junction points and sym-bolic links are fol-lowed, so in-for-m a-tion is given about the [211] [212] Underfull \hbox (badness 2573) in paragraph at lines 14770--14772 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as []\T1/pcr /m/n/10 PATH []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 R_LIBS []\T1/ptm/m/n/10 with []\T1/pcr/m/n/10 fsep = [213] [214] Underfull \hbox (badness 10000) in paragraph at lines 14929--14931 []\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See [215] [216] Underfull \hbox (badness 10000) in paragraph at lines 15050--15054 [][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil e.access[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.path[][][][]\T1/ptm/ m/n/10 , [][][]\T1/pcr/m/n/10 file.show[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 list.files[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 unlink[][][][]\T1 /ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 15061--15064 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Overfull \hbox (47.58038pt too wide) in paragraph at lines 15082--15082 [] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B as it exists already[] [217] Overfull \hbox (30.78088pt too wide) in paragraph at lines 15107--15107 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [218] Underfull \hbox (badness 10000) in paragraph at lines 15204--15207 [][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil e.exists[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.path[][][][]\T1/ptm/ m/n/10 , [][][]\T1/pcr/m/n/10 list.files[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/ m/n/10 unlink[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 basename[][][][]\T1/ ptm/m/n/10 , Overfull \hbox (9.78043pt too wide) in paragraph at lines 15214--15214 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu rsive = TRUE)[] [219] Underfull \hbox (badness 10000) in paragraph at lines 15280--15283 []\T1/pcr/m/n/10 packageNotFoundError []\T1/ptm/m/n/10 cre-ates an er-ror con-d i-tion ob-ject of class Overfull \hbox (20.58041pt too wide) in paragraph at lines 15297--15297 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio ns it is found:[] [220] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15326--15326 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE, Underfull \hbox (badness 3965) in paragraph at lines 15358--15362 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [221] [222] [223] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15522--15522 [] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING) Overfull \hbox (0.78088pt too wide) in paragraph at lines 15523--15523 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING)[] [224] [225] [226] [227] Overfull \hbox (63.78036pt too wide) in paragraph at lines 15765--15765 []\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have type symbol (aka name).[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15768--15768 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co mbination with[] [228] Underfull \hbox (badness 1168) in paragraph at lines 15854--15858 []\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real or com-plex vec- Underfull \hbox (badness 2012) in paragraph at lines 15854--15858 \T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger penalty (see [229] Underfull \hbox (badness 6944) in paragraph at lines 15951--15954 [][][]\T1/pcr/m/n/10 formatC[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 paste [][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 as.character[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/pcr/m/n/10 sprintf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 p rint[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 prettyNum[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 toString[][][][]\T1/ptm/m/n/10 , [230] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15976--15976 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1 0,100,1000),[] [231] [232] Underfull \hbox (badness 10000) in paragraph at lines 16114--16116 []\T1/pcr/m/n/10 prettyNum() []\T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (p os-si-bly for-mat-ted) num-bers, also in Overfull \hbox (48.78088pt too wide) in paragraph at lines 16134--16134 [] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = decimal.mark,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16140--16140 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric (x)),[] Underfull \hbox (badness 2790) in paragraph at lines 16147--16150 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] []\T1/pcr/m/n/10 complex[][][] []\T1/ptm/m/n/10 only for [233] Underfull \hbox (badness 1024) in paragraph at lines 16178--16185 []\T1/pcr/m/n/10 "f" []\T1/ptm/m/n/10 gives num-bers in the usual []\T1/pcr/m/n /10 xxx.xxx []\T1/ptm/m/n/10 for-mat; []\T1/pcr/m/n/10 "e" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "E" []\T1/ptm/m/n/10 give [234] Underfull \hbox (badness 10000) in paragraph at lines 16253--16255 []\T1/ptm/m/n/10 This works via []\T1/pcr/m/n/10 prettyNum()[]\T1/ptm/m/n/10 , which calls []\T1/pcr/m/n/10 .format.zeros(*, Underfull \hbox (badness 10000) in paragraph at lines 16275--16280 []\T1/ptm/m/n/10 For num-bers, []\T1/pcr/m/n/10 formatC() []\T1/ptm/m/n/10 call s []\T1/pcr/m/n/10 prettyNum() []\T1/ptm/m/n/10 when needed which it-self calls Underfull \hbox (badness 2426) in paragraph at lines 16281--16283 []\T1/ptm/m/n/10 If you set []\T1/pcr/m/n/10 format []\T1/ptm/m/n/10 it over-ri des the set-ting of []\T1/pcr/m/n/10 mode[]\T1/ptm/m/n/10 , so []\T1/pcr/m/n/10 formatC(123.45, mode = Underfull \hbox (badness 10000) in paragraph at lines 16292--16300 []\T1/pcr/m/n/10 prettyNum []\T1/ptm/m/n/10 is the util-ity func-tion for pret- ti-fy-ing []\T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 x []\T1/ptm/m/n /10 can be com-plex (or [235] [236] Overfull \hbox (4.38043pt too wide) in paragraph at lines 16400--16400 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big .mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 16422--16422 []\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you want see the effect[] Underfull \vbox (badness 10000) has occurred while \output is active [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17256--17256 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil l a DLLInfoList[] [249] [250] Underfull \hbox (badness 2418) in paragraph at lines 17365--17369 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing [ ]\T1/pcr/m/n/10 CRoutine[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 CallRoutine[]\T1/pt m/m/n/10 , Underfull \hbox (badness 6510) in paragraph at lines 17372--17375 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 name []\T1/ptm/m/n/10 con-tains only one s ym-bol name and []\T1/pcr/m/n/10 unlist []\T1/ptm/m/n/10 is []\T1/pcr/m/n/10 TR UE[]\T1/ptm/m/n/10 , then the sin-gle Underfull \hbox (badness 2326) in paragraph at lines 17407--17414 [][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][][]\T1/ptm/m/n/10 , [][][]\T1 /pcr/m/n/10 is.loaded[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .C[][][][]\T 1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .Fortran[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 .External[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .Call[][][][] \T1/ptm/m/n/10 , [251] [252] Underfull \hbox (badness 10000) in paragraph at lines 17513--17517 []\T1/ptm/m/n/10 The spe-cial case []\T1/pcr/m/n/10 bindtextdomain(NULL) []\T1/ ptm/m/n/10 calls C level Underfull \hbox (badness 3302) in paragraph at lines 17513--17517 []\T1/pcr/m/n/10 textdomain(textdomain(NULL)) []\T1/ptm/m/n/10 for the pur-pose of flush-ing (i.e., emp-ty-ing) the [253] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17580--17580 []\T1/pcr/m/n/9 if(is.na(thisLang) || !nzchar(thisLang)) thisLang <- "en" # "f actory" default[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 17583--17583 []\T1/pcr/m/n/9 gettext(enT, domain="R-stats")# "leeres Modell angegeben" (if translation works)[] Underfull \vbox (badness 10000) has occurred while \output is active [254] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17614--17614 []\T1/pcr/m/n/9 ## Here, we reset to the *original* setting before the full ex ample started:[] [255] [256] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17751--17751 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE, Underfull \hbox (badness 1867) in paragraph at lines 17779--17786 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [257] [258] [259] [260] [261] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18097--18097 [] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around "checking hack"[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 18126--18126 []\T1/pcr/m/n/9 name.rex <- "(?[[:upper:]][[:lower:]]+) (?[[:uppe r:]][[:lower:]]+)"[] Underfull \vbox (badness 10000) has occurred while \output is active [262] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18182--18182 [] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F ALSE)[] [263] [264] [265] [266] [267] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18575--18575 []\T1/pcr/m/n/9 (ii <- grouping(x <- c(1, 1, 3:1, 1:4, 3), y <- c(9, 9:1), z < - c(2, 1:9))) [268] Overfull \hbox (4.38043pt too wide) in paragraph at lines 18640--18640 []\T1/pcr/m/n/9 z <- gzcon(url("https://www.stats.ox.ac.uk/pub/datasets/csb/ch 12.dat.gz"))[] [269] [270] [271] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18853--18853 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F ALSE) [272] [273] Underfull \hbox (badness 1360) in paragraph at lines 19017--19022 []\T1/ptm/m/n/10 The most portable name for the ISO 8859-15 en-cod-ing, com-mon ly known as `Latin 9', Underfull \hbox (badness 1953) in paragraph at lines 19017--19022 \T1/ptm/m/n/10 is []\T1/pcr/m/n/10 "iso885915"[]\T1/ptm/m/n/10 : most plat-form s sup-port both []\T1/pcr/m/n/10 "latin-9" []\T1/ptm/m/n/10 and[]\T1/pcr/m/n/10 "latin9" []\T1/ptm/m/n/10 but GNU [274] [275] [276] Underfull \hbox (badness 1163) in paragraph at lines 19233--19235 []\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1 0 https : / / unicode-[]org . github . io / icu / Overfull \hbox (9.78043pt too wide) in paragraph at lines 19241--19241 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s ettings, we can only reset to the default.[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 19271--19271 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE, [277] [278] Overfull \hbox (30.78088pt too wide) in paragraph at lines 19365--19365 [] \T1/pcr/m/n/10 num.eq = FALSE, single.NA = FALSE, attrib.as.se t = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19366--19366 [] \T1/pcr/m/n/10 ignore.bytecode = FALSE, ignore.environment = F ALSE,[] [279] Overfull \hbox (25.98041pt too wide) in paragraph at lines 19419--19419 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------ ----------------[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 19425--19425 []\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is ignored by default[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 19428--19428 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share an environment:[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19434--19434 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi ng "srcref" :[] [280] [281] Overfull \hbox (4.38043pt too wide) in paragraph at lines 19561--19561 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u se ifelse(),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19569--19569 []\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[] [282] [283] [284] Underfull \hbox (badness 10000) in paragraph at lines 19774--19776 []\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][][]\T 1/pcr/m/n/10 stop[][][] []\T1/ptm/m/n/10 and [285] [286] [287] [288] [289] Underfull \hbox (badness 10000) in paragraph at lines 20114--20120 Underfull \hbox (badness 10000) in paragraph at lines 20127--20129 []\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac le . com / cd / E19957-[]01 / 806-[]3568 / ncg _ [290] [291] [292] [293] Underfull \hbox (badness 4699) in paragraph at lines 20371--20374 []\T1/pcr/m/n/10 is.atomic []\T1/ptm/m/n/10 is true for the [][]atomic[][][] ty pes ([]\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "integer"[]\ T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "numeric"[]\T1/ptm/m/n/10 , [294] [295] Overfull \hbox (0.78088pt too wide) in paragraph at lines 20499--20499 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [296] [297] Underfull \hbox (badness 4739) in paragraph at lines 20634--20636 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [298] Overfull \hbox (36.7804pt too wide) in paragraph at lines 20683--20683 []\T1/pcr/m/n/9 isSymmetric(D3) # FALSE (as row and co lumn names differ)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20684--20684 []\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE (as names are not checked)[] [299] [300] Underfull \hbox (badness 2961) in paragraph at lines 20861--20864 []\T1/ptm/m/n/10 LAPACK and LIN-PACK are from [][]$\T1/pcr/m/n/10 https : / / n etlib . org / lapack/$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / [301] [302] [303] [304] [305] [306] [307] Underfull \hbox (badness 1975) in paragraph at lines 21302--21305 []\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to [308] [309] [310] [311] [312] [313] Underfull \hbox (badness 1077) in paragraph at lines 21718--21723 []\T1/ptm/m/n/10 In late 2017 a []\T1/pcr/m/n/10 libcurl []\T1/ptm/m/n/10 in-st al-la-tion was seen di-vided into two li-braries, []\T1/pcr/m/n/10 libcurl []\T 1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 21732--21739 [][][]$\T1/pcr/m/n/10 https : / / curl . se / docs / sslcerts . html$[][] \T1/p tm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / curl . se / docs / [314] Underfull \hbox (badness 1112) in paragraph at lines 21805--21814 []\T1/ptm/m/n/10 At startup, the li-brary search path is ini-tial-ized from the en-vi-ron-ment vari-ables []\T1/pcr/m/n/10 R_LIBS[]\T1/ptm/m/n/10 , [315] Underfull \hbox (badness 2970) in paragraph at lines 21863--21866 []\T1/pcr/m/n/10 LOCALAPPDATA []\T1/ptm/m/n/10 (usu-ally []\T1/pcr/m/n/10 C:\Us ers\username\AppData\Local[]\T1/ptm/m/n/10 ) on Win-dows is a Underfull \hbox (badness 2951) in paragraph at lines 21863--21866 \T1/ptm/m/n/10 hid-den di-rec-tory and may not be viewed by some soft-ware. It may be opened by [316] [317] Underfull \hbox (badness 10000) in paragraph at lines 21976--21980 []\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use Underfull \hbox (badness 1454) in paragraph at lines 21976--21980 [][][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][][]\T1/ptm/m/n/10 : thi s will sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self Underfull \hbox (badness 1221) in paragraph at lines 21981--21988 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 library []\T1/ptm/m/n/10 is called with no []\T1/pcr/m/n/10 package []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 help []\T1/ptm/m /n/10 ar-gu-ment, it lists all avail-able pack- [318] [319] Underfull \hbox (badness 10000) in paragraph at lines 22110--22117 [][][]\T1/pcr/m/n/10 attach[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 detach [][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 search[][][][]\T1/ptm/m/n/10 , [] [][]\T1/pcr/m/n/10 objects[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 autoloa d[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 requireNamespace[][][][]\T1/ptm/ m/n/10 , [320] Underfull \hbox (badness 10000) in paragraph at lines 22231--22235 []\T1/ptm/m/n/10 Do not use [][][]\T1/pcr/m/n/10 dyn.unload[][][] []\T1/ptm/m/n /10 on a DLL loaded by []\T1/pcr/m/n/10 library.dynam[]\T1/ptm/m/n/10 : use [321] Underfull \hbox (badness 5161) in paragraph at lines 22301--22306 []\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di s-tributed un-der the Underfull \hbox (badness 6592) in paragraph at lines 22301--22306 \T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c opy of Underfull \hbox (badness 5133) in paragraph at lines 22301--22306 \T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L GPL-2.1\T1/ptm/m/n/10 ' and can be viewed Underfull \hbox (badness 10000) in paragraph at lines 22301--22306 \T1/ptm/m/n/10 by []\T1/pcr/m/n/10 RShowDoc("LGPL-2.1")[]\T1/ptm/m/n/10 . Ver-s ion 3 of the li-cense can be dis-played by [322] [323] [324] Overfull \hbox (6.78088pt too wide) in paragraph at lines 22469--22469 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 22473--22473 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] [325] Underfull \hbox (badness 3343) in paragraph at lines 22534--22538 [][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil e.access[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 files[][][] []\T1/ptm/ m/n/10 for many more file han-dling func-tions and [326] [327] Overfull \hbox (4.38043pt too wide) in paragraph at lines 22672--22672 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 22683--22683 [] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1, prob = 0.2))),[] [328] [329] Overfull \hbox (9.78043pt too wide) in paragraph at lines 22794--22794 []\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the same names ![] Overfull \hbox (74.58035pt too wide) in paragraph at lines 22797--22797 []\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w / same name in .GlobalEnv[] Underfull \hbox (badness 6380) in paragraph at lines 22844--22852 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- [330] [331] Underfull \hbox (badness 2564) in paragraph at lines 22947--22950 []\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/ ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of Overfull \hbox (4.38043pt too wide) in paragraph at lines 22988--22988 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other Unix-alikes[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 22992--22992 []\T1/pcr/m/n/9 c(m = months(then), wd = weekdays(then)) # in C_TIME locale \T S1/pcr/m/n/9 '\T1/pcr/m/n/9 cT\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 ; typically German [] Overfull \hbox (42.18039pt too wide) in paragraph at lines 22996--22996 []\T1/pcr/m/n/9 c(m = months(then), wd = weekdays(then)) # "standard" (still p latform specific ?)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 23003--23003 []\T1/pcr/m/n/9 ## Not run: Sys.setlocale("LC_COLLATE", "C") # turn off loca le-specific sorting,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 23005--23005 []\T1/pcr/m/n/9 Sys.setenv("LANGUAGE" = "es") # set the language for error/war ning messages[] [332] [333] [334] Underfull \hbox (badness 1400) in paragraph at lines 23179--23183 [][][]\T1/pcr/m/n/10 raw[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logical[] [][] []\T1/ptm/m/n/10 or `number-like' vec-tors (i.e., of types [][][]\T1/pcr/m /n/10 double[][][] []\T1/ptm/m/n/10 (class [335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] Overfull \hbox (52.98038pt too wide) in paragraph at lines 24021--24021 []\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary = r ), complex(real = r , imaginary = NA ),[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 24022--24022 [] \T1/pcr/m/n/9 complex(real = r , imaginary = NaN), complex(real = N aN, imaginary = r ))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 24025--24025 []\T1/pcr/m/n/9 zM ##--> many "NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s" (= 1) and th e four non-NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s (3 different ones, at 7,9,10)[] [347] [348] Overfull \hbox (20.58041pt too wide) in paragraph at lines 24122--24122 []\T1/pcr/m/n/9 match.arg(c("a", ""), c("", NA, "bb", "abc"), several.ok=TRUE ) # |--> "abc"[] Underfull \hbox (badness 1655) in paragraph at lines 24156--24160 []\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion (also known as a `clo-sure'): [349] [350] [351] [352] Underfull \hbox (badness 2277) in paragraph at lines 24407--24410 []\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross\T1/ptm/m/n/10 products, [][] []\T1/pcr/m/n/10 crossprod[][][]() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 tcross prod() []\T1/ptm/m/n/10 are typ-i-cally prefer-able. [353] [354] [355] [356] [357] [358] [359] [360] [361] Underfull \hbox (badness 1484) in paragraph at lines 25007--25015 []\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less the OS's de-fault has been Underfull \hbox (badness 1152) in paragraph at lines 25007--25015 \T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http s : / / docs . microsoft . com / en-[]gb / [362] Overfull \hbox (0.78088pt too wide) in paragraph at lines 25081--25081 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] [363] [364] [365] [366] [367] [368] [369] [370] Underfull \hbox (badness 1448) in paragraph at lines 25633--25641 []\T1/pcr/m/n/10 anyNA(recursive = FALSE) []\T1/ptm/m/n/10 works the same way a s []\T1/pcr/m/n/10 is.na[]\T1/ptm/m/n/10 ; []\T1/pcr/m/n/10 anyNA(recursive = [371] [372] Underfull \hbox (badness 3849) in paragraph at lines 25748--25753 []\T1/pcr/m/n/10 as.name []\T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter- nally to a char-ac-ter vec-tor (so meth-ods for [373] Underfull \hbox (badness 2165) in paragraph at lines 25825--25831 []\T1/ptm/m/n/10 For an [][][]\T1/pcr/m/n/10 environment[][][] env[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 names(env) []\T1/ptm/m/n/10 gives the names of the cor-r e-spond-ing list, Underfull \hbox (badness 1199) in paragraph at lines 25825--25831 \T1/ptm/m/n/10 i.e., []\T1/pcr/m/n/10 names(as.list(env, all.names = TRUE)) []\ T1/ptm/m/n/10 which are also given by [][][]\T1/pcr/m/n/10 ls[][][](env, Underfull \hbox (badness 3148) in paragraph at lines 25825--25831 \T1/pcr/m/n/10 all.names = TRUE, sorted = FALSE)[]\T1/ptm/m/n/10 . If the en-vi -ron-ment is used as a hash ta-ble, [374] [375] Underfull \hbox (badness 2237) in paragraph at lines 25988--25990 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of []\T1/pcr/m/n/1 0 c("bytes", "chars", [376] [377] [378] Underfull \hbox (badness 6188) in paragraph at lines 26215--26218 []\T1/ptm/m/n/10 optional [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 e ven-tu-ally to be passed to []\T1/pcr/m/n/10 print()[]\T1/ptm/m/n/10 , used by [379] [380] [381] Underfull \hbox (badness 1521) in paragraph at lines 26405--26419 \T1/ptm/m/n/10 tion []\T1/pcr/m/n/10 GetFinalPathNameByHandle []\T1/ptm/m/n/10 and in case of an er-ror (such as in-suf-fi-cient per- [382] [383] [384] [385] [386] Underfull \hbox (badness 2197) in paragraph at lines 26719--26723 []\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s tartup mes-sages given by Underfull \hbox (badness 4048) in paragraph at lines 26719--26723 []\T1/pcr/m/n/10 .onAttach[]\T1/ptm/m/n/10 . These mes-sages (and any es-sen-ti al ones from []\T1/pcr/m/n/10 .onLoad[]\T1/ptm/m/n/10 ) should use Underfull \hbox (badness 2846) in paragraph at lines 26733--26737 []\T1/ptm/m/n/10 Uses of []\T1/pcr/m/n/10 library []\T1/ptm/m/n/10 with ar-gu-m ent []\T1/pcr/m/n/10 help []\T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion ab out the pack- Underfull \hbox (badness 1990) in paragraph at lines 26733--26737 \T1/ptm/m/n/10 age should use []\T1/pcr/m/n/10 format []\T1/ptm/m/n/10 on the c om-puted pack-age in-for-ma-tion ob-ject and pass this to Overfull \hbox (12.78088pt too wide) in paragraph at lines 26775--26775 []\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ e.only) [387] Overfull \hbox (0.78088pt too wide) in paragraph at lines 26779--26779 [] \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk gs"))[] [388] Underfull \hbox (badness 10000) in paragraph at lines 26828--26834 []\T1/pcr/m/n/10 loadNamespace []\T1/ptm/m/n/10 does not at-tach the name space it loads to the search path. Underfull \hbox (badness 1168) in paragraph at lines 26828--26834 []\T1/pcr/m/n/10 attachNamespace []\T1/ptm/m/n/10 can be used to at-tach a fram e con-tain-ing the ex-ported val-ues of a Underfull \hbox (badness 10000) in paragraph at lines 26841--26843 []\T1/pcr/m/n/10 isNamespaceLoaded(pkg) []\T1/ptm/m/n/10 is equiv-a-lent to but more ef-fi-cient than []\T1/pcr/m/n/10 pkg %in% [389] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26908--26908 [] \T1/pcr/m/n/9 ## The string "foo" and the symbol \TS1/pcr/m/n/9 '\T1/pcr/m/ n/9 foo\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 can be used interchangably here:[] [390] [391] Underfull \hbox (badness 8189) in paragraph at lines 27103--27109 []\T1/ptm/m/n/10 The de-fault method for []\T1/pcr/m/n/10 is.numeric []\T1/ptm/ m/n/10 re-turns []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode[][][] [392] [393] [394] Underfull \hbox (badness 2591) in paragraph at lines 27329--27337 \T1/ptm/m/n/10 ject as ob-tained by [][][]\T1/pcr/m/n/10 R.version[][][][]\T1/p tm/m/n/10 . For []\T1/pcr/m/n/10 as.numeric_version []\T1/ptm/m/n/10 and [395] [396] [397] [398] [399] Underfull \hbox (badness 1603) in paragraph at lines 27611--27613 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [400] Underfull \hbox (badness 1210) in paragraph at lines 27738--27747 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini- [401] [402] [403] Underfull \hbox (badness 3271) in paragraph at lines 27960--27963 []\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men t vari-able [404] [405] [406] Underfull \hbox (badness 3138) in paragraph at lines 28273--28279 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][][]\T1/pcr/ m/n/10 setRepositories[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 28273--28279 \T1/ptm/m/n/10 e.g. the de-fault `[]\T1/pcr/m/n/10 "https://bioconductor.org"[] \T1/ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 2088) in paragraph at lines 28273--28279 \T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de "[]\T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 1194) in paragraph at lines 28286--28289 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][][]\T1/pcr/m/n/10 create.post[ ][][] []\T1/ptm/m/n/10 (and hence[][][]\T1/pcr/m/n/10 bug.report[][][] []\T1/pt m/m/n/10 and Underfull \hbox (badness 1389) in paragraph at lines 28312--28314 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [407] Underfull \hbox (badness 10000) in paragraph at lines 28339--28345 []\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by Underfull \hbox (badness 3826) in paragraph at lines 28354--28359 []\T1/ptm/m/n/10 Used by [][][]\T1/pcr/m/n/10 install.packages[][][] []\T1/ptm/ m/n/10 (and in-di-rectly Underfull \hbox (badness 1009) in paragraph at lines 28372--28375 []\T1/ptm/m/n/10 default email-ing method used by [][][]\T1/pcr/m/n/10 create.p ost[][][] []\T1/ptm/m/n/10 and hence [][][]\T1/pcr/m/n/10 bug.report[][][] []\T 1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 28388--28391 []\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle d -- see Underfull \hbox (badness 10000) in paragraph at lines 28396--28402 []\T1/pcr/m/n/10 "source" []\T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma-cOS Underfull \hbox (badness 10000) in paragraph at lines 28396--28402 \T1/ptm/m/n/10 build), []\T1/pcr/m/n/10 "mac.binary" []\T1/ptm/m/n/10 and []\T1 /pcr/m/n/10 "both" []\T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS Underfull \hbox (badness 10000) in paragraph at lines 28396--28402 \T1/ptm/m/n/10 builds). ([]\T1/pcr/m/n/10 "mac.binary.el-capitan"[]\T1/ptm/m/n/ 10 , []\T1/pcr/m/n/10 "mac.binary.mavericks"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 5091) in paragraph at lines 28396--28402 []\T1/pcr/m/n/10 "mac.binary.leopard" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "ma c.binary.universal" []\T1/ptm/m/n/10 are no longer [408] [409] [410] [411] [412] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28777--28777 []\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec, 300X faster[] [413] Underfull \hbox (badness 10000) in paragraph at lines 28790--28794 []\T1/ptm/m/n/10 where el-e-ment []\T1/pcr/m/n/10 A[c(arrayindex.x, arrayindex. y)] = FUN(X[arrayindex.x], [414] [415] Underfull \hbox (badness 1210) in paragraph at lines 28937--28940 []\T1/pcr/m/n/10 str2expression(s) []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 str2la ng(s) []\T1/ptm/m/n/10 re-turn spe-cial ver-sions of []\T1/pcr/m/n/10 parse(tex t=s, [416] [417] Overfull \hbox (25.98041pt too wide) in paragraph at lines 29133--29133 []\T1/pcr/m/n/9 tryCatch(parse(text = txt, srcfile = sf), error = function(e) "Syntax error.")[] [418] Underfull \hbox (badness 1478) in paragraph at lines 29163--29168 \T1/ptm/m/n/10 zero-length [][][]\T1/pcr/m/n/10 character[][][](0)[]\T1/ptm/m/n /10 . Note that when []\T1/pcr/m/n/10 collapse []\T1/ptm/m/n/10 is a string, [419] Underfull \hbox (badness 7133) in paragraph at lines 29222--29228 [][][]\T1/pcr/m/n/10 toString[][][] []\T1/ptm/m/n/10 typ-i-cally calls []\T1/pc r/m/n/10 paste(*, collapse=", ")[]\T1/ptm/m/n/10 . String ma-nip-u-la-tion with Overfull \hbox (42.18039pt too wide) in paragraph at lines 29244--29244 []\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as the longest input.[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 29256--29256 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha t you wanted[] Overfull \hbox (17.87582pt too wide) in paragraph at lines 29269--29269 []\T1/pcr/m/n/9 ## zero length arguments recycled as \TS1/cmtt/m/n/9 `\T1/pcr/ m/n/9 ""\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 -- NB: \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 { }\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 <==> character(0) here[] [420] Overfull \hbox (15.18042pt too wide) in paragraph at lines 29272--29272 []\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 recycle0 = TRUE\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 allows standard vectorized behaviour, i.e., zero-length[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 29273--29273 []\T1/pcr/m/n/9 ## recycling resulting in zero-length result character(0):[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 29276--29276 []\T1/pcr/m/n/9 paste("The value is", val[valid], "-- not so good!") # -> ".. value is -- not .."[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 29277--29277 []\T1/pcr/m/n/9 paste("The value is", val[valid], "-- good: empty!", recycle0= TRUE) # -> character(0)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29280--29280 []\T1/pcr/m/n/9 paste("foo", {}, "bar", collapse = "|") # |-- > "foo bar"[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29282--29282 []\T1/pcr/m/n/9 ## If all arguments are empty (and collapse a string), "" r esults always[] [421] [422] [423] Overfull \hbox (25.98041pt too wide) in paragraph at lines 29471--29471 []\T1/pcr/m/n/9 mtcars |> subset(cyl == 4) |> nrow() # same as nrow(subset(mt cars, cyl == 4))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 29489--29489 []\T1/pcr/m/n/9 stop() |> (function(...) {})() # stop() is not used on RHS so is not evaluated[] [424] Underfull \hbox (badness 1360) in paragraph at lines 29544--29548 []\T1/ptm/m/n/10 All other []\T1/pcr/m/n/10 type[]\T1/ptm/m/n/10 s give a warn- ing or an er-ror; us-ing, e.g., []\T1/pcr/m/n/10 type = [425] [426] [427] [428] Underfull \hbox (badness 2277) in paragraph at lines 29856--29861 \T1/ptm/m/n/10 i.e., strictly in-clude the bounds of []\T1/pcr/m/n/10 x[]\T1/pt m/m/n/10 . New from \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0, al-low-ing [429] [430] Underfull \hbox (badness 1701) in paragraph at lines 29972--29976 []\T1/ptm/m/n/10 This func-tion is al-most never used: []\TS1/cmtt/m/n/10 `\T1/ pcr/m/n/10 name\TS1/cmtt/m/n/10 ` []\T1/ptm/m/n/10 or, more care-fully, [][][]\ T1/pcr/m/n/10 get[][][](name, envir = [431] Underfull \hbox (badness 1796) in paragraph at lines 30040--30043 []\T1/ptm/m/n/10 character string (or []\T1/pcr/m/n/10 NULL[]\T1/ptm/m/n/10 ) i n-di-cat-ing [][][]\T1/pcr/m/n/10 NA[][][] []\T1/ptm/m/n/10 val-ues in printed out-put, see [432] [433] [434] [435] Underfull \hbox (badness 10000) in paragraph at lines 30244--30247 []\T1/ptm/m/n/10 Option []\T1/pcr/m/n/10 width []\T1/ptm/m/n/10 con-trols the p rint-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion [436] [437] [438] [439] [440] [441] [442] [443] Underfull \hbox (badness 2961) in paragraph at lines 30790--30793 []\T1/ptm/m/n/10 LAPACK and LIN-PACK are from [][]$\T1/pcr/m/n/10 https : / / n etlib . org / lapack/$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / [444] [445] Overfull \hbox (25.98041pt too wide) in paragraph at lines 30939--30939 [] \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 = rep(c(0,0,1),2))[] [446] [447] [448] [449] Overfull \hbox (15.18042pt too wide) in paragraph at lines 31232--31232 []\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3 \u147b\u203c")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 31243--31243 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\ U147b\U203c"[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 31249--31249 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm l#Literal-constants[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 31255--31255 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow ed (parse errors)[] Underfull \vbox (badness 10000) has occurred while \output is active [450] [451] Underfull \hbox (badness 7415) in paragraph at lines 31352--31358 []\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use []\T1/pcr/m/n/10 R.v ersion$os []\T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use Overfull \hbox (42.18039pt too wide) in paragraph at lines 31376--31376 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu l bottom-right note[] [452] Overfull \hbox (6.78088pt too wide) in paragraph at lines 31422--31422 []\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind = NULL)[] [453] [454] Underfull \hbox (badness 3713) in paragraph at lines 31567--31578 []\T1/pcr/m/n/10 normal.kind []\T1/ptm/m/n/10 can be []\T1/pcr/m/n/10 "Kinderma n-Ramage"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Buggy Kinderman-Ramage" []\T1/ptm /m/n/10 (not [455] Underfull \hbox (badness 1248) in paragraph at lines 31719--31726 \T1/ptm/m/n/10 uni-form pseudo-random num-ber gen-er-a-tor, \T1/ptm/m/it/10 ACM Trans-ac-tions on Mod-el-ing and Com-puter Underfull \hbox (badness 10000) in paragraph at lines 31719--31726 \T1/ptm/m/n/10 Now see [][]$\T1/pcr/m/n/10 http : / / www . math . sci . hirosh ima-[]u . ac . jp / ~m-[]mat / MT / VERSIONS / [456] [457] Underfull \hbox (badness 1533) in paragraph at lines 31837--31840 []\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the [458] [459] Overfull \hbox (42.78088pt too wide) in paragraph at lines 31982--31982 [] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m ax", "min"))[] [460] Underfull \hbox (badness 1038) in paragraph at lines 32000--32011 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no []\T1/pcr/m/n/10 N A[]\T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [461] [462] Overfull \hbox (15.18042pt too wide) in paragraph at lines 32144--32144 []\T1/pcr/m/n/9 rapply(X, function(x) x, how = "replace") -> X.; stopifnot(ide ntical(X, X.))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 32146--32146 []\T1/pcr/m/n/9 rapply(X, deparse, control = "all") # passing extras. argument of deparse()[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 32147--32147 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h ow = "list")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 32148--32148 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h ow = "unlist")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 32149--32149 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", h ow = "unlist")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 32156--32156 []\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h ow = "unlist")[] [463] [464] [465] [466] [467] Overfull \hbox (25.98041pt too wide) in paragraph at lines 32464--32464 []\T1/pcr/m/n/9 ## Bit representation [ sign | exponent | mantissa ] of doubl e prec numbers :[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 32466--32466 []\T1/pcr/m/n/9 bitC <- function(x) noquote(vapply(as.double(x), function(x) { # split one double[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 32476--32476 []\T1/pcr/m/n/9 d2bI <- function(x) vapply(as.double(x), function(x) intToBits (numToInts(x)), raw(64L))[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 32477--32477 []\T1/pcr/m/n/9 d2b <- function(x) vapply(as.double(x), function(x) numToBits(x) , raw(64L))[] [468] Underfull \hbox (badness 4048) in paragraph at lines 32572--32577 []\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor to Underfull \hbox (badness 4582) in paragraph at lines 32572--32577 \T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the mode: Underfull \hbox (badness 1824) in paragraph at lines 32572--32577 \T1/ptm/m/n/10 one of []\T1/pcr/m/n/10 "numeric"[]\T1/ptm/m/n/10 , []\T1/pcr/m/ n/10 "double"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "integer"[]\T1/ptm/m/n/10 , [] \T1/pcr/m/n/10 "int"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/ 10 , [469] [470] [471] [472] [473] [474] [475] [476] Underfull \hbox (badness 2080) in paragraph at lines 33112--33122 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 infoRDS[]\T1/ptm/m/n/10 , an \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 list with el-e-ments []\T1/pcr/m/n/10 version []\T1/ptm/m/n /10 (ver-sion num-ber, cur-rently 2 or 3), [477] Overfull \hbox (4.38043pt too wide) in paragraph at lines 33146--33146 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene d as needed.[] [478] [479] [480] [481] [482] [483] [484] Underfull \hbox (badness 7558) in paragraph at lines 33666--33670 []\T1/pcr/m/n/10 regexpr []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 gregexpr []\T1/p tm/m/n/10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1968) in paragraph at lines 33676--33678 []\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P OSIX stan-dard, and the Underfull \hbox (badness 10000) in paragraph at lines 33687--33689 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / Underfull \hbox (badness 1975) in paragraph at lines 33690--33694 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 pcre2pattern []\T1/ptm/m/n/10 or []\T1/pc r/m/n/10 pcrepattern man []\T1/ptm/m/n/10 page (found as part of [][]$\T1/pcr/m /n/10 https : / / www . [485] [486] Underfull \vbox (badness 10000) has occurred while \output is active [487] [488] [489] [490] Overfull \hbox (4.38043pt too wide) in paragraph at lines 34061--34061 []\T1/pcr/m/n/9 rep(1:4, each = 2, times = 3) # length 24, 3 complete replications[] [491] Underfull \hbox (badness 10000) in paragraph at lines 34132--34136 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [492] [493] [494] Underfull \hbox (badness 2302) in paragraph at lines 34365--34370 []\T1/pcr/m/n/10 signif []\T1/ptm/m/n/10 rounds the val-ues in its first ar-gu- ment to the spec-i-fied num-ber of \T1/ptm/m/it/10 sig-nif-i-cant Underfull \hbox (badness 1824) in paragraph at lines 34365--34370 \T1/ptm/m/n/10 dig-its. Hence, for []\T1/pcr/m/n/10 numeric x[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 signif(x, dig) []\T1/ptm/m/n/10 is the same as []\T1/pcr/m/n/ 10 round(x, dig - [495] [496] Overfull \hbox (12.78088pt too wide) in paragraph at lines 34498--34498 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"))[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 34501--34501 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 34508--34508 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] [497] [498] [499] [500] [501] [502] [503] Overfull \hbox (66.78088pt too wide) in paragraph at lines 34956--34956 [] \T1/pcr/m/n/10 useHash = (n > 1e+07 && !replace && is.null(prob) && size <= n/2))[] [504] [505] [506] [507] [508] [509] Overfull \hbox (12.78088pt too wide) in paragraph at lines 35393--35393 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)[] [510] [511] Underfull \hbox (badness 1158) in paragraph at lines 35497--35502 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 strip.white []\T1/ptm/m/n/10 is of length 1, it ap-plies to all fields; oth-er-wise, if [512] [513] Overfull \hbox (15.18042pt too wide) in paragraph at lines 35683--35683 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data ", sep = "\n") [514] [515] [516] Underfull \hbox (badness 4752) in paragraph at lines 35942--35945 []\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence []\T1/pcr/ m/n/10 1, 2, ..., length(along.with)[]\T1/ptm/m/n/10 . Underfull \hbox (badness 5563) in paragraph at lines 35946--35952 []\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence []\T1/pcr/m/n/10 1, 2 , ..., length(from) []\T1/ptm/m/n/10 (as if ar-gu-ment [517] [518] [519] [520] [521] [522] [523] [524] [525] Underfull \hbox (badness 6094) in paragraph at lines 36532--36536 []\T1/pcr/m/n/10 getAllConnections []\T1/ptm/m/n/10 re-turns a se-quence of in- te-ger con-nec-tion de-scrip-tors for use Underfull \hbox (badness 6559) in paragraph at lines 36532--36536 \T1/ptm/m/n/10 with []\T1/pcr/m/n/10 getConnection[]\T1/ptm/m/n/10 , cor-re-spo nd-ing to the row names of the ta-ble re-turned by [526] [527] Underfull \hbox (badness 3826) in paragraph at lines 36623--36634 []\T1/ptm/m/n/10 In Win-dows, com-mand line in-ter-pre-ta-tion is done by the a p-pli-ca-tion as well as the Underfull \hbox (badness 3492) in paragraph at lines 36623--36634 \T1/ptm/m/n/10 shell. It may de-pend on the com-piler used: Mi-crosoft's rules for the C run-time Underfull \hbox (badness 10000) in paragraph at lines 36623--36634 \T1/ptm/m/n/10 are given at [][]$\T1/pcr/m/n/10 https : / / learn . microsoft . com / en-[]us / cpp / c-[]language / Underfull \hbox (badness 1635) in paragraph at lines 36623--36634 \T1/pcr/m/n/10 parsing-[]c-[]command-[]line-[]arguments ? view = msvc-[]160$[][ ]\T1/ptm/m/n/10 . It may de-pend on the [528] [529] [530] [531] [532] [533] [534] [535] Overfull \hbox (66.78088pt too wide) in paragraph at lines 37177--37177 [] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index .return = FALSE)[] [536] [537] [538] [539] Overfull \hbox (6.78088pt too wide) in paragraph at lines 37429--37429 [] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length = Inf,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 37431--37431 [] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes" , "keepNA"),[] Underfull \hbox (badness 4954) in paragraph at lines 37474--37480 [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 vec-tor, passed as []\T1/ pcr/m/n/10 control []\T1/ptm/m/n/10 to [][][]\T1/pcr/m/n/10 deparse[][][]()[]\T 1/ptm/m/n/10 , see also Underfull \hbox (badness 5050) in paragraph at lines 37474--37480 [][][]\T1/pcr/m/n/10 .deparseOpts[][][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \ T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to [540] [541] Overfull \hbox (20.58041pt too wide) in paragraph at lines 37585--37585 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments should print:)[] [542] [543] [544] [545] [546] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37928--37928 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m /n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37943--37943 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is being added[] [547] [548] [549] Underfull \hbox (badness 10000) in paragraph at lines 38168--38170 [][][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919 799 / functions / [550] [551] [552] Overfull \hbox (12.78088pt too wide) in paragraph at lines 38395--38395 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known") Overfull \hbox (12.78088pt too wide) in paragraph at lines 38396--38396 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile = FALSE)[] [553] [554] [555] [556] [557] Overfull \hbox (63.78036pt too wide) in paragraph at lines 38727--38727 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS E, nowadays often three [558] Underfull \hbox (badness 6110) in paragraph at lines 38823--38833 []\T1/ptm/m/n/10 A func-tion []\T1/pcr/m/n/10 .First []\T1/ptm/m/n/10 (and [][] []\T1/pcr/m/n/10 .Last[][][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-at e `\T1/pcr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or Underfull \hbox (badness 2635) in paragraph at lines 38823--38833 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have been saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want a dif-fer-ent Underfull \hbox (badness 1237) in paragraph at lines 38823--38833 \T1/ptm/m/n/10 set of pack-ages than the de-fault ones when you start, in-sert a call to [][][]\T1/pcr/m/n/10 options[][][] []\T1/ptm/m/n/10 in the Underfull \hbox (badness 1231) in paragraph at lines 38823--38833 \T1/pcr/m/n/10 = character()) []\T1/ptm/m/n/10 will at-tach no ex-tra pack-ages on startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (or Underfull \hbox (badness 1112) in paragraph at lines 38823--38833 \T1/ptm/m/n/10 set []\T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL []\T1/ptm/m/n/10 as an en-vi-ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/10 ). Us-ing [559] Underfull \hbox (badness 10000) in paragraph at lines 38879--38885 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 38879--38885 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1496) in paragraph at lines 38879--38885 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be Underfull \hbox (badness 1460) in paragraph at lines 38894--38901 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 38894--38901 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 38894--38901 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment [560] Overfull \hbox (4.38043pt too wide) in paragraph at lines 38956--38956 []\T1/pcr/m/n/9 # Variable expansion in double quotes, string literals with ba ckslashes in[] [561] [562] [563] Underfull \hbox (badness 1484) in paragraph at lines 39129--39133 []\T1/ptm/m/n/10 alternative to []\T1/pcr/m/n/10 exprs []\T1/ptm/m/n/10 or []\T 1/pcr/m/n/10 ...[]\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an Overfull \hbox (60.78088pt too wide) in paragraph at lines 39194--39194 [] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e xprs = exprs))) [564] Overfull \hbox (9.78043pt too wide) in paragraph at lines 39220--39220 []\T1/pcr/m/n/9 stopifnot(all.equal(pi, 3.141593), 2 < 2, (1:10 < 12), "a" < "b") |> try()[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 39236--39236 []\T1/pcr/m/n/9 stopifnot(all.equal(rep(list(pi),4), list(3.1, 3.14, 3.141, 3. 1415))) |> try()[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 39244--39244 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 {Yes, learn how to use do.c all(substitute, ...) in a powerful manner !!}[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 39246--39246 []\T1/pcr/m/n/9 bdy <- do.call(substitute, list(bdy, list(stopifnot = quote(warnifnot))))[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 39247--39247 []\T1/pcr/m/n/9 bdy[[N-1]] <- do.call(substitute, list(bdy[[N-1]], list(stop = quote(warning))))[] [565] Underfull \hbox (badness 1436) in paragraph at lines 39307--39311 []\T1/ptm/m/n/10 integer de-ter-min-ing the []\T1/pcr/m/n/10 format()[]\T1/ptm/ m/n/10 ing of sec-onds when needed. Note [566] [567] [568] [569] [570] Overfull \hbox (15.18042pt too wide) in paragraph at lines 39700--39700 []\T1/pcr/m/n/9 z3 # prints without fractional seconds by default, digits.sec = NULL ("= 0")[] [571] Overfull \hbox (9.78043pt too wide) in paragraph at lines 39728--39728 []\T1/pcr/m/n/9 format(s1 <- seq.Date(as.Date(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 19 78-01-01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ), by = \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 day \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , len = 7), "%a")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 39729--39729 []\T1/pcr/m/n/9 format(s2 <- seq.Date(as.Date(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 20 00-01-01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ), by = \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 mon th\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , len = 12), "%b")[] [572] [573] Overfull \hbox (0.78088pt too wide) in paragraph at lines 39841--39841 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [574] [575] [576] Overfull \hbox (6.78088pt too wide) in paragraph at lines 40104--40104 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] [577] Overfull \hbox (4.38043pt too wide) in paragraph at lines 40148--40148 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [578] [579] [580] [581] [582] [583] [584] Overfull \hbox (52.98038pt too wide) in paragraph at lines 40595--40595 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e verything gets added.[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 40598--40598 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also missing, ....[] [585] Underfull \hbox (badness 10000) in paragraph at lines 40649--40656 []\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][][]\T1/pcr/m/n/ 10 signif[][][]() []\T1/ptm/m/n/10 (for Underfull \hbox (badness 10000) in paragraph at lines 40649--40656 []\T1/pcr/m/n/10 summary.default[]\T1/ptm/m/n/10 ) or [][][]\T1/pcr/m/n/10 form at[][][]() []\T1/ptm/m/n/10 (for []\T1/pcr/m/n/10 summary.data.frame[]\T1/ptm/m /n/10 ). [586] Overfull \hbox (4.38043pt too wide) in paragraph at lines 40702--40702 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision [587] [588] [589] [590] Overfull \hbox (31.3804pt too wide) in paragraph at lines 41016--41016 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw ise: last"),"\n")[] [591] [592] [593] [594] Overfull \hbox (20.58041pt too wide) in paragraph at lines 41221--41221 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, macOS, FreeBSD:[] Underfull \hbox (badness 2293) in paragraph at lines 41251--41257 []\T1/ptm/m/n/10 This ex-pands tilde (see [][]tilde ex-pan-sion[][][]) and wild -cards in file paths. For pre-cise de- Underfull \hbox (badness 1237) in paragraph at lines 41251--41257 \T1/ptm/m/n/10 tails of wild-cards ex-pan-sion, see your sys-tem's doc-u-men-ta -tion on the []\T1/pcr/m/n/10 glob []\T1/ptm/m/n/10 sys-tem call. Underfull \hbox (badness 4792) in paragraph at lines 41270--41275 []\T1/ptm/m/n/10 If a file-name starts with []\T1/pcr/m/n/10 . []\T1/ptm/m/n/10 this may need to be matched ex-plic-itly: for ex-am-ple Underfull \hbox (badness 1107) in paragraph at lines 41270--41275 []\T1/pcr/m/n/10 Sys.glob("*.RData") []\T1/ptm/m/n/10 may or may not match `\T1 /pcr/m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match [595] [596] [597] [598] Underfull \hbox (badness 10000) in paragraph at lines 41558--41562 []\T1/pcr/m/n/10 sys.status() []\T1/ptm/m/n/10 re-turns a list with com-po-nent s []\T1/pcr/m/n/10 sys.calls[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sys.parents []\ T1/ptm/m/n/10 and Underfull \hbox (badness 1584) in paragraph at lines 41573--41576 []\T1/pcr/m/n/10 sys.call []\T1/ptm/m/n/10 re-turns a call, []\T1/pcr/m/n/10 sy s.function []\T1/ptm/m/n/10 a func-tion def-i-ni-tion, and []\T1/pcr/m/n/10 sys .frame []\T1/ptm/m/n/10 and [599] [600] [601] Overfull \hbox (25.98041pt too wide) in paragraph at lines 41711--41711 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths ), keepNA=TRUE))[] [602] Overfull \hbox (19.22812pt too wide) in paragraph at lines 41792--41792 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/cmtt /m/n/9 `\T1/pcr/m/n/9 A+C\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 could also be used [603] [604] Underfull \hbox (badness 1082) in paragraph at lines 41937--41940 []\T1/ptm/m/n/10 logical. If []\T1/pcr/m/n/10 TRUE[]\T1/ptm/m/n/10 , func-tions keep their source in-clud-ing com-ments, see Underfull \hbox (badness 10000) in paragraph at lines 41964--41966 [][][]\T1/pcr/m/n/10 source[][][][]\T1/ptm/m/n/10 , and [][][]\T1/pcr/m/n/10 lo adNamespace[][][] []\T1/ptm/m/n/10 which is called from [][][]\T1/pcr/m/n/10 li brary[][][](.) []\T1/ptm/m/n/10 and uses [605] [606] [607] Underfull \hbox (badness 1038) in paragraph at lines 42130--42133 []\T1/ptm/m/n/10 a log-i-cal (not []\T1/pcr/m/n/10 NA[]\T1/ptm/m/n/10 ) in-di-c at-ing whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or [608] [609] [610] [611] [612] Underfull \hbox (badness 1442) in paragraph at lines 42495--42499 \T1/ptm/m/n/10 con-sider it to be piped or redi-rected: []\T1/pcr/m/n/10 stdout = TRUE []\T1/ptm/m/n/10 uses a pipe whereas []\T1/pcr/m/n/10 stdout = [613] [614] [615] [616] Underfull \hbox (badness 4096) in paragraph at lines 42749--42752 []\T1/ptm/m/n/10 Use [][][]\T1/pcr/m/n/10 ftable[][][] []\T1/ptm/m/n/10 for pri nt-ing (and more) of mul-ti-di-men-sional ta-bles. [][][]\T1/pcr/m/n/10 margin. table[][][][]\T1/ptm/m/n/10 , [617] Underfull \hbox (badness 7888) in paragraph at lines 42863--42867 []\T1/ptm/m/n/10 On 64-bit plat-forms []\T1/pcr/m/n/10 bin []\T1/ptm/m/n/10 can have $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., []\T1/pcr/ m/n/10 length(bin) > [618] [619] [620] Overfull \hbox (63.78036pt too wide) in paragraph at lines 43025--43025 [] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1" , "2"), c("A", "B")))),[] Overfull \hbox (30.0281pt too wide) in paragraph at lines 43027--43027 [] \T1/pcr/m/n/9 array(list(\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 2\TS1/cm tt/m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), names = nq),[] Overfull \hbox (55.67578pt too wide) in paragraph at lines 43029--43029 [] \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 4\TS1/cmtt/m/n/9 ` \T1/pcr/m /n/9 = NULL, \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 5\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 = NULL), dim=4, dimnames=list(as.character(2:5)))))[] Underfull \hbox (badness 10000) in paragraph at lines 43042--43044 []\T1/pcr/m/n/10 removeTaskCallback []\T1/ptm/m/n/10 un-registers a func-tion t hat was reg-is-tered ear-lier via [621] Underfull \hbox (badness 10000) in paragraph at lines 43122--43125 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . [622] [623] Underfull \hbox (badness 3872) in paragraph at lines 43240--43243 []\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call -backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer . [624] Underfull \hbox (badness 5475) in paragraph at lines 43306--43310 [][][]\T1/pcr/m/n/10 addTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 removeTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 taskCallback Manager[][][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / [625] [626] [627] [628] [629] [630] Underfull \hbox (badness 1655) in paragraph at lines 43729--43736 \T1/ptm/m/n/10 may also be known as `[]\T1/pcr/m/n/10 GB[]\T1/ptm/m/n/10 ', `[] \T1/pcr/m/n/10 GB-Eire[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 Europe/Belfast[]\T1 /ptm/m/n/10 ', `[]\T1/pcr/m/n/10 Europe/Guernsey[]\T1/ptm/m/n/10 ', Underfull \hbox (badness 2253) in paragraph at lines 43737--43742 []\T1/pcr/m/n/10 OlsonNames []\T1/ptm/m/n/10 re-turns a char-ac-ter vec-tor, se e the ex-am-ples for typ-i-cal cases. It may Underfull \hbox (badness 1655) in paragraph at lines 43737--43742 \T1/ptm/m/n/10 have an at-tribute []\T1/pcr/m/n/10 "Version"[]\T1/ptm/m/n/10 , some-thing like `[]\T1/pcr/m/n/10 "2023a"[]\T1/ptm/m/n/10 '. (It does on sys-te ms us-ing [631] Underfull \hbox (badness 4467) in paragraph at lines 43787--43796 []\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 OlsonNames []\T1/ptm/m/n/10 re- turns the time-zone names known to the cur-rently se- Underfull \hbox (badness 3954) in paragraph at lines 43787--43796 \T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t he file sys-tem varies, [632] Underfull \hbox (badness 1337) in paragraph at lines 43890--43898 \T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 / usr/local/etc\T1/ptm/m/n/10 ' or Underfull \hbox (badness 10000) in paragraph at lines 43899--43902 []\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym -link tar-get name of [633] Underfull \hbox (badness 3460) in paragraph at lines 43955--43958 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / data . iana . org / Underfull \hbox (badness 4429) in paragraph at lines 43959--43961 [][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol- Overfull \hbox (31.3804pt too wide) in paragraph at lines 43968--43968 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET", "Eire", ..., but[] [634] [635] [636] [637] [638] Overfull \hbox (15.18042pt too wide) in paragraph at lines 44311--44311 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15 g)\n", ncp))),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 44313--44313 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp root finding:[] [639] [640] Overfull \hbox (84.78088pt too wide) in paragraph at lines 44413--44413 [] \T1/pcr/m/n/10 getOption("deparse .max.lines", -1L)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 44415--44415 [] \T1/pcr/m/n/10 getOption("deparse .max.lines", -1L)))[] [641] [642] [643] Underfull \hbox (badness 6542) in paragraph at lines 44689--44691 []\T1/pcr/m/n/10 cospi(x)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sinpi(x)[]\T1/ptm/ m/n/10 , and []\T1/pcr/m/n/10 tanpi(x)[]\T1/ptm/m/n/10 , com-pute []\T1/pcr/m/n /10 cos(pi*x)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sin(pi*x)[]\T1/ptm/m/n/10 , an d [644] [645] Overfull \hbox (30.78088pt too wide) in paragraph at lines 44808--44808 []\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[ \t\r\n]") [646] Underfull \hbox (badness 1708) in paragraph at lines 44876--44884 []\T1/pcr/m/n/10 try []\T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any er-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 3713) in paragraph at lines 44876--44884 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ][]\T1/pcr/m/n/10 stderr[][][] []\T1/ptm/m/n/10 con-nec-tion un-less [647] Underfull \hbox (badness 4859) in paragraph at lines 44916--44921 [][][]\T1/pcr/m/n/10 options[][][] []\T1/ptm/m/n/10 for set-ting er-ror han-dle rs and sup-press-ing the print-ing of er-ror mes-sages; [648] Underfull \hbox (badness 3895) in paragraph at lines 44978--44990 []\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the struc-ture []\T1/pcr/m/n/10 TypeTable []\T1/ptm/m/n/10 in Underfull \hbox (badness 1303) in paragraph at lines 44978--44990 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue s are the vec-tor types []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/ m/n/10 "integer"[]\T1/ptm/m/n/10 , [649] [650] [651] [652] [653] Overfull \hbox (9.78043pt too wide) in paragraph at lines 45326--45326 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp ression(1+x))[] [654] [655] Underfull \hbox (badness 1137) in paragraph at lines 45420--45427 []\T1/ptm/m/n/10 When a func-tion call-ing []\T1/pcr/m/n/10 UseMethod("fun") [] \T1/ptm/m/n/10 is ap-plied to an ob-ject with class vec-tor [656] [657] [658] [659] [660] Overfull \hbox (4.38043pt too wide) in paragraph at lines 45798--45798 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local es and fonts[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 45807--45807 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little- endian platforms[] [661] Underfull \hbox (badness 2057) in paragraph at lines 45873--45879 [][][]\T1/pcr/m/n/10 file[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.acc ess[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.append[][][][]\T1/ptm/m/n /10 , [][][]\T1/pcr/m/n/10 file.copy[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 file.create[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.exists[][][][] \T1/ptm/m/n/10 , Underfull \hbox (badness 3861) in paragraph at lines 45882--45887 [][][]\T1/pcr/m/n/10 dir.create[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 di r.exists[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 normalizePath[][][][]\T1/ ptm/m/n/10 , [][][]\T1/pcr/m/n/10 path.expand[][][][]\T1/ptm/m/n/10 , [][][]\T1 /pcr/m/n/10 pipe[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Sys.glob[][][][]\ T1/ptm/m/n/10 , [662] Overfull \hbox (36.7804pt too wide) in paragraph at lines 45975--45975 []\T1/pcr/m/n/9 try( substr(x, 1,1) ) # gives \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 in valid multibyte string\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 error in a UTF-8 locale[] [663] Underfull \hbox (badness 1803) in paragraph at lines 46038--46041 []\T1/ptm/m/n/10 The atomic modes are []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "integer"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "numeric" []\ T1/ptm/m/n/10 (syn-onym []\T1/pcr/m/n/10 "double"[]\T1/ptm/m/n/10 ), Underfull \hbox (badness 3471) in paragraph at lines 46042--46048 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 mode = "any"[]\T1/ptm/m/n/10 , []\T1/pcr/m /n/10 is.vector []\T1/ptm/m/n/10 may re-turn []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/ n/10 for the atomic modes, [][][]\T1/pcr/m/n/10 list[][][] []\T1/ptm/m/n/10 and [664] [665] [666] [667] Underfull \hbox (badness 1014) in paragraph at lines 46271--46274 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the warn-ing should be out-put im-me -di-ately, even if [668] Overfull \hbox (36.78088pt too wide) in paragraph at lines 46380--46380 [] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes sages:\n"),[] [669] Overfull \hbox (4.38043pt too wide) in paragraph at lines 46455--46455 []\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n /9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 46463--46463 []\T1/pcr/m/n/9 x <- 1:36; for(n in 1:13) for(m in 1:12) A <- matrix(x, n,m) # There were 105 warnings ...[] [670] Underfull \hbox (badness 1783) in paragraph at lines 46528--46530 []\T1/pcr/m/n/10 weekdays []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 months []\T1/pt m/m/n/10 re-turn a char-ac-ter vec-tor of names in the lo-cale in use, i.e., [671] Overfull \hbox (25.98041pt too wide) in paragraph at lines 46558--46558 []\T1/pcr/m/n/9 ## Show how easily you get month, day, year, day (of {month, w eek, yr}), ... :[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 46570--46570 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Even simpler: Date -> Matrix - dropping time info {sec,min,hour, isdst}[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 46573--46573 []\T1/pcr/m/n/9 d2mat(seq(as.Date("2000-02-02"), by=1, length.out=30)) # has R 1.0.0\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s release date[] [672] Underfull \hbox (badness 10000) in paragraph at lines 46635--46640 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 arr.ind == TRUE []\T1/ptm/m/n/10 and []\T1 /pcr/m/n/10 x []\T1/ptm/m/n/10 is an [][][]\T1/pcr/m/n/10 array[][][] []\T1/ptm /m/n/10 (has a [][][]\T1/pcr/m/n/10 dim[][][] []\T1/ptm/m/n/10 at-tribute), the re-sult is Underfull \hbox (badness 2564) in paragraph at lines 46635--46640 []\T1/pcr/m/n/10 arrayInd(which(x), dim(x), dimnames(x))[]\T1/ptm/m/n/10 , name ly a ma-trix whose rows each [673] Underfull \hbox (badness 2818) in paragraph at lines 46731--46737 []\T1/ptm/m/n/10 For a [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 vec- tor []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 with both []\T1/pcr/m/n/10 FALSE []\T1/ ptm/m/n/10 and []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 val-ues, []\T1/pcr/m/n/10 which.min(x) []\T1/ptm/m/n/10 and [674] Overfull \hbox (15.18042pt too wide) in paragraph at lines 46766--46766 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is at least one:[] [675] [676] [677] [678] [679] [680] Underfull \hbox (badness 2846) in paragraph at lines 47227--47231 []\T1/pcr/m/n/10 .packages() []\T1/ptm/m/n/10 re-turns the names of the cur-ren tly at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [681] Overfull \hbox (4.38043pt too wide) in paragraph at lines 47267--47267 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 47288--47292 []\T1/pcr/m/n/10 .standard_regexps []\T1/ptm/m/n/10 re-turns a list of `stan-da rd' reg-exps, in-clud-ing el-e-ments named [682]) (./compiler-pkg.tex Chapter 2. [683] Underfull \hbox (badness 2884) in paragraph at lines 106--120 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 options []\T1/ptm/m/n/10 ar-gu-ment can b e used to con-trol com-piler op-er-a-tion. There are cur- Underfull \hbox (badness 10000) in paragraph at lines 106--120 \T1/ptm/m/n/10 rently four op-tions: []\T1/pcr/m/n/10 optimize[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 suppressAll[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 suppressUndef ined[]\T1/ptm/m/n/10 , and [684] [685] [686]) (./datasets-pkg.tex Chapter 3. [687] [688] [689] [690] [691] Overfull \hbox (15.18042pt too wide) in paragraph at lines 301--301 [] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang e", cex = 1.2,[] [692] Overfull \hbox (4.38043pt too wide) in paragraph at lines 379--379 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi ven = FALSE)[] [693] [694] [695] [696] Overfull \hbox (4.38043pt too wide) in paragraph at lines 617--617 [] \T1/pcr/m/n/9 start = c(lrc = log(.35)), algorithm = "plinear", t race = TRUE)[] [697] Underfull \hbox (badness 4779) in paragraph at lines 704--707 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [698] [699] Underfull \hbox (badness 4779) in paragraph at lines 837--840 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [700] [701] [702] Underfull \hbox (badness 1097) in paragraph at lines 1037--1041 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [703] Underfull \hbox (badness 4779) in paragraph at lines 1152--1155 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [704] [705] [706] [707] [708] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1464--1464 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption time (sec)")[] [709] [710] Underfull \hbox (badness 10000) in paragraph at lines 1549--1552 []\T1/ptm/m/n/10 Finally, []\T1/pcr/m/n/10 freeny []\T1/ptm/m/n/10 is a data fr ame with vari-ables []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lag.q uarterly.revenue[]\T1/ptm/m/n/10 , Underfull \hbox (badness 2903) in paragraph at lines 1549--1552 []\T1/pcr/m/n/10 price.index[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 income.level[]\ T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 market.potential []\T1/ptm/m/n/10 ob-taine d from the above [711] [712] [713] Underfull \hbox (badness 4779) in paragraph at lines 1738--1741 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [714] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1832--1832 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil y = binomial())[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1840--1840 [] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum), data = infert)[] [715] [716] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1956--1956 [] \T1/pcr/m/n/9 sub(" W.",".Width", dn i3[[2]])))),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1957--1957 [] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d ni3[[3]]))))[] [717] [718] [719] [720] Underfull \hbox (badness 4779) in paragraph at lines 2160--2163 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [721] [722] [723] [724] [725] [726] [727] [728] Underfull \hbox (badness 4779) in paragraph at lines 2725--2728 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [729] [730] [731] [732] [733] [734] [735] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3154--3154 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 1.2, pch = ".")[] [736] [737] [738] [739] [740] [741] Overfull \hbox (47.58038pt too wide) in paragraph at lines 3505--3505 []\T1/pcr/m/n/9 ## Alaska and Hawaii are placed just off the West Coast (for c ompact map drawing):[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3507--3507 []\T1/pcr/m/n/9 ## state.center2 := version of state.center with "correct" coo rdinates for AK & HI:[] Overfull \hbox (85.38034pt too wide) in paragraph at lines 3508--3508 []\T1/pcr/m/n/9 ## From https://pubs.usgs.gov/gip/Elevations-Distances/elvadis t.html#Geographic%20Centers[] [742] [743] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3639--3639 [] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t he monthly one:[] [744] [745] Underfull \hbox (badness 4779) in paragraph at lines 3787--3790 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [746] [747] [748] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3996--3996 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] [749] Underfull \hbox (badness 10000) in paragraph at lines 4034--4036 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/pcr/m/n/10 h ttps : / / web . archive . org / web / Underfull \hbox (badness 10000) in paragraph at lines 4034--4036 \T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma n / sitephotos / [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762]) (./grDevices-pkg.tex Chapter 4. [763] [764] [765] [766] Underfull \hbox (badness 4752) in paragraph at lines 298--303 []\T1/ptm/m/n/10 Apart from that, [][][]\T1/pcr/m/n/10 axisTicks[][][]() []\T1/ ptm/m/n/10 just calls the C func-tion []\T1/pcr/m/n/10 CreateAtVector() []\T1/p tm/m/n/10 in [767] [768] [769] [770] Overfull \hbox (6.78088pt too wide) in paragraph at lines 519--519 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d .pdf",[] [771] [772] [773] [774] [775] [776] [777] [778] [779] [780] Underfull \hbox (badness 5175) in paragraph at lines 1193--1195 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [781] [782] [783] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1364--1364 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", scale.in = 255))[] [784] [785] [786] Underfull \hbox (badness 3302) in paragraph at lines 1625--1629 []\T1/ptm/m/n/10 character: Does the de-vice sup-port pat-tern fills? One or mo re of Underfull \hbox (badness 10000) in paragraph at lines 1625--1629 []\T1/pcr/m/n/10 c("LinearGradient", "RadialGradient", "TilingPattern") [787] [788] [789] [790] [791] Underfull \hbox (badness 1565) in paragraph at lines 1916--1921 []\T1/ptm/m/n/10 The de-fault for []\T1/pcr/m/n/10 dev.print []\T1/ptm/m/n/10 i s to pro-duce and print a postscript copy. This will not Underfull \hbox (badness 1354) in paragraph at lines 1916--1921 \T1/ptm/m/n/10 sys-tem: see [][][]\T1/pcr/m/n/10 postscript[][][] []\T1/ptm/m/n /10 for how to set this up. Win-dows users may pre-fer to use [792] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1999--1999 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] [793] Underfull \hbox (badness 1184) in paragraph at lines 2040--2050 []\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of []\T1/pcr /m/n/10 ghostscript[]\T1/ptm/m/n/10 , but are likely to in- Underfull \hbox (badness 2057) in paragraph at lines 2040--2050 []\T1/pcr/m/n/10 "tiffg4"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiffgray"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "tifflzw"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiffp ack"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiff12nc"[]\T1/ptm/m/n/10 , []\T1/pcr/ m/n/10 "tiff24nc"[]\T1/ptm/m/n/10 , [794] Underfull \hbox (badness 10000) in paragraph at lines 2152--2154 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [795] [796] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2288--2288 []\T1/pcr/m/n/10 embedGlyphs(file, glyphInfo, outfile = file, options = charac ter())[] [797] Underfull \hbox (badness 6758) in paragraph at lines 2338--2341 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [798] [799] Underfull \hbox (badness 2326) in paragraph at lines 2456--2466 []\T1/ptm/m/n/10 are given, then it uses those in a call to []\T1/pcr/m/n/10 se tGraphicsEventHandlers []\T1/ptm/m/n/10 to re-place Underfull \hbox (badness 2318) in paragraph at lines 2456--2466 \T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co m-pat-i-bil-ity with pre-2.12.0 Underfull \hbox (badness 2460) in paragraph at lines 2456--2466 \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e vent han-dlers is to set them us-ing Underfull \hbox (badness 1221) in paragraph at lines 2456--2466 []\T1/pcr/m/n/10 setGraphicsEventHandlers []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 setGraphicsEventEnv []\T1/ptm/m/n/10 on one or more graph-ics [800] [801] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2559--2559 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r" , yaxs = "r") {[] Underfull \vbox (badness 10000) has occurred while \output is active [802] [803] [804] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2815--2815 []\T1/pcr/m/n/10 gray.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re v = FALSE) Overfull \hbox (30.78088pt too wide) in paragraph at lines 2816--2816 []\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re v = FALSE)[] [805] [806] [807] [808] [809] Underfull \hbox (badness 10000) in paragraph at lines 3089--3090 [810] [811] [812] [813] [814] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3422--3422 []\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized = FALSE)[] [815] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3506--3506 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", scale.in = 255))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3507--3507 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale. out = NULL))[] [816] [817] [818] Underfull \hbox (badness 10000) in paragraph at lines 3665--3671 []\T1/pcr/m/n/10 nclass.FD []\T1/ptm/m/n/10 uses the Freedman-Diaconis choice b ased on the inter-quartile range [819] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3740--3740 []\T1/pcr/m/n/10 palette.colors(n = NULL, palette = "Okabe-Ito", alpha, recycl e = FALSE)[] [820] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3824--3824 []\T1/pcr/m/n/9 (palette(gray(seq(0,.9,length.out = 25)))) # gray scales; prin t old palette[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3844--3844 []\T1/pcr/m/n/9 ## Demonstrate the colors 1:8 in different palettes using a cu stom matplot()[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3851--3851 [] \T1/pcr/m/n/9 matplot(x, type = "l", lwd = 4, lty = 1, col = 1:8, ylab = "", main=main)[] [821] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3907--3907 []\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE, fixup = TRUE) [822] Underfull \hbox (badness 8170) in paragraph at lines 3936--3939 []\T1/ptm/m/n/10 the type of palettes to list: []\T1/pcr/m/n/10 "qualitative"[] \T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sequential"[]\T1/ptm/m/n/10 , [823] Underfull \hbox (badness 2189) in paragraph at lines 3997--4002 []\T1/ptm/m/n/10 For ex-am-ple, []\T1/pcr/m/n/10 "Dark 3" []\T1/ptm/m/n/10 work s well for shad-ing points or lines in up to five groups, Underfull \hbox (badness 10000) in paragraph at lines 4035--4039 \T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space & oldid = 883465135$[][]\T1/ptm/m/n/10 . [824] Underfull \vbox (badness 10000) has occurred while \output is active [825] Underfull \hbox (badness 5260) in paragraph at lines 4165--4168 []\T1/ptm/m/n/10 For use with []\T1/pcr/m/n/10 onefile = FALSE []\T1/ptm/m/n/10 give a C in-te-ger for-mat such as [826] [827] [828] [829] [830] Underfull \hbox (badness 5939) in paragraph at lines 4504--4509 []\T1/ptm/m/n/10 arguments []\T1/pcr/m/n/10 width[]\T1/ptm/m/n/10 , []\T1/pcr/m /n/10 height[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 onefile[]\T1/ptm/m/n/10 , []\T1 /pcr/m/n/10 family[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 title[]\T1/ptm/m/n/10 , [ ]\T1/pcr/m/n/10 fonts[]\T1/ptm/m/n/10 , [831] [832] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.symbol}) has been already used, duplicate ignored \relax l.4681 \aliasA{symbol}{plotmath}{symbol} [833] [834] [835] [836] [837] [838] Overfull \hbox (60.78088pt too wide) in paragraph at lines 5025--5025 [] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz w+p", "zip+p"),[] [839] [840] Underfull \hbox (badness 1348) in paragraph at lines 5236--5239 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, [][]$\T1/pcr/m/n/10 https : / / ww w . iso . org / standard / 34342 . html$[][]\T1/ptm/m/n/10 . See also [841] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5263--5263 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, height = 768)[] Underfull \hbox (badness 7522) in paragraph at lines 5304--5310 []\T1/ptm/m/n/10 For use with []\T1/pcr/m/n/10 onefile = FALSE []\T1/ptm/m/n/10 give a []\T1/pcr/m/n/10 printf []\T1/ptm/m/n/10 for-mat such as [842] Underfull \hbox (badness 1112) in paragraph at lines 5337--5341 []\T1/ptm/m/n/10 as `\T1/pcr/m/n/10 "CP1250.enc"\T1/ptm/m/n/10 ' (Cen-tral Eu-r o-pean), []\T1/pcr/m/n/10 "CP1251.enc" [843] [844] Underfull \hbox (badness 1755) in paragraph at lines 5481--5483 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [845] [846] Underfull \hbox (badness 7344) in paragraph at lines 5664--5666 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso Underfull \hbox (badness 7397) in paragraph at lines 5675--5679 [][][]\T1/pcr/m/n/10 postscriptFonts[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 Devices[][][][]\T1/ptm/m/n/10 , and [][][]\T1/pcr/m/n/10 check.options[][][] []\T1/ptm/m/n/10 which is called from both [847] [848] Underfull \hbox (badness 1552) in paragraph at lines 5802--5811 []\T1/pcr/m/n/10 "AvantGarde"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Bookman"[]\T1 /ptm/m/n/10 , []\T1/pcr/m/n/10 "Courier"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "He lvetica"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Helvetica-Narrow"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5802--5811 []\T1/pcr/m/n/10 "NewCenturySchoolbook"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Pal atino" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "Times"[]\T1/ptm/m/n/10 ; []\T1/pc r/m/n/10 "URWGothic"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5802--5811 []\T1/pcr/m/n/10 "URWBookman"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "NimbusMon"[]\ T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "NimbusSan" []\T1/ptm/m/n/10 (syn-onym []\T1/p cr/m/n/10 "URWHelvetica"[]\T1/ptm/m/n/10 ), Underfull \hbox (badness 2221) in paragraph at lines 5812--5814 []\T1/ptm/m/n/10 There are also map-pings for []\T1/pcr/m/n/10 "ComputerModern" []\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ComputerModernItalic" []\T1/ptm/m/n/10 and Underfull \hbox (badness 4686) in paragraph at lines 5844--5850 []\T1/pcr/m/n/10 "Japan1"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Japan1HeiMin"[]\T 1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Japan1GothicBBB"[]\T1/ptm/m/n/10 , and []\T1/p cr/m/n/10 "Japan1Ryumin" []\T1/ptm/m/n/10 for [849] Underfull \hbox (badness 5388) in paragraph at lines 5870--5872 []\T1/pcr/m/n/10 BousungEG-Light-GB []\T1/ptm/m/n/10 can be found at [][]$\T1/p cr/m/n/10 https : / / ftp . gnu . org / pub / non-[]gnu / [850] [851] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5974--5974 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r eg-tests-1c.R[] [852] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6086--6086 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100 , ...)[] [853] [854] Underfull \hbox (badness 10000) in paragraph at lines 6173--6175 []\T1/ptm/m/n/10 Calling []\T1/pcr/m/n/10 quartz() []\T1/ptm/m/n/10 sets [][][] \T1/pcr/m/n/10 .Device[][][] []\T1/ptm/m/n/10 to []\T1/pcr/m/n/10 "quartz" []\T 1/ptm/m/n/10 for on-screen de-vices and to [855] [856] [857] [858] [859] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6540--6540 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15, sep = "."))[] Underfull \hbox (badness 10000) in paragraph at lines 6554--6557 []\T1/pcr/m/n/10 rgb2hsv []\T1/ptm/m/n/10 trans-forms col-ors from RGB space (r ed/green/blue) into HSV space [860] [861] [862] [863] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6774--6774 []\T1/pcr/m/n/9 p <- persp(x, y, fxy <- outer(x,y), phi = 20, theta = 15, r = 3, ltheta = -75,[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6785--6785 []\T1/pcr/m/n/9 ## now some "horizontal rays" (going from center to very left or very right):[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 6787--6787 [] \T1/pcr/m/n/9 lines(trans3d(x=seq(x1, x2, by=0.5), y= -0.7, z = z, pmat = p, continuous = CNT),[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6789--6789 []\T1/pcr/m/n/9 doHor(-10, 0, z = -0.5, col = 2) # x in [-10, 0] -- to the v ery left : fine[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 6790--6790 []\T1/pcr/m/n/9 doHor(-.5, 2, z = -0.52,col = 4) # x in [-0.5, 2] only {to th e right} --> all fine[] Overfull \hbox (117.7803pt too wide) in paragraph at lines 6791--6791 []\T1/pcr/m/n/9 ## but now, x in [-0.5, 20] -- "too far" ==> "wrap around" pro blem (without \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 continuous=TRUE\TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 ):[] [864] [865] Overfull \hbox (0.78088pt too wide) in paragraph at lines 6923--6923 []\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp inch, Overfull \hbox (0.78088pt too wide) in paragraph at lines 6930--6930 []\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize = 12,[] [866] [867] [868] [869] Underfull \hbox (badness 10000) in paragraph at lines 7196--7201 []\T1/ptm/m/n/10 arguments []\T1/pcr/m/n/10 width[]\T1/ptm/m/n/10 , []\T1/pcr/m /n/10 height[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pointsize[]\T1/ptm/m/n/10 , []\ T1/pcr/m/n/10 record[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 rescale[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1803) in paragraph at lines 7196--7201 []\T1/pcr/m/n/10 xpinch[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 ypinch[]\T1/ptm/m/n/ 10 , []\T1/pcr/m/n/10 bg[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 canvas[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 gamma[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 xpos[]\T1/ptm/m /n/10 , []\T1/pcr/m/n/10 ypos[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 buffered[]\T1/ ptm/m/n/10 , Underfull \hbox (badness 2941) in paragraph at lines 7196--7201 []\T1/pcr/m/n/10 restoreConsole[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 clickToConfi rm[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 title[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 fillOddEven []\T1/ptm/m/n/10 and [870] [871] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7302--7302 []\T1/pcr/m/n/9 windows() # make sure we have the right device type (availabl e on Windows only)[] Underfull \hbox (badness 3590) in paragraph at lines 7341--7344 []\T1/ptm/m/n/10 The \T1/phv/m/n/10 R \T1/ptm/m/n/10 func-tion is a wrap-per fo r two de-vices, one based on Xlib ([][]$\T1/pcr/m/n/10 https : / / Underfull \hbox (badness 2393) in paragraph at lines 7341--7344 \T1/pcr/m/n/10 en . wikipedia . org / wiki / Xlib$[][]\T1/ptm/m/n/10 ) and one us-ing cairo-graph-ics ([][]$\T1/pcr/m/n/10 https : / / www . Overfull \hbox (12.78088pt too wide) in paragraph at lines 7352--7352 [] \T1/pcr/m/n/10 fonts, family, xpos, ypos, title, type, antialias, symbol family)[] [872] Underfull \hbox (badness 1189) in paragraph at lines 7417--7419 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [873] [874] Underfull \hbox (badness 10000) in paragraph at lines 7522--7524 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" []\T1/ptm/m/n/10 for CJ K lan-guages and Underfull \hbox (badness 10000) in paragraph at lines 7568--7575 []\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of [] \T1/pcr/m/n/10 quote(pi) []\T1/ptm/m/n/10 and Underfull \hbox (badness 2469) in paragraph at lines 7568--7575 []\T1/pcr/m/n/10 expression(10^degree)[]\T1/ptm/m/n/10 ) have been seen on Linu x sys-tems which have the Wine [875] Underfull \hbox (badness 5607) in paragraph at lines 7652--7656 []\T1/pcr/m/n/10 type = "Xlib" []\T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-d o-Color', `GrayScale', []\T1/pcr/m/n/10 StaticGray []\T1/ptm/m/n/10 and [876] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7704--7704 [] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height = 6, xpos = 0,[] [877] [878] Underfull \hbox (badness 5637) in paragraph at lines 7836--7842 []\T1/pcr/m/n/10 "Courier"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Helvetica" []\T1 /ptm/m/n/10 (the de-fault), []\T1/pcr/m/n/10 "Helvetica-Narrow"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1721) in paragraph at lines 7869--7872 []\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt p : / / www . schmidt-[]web-[]berlin . de / [879] [880] Overfull \hbox (63.78036pt too wide) in paragraph at lines 8004--8004 []\T1/pcr/m/n/9 op <- options(warn = 2)# ==> warnings would be errors, we supp ress the one "we know":[] [881] Underfull \hbox (badness 1231) in paragraph at lines 8043--8045 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., []\T1/pcr/m/n/10 number[i] []\T1/ptm/m/n/10 is the mul-ti-plic-ity of [882] [883] [884]) (./graphics-pkg.tex Chapter 5. Underfull \hbox (badness 4647) in paragraph at lines 16--18 []\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag es, use []\T1/pcr/m/n/10 library(help = [885] [886] [887] [888] [889] [890] [891] Overfull \hbox (6.05087pt too wide) in paragraph at lines 450--450 [] \T1/pcr/m/n/10 gap.axis <- if(perpendicular(side, las)) 0.25 else 1[] Underfull \hbox (badness 4048) in paragraph at lines 482--488 []\T1/ptm/m/n/10 When []\T1/pcr/m/n/10 at = NULL[]\T1/ptm/m/n/10 , pretty tick mark lo-ca-tions are com-puted in-ter-nally (the same way [892] [893] Overfull \hbox (47.58038pt too wide) in paragraph at lines 580--580 []\T1/pcr/m/n/9 ## now shrink the window (in x- and y-direction) and observe t he axis labels drawn[] [894] Overfull \hbox (15.18042pt too wide) in paragraph at lines 692--692 []\T1/pcr/m/n/9 axis.Date(3, at = as.integer(as.Date("2023-04-01")), col.axis = "darkgreen")[] [895] Overfull \hbox (15.18042pt too wide) in paragraph at lines 707--707 []\T1/pcr/m/n/9 axis.POSIXct(3, at = as.POSIXct("2022-10-01 00:01:30"), col.ax is = "orange")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 712--712 []\T1/pcr/m/n/9 axis.POSIXct(3, at = as.numeric(as.POSIXct("2022-10-01 00:00:3 0")) + 0.25,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 713--713 [] \T1/pcr/m/n/9 col.axis = "forestgreen", col = "darkgreen", m gp = c(3,2,0))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 719--719 []\T1/pcr/m/n/9 plot(data.frame(HST, y = 1), xaxt = "n", xlab = "Hawaii Standa rd Time (HST)")[] Underfull \hbox (badness 10000) in paragraph at lines 746--750 []\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][][]\T1/pcr /m/n/10 par[][][]("xaxp") []\T1/ptm/m/n/10 or Underfull \hbox (badness 3250) in paragraph at lines 746--750 [][][]\T1/pcr/m/n/10 par[][][]("yaxp") []\T1/ptm/m/n/10 de-pend-ing on the []\T 1/pcr/m/n/10 side []\T1/ptm/m/n/10 ar-gu-ment ([]\T1/pcr/m/n/10 par("xaxp") []\ T1/ptm/m/n/10 if [896] [897] Overfull \hbox (4.38043pt too wide) in paragraph at lines 833--833 [] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n intLog = 5))[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 870--870 [] \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend = NULL, ...)[] [898] [899] Underfull \hbox (badness 10000) in paragraph at lines 1017--1021 [][][]\T1/pcr/m/n/10 plot[][][](..., type = "h")[]\T1/ptm/m/n/10 , [][][]\T1/pc r/m/n/10 dotchart[][][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 hist[][][] []\T1 /ptm/m/n/10 for bars of a \T1/ptm/m/it/10 con-tin-u-ous \T1/ptm/m/n/10 vari-abl e. [900] Overfull \hbox (133.98029pt too wide) in paragraph at lines 1034--1034 [] \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = " # {passengers}", legend.text = TRUE)[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1036--1036 []\T1/pcr/m/n/9 (xt <- xtabs(Freq ~ Survived + Class + Sex, d.Titanic, subset = Age=="Adult"))[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 1038--1038 []\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur vived, *)", color=TRUE)[] Underfull \vbox (badness 10000) has occurred while \output is active [901] [902] [903] [904] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1322--1322 []\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches .. outside hinges"):[] [905] [906] [907] Underfull \hbox (badness 2503) in paragraph at lines 1484--1493 \T1/ptm/m/n/10 when []\T1/pcr/m/n/10 horizontal []\T1/ptm/m/n/10 is false, and []\T1/pcr/m/n/10 xlim []\T1/ptm/m/n/10 hor-i-zon-tally. []\T1/pcr/m/n/10 xaxt[] \T1/ptm/m/n/10 , []\T1/pcr/m/n/10 yaxt[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3375) in paragraph at lines 1519--1521 []\T1/ptm/m/n/10 whisker line type (de-fault: []\T1/pcr/m/n/10 "dashed"[]\T1/pt m/m/n/10 ), [908] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1593--1593 []\T1/pcr/m/n/9 boxplot(z, col.axis = "skyblue3", main = "boxplot(*, col.axi s=..,main=..)")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1594--1594 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main = "plot(*, col.axi s=..,main=..)")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1600--1600 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill = "grey40",[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1601--1601 [] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl ty = 1, outpch = NA)[] [909] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1634--1634 [] \T1/pcr/m/n/10 yaxlabels = NULL, xlim = NULL, ylim = c(0, 1), weights = NU LL, ...)[] [910] [911] [912] [913] Underfull \hbox (badness 10000) in paragraph at lines 1907--1913 [][][]\T1/pcr/m/n/10 contourLines[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 filled.contour[][][] []\T1/ptm/m/n/10 for color-filled con-tours, [][][]\T1/pcr /m/n/10 contourplot[][][] []\T1/ptm/m/n/10 (and [914] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1927--1927 []\T1/pcr/m/n/9 contour(x, x, z, ylim = c(-6, 6), nlevels = 20, lty = 2, metho d = "simple",[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 1939--1939 []\T1/pcr/m/n/9 contour(z, levels=levs[-c(1,length(levs))], col = 1:5, lwd = 1 :3 *1.5, lty = 1:3)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1955--1955 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1964--1964 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [915] [916] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2049--2049 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [917] [918] Overfull \hbox (31.3804pt too wide) in paragraph at lines 2178--2178 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.values = given .depth, rows = 1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2183--2183 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c( TRUE, FALSE))[] [919] [920] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2357--2357 []\T1/pcr/m/n/10 dotchart(x, labels = NULL, groups = NULL, gdata = NULL, offse t = 1/8, Overfull \hbox (54.78088pt too wide) in paragraph at lines 2358--2358 [] \T1/pcr/m/n/10 ann = par("ann"), xaxt = par("xaxt"), frame.plot = T RUE, log = "",[] [921] Underfull \hbox (badness 1430) in paragraph at lines 2388--2390 []\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use []\T1/pcr/m/n/10 "n" []\T1/ptm/m/n/10 to sup-press and see also [922] Overfull \hbox (78.78088pt too wide) in paragraph at lines 2469--2469 [] \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO rRd", rev = TRUE),[] Underfull \hbox (badness 1009) in paragraph at lines 2481--2488 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [923] Underfull \hbox (badness 7273) in paragraph at lines 2563--2567 [][][]\T1/pcr/m/n/10 contour[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 image [][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 hcl.colors[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gray.colors[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 palette[][][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 contourplot[][][] []\T1/p tm/m/n/10 and [924] [925] [926] [927] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2811--2811 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [928] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2848--2848 [] \T1/pcr/m/n/10 density = NULL, angle = 45, col = "lightgray", border = NULL,[] [929] [930] Underfull \hbox (badness 1226) in paragraph at lines 2975--2979 \T1/pcr/m/n/10 1)[]\T1/ptm/m/n/10 , they are the rel-a-tive fre-quen-cies []\T1 /pcr/m/n/10 counts/n []\T1/ptm/m/n/10 and in gen-eral sat-isfy [931] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3028--3028 []\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3032--3032 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a suggestion only"[] [932] Underfull \hbox (badness 10000) in paragraph at lines 3094--3097 [][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][][]\T1 /pcr/m/n/10 hist.default[][][] []\T1/ptm/m/n/10 such as Overfull \hbox (15.18042pt too wide) in paragraph at lines 3145--3145 []\T1/pcr/m/n/9 ## The default fuzz in hist.default() "kills" this, with a "w rong" message:[] [933] [934] [935] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3309--3309 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL SE, pch = 19, ...)[] Overfull \hbox (79.98035pt too wide) in paragraph at lines 3314--3314 [] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel) , n = 1, plot = plot, ...)[] [936] [937] Underfull \hbox (badness 10000) in paragraph at lines 3456--3461 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 useRaster []\T1/ptm/m/n/10 is not spec-i-f ied, raster im-ages are used when the Underfull \hbox (badness 10000) in paragraph at lines 3456--3461 [][][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") []\T1/ptm/m/n/10 is true, the grid is reg-u-lar and ei-ther Underfull \hbox (badness 10000) in paragraph at lines 3456--3461 [][][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage []\T1/pt m/m/n/10 is []\T1/pcr/m/n/10 "yes" []\T1/ptm/m/n/10 or it is Overfull \hbox (31.3804pt too wide) in paragraph at lines 3491--3491 []\T1/pcr/m/n/9 # Visualize as matrix. Need to transpose matrix and then flip it horizontally:[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 3493--3493 []\T1/pcr/m/n/9 imageM <- function(m, grid = max(dim(m)) <= 25, asp = (nrow(m) -1)/(ncol(m)-1), ...) {[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3496--3496 [] \T1/pcr/m/n/9 axis(side, at=at, labels=as.character(j+1L), col="gray ", col.axis=1, ...)[] [938] [939] [940] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3653--3653 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 0, horiz = TRUE)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3672--3672 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3676--3676 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [941] [942] [943] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3861--3861 [] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c ex = 0.8, adj = 0)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3862--3862 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3866--3866 [] \T1/pcr/m/n/9 cex = 1+(-1:2)/8, trace = TRUE)# trace: show computed l engths & coords[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3876--3876 [] \T1/pcr/m/n/9 title("legend(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 top\TS1/pcr/m/n/ 9 '\T1/pcr/m/n/9 , lty = c(2, -1, 1), pch = c(NA, 3, 4), merge = TRUE)",[] [944] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3907--3907 [] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj = c(0, 0.3))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3933--3933 []\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Filled\TS1/pcr/m/n/9 ' \T1/pc r/m/n/9 boxes -- see also example(barplot) which may call legend(*, fill=)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3935--3935 []\T1/pcr/m/n/9 legend("topright", rownames(VADeaths), fill = gray.colors(nrow (VADeaths)))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3946--3946 []\T1/pcr/m/n/9 legend("bottomright", paste("sin(", 1:7, "pi * x)"), col = 1:7 , lty = 1:7,[] Underfull \vbox (badness 10000) has occurred while \output is active [945] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3961--3961 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c ol = "blue")[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3969--3969 []\T1/pcr/m/n/9 legend("topleft", "(x,y)", pch=1, title= "topleft, inset = .05", inset = .05)[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3971--3971 []\T1/pcr/m/n/9 legend("topright", "(x,y)", pch=1, title= "topright, inset = .02",inset = .02)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3979--3979 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3989--3989 []\T1/pcr/m/n/9 legend("bottomleft", c("This legend", "has", "optimally sized" , "columns."),[] [946] Underfull \hbox (badness 10000) in paragraph at lines 4051--4055 [][][]\T1/pcr/m/n/10 lines.formula[][][] []\T1/ptm/m/n/10 for the for-mula meth od; [][][]\T1/pcr/m/n/10 points[][][][]\T1/ptm/m/n/10 , par-tic-u-larly for []\ T1/pcr/m/n/10 type %in% [947] [948] Overfull \hbox (6.78088pt too wide) in paragraph at lines 4163--4163 [] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb ose"))[] [949] [950] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4317--4317 []\T1/pcr/m/n/9 nd <- length(dv <- seq(as.Date("1959-02-21"), by = "weeks", le ngth.out = 100))[] [951] Underfull \hbox (badness 3930) in paragraph at lines 4396--4398 []\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a mul-ti-ple of [952] [953] [954] [955] [956] Underfull \hbox (badness 1286) in paragraph at lines 4707--4710 []\T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify []\T1/pcr/m/n /10 oma []\T1/ptm/m/n/10 when chang-ing Underfull \hbox (badness 3229) in paragraph at lines 4715--4720 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used, see [957] [958] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4811--4811 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel = panel.cor,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4816--4816 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] [959] Underfull \hbox (badness 1264) in paragraph at lines 5007--5020 \T1/ptm/m/n/10 func-tions such as [][][]\T1/pcr/m/n/10 plot.default[][][][]\T1/ ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.window[][][][]\T1/ptm/m/n/10 , [][][]\T1 /pcr/m/n/10 points[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lines[][][][]\T 1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 abline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc r/m/n/10 axis[][][][]\T1/ptm/m/n/10 , [960] [961] [962] [963] Underfull \hbox (badness 10000) in paragraph at lines 5273--5276 [964 ] Underfull \hbox (badness 10000) in paragraph at lines 5334--5336 [965 ] [966] [967] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5580--5580 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, physicians = 9,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5581--5581 [] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t eachers = 4,[] Underfull \vbox (badness 10000) has occurred while \output is active [968] [969] [970] [971] [972] [973] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5945--5945 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p yramid" = 5),[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 5946--5946 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] [974] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot}) ha s been already used, duplicate ignored \relax l.6005 \aliasA{plot}{plot.default}{plot} [975] [976] [977] [978] [979] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6337--6337 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6343--6343 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [980] [981] Overfull \hbox (66.78088pt too wide) in paragraph at lines 6467--6467 [] \T1/pcr/m/n/10 main = paste("Histogram of", paste(x$xname, co llapse = "\n")),[] [982] [983] [984] [985] Underfull \hbox (badness 10000) in paragraph at lines 6772--6774 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [986] [987] Underfull \hbox (badness 1028) in paragraph at lines 6866--6868 []\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th is works as a mul-ti-ple of Overfull \hbox (31.57222pt too wide) in paragraph at lines 6909--6910 [][] [988 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7003--7003 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [989] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7034--7034 [] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab = "", main = main)[] Underfull \vbox (badness 10000) has occurred while \output is active [990] [991] Underfull \hbox (badness 10000) in paragraph at lines 7156--7158 []\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev in Buhr Overfull \hbox (15.18042pt too wide) in paragraph at lines 7183--7183 [] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b order = "red")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7189--7189 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [992] Underfull \hbox (badness 2600) in paragraph at lines 7246--7248 []\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther []\T 1/pcr/m/n/10 "winding" []\T1/ptm/m/n/10 or [993] [994] [995] [996] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7478--7478 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7 , end = 0.1))[] [997] [998] [999] [1000] [1001] [1002] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7865--7865 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp ace = "Lab")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7869--7869 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [1003] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7881--7881 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 7908--7908 [] \T1/pcr/m/n/10 xlim = NULL, ylim = c(0, 1), axes = TRUE, weights = NULL, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 7917--7917 [] \T1/pcr/m/n/10 subset = NULL, weights = NULL, drop.unused.levels = FALSE)[] [1004] [1005] [1006] [1007] [1008] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8234--8234 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8237--8237 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] [1009] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8241--8241 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [1010] [1011] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8412--8412 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...) Overfull \hbox (36.78088pt too wide) in paragraph at lines 8413--8413 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [1012] [1013] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8517--8517 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] [1014] Underfull \hbox (badness 1112) in paragraph at lines 8576--8580 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 number[i] == 1[]\T1/ptm/m/n/10 , a (sligh tly en-larged) usual plot-ting sym-bol ([]\T1/pcr/m/n/10 pch[]\T1/ptm/m/n/10 ) is drawn. For [1015] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8636--8636 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035 , seg.lwd = .8)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8651--8651 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [1016] [1017] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8788--8788 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [1018] [1019] [1020] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8973--8973 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est facile: Règles, Liberté, Egalité, Fraternité...")[] Underfull \hbox (badness 1215) in paragraph at lines 9001--9003 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color []\T1/pcr/m /n/10 par(c("font.sub", Underfull \hbox (badness 1584) in paragraph at lines 9035--9041 []\T1/ptm/m/n/10 The po-si-tions of []\T1/pcr/m/n/10 xlab[]\T1/ptm/m/n/10 , []\ T1/pcr/m/n/10 ylab []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 sub []\T1/ptm/m/n/10 a re []\T1/pcr/m/n/10 line []\T1/ptm/m/n/10 (de-fault for []\T1/pcr/m/n/10 xlab [ ]\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 ylab []\T1/ptm/m/n/10 be-ing [1021] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.units}) h as been already used, duplicate ignored \relax l.9083 \HeaderA{units}{Graphical Units}{units} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.units.1}) has been already used, duplicate ignored \relax l.9083 \HeaderA{units}{Graphical Units}{units} [1022] Underfull \hbox (badness 1205) in paragraph at lines 9148--9150 []\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th e poly-gon. See [1023] [1024] Overfull \hbox (25.98041pt too wide) in paragraph at lines 9267--9267 []\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code = 2, length = 0.1)[] [1025]) (./grid-pkg.tex [1026] Chapter 6. [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] Underfull \hbox (badness 4859) in paragraph at lines 634--637 []\T1/ptm/m/n/10 Modification of the view-port (should all be valid ar-gu-ments to the [1037] [1038] [1039] [1040] [1041] [1042] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1028--1028 [] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un it(1, "inches")))[] [1043] [1044] [1045] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1239--1239 [] \T1/pcr/m/n/9 vpList(vpStack(viewport(x=0.1, y=0.1, width=0.5 , height=0.5,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1240--1240 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1241--1241 [] \T1/pcr/m/n/9 viewport(x=0.1, y=0.1, width=0.5 , height=0.5,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1242--1242 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1243--1243 [] \T1/pcr/m/n/9 viewport(x=0.1, y=0.1, width=0.5 , height=0.5,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1244--1244 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] [1046] [1047] [1048] [1049] Underfull \hbox (badness 3219) in paragraph at lines 1503--1506 []\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject de-scrib-ing a cir-cle), but only [1050] [1051] [1052] [1053] [1054] [1055] [1056] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1891--1891 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [1057] [1058] [1059] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2105--2105 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla ck"), name="r1")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2106--2106 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey" ), name="r2")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2107--2107 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [1060] Underfull \hbox (badness 2961) in paragraph at lines 2142--2147 []\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio ns []\T1/pcr/m/n/10 preDrawDetails[]\T1/ptm/m/n/10 , [1061] Underfull \hbox (badness 4479) in paragraph at lines 2230--2233 []\T1/ptm/m/n/10 Both func-tions call []\T1/pcr/m/n/10 editDetails []\T1/ptm/m/ n/10 to al-low a grob to per-form cus-tom ac-tions and [1062] [1063] [1064] Underfull \hbox (badness 2894) in paragraph at lines 2437--2444 []\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de -scrib-ing a frame), but only [1065] [1066] [1067] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2593--2593 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] [1068] Underfull \hbox (badness 1014) in paragraph at lines 2679--2684 []\T1/ptm/m/n/10 The jus-ti-fi-ca-tion of the glyphs rel-a-tive to the ([]\T1/p cr/m/n/10 x[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 ) lo-ca-tion. Can be [1069] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2725--2725 []\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs = FALSE,[] [1070] [1071] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2887--2887 [] \T1/pcr/m/n/9 children=gList(grob(name="child", vp ="vp1::vp2")),[] [1072] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2919--2919 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [1073] [1074] Underfull \hbox (badness 10000) in paragraph at lines 3102--3104 []\T1/ptm/m/n/10 A func-tion that re-turns an affine trans-for-ma-tion ma-trix; see [1075] Underfull \hbox (badness 1077) in paragraph at lines 3119--3138 []\T1/ptm/m/n/10 Another pos-si-ble use of []\T1/pcr/m/n/10 grid.group() []\T1/ ptm/m/n/10 is to spec-ify both []\T1/pcr/m/n/10 src []\T1/ptm/m/n/10 and []\T1/ pcr/m/n/10 dst []\T1/ptm/m/n/10 and com-bine Underfull \hbox (badness 1622) in paragraph at lines 3119--3138 []\T1/ptm/m/n/10 is only drawn where it is NOT over-lapped by []\T1/pcr/m/n/10 src[]\T1/ptm/m/n/10 . The fol-low-ing (ex-tended) Porter- Underfull \hbox (badness 2057) in paragraph at lines 3119--3138 []\T1/pcr/m/n/10 "multiply"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "screen"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "overlay"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "darke n"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lighten"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n /10 "color.dodge"[]\T1/ptm/m/n/10 , [1076] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3191--3191 [] \T1/pcr/m/n/9 mask <- as.mask(rectGrob(gp=gpar(col=NA, fill="grey50")), ty pe="luminance")[] [1077] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3307--3307 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [1078] [1079] [1080] [1081] [1082] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3622--3622 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [1083] [1084] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3718--3718 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, width=0.25, height=0.25, just= c("left", "bottom")))[] Underfull \hbox (badness 2799) in paragraph at lines 3755--3761 []\T1/ptm/m/n/10 There are two hooks called []\T1/pcr/m/n/10 "before.grid.newpa ge" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "grid.newpage" []\T1/ptm/m/n/10 (see [1085] [1086] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3847--3847 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3854--3854 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [1087] [1088] [1089] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4055--4055 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] [1090] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4070--4070 [] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other anti-clockwise")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4091--4091 []\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s ame path, thus[] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] Underfull \hbox (badness 1067) in paragraph at lines 4840--4843 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1103] [1104] [1105] [1106] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5056--5056 [] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un it(1, "inches")))[] [1107] [1108] Underfull \hbox (badness 7256) in paragraph at lines 5191--5193 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1109] Overfull \hbox (69.18036pt too wide) in paragraph at lines 5258--5258 []\T1/pcr/m/n/9 grid.text(quote(frac(e^{-x^2/2}, sqrt(2*pi))), x=x, y=y, rot=s tats::runif(20, -45,45),[] [1110] [1111] [1112] [1113] [1114] [1115] Underfull \hbox (badness 2726) in paragraph at lines 5645--5649 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 gridCoords []\T1/ptm/m/n/10 a nu-meric ve c-tor. For []\T1/pcr/m/n/10 gridGrobCoords []\T1/ptm/m/n/10 a list Underfull \hbox (badness 1231) in paragraph at lines 5645--5649 \T1/ptm/m/n/10 of []\T1/pcr/m/n/10 "GridCoords" []\T1/ptm/m/n/10 ob-jects. For []\T1/pcr/m/n/10 gridGTreeCoords []\T1/ptm/m/n/10 a list of ei-ther [1116] Underfull \hbox (badness 2080) in paragraph at lines 5727--5732 []\T1/ptm/m/n/10 Either a []\T1/pcr/m/n/10 "GridGrobCoords" []\T1/ptm/m/n/10 ob -ject (a list of lists with com-po-nents []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 an d []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 ) or a [1117] [1118] [1119] Underfull \hbox (badness 10000) in paragraph at lines 5907--5909 []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 grid.legend()[]\T1/ptm/m/n/10 : all the a r-gu-ments above are passed to [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7002--7002 []\T1/pcr/m/n/9 unitType(min(unit(1, "in"), unit(1, "npc") + unit(1, "mm")), r ecurse=TRUE)[] [1137] [1138] Overfull \hbox (54.78088pt too wide) in paragraph at lines 7122--7122 []\T1/pcr/m/n/10 viewportTransform(group, shear=groupShear(), flip=groupFlip() , device=TRUE) [1139] Underfull \hbox (badness 1867) in paragraph at lines 7224--7226 []\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for use in []\T1/pcr/m/n/10 downViewport []\T1/ptm/m/n/10 or [1140] Underfull \hbox (badness 10000) in paragraph at lines 7261--7267 [][][]\T1/pcr/m/n/10 viewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 push Viewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 popViewport[][][][]\T1/pt m/m/n/10 , [][][]\T1/pcr/m/n/10 downViewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 seekViewport[][][][]\T1/ptm/m/n/10 , [1141] [1142] [1143] Underfull \vbox (badness 10000) has occurred while \output is active [1144] [1145] [1146] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7597--7597 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp ar(col="red"))))[] [1147]) (./methods-pkg.tex [1148] Chapter 7. [1149] [1150] Underfull \hbox (badness 1688) in paragraph at lines 166--171 []\T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how co-erce meth-ods work. Use [1151] [1152] [1153] Underfull \hbox (badness 1348) in paragraph at lines 392--395 [][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] []\T1/ptm/m/n/10 for other in- for-ma-tion about group generic func-tions; [][]Meth- [1154] [1155] Overfull \hbox (15.18042pt too wide) in paragraph at lines 558--558 []\T1/pcr/m/n/9 ## vector. The next method will always be the default, usuall y a primitive.[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w ith no arguments[] [1156] Overfull \hbox (4.38043pt too wide) in paragraph at lines 619--619 []\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho ut arguments[] Underfull \vbox (badness 10000) has occurred while \output is active [1157] Overfull \hbox (25.98041pt too wide) in paragraph at lines 637--637 []\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th e default method[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 640--640 []\T1/pcr/m/n/9 ## call f() with 1 argument: the default "B0" is not passed b y callNextMethod[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 657--657 []\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the "B0" method[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 672--672 []\T1/pcr/m/n/9 ## Although the argument here is numeric, it\TS1/pcr/m/n/9 '\T 1/pcr/m/n/9 s still the "B0" method that\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s called[ ] Underfull \vbox (badness 10000) has occurred while \output is active [1158] [1159] [1160] [1161] [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1794--1794 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N umber" method[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1796--1796 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE)) ) # the default[] [1173] [1174] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to []\T1/pcr/m/n/10 insertSource []\T1/ptm/m/n/ 10 can be an ob-ject of class [1175] [1176] [1177] Underfull \hbox (badness 1478) in paragraph at lines 2213--2218 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use []\T1/pcr/m/n/10 where = [1178] [1179] Underfull \hbox (badness 10000) in paragraph at lines 2327--2331 []\T1/ptm/m/n/10 To see the ac-tual ta-ble (an [][][]\T1/pcr/m/n/10 environment [][][][]\T1/ptm/m/n/10 ) used for meth-ods dis-patch, call [1180] [1181] [1182] Underfull \hbox (badness 3792) in paragraph at lines 2573--2576 []\T1/ptm/m/n/10 As you might ex-pect [][][]\T1/pcr/m/n/10 setGeneric[][][] []\ T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 setGroupGeneric[][][] []\T1/ptm/m/n/10 c re-ate ob-jects of class Underfull \hbox (badness 1194) in paragraph at lines 2604--2608 []\T1/ptm/m/n/10 Object of class []\T1/pcr/m/n/10 "optionalMethod" []\T1/ptm/m/ n/10 (a union of classes []\T1/pcr/m/n/10 "function" []\T1/ptm/m/n/10 and [1183] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2660--2660 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin g(where))[] [1184] [1185] [1186] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2879--2879 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers ions visible:[] [1187] [1188] [1189] [1190] [1191] [1192] [1193] Underfull \hbox (badness 10000) in paragraph at lines 3402--3407 []\T1/ptm/m/n/10 Function []\T1/pcr/m/n/10 implicitGeneric() []\T1/ptm/m/n/10 r e-turns the im-plicit generic ver-sion, Underfull \hbox (badness 6268) in paragraph at lines 3402--3407 []\T1/pcr/m/n/10 setGenericImplicit() []\T1/ptm/m/n/10 turns a generic im-plici t, []\T1/pcr/m/n/10 prohibitGeneric() []\T1/ptm/m/n/10 pre-vents [1194] [1195] Underfull \hbox (badness 10000) in paragraph at lines 3530--3534 []\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][][]\T1/pcr/m/n/10 getClass[][][] []\T1/ptm/m/n/10 and the de-scrip-tion of class [1196] Overfull \hbox (14.78088pt too wide) in paragraph at lines 3641--3650 [] [1197] [1198] Underfull \hbox (badness 10000) in paragraph at lines 3761--3762 [] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longit ude = Underfull \hbox (badness 10000) in paragraph at lines 3808--3809 []\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) { [1199] Underfull \hbox (badness 10000) in paragraph at lines 3845--3846 []\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , Underfull \hbox (badness 6157) in paragraph at lines 3907--3911 []\T1/ptm/m/n/10 A call to [][][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) [] \T1/ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to [1200] [1201] [1202] [1203] [1204] [1205] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4312--4312 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char acter(), Overfull \hbox (0.78088pt too wide) in paragraph at lines 4313--4313 [] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac cess,[] [1206] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4370--4370 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w here) [1207] [1208] [1209] Underfull \hbox (badness 2126) in paragraph at lines 4578--4586 []\T1/ptm/m/n/10 For ad-di-tional in-for-ma-tion see doc-u-men-ta-tion for the im-por-tant steps: ([][][]\T1/pcr/m/n/10 setMethod[][][]()[]\T1/ptm/m/n/10 , [1210] [1211] [1212] Underfull \hbox (badness 10000) in paragraph at lines 4815--4824 []\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha t eval-u-ates a call to [1213] [1214] [1215] [1216] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5203--5203 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate inheritance[] [1217] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5231--5231 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli er fails here)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5245--5245 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho d for classB[] Underfull \vbox (badness 10000) has occurred while \output is active [1218] [1219] Underfull \hbox (badness 10000) in paragraph at lines 5363--5364 []\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1220] [1221] Underfull \hbox (badness 3803) in paragraph at lines 5520--5522 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1222] [1223] [1224] Underfull \hbox (badness 1087) in paragraph at lines 5752--5757 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1225] [1226] [1227] [1228] [1229] [1230] Underfull \hbox (badness 10000) in paragraph at lines 6218--6234 []\T1/ptm/m/n/10 The de-fault method for []\T1/pcr/m/n/10 $initialize() []\T1/p tm/m/n/10 is equiv-a-lent to in-vok-ing the method [1231] [1232] Underfull \hbox (badness 1248) in paragraph at lines 6351--6355 []\T1/ptm/m/n/10 Typically, a spe-cial-ized []\T1/pcr/m/n/10 $initialize() []\T 1/ptm/m/n/10 method car-ries out its own com-pu-ta-tions, Underfull \hbox (badness 1960) in paragraph at lines 6351--6355 \T1/ptm/m/n/10 then in-vokes []\T1/pcr/m/n/10 $initFields() []\T1/ptm/m/n/10 to per-form stan-dard ini-tial-iza-tion, as shown in the [1233] Underfull \hbox (badness 4647) in paragraph at lines 6506--6508 []\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func- tion re-turned by [1234] [1235] Underfull \hbox (badness 2875) in paragraph at lines 6655--6664 []\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen se as any S4 class (see Underfull \hbox (badness 1436) in paragraph at lines 6655--6664 [][][]\T1/pcr/m/n/10 setValidity[][][][]\T1/ptm/m/n/10 ). Such meth-ods are of- ten a good idea; they will be called by call-ing [1236] Underfull \vbox (badness 10000) has occurred while \output is active [1237] [1238] [1239] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6981 \aliasA{S4}{S3Part}{S4} [1240] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7017--7017 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement version of as().[] [1241] [1242] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7208--7208 []\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data = datasets::iris)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7212--7212 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con tains = "mlm")[] [1243] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Complex}) has been already used, duplicate ignored \relax l.7237 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Logic}) h as been already used, duplicate ignored \relax l.7239 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) ha s been already used, duplicate ignored \relax l.7240 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7242 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignored \relax l.7243 \aliasA{Summary}{S4groupGeneric}{Summary} Underfull \hbox (badness 2050) in paragraph at lines 7304--7308 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1244] Underfull \hbox (badness 6708) in paragraph at lines 7317--7329 []\T1/pcr/m/n/10 "abs"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sign"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "sqrt"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ceiling"[]\T1/p tm/m/n/10 , []\T1/pcr/m/n/10 "floor"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "trunc" []\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cummax"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 2012) in paragraph at lines 7317--7329 []\T1/pcr/m/n/10 "acosh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "asin"[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 "asinh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "atan"[]\T1/p tm/m/n/10 , []\T1/pcr/m/n/10 "atanh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "exp"[] \T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "expm1"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "c os"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3209) in paragraph at lines 7317--7329 []\T1/pcr/m/n/10 "cosh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cospi"[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 "sin"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sinh"[]\T1/ptm /m/n/10 , []\T1/pcr/m/n/10 "sinpi"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tan"[]\T 1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tanh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tanp i"[]\T1/ptm/m/n/10 , [1245] [1246] Underfull \hbox (badness 1694) in paragraph at lines 7480--7482 []\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t ion ob-ject (see Underfull \hbox (badness 10000) in paragraph at lines 7504--7507 []\T1/ptm/m/n/10 The typ-i-cal user level func-tion is []\T1/pcr/m/n/10 selectS uperClasses() []\T1/ptm/m/n/10 which calls [1247] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7525--7525 []\T1/pcr/m/n/9 selectSuperClasses("C", dropVirtual=TRUE, directOnly=FALSE)# d itto w/o "Root"[] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8630--8630 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact er(), [1261] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8705--8705 [] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class Def =,[] [1262] [1263] [1264] [1265] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8967--8967 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col umn matrices[] [1266] [1267] [1268] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9175--9175 [] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns), "setCount")[] [1269] [1270] [1271] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9437--9437 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo rmal arguments[] [1272] [1273] [1274] [1275] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9745--9745 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre es of freedom[] [1276] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9855--9855 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9866--9866 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] Underfull \hbox (badness 10000) in paragraph at lines 10564--10566 []\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., []\T1/pcr/m/n/10 "functi on" []\T1/ptm/m/n/10 for class Underfull \hbox (badness 1852) in paragraph at lines 10572--10576 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., Underfull \hbox (badness 1681) in paragraph at lines 10572--10576 []\T1/pcr/m/n/10 "functionWithTrace" []\T1/ptm/m/n/10 ex-tends []\T1/pcr/m/n/10 "function"[]\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends [1287] [1288] [1289]) (./parallel-pkg.tex [1290] Chapter 8. Underfull \hbox (badness 2418) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `[]\T1/p cr/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"[]\T1/ptm/m/n/10 ' [][] RNG[][][]: see [1291] Underfull \hbox (badness 4242) in paragraph at lines 97--99 []\T1/ptm/m/n/10 a vec-tor for []\T1/pcr/m/n/10 clusterApply []\T1/ptm/m/n/10 a nd []\T1/pcr/m/n/10 clusterApplyLB[]\T1/ptm/m/n/10 , a ma-trix for [1292] [1293] Underfull \hbox (badness 1024) in paragraph at lines 214--217 []\T1/ptm/m/n/10 Two ex-cep-tions: []\T1/pcr/m/n/10 parLapply []\T1/ptm/m/n/10 has ar-gu-ment []\T1/pcr/m/n/10 X []\T1/ptm/m/n/10 not []\T1/pcr/m/n/10 x []\T1 /ptm/m/n/10 for con-sis-tency with [][][]\T1/pcr/m/n/10 lapply[][][][]\T1/ptm/m /n/10 , and [1294] Underfull \hbox (badness 1320) in paragraph at lines 301--304 []\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD, So-laris and Win-dows. [1295] [1296] Underfull \hbox (badness 10000) in paragraph at lines 437--439 []\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for []\T1/pcr/m/ n/10 Rscript []\T1/ptm/m/n/10 such as [1297] [1298] [1299] [1300] [1301] Underfull \hbox (badness 1917) in paragraph at lines 771--780 []\T1/pcr/m/n/10 mcfork []\T1/ptm/m/n/10 re-turns an ob-ject of the class []\T1 /pcr/m/n/10 "childProcess" []\T1/ptm/m/n/10 to the mas-ter and of class Underfull \hbox (badness 1178) in paragraph at lines 771--780 []\T1/pcr/m/n/10 "masterProcess" []\T1/ptm/m/n/10 to the child: both the classe s in-herit from class []\T1/pcr/m/n/10 "process"[]\T1/ptm/m/n/10 . If [1302] Overfull \hbox (60.78088pt too wide) in paragraph at lines 864--864 [] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini ty.list = NULL)[] [1303] [1304] [1305] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1055--1055 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit y.list = affL)[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 1059--1059 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch eduled to suitable CPUs[] [1306] [1307] Underfull \hbox (badness 5388) in paragraph at lines 1174--1179 []\T1/pcr/m/n/10 mcparallel []\T1/ptm/m/n/10 re-turns an ob-ject of the class [ ]\T1/pcr/m/n/10 "parallelJob" []\T1/ptm/m/n/10 which in-her-its from Underfull \hbox (badness 10000) in paragraph at lines 1198--1206 []\T1/ptm/m/n/10 The be-haviour with []\T1/pcr/m/n/10 mc.set.seed = TRUE []\T1/ ptm/m/n/10 is dif-fer-ent only if [1308] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1235--1235 []\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[] [1309] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1351--1351 [] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif (N, 1, 28)))[] [1310] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1365--1365 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format = "%Y-%m-%d")))[] Underfull \hbox (badness 1577) in paragraph at lines 1394--1397 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by []\T1/pcr/m/n/10 .Random.seed []\T1/ptm/m/n/10 when the [1311] Underfull \hbox (badness 3375) in paragraph at lines 1441--1443 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 nextRNGStream []\T1/ptm/m/n/10 and []\T1/ pcr/m/n/10 nextRNGSubStream[]\T1/ptm/m/n/10 , a value which can be as-signed to [1312] [1313]) (./splines-pkg.tex [1314] Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1315] [1316] [1317] [1318] [1319] [1320] [1321] [1322] Overfull \hbox (4.38043pt too wide) in paragraph at lines 499--499 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl ine = TRUE))[] [1323] Underfull \hbox (badness 1043) in paragraph at lines 600--602 []\T1/ptm/m/n/10 An in-te-ger be-tween 0 and []\T1/pcr/m/n/10 splineOrder(objec t) - 1 []\T1/ptm/m/n/10 spec-i-fy-ing the [1324] [1325] Overfull \hbox (25.98041pt too wide) in paragraph at lines 715--715 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, sparse = TRUE)))[] [1326] [1327] [1328]) (./stats-pkg.tex Chapter 10. [1329] Underfull \hbox (badness 1077) in paragraph at lines 71--74 []\T1/pcr/m/n/10 .MFclass() []\T1/ptm/m/n/10 re-turns a char-ac-ter string, one of []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ordered"[]\T 1/ptm/m/n/10 , []\T1/pcr/m/n/10 "factor"[]\T1/ptm/m/n/10 , Overfull \hbox (69.18036pt too wide) in paragraph at lines 91--91 []\T1/pcr/m/n/9 (xl <- .getXlevels(terms(mf), mf)) # a list with one entry " $ Species" with 3 levels:[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 94--94 [] \T1/pcr/m/n/9 identical(.getXlevels(terms(mc), mc), xl[0]) # a empty named list, as no factors[] [1330] [1331] [1332] [1333] [1334] Overfull \hbox (20.58041pt too wide) in paragraph at lines 445--445 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea rson Chi-square[] [1335] Overfull \hbox (6.78088pt too wide) in paragraph at lines 468--468 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = FALSE) [1336] [1337] [1338] [1339] [1340] [1341] Underfull \hbox (badness 1024) in paragraph at lines 901--903 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from []\T1/pcr/m/n/10 l m []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 aov[]\T1/ptm/m/n/10 , or a for-mula for [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1640--1640 [] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm = TRUE)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1643--1643 [] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm = TRUE)[] [1354] [1355] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1790--1790 [] \T1/pcr/m/n/9 approx(xn, yn, xout=xout, method=M, rule=R, n a.rm=na.)$y),[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1802--1802 []\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$y) # warning, can be avoided by specifying \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ties=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[ ] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2820--2820 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F ALSE) [1371] [1372] [1373] [1374] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3068--3068 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co l = "green")[] [1375] [1376] [1377] Underfull \hbox (badness 10000) in paragraph at lines 3279--3281 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Bartlett test of homo geneity of [1378] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3328--3328 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3329--3329 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1379] [1380] [1381] [1382] Package amsmath Warning: Foreign command \atopwithdelims; (amsmath) \frac or \genfrac should be used instead (amsmath) on input line 3658. [1383] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3724--3724 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = " log density",[] [1384] [1385] [1386] [1387] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4003--4003 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0) [1388] [1389] [1390] [1391] [1392] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4292--4292 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4293--4293 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1393] [1394] [1395] [1396] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4534--4534 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1397] [1398] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4709--4709 [] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df = df, ncp = L)),[] [1399] [1400] Underfull \hbox (badness 3989) in paragraph at lines 4803--4810 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1401] [1402] [1403] [1404] [1405] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5192--5192 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1)) , ci = c(-1,-1))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5194--5194 []\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci = c(-0.9,0.1))[] [1406] [1407] [1408] [1409] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5416--5416 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works with these :[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5434--5434 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter")) [1410] [1411] [1412] Underfull \hbox (badness 1436) in paragraph at lines 5644--5649 []\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i ng co-vari-ances Underfull \hbox (badness 1377) in paragraph at lines 5644--5649 \T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi -a-tion of) Underfull \hbox (badness 1448) in paragraph at lines 5644--5649 \T1/ptm/m/n/10 one of the strings []\T1/pcr/m/n/10 "everything"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "all.obs"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "complete.obs" []\T1/ptm/m/n/10 , [1413] [1414] Underfull \vbox (badness 10000) has occurred while \output is active [1415] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5847--5847 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1416] [1417] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6014--6014 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE, [1418] [1419] [1420] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6199--6199 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL) [1421] [1422] Overfull \hbox (84.78088pt too wide) in paragraph at lines 6307--6307 []\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en v = parent.frame())[] [1423] [1424] [1425] [1426] Underfull \hbox (badness 5954) in paragraph at lines 6570--6572 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1427] Underfull \hbox (badness 2503) in paragraph at lines 6652--6655 []\T1/ptm/m/n/10 Objects of class []\T1/pcr/m/n/10 "hclust" []\T1/ptm/m/n/10 ca n be con-verted to class []\T1/pcr/m/n/10 "dendrogram" []\T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 5563) in paragraph at lines 6656--6658 []\T1/pcr/m/n/10 rev.dendrogram []\T1/ptm/m/n/10 sim-ply re-turns the den-dro-g ram []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 with re-versed nodes, see also Underfull \hbox (badness 1655) in paragraph at lines 6659--6664 \T1/ptm/m/n/10 has []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 y [ ]\T1/ptm/m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be- fore \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.1.2, [1428] Underfull \hbox (badness 7238) in paragraph at lines 6695--6698 [][][]\T1/pcr/m/n/10 dendrapply[][][] []\T1/ptm/m/n/10 for ap-ply-ing a func-ti on to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][][]\T1/pcr/m/n/10 order.dend rogram[][][] []\T1/ptm/m/n/10 and Overfull \hbox (4.38043pt too wide) in paragraph at lines 6707--6707 []\T1/pcr/m/n/9 str(dend1, max.level = 2, last.str = "\TS1/pcr/m/n/9 '\T1/pcr /m/n/9 ") # only the first two sub-levels[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6730--6730 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, type = "tr")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6745--6745 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] [1429] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6760--6760 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h oriz = TRUE)[] [1430] [1431] [1432] Underfull \vbox (badness 10000) has occurred while \output is active [1433] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7028--7028 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] [1434] [1435] Underfull \vbox (badness 10000) has occurred while \output is active [1436] [1437] [1438] [1439] Underfull \hbox (badness 10000) in paragraph at lines 7428--7432 []\T1/pcr/m/n/10 "maximum"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "manhattan"[]\T1/ ptm/m/n/10 , []\T1/pcr/m/n/10 "canberra"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "bi nary" []\T1/ptm/m/n/10 or [1440] Underfull \hbox (badness 6493) in paragraph at lines 7531--7534 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][][] \T1/pcr/m/n/10 dist[][][]()[]\T1/ptm/m/n/10 , the [1441] [1442] Underfull \hbox (badness 10000) in paragraph at lines 7668--7671 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht tps : / / CRAN . R-[]project . org / view = [1443] [1444] [1445] [1446] [1447] [1448] Underfull \hbox (badness 10000) in paragraph at lines 8080--8085 []\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences [] \T1/pcr/m/n/10 x[t][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 x[t-1][]\T1/ptm/m/n/10 , ..., [1449] [1450] [1451] [1452] [1453] [1454] Underfull \hbox (badness 1210) in paragraph at lines 8435--8437 []\T1/ptm/m/n/10 Components of []\T1/pcr/m/n/10 control []\T1/ptm/m/n/10 can al so be sup-plied as named ar-gu-ments to [1455] [1456] [1457] [1458] [1459] [1460] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8901--8901 []\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q uasipoisson())[] [1461] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8946--8946 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link = "log")) # fails[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 8949--8949 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit "), start = c(0,1))[] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9529--9529 [] \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4 0k", "> 40k"),[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 9530--9530 [] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod erateS", "VeryS")))[] [1470] [1471] [1472] Underfull \hbox (badness 7291) in paragraph at lines 9709--9711 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Fligner-Killeen test of homogeneity of [1473] [1474] [1475] [1476] [1477] [1478] [1479] Underfull \hbox (badness 6944) in paragraph at lines 10201--10207 [][][]\T1/pcr/m/n/10 ftable.formula[][][] []\T1/ptm/m/n/10 for the for-mula in- ter-face (which al-lows a []\T1/pcr/m/n/10 data = . []\T1/ptm/m/n/10 ar-gu-ment ); [1480] [1481] [1482] Underfull \hbox (badness 3758) in paragraph at lines 10415--10418 []\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or [1483] [1484] [1485] [1486] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10659--10659 [] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL , ...)[] Underfull \hbox (badness 4518) in paragraph at lines 10685--10690 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1487] Underfull \hbox (badness 4132) in paragraph at lines 10724--10728 []\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth od Underfull \hbox (badness 1112) in paragraph at lines 10778--10784 []\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form []\T1/pcr/m/n/10 first:second []\T1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak- [1488] Underfull \hbox (badness 10000) in paragraph at lines 10829--10832 []\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][][]\T1/pcr/m/n/10 coeffic ients[][][][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 effects[]\T1/ptm/m/n/10 , []\T1/ pcr/m/n/10 fitted.values []\T1/ptm/m/n/10 and [1489] [1490] [1491] Underfull \hbox (badness 2142) in paragraph at lines 11046--11049 []\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1 0 dev \OMS/cmsy/m/n/10 ^^@ [1492] Underfull \hbox (badness 1708) in paragraph at lines 11127--11131 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1493] Underfull \hbox (badness 10000) in paragraph at lines 11169--11175 [][][]\T1/pcr/m/n/10 glm[][][] []\T1/ptm/m/n/10 for com-put-ing []\T1/pcr/m/n/1 0 glm.obj[]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 anova.glm[][][][]\T1/ptm/m/n/1 0 ; the cor-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions, Underfull \hbox (badness 1418) in paragraph at lines 11207--11212 []\T1/pcr/m/n/10 "average" []\T1/ptm/m/n/10 (= UP-GMA), []\T1/pcr/m/n/10 "mcqui tty" []\T1/ptm/m/n/10 (= WPGMA), []\T1/pcr/m/n/10 "median" []\T1/ptm/m/n/10 (= [1494] [1495] Underfull \hbox (badness 2635) in paragraph at lines 11340--11343 \T1/ptm/m/n/10 There are [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/n/10 , [][ ][]\T1/pcr/m/n/10 plot[][][] []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 identify []\ T1/ptm/m/n/10 (see [][][]\T1/pcr/m/n/10 identify.hclust[][][][]\T1/ptm/m/n/10 ) meth-ods and the [1496] [1497] [1498] Underfull \hbox (badness 1694) in paragraph at lines 11523--11526 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1499] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11621--11621 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col SideColors = cc,[] [1500] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11654--11654 [] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 0.1),[] Underfull \hbox (badness 10000) in paragraph at lines 11667--11671 []\T1/ptm/m/n/10 Character string to se-lect an []\T1/pcr/m/n/10 "additive" []\ T1/ptm/m/n/10 (the de-fault) or [1501] [1502] [1503] [1504] [1505] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11989--11989 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] [1506] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.12004 \aliasA{hat}{influence.measures}{hat} Overfull \hbox (0.78088pt too wide) in paragraph at lines 12064--12064 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] [1507] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12076--12076 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] Underfull \hbox (badness 1062) in paragraph at lines 12129--12134 []\T1/ptm/m/n/10 The op-tional []\T1/pcr/m/n/10 infl[]\T1/ptm/m/n/10 , []\T1/pc r/m/n/10 res []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 sd []\T1/ptm/m/n/10 ar-gu-me nts are there to en-cour-age the use of these di- Underfull \hbox (badness 1052) in paragraph at lines 12146--12148 []\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 hat() []\T1/ptm/m/n/10 ex-ists mainly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1508] [1509] [1510] [1511] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12401--12401 [] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = TRUE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12402--12402 [] \T1/pcr/m/n/10 trace.label = deparse1(substitute(trace.fact or)),[] [1512] [1513] [1514] [1515] [1516] [1517] Underfull \hbox (badness 10000) in paragraph at lines 12749--12751 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][][]\T1/pcr/m/n/10 solve.de fault[][][] []\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 SSinit = Underfull \hbox (badness 4739) in paragraph at lines 12772--12774 []\T1/ptm/m/n/10 the es-ti-mate at time $\OML/cmm/m/it/10 t \OMS/cmsy/m/n/10 ^^ @ \OT1/cmr/m/n/10 1$ \T1/ptm/m/n/10 of the state un-cer-tainty ma-trix $\OML/cm m/m/it/10 Q$ \T1/ptm/m/n/10 (not up-dated by [1518] [1519] [1520] [1521] [1522] Underfull \hbox (badness 3417) in paragraph at lines 13079--13081 []\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class []\T1/pcr/ m/n/10 "kmeans"[]\T1/ptm/m/n/10 , typ-i-cally the re-sult []\T1/pcr/m/n/10 ob [ ]\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 ob <- Underfull \hbox (badness 2894) in paragraph at lines 13085--13089 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method Underfull \hbox (badness 1038) in paragraph at lines 13085--13089 \T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 "Hartigan-Wong"[]\T1/ptm/m/n/10 ): if pos-i-ti ve (or true), trac-ing in-for-ma-tion on the [1523] [1524] [1525] [1526] [1527] [1528] Underfull \hbox (badness 1496) in paragraph at lines 13508--13514 []\T1/ptm/m/n/10 Gunar Schröer and Di-et-rich Tren-kler (1995). Ex-act and Ran- dom-iza-tion Dis-tri-bu-tions of [1529] [1530] [1531] [1532] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13757--13757 []\T1/pcr/m/n/9 lag.plot(sqrt(sunspots), set.lags = c(1:4, 9:12), pch = ".", c ol = "gold")[] [1533] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13858--13858 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep t", "slope"))[] [1534] Underfull \hbox (badness 4518) in paragraph at lines 13906--13911 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1535] [1536] [1537] Underfull \hbox (badness 10000) in paragraph at lines 14107--14111 []\T1/ptm/m/n/10 More []\T1/pcr/m/n/10 lm() []\T1/ptm/m/n/10 ex-am-ples are ava il-able e.g., in [][][]\T1/pcr/m/n/10 anscombe[][][][]\T1/ptm/m/n/10 , [][][]\T 1/pcr/m/n/10 attitude[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 freeny[][][] []\T1/ptm/m/n/10 , [1538] [1539] [1540] [1541] [1542] Underfull \hbox (badness 1163) in paragraph at lines 14446--14454 \T1/ptm/m/n/10 els, [][][]\T1/pcr/m/n/10 influence[][][] []\T1/ptm/m/n/10 (etc on that page) for re-gres-sion di-ag-nos-tics, [][][]\T1/pcr/m/n/10 weighted.re siduals[][][][]\T1/ptm/m/n/10 , [1543] [1544] Underfull \hbox (badness 4518) in paragraph at lines 14566--14571 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1545] [1546] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14754--14754 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14755--14755 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1547] [1548] [1549] [1550] [1551] Overfull \hbox (6.78088pt too wide) in paragraph at lines 15098--15098 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 15099--15099 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1552] [1553] Overfull \hbox (18.78088pt too wide) in paragraph at lines 15192--15192 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra nge(x))) [1554] [1555] [1556] [1557] [1558] [1559] Underfull \hbox (badness 2726) in paragraph at lines 15601--15604 []\T1/ptm/m/n/10 character; one of []\T1/pcr/m/n/10 "logit"[]\T1/ptm/m/n/10 , [ ]\T1/pcr/m/n/10 "probit"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cauchit"[]\T1/ptm/ m/n/10 , []\T1/pcr/m/n/10 "cloglog"[]\T1/ptm/m/n/10 , [1560] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15695--15695 []\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i n R <= 3.5.0[] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] Overfull \hbox (31.3804pt too wide) in paragraph at lines 16324--16324 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc gp, data = esoph) [1571] [1572] Underfull \hbox (badness 1490) in paragraph at lines 16471--16476 \T1/ptm/m/n/10 those spec-i-fied in []\T1/pcr/m/n/10 ... []\T1/ptm/m/n/10 which are re-cy-cled to the num-ber of data frame rows. Un-like [1573] Underfull \hbox (badness 1648) in paragraph at lines 16539--16541 []\T1/ptm/m/n/10 a data frame cre-ated with [][][]\T1/pcr/m/n/10 model.frame[][ ][][]\T1/ptm/m/n/10 . If an-other sort of ob-ject, [1574] Overfull \hbox (36.7804pt too wide) in paragraph at lines 16624--16624 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts.arg = list(a = "contr.sum" , b = contr.poly))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16625--16625 []\T1/pcr/m/n/9 m.orth <- model.matrix(~a+b, dd, contrasts.arg = list(a = "con tr.helmert"))[] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17182--17182 []\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3)) # does not affect objects with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[] [1584] [1585] [1586] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17414--17414 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, s, prob = 0.4)),[] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] Underfull \vbox (badness 10000) has occurred while \output is active [1597] Overfull \hbox (42.18039pt too wide) in paragraph at lines 18136--18136 []\T1/pcr/m/n/9 ## adjusting the convergence test by adding \TS1/pcr/m/n/9 '\T 1/pcr/m/n/9 scaleOffset\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 to its denominator RSS:[] Underfull \vbox (badness 10000) has occurred while \output is active [1598] Overfull \hbox (74.58035pt too wide) in paragraph at lines 18154--18154 []\T1/pcr/m/n/9 ## Here, requiring close convergence, must use more accurate n umerical differentiation,[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 18155--18155 []\T1/pcr/m/n/9 ## as this typically gives Error: "step factor .. reduced belo w \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 minFactor\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 .."[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 18159--18159 []\T1/pcr/m/n/9 ## central differencing works here typically (PR#18165: not co nverging on *some*):[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18160--18160 []\T1/pcr/m/n/9 ctr2 <- nls.control(nDcentral=TRUE, tol = 8e-8, # <- even smal ler than above[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 18163--18163 [] \T1/pcr/m/n/9 (grepl("^aarch64.*linux", R.version$platform) && grepl ("^NixOS", osVersion)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18195--18195 [] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21 ), th = b[1]))[] [1599] [1600] [1601] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18371--18371 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi ty), DNase.2)[] [1602] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18418--18418 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18465--18465 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1603] [1604] [1605] [1606] Overfull \hbox (102.78088pt too wide) in paragraph at lines 18678--18678 [] \T1/pcr/m/n/10 eps = .Machine$double.eps ^ (1/if(central) 3 els e 2), central = FALSE)[] [1607] [1608] [1609] [1610] [1611] Underfull \hbox (badness 1248) in paragraph at lines 18993--18996 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 1661) in paragraph at lines 19006--19010 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 1478) in paragraph at lines 19014--19018 \T1/ptm/m/n/10 if []\T1/pcr/m/n/10 control$trace []\T1/ptm/m/n/10 is pos-i-tive . De-faults to ev-ery 10 it-er-a-tions for []\T1/pcr/m/n/10 "BFGS" []\T1/ptm/m/ n/10 and [1612] Underfull \hbox (badness 2042) in paragraph at lines 19072--19074 []\T1/ptm/m/n/10 indicates an er-ror from the []\T1/pcr/m/n/10 "L-BFGS-B" []\T1 /ptm/m/n/10 method; see com-po-nent [1613] Overfull \hbox (15.18042pt too wide) in paragraph at lines 19178--19178 [] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no t* at boundary[] [1614] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19221--19221 [] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", axes = FALSE)[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 19239--19239 []\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 19242--19242 []\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 19262--19262 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max (interval), [1615] Overfull \hbox (36.78088pt too wide) in paragraph at lines 19265--19265 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max (interval),[] Underfull \hbox (badness 2564) in paragraph at lines 19300--19311 []\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 f []\T1/ptm/m/n/10 is never eva l-u-ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m /n/10 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/ 10 tol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 , Underfull \hbox (badness 1082) in paragraph at lines 19300--19311 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately []\T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) []\T1/ptm/m/n/10 and $\OML /cmm/m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa [1616] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19363--19363 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1617] [1618] [1619] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19590--19590 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 1, lty = 1:6,[] [1620] [1621] Underfull \hbox (badness 1337) in paragraph at lines 19701--19704 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1622] [1623] [1624] [1625] [1626] Overfull \hbox (0.78088pt too wide) in paragraph at lines 20020--20020 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1627] [1628] Overfull \hbox (24.78088pt too wide) in paragraph at lines 20108--20108 [] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist vs Leverage* " * h[ii] / (1 - h[ii]))),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 20110--20110 [] \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else points,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20112--20112 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1629] Underfull \hbox (badness 10000) in paragraph at lines 20172--20178 \T1/pcr/m/n/10 "bottomleft", legend = "Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s di stance", lty = cook.lty, Underfull \hbox (badness 10000) in paragraph at lines 20172--20178 \T1/pcr/m/n/10 col = cook.col, text.col = cook.col, bty = "n", x.intersp Underfull \hbox (badness 10000) in paragraph at lines 20180--20186 []\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment []\T 1/pcr/m/n/10 iter []\T1/ptm/m/n/10 in Underfull \hbox (badness 10000) in paragraph at lines 20191--20194 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 1 or 2, to be used in []\T1/pcr/m /n/10 ylim <- [1630] [1631] [1632] [1633] [1634] Overfull \hbox (0.78088pt too wide) in paragraph at lines 20500--20500 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] Underfull \hbox (badness 1194) in paragraph at lines 20510--20513 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1635] Underfull \hbox (badness 1107) in paragraph at lines 20568--20570 []\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate [] \T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . De-faults to [1636] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20623--20623 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange ") # all colors[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 20630--20630 []\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 1, y.intersp = 1)[] [1637] [1638] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20724--20724 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1639] [1640] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20853--20853 [] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no cancellation[] [1641] Underfull \hbox (badness 7740) in paragraph at lines 20916--20918 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Exact Poisson test" [ ]\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 "Comparison of Overfull \hbox (6.78088pt too wide) in paragraph at lines 20964--20964 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) [1642] Underfull \hbox (badness 10000) in paragraph at lines 21020--21022 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 poly(*, simple=TRUE)[]\T1/ptm/m/n/10 , [] \T1/pcr/m/n/10 polym(*, coefs=)[]\T1/ptm/m/n/10 , and [1643] Overfull \hbox (4.38043pt too wide) in paragraph at lines 21057--21057 [] \T1/pcr/m/n/9 zm <- zapsmall(polym ( 1:4, c(1, 4:6), degree = 3)) # or just poly():[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 21062--21062 []\T1/pcr/m/n/9 ## poly(, df) --- used to fail till July 14 (vive la F rance!), 2017:[] [1644] [1645] [1646] [1647] [1648] [1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656] Overfull \hbox (58.38037pt too wide) in paragraph at lines 21917--21917 [] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tolerance = 1e-15)) # e xactly equal typically[] [1657] Underfull \hbox (badness 6859) in paragraph at lines 21984--21991 [][][]\T1/pcr/m/n/10 predict.glm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 p redict.lm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.loess[][][][]\T1 /ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.nls[][][][]\T1/ptm/m/n/10 , [][][]\T 1/pcr/m/n/10 predict.poly[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 21995--22001 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][][]\T1/pcr/m/n/10 predict.ar[ ][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.Arima[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/pcr/m/n/10 predict.arima0[][][][]\T1/ptm/m/n/10 , [1658] [1659] [1660] [1661] [1662] Overfull \hbox (54.78088pt too wide) in paragraph at lines 22283--22283 [] \T1/pcr/m/n/10 rankdeficient = c("warnif", "simple", "non-estim", "N A", "NAwarn"),[] Underfull \hbox (badness 10000) in paragraph at lines 22309--22312 []\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string spec-i-fy-ing what should hap-pen in the Underfull \hbox (badness 10000) in paragraph at lines 22309--22312 \T1/ptm/m/n/10 case of a rank de-fi-cient model, i.e., when []\T1/pcr/m/n/10 ob ject$rank < [1663] Underfull \hbox (badness 5832) in paragraph at lines 22314--22319 \T1/ptm/m/n/10 cases, i.e., vec-tors not in the same pre-dic-tor sub-space as t he Underfull \hbox (badness 8151) in paragraph at lines 22314--22319 \T1/ptm/m/n/10 orig-i-nal data (with tol-er-ance []\T1/pcr/m/n/10 tol[]\T1/ptm/ m/n/10 ). In that case, the non- Underfull \hbox (badness 1184) in paragraph at lines 22314--22319 \T1/ptm/m/n/10 estimable in-dices are also re-turned as at-tribute []\T1/pcr/m/ n/10 "non-estim" []\T1/ptm/m/n/10 (see [1664] [1665] [1666] [1667] [1668] [1669] [1670] Overfull \hbox (48.78088pt too wide) in paragraph at lines 22782--22782 [] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign = TRUE, ...)[] [1671] [1672] [1673] [1674] Overfull \hbox (0.78088pt too wide) in paragraph at lines 23066--23066 [] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x )) &&[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 23067--23067 [] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr(" , "p-v"),[] [1675] [1676] [1677] [1678] [1679] Underfull \hbox (badness 1337) in paragraph at lines 23393--23399 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1680] [1681] [1682] [1683] [1684] Overfull \hbox (15.18042pt too wide) in paragraph at lines 23705--23705 []\T1/pcr/m/n/9 with(d, qqplot(Female, Male, pch = 19, xlim = c(-31, 31), ylim = c(-31, 31),[] [1685] [1686] [1687] [1688] Underfull \hbox (badness 10000) in paragraph at lines 24017--24019 []\T1/ptm/m/n/10 Wicklin, R. (2017) Sam-ple quan-tiles: A com-par-i-son of 9 de f-i-ni-tions; Underfull \hbox (badness 10000) in paragraph at lines 24017--24019 \T1/ptm/m/n/10 SAS Blog. [][]$\T1/pcr/m/n/10 https : / / blogs . sas . com / co ntent / iml / 2017 / 05 / 24 / [1689] Underfull \hbox (badness 10000) in paragraph at lines 24024--24025 []\T1/ptm/m/n/10 Wikipedia: [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . or g / wiki / Quantile # Estimating _ [1690] Overfull \hbox (48.78088pt too wide) in paragraph at lines 24135--24135 [] \T1/pcr/m/n/10 method = c("non.compact", "row.compact", "col.compact" , "compact"),[] [1691] Underfull \hbox (badness 1028) in paragraph at lines 24193--24196 []\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for []\T 1/pcr/m/n/10 write() []\T1/ptm/m/n/10 and [1692] [1693] Underfull \hbox (badness 10000) in paragraph at lines 24308--24311 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1694] Underfull \hbox (badness 7099) in paragraph at lines 24363--24365 []\T1/ptm/m/n/10 This, as [][][]\T1/pcr/m/n/10 reorder[][][]()[]\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [][][]\T1/pcr/m/n/10 factor[][][](x, l evels = [1695] Underfull \hbox (badness 7099) in paragraph at lines 24427--24429 []\T1/ptm/m/n/10 This, as [][][]\T1/pcr/m/n/10 relevel[][][]()[]\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [][][]\T1/pcr/m/n/10 factor[][][](x, l evels = Overfull \hbox (31.3804pt too wide) in paragraph at lines 24462--24462 []\T1/pcr/m/n/9 bymedianR <- with(InsectSprays, reorder(spray, count, median, decreasing=TRUE))[] [1696] [1697] Overfull \hbox (9.78043pt too wide) in paragraph at lines 24538--24538 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")[] [1698] [1699] Overfull \hbox (0.78088pt too wide) in paragraph at lines 24655--24655 []\T1/pcr/m/n/10 # varying = ___, # list / matrix / vector (use with care)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 24656--24656 []\T1/pcr/m/n/10 # v.names = ___, # vector of variable names in long format[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 24657--24657 []\T1/pcr/m/n/10 # timevar, times, # name / values of constructed time variable[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 24658--24658 []\T1/pcr/m/n/10 # idvar, ids) # name / values of constructed id v ariable[] [1700] [1701] Underfull \hbox (badness 10000) in paragraph at lines 24818--24823 [][][]\T1/pcr/m/n/10 stack[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 aperm[] [][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 relist[][][] []\T1/ptm/m/n/10 for r e-shap-ing the re-sult of [][][]\T1/pcr/m/n/10 unlist[][][][]\T1/ptm/m/n/10 . [ ][][]\T1/pcr/m/n/10 xtabs[][][] []\T1/ptm/m/n/10 and Underfull \hbox (badness 2495) in paragraph at lines 24818--24823 [][][]\T1/pcr/m/n/10 as.data.frame.table[][][] []\T1/ptm/m/n/10 for cre-at-ing con-tin-gency ta-bles and con-vert-ing them back to Overfull \hbox (15.18042pt too wide) in paragraph at lines 24829--24829 []\T1/pcr/m/n/9 ## long to wide (direction = "wide") requires idvar and timeva r at a minimum[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 24830--24830 []\T1/pcr/m/n/9 reshape(Indometh, direction = "wide", idvar = "Subject", timev ar = "time")[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 24849--24849 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide ", v.names = "x")[] [1702] [1703] Overfull \hbox (60.78088pt too wide) in paragraph at lines 24953--24953 [] \T1/pcr/m/n/10 na.action = c("+Big_alternate", "-Big_alternate", "na. omit", "fail"),[] Underfull \hbox (badness 1033) in paragraph at lines 24996--25002 \T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/ m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where [1704] Underfull \hbox (badness 10000) in paragraph at lines 25017--25020 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult []\T1/pcr/m/n/10 y = r unmed(x, k) []\T1/ptm/m/n/10 sim-ply has []\T1/pcr/m/n/10 y[j] = [1705] Overfull \hbox (9.78043pt too wide) in paragraph at lines 25099--25099 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi ans Example")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 25128--25128 []\T1/pcr/m/n/9 ## An example with initial NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s - used to fail badly (notably for "Turlach"):[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 25140--25140 []\T1/pcr/m/n/9 matplot(y = cbind(x15, rT15), type = "b", ylim = c(1,9), pch=1 :5, xlab = NA,[] [1706] [1707] [1708] [1709] [1710] [1711] Underfull \vbox (badness 10000) has occurred while \output is active [1712] [1713] Underfull \hbox (badness 6268) in paragraph at lines 25599--25604 [][][]\T1/pcr/m/n/10 SSasympOrig[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 S Sbiexp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSfol[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSfpl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSgo mpertz[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSlogis[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 SSmicmen[][][][]\T1/ptm/m/n/10 , [1714] [1715] [1716] Underfull \hbox (badness 1867) in paragraph at lines 25809--25811 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 25825--25829 []\T1/ptm/m/n/10 where []\T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallba ck = use.fallback) []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 PP Underfull \hbox (badness 10000) in paragraph at lines 25825--25829 \T1/pcr/m/n/10 <- sum(!is.na([][]coef[][][](object))) []\T1/ptm/m/n/10 -- where in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was [1717] Overfull \hbox (20.58041pt too wide) in paragraph at lines 25867--25867 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr om summary(lm1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 25874--25874 []\T1/pcr/m/n/9 stopifnot(all.equal(sigma(fm.DN1), summary(fm.DN1)$sigma, tole rance=1e-15))[] [1718] [1719] [1720] Underfull \hbox (badness 2495) in paragraph at lines 26057--26066 []\T1/ptm/m/n/10 For an in-verse gaus-sian GLM the model as-sumed is $\OML/cmm/ m/it/10 IG\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^V[]; ^^Uw[]\OT1/cmr/m/n/10 )$ \T1 /ptm/m/n/10 (see [][]$\T1/pcr/m/n/10 https : / / en . [1721] [1722] Underfull \hbox (badness 2197) in paragraph at lines 26199--26202 []\T1/pcr/m/n/10 psmirnov []\T1/ptm/m/n/10 gives the dis-tri-bu-tion func-tion, []\T1/pcr/m/n/10 qsmirnov []\T1/ptm/m/n/10 gives the quan-tile func-tion, and Overfull \hbox (24.78088pt too wide) in paragraph at lines 26219--26219 [] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)[] Underfull \hbox (badness 1412) in paragraph at lines 26226--26228 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1723] Overfull \hbox (25.98041pt too wide) in paragraph at lines 26313--26313 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS S"), smooth(x)))[] [1724] Overfull \hbox (84.78088pt too wide) in paragraph at lines 26338--26338 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda = NULL, cv = FALSE, Overfull \hbox (66.78088pt too wide) in paragraph at lines 26341--26341 [] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee p.stuff = FALSE)[] [1725] [1726] [1727] Overfull \hbox (6.78088pt too wide) in paragraph at lines 26576--26576 [] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / t ol) ))[] Underfull \hbox (badness 2547) in paragraph at lines 26580--26586 []\T1/ptm/m/n/10 The de-fault []\T1/pcr/m/n/10 all.knots = FALSE []\T1/ptm/m/n/ 10 and []\T1/pcr/m/n/10 nknots = .nknots.smspl[]\T1/ptm/m/n/10 , en-tails us-in g only [1728] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26627--26627 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi ng splines")[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 26648--26648 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # = = unique(cars$speed)[] Underfull \vbox (badness 10000) has occurred while \output is active [1729] [1730] [1731] Overfull \hbox (0.78088pt too wide) in paragraph at lines 26840--26840 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail, [1732] [1733] [1734] [1735] [1736] [1737] Overfull \hbox (36.78088pt too wide) in paragraph at lines 27220--27220 [] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC" , "hyman"),[] [1738] [1739] Overfull \hbox (69.18036pt too wide) in paragraph at lines 27401--27401 []\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi * x) + rnorm(30)/10, 3)[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 27407--27407 []\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean)) for when x has ties")[] Underfull \vbox (badness 10000) has occurred while \output is active [1740] Overfull \hbox (31.3804pt too wide) in paragraph at lines 27416--27416 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c ol = 3, n = 1001)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 27417--27417 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c ol = 4, n = 1001)[] [1741] Underfull \hbox (badness 2922) in paragraph at lines 27486--27491 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (9.78043pt too wide) in paragraph at lines 27523--27523 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim = c(-.3, 5),[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 27526--27526 [] \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^ {-e^{phi[3]}*~x}}))[] [1742] Overfull \hbox (20.58041pt too wide) in paragraph at lines 27535--27535 [] \T1/pcr/m/n/9 c(0 , 1 ), 1, length = 0.08, angle = 25); text(0. 5, 1, quote(1))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27536--27536 [] \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3 # (Asym + R0)/2[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 27540--27540 [] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi [1]+phi[2],2), phi[1]),[] Underfull \hbox (badness 3240) in paragraph at lines 27594--27597 [][][]\T1/pcr/m/n/10 nls[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 selfStart [][][][]\T1/ptm/m/n/10 ; []\T1/pcr/m/n/10 example(SSasympOff) []\T1/ptm/m/n/10 gives graph show-ing the []\T1/pcr/m/n/10 SSasympOff [1743] Overfull \hbox (36.7804pt too wide) in paragraph at lines 27615--27615 [] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log( 0.4), c0 = 3/4)) )[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27618--27618 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim = c(-1, 8),[] [1744] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27701--27701 [] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log (log(2)))) )[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27705--27705 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim = c(-1/4, 5),[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 27715--27715 [] \T1/pcr/m/n/9 axis(2, at = 5*c(1/2,1), labels= expression(frac(phi[1],2), phi[1]), pos=0, las=1)[] [1745] Overfull \hbox (106.98032pt too wide) in paragraph at lines 27720--27720 [] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] Underfull \hbox (badness 2922) in paragraph at lines 27756--27762 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 27778--27778 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat a = Indo.1),[] [1746] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27794--27794 [] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 1.5 * exp(-x)"),[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 27808--27808 []\T1/pcr/m/n/9 ## Fails by default (scaleOffset=0) on most platforms {also af ter increasing maxiter !}[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27810--27810 [] \T1/pcr/m/n/9 nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d atN, trace=TRUE)[] Overfull \hbox (128.58029pt too wide) in paragraph at lines 27813--27813 []\T1/pcr/m/n/9 fmX1 <- nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d atN, control = list(scaleOffset=1))[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 27815--27815 [] \T1/pcr/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol=1 e-11, nDcentral=TRUE), trace=TRUE)[] [1747] [1748] Overfull \hbox (30.78088pt too wide) in paragraph at lines 27927--27927 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK a)*input)) [1749] Underfull \hbox (badness 2922) in paragraph at lines 27989--27994 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1750] Overfull \hbox (69.18036pt too wide) in paragraph at lines 28027--28027 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm id", phi[4] == "scal")))[] Underfull \hbox (badness 2922) in paragraph at lines 28076--28081 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1751] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28107--28107 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = " red", lwd=2)[] Underfull \hbox (badness 2922) in paragraph at lines 28141--28146 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1752] Overfull \hbox (25.98041pt too wide) in paragraph at lines 28166--28166 []\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number of iter...: 0" :[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 28170--28170 []\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR UE), trace = TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28190--28190 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] == "scal")))[] [1753] Overfull \hbox (20.58041pt too wide) in paragraph at lines 28200--28200 [] \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0, 2.5,3.5), # NB. SSlogis(x = xmid = 2) = 2.5[] Underfull \hbox (badness 2922) in paragraph at lines 28235--28240 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 28257--28257 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt), digits = 3)[] [1754] Overfull \hbox (15.18042pt too wide) in paragraph at lines 28275--28275 [] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS micmen model")[] [1755] Underfull \hbox (badness 6493) in paragraph at lines 28327--28332 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 x[]\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 28355--28355 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28358--28358 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 28361--28361 []\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul l() fit to Chick.6")[] Overfull \hbox (69.18036pt too wide) in paragraph at lines 28364--28364 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f m1)[["Drop"]]), lty = 3)[] [1756] [1757] [1758] [1759] [1760] [1761] [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] Underfull \hbox (badness 3396) in paragraph at lines 29248--29250 []\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.glm"[]\T1/ptm/m/ n/10 , usu-ally, a re-sult of a call to [1770] [1771] [1772] Underfull \hbox (badness 2237) in paragraph at lines 29427--29429 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /pcr/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1773] [1774] Underfull \hbox (badness 2591) in paragraph at lines 29591--29593 []\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.nls"[]\T1/ptm/m/ n/10 , usu-ally the re-sult of a call to [1775] Underfull \hbox (badness 2237) in paragraph at lines 29637--29640 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /pcr/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1776] Overfull \hbox (48.78088pt too wide) in paragraph at lines 29710--29710 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t race = FALSE) [1777] [1778] Underfull \hbox (badness 3407) in paragraph at lines 29819--29823 []\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m ented\T1/ptm/m/n/10 , see []\T1/pcr/m/n/10 corr []\T1/ptm/m/n/10 be-low) [1779] Overfull \hbox (47.58038pt too wide) in paragraph at lines 29889--29889 []\T1/pcr/m/n/9 symnum(ii, cutpoints = 2*(0:4), symbols = c(".", "-", "+", "$ "), show.max = TRUE)[] [1780] Underfull \hbox (badness 1337) in paragraph at lines 29952--29956 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1781] [1782] [1783] [1784] Overfull \hbox (9.78043pt too wide) in paragraph at lines 30219--30219 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, main = t.tit,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30262--30262 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] [1785] Underfull \hbox (badness 1616) in paragraph at lines 30288--30291 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1786] Overfull \hbox (20.58041pt too wide) in paragraph at lines 30367--30367 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1787] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30445--30445 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1788] [1789] Underfull \hbox (badness 2205) in paragraph at lines 30540--30545 []\T1/ptm/m/n/10 If a []\T1/pcr/m/n/10 specials []\T1/ptm/m/n/10 ar-gu-ment was given to [][][]\T1/pcr/m/n/10 terms.formula[][][] []\T1/ptm/m/n/10 there is a [1790] [1791] Overfull \hbox (12.78088pt too wide) in paragraph at lines 30681--30681 []\T1/pcr/m/n/10 toeplitz2(x, nrow = length(x) +1 - ncol, ncol = length(x) +1 - nrow)[] Underfull \hbox (badness 2913) in paragraph at lines 30687--30691 []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 toeplitz(x, *)[]\T1/ptm/m/n/10 : the firs t col-umn of the Toeplitz ma-trix; for [1792] Overfull \hbox (36.7804pt too wide) in paragraph at lines 30724--30724 []\T1/pcr/m/n/9 # Matrix of character (could also have logical, raw, complex . .) {also warning}:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 30737--30737 [] \T1/pcr/m/n/9 colnames(W) <- paste0(",", if(n <= 9) 1:n else c(1:9, lette rs[seq_len(n-9)]))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 30748--30748 []\T1/pcr/m/n/9 y.hat <- W. %*% y # y.hat := smoothed(y) ("mass preserving" -> longer than y)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 30750--30750 []\T1/pcr/m/n/9 plot(x,y, type="b", xlim=c(1,m)); curve(f(x), 1,n, col="gray", lty=2, add=TRUE)[] [1793] Overfull \hbox (30.78088pt too wide) in paragraph at lines 30780--30780 [] \T1/pcr/m/n/10 class = if(nseries > 1) c("mts", "ts", "matrix", "array") else "ts",[] [1794] Underfull \hbox (badness 1655) in paragraph at lines 30858--30861 []\T1/pcr/m/n/10 is.mts(x) []\T1/ptm/m/n/10 tests if an ob-ject []\T1/pcr/m/n/1 0 x []\T1/ptm/m/n/10 is a mul-ti-vari-ate time se-ries, i.e., ful-fills []\T1/p cr/m/n/10 is.ts(x)[]\T1/ptm/m/n/10 , [1795] [1796] [1797] [1798] [1799] Overfull \hbox (12.78088pt too wide) in paragraph at lines 31222--31222 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE) Overfull \hbox (12.78088pt too wide) in paragraph at lines 31223--31223 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1800] [1801] [1802] [1803] [1804] Overfull \hbox (30.78088pt too wide) in paragraph at lines 31523--31523 [] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con v = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 31524--31524 [] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace = 0)[] [1805] [1806] Overfull \hbox (31.3804pt too wide) in paragraph at lines 31653--31653 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 31662--31662 []\T1/pcr/m/n/9 ## where as \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 simply first enlarges the search interval:[] Underfull \vbox (badness 10000) has occurred while \output is active [1807] [1808] [1809] Underfull \hbox (badness 1337) in paragraph at lines 31879--31883 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1810] [1811] [1812] [1813] [1814] [1815] [1816] [1817] Underfull \hbox (badness 1337) in paragraph at lines 32408--32412 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1818] [1819] [1820] Overfull \hbox (117.7803pt too wide) in paragraph at lines 32616--32616 []\T1/pcr/m/n/9 wilcox.test( 4:2, 3:1, paired=TRUE) # Warning: canno t compute exact p-value with ties[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 32618--32618 []\T1/pcr/m/n/9 wilcox.test((4:2)/10, (3:1)/10, paired=TRUE, digits.rank = 9) # same ties as (4:2, 3:1)[] [1821] [1822] [1823] Overfull \hbox (138.78088pt too wide) in paragraph at lines 32777--32777 [] \T1/pcr/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps = getOption("ts.eps"), ...)[] [1824] Overfull \hbox (0.78088pt too wide) in paragraph at lines 32862--32862 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, [1825] [1826] Overfull \hbox (47.58038pt too wide) in paragraph at lines 32995--32995 []\T1/pcr/m/n/9 ## The Female:Rejected combination has NA \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 Freq\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 (and NA prints \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 invisibly\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 as "")[] [1827]) (./stats4-pkg.tex [1828] Chapter 11. [1829] [1830] [1831] Overfull \hbox (15.18042pt too wide) in paragraph at lines 224--224 [] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf)) , log = TRUE))[] Underfull \vbox (badness 10000) has occurred while \output is active [1832] Overfull \hbox (9.78043pt too wide) in paragraph at lines 278--278 []\T1/pcr/m/n/9 ## Boundary case: This works, but fails if limits are set clos er to 0 and 1[] [1833] [1834] [1835] [1836] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdas h.methods}) has been already used, duplicate ignored \relax l.503 ...Package \pkg{stats4}}{show.Rdash.methods} [1837] [1838] [1839]) (./tcltk-pkg.tex [1840] Chapter 12. [1841] [1842] [1843] [1844] [1845] Overfull \hbox (36.7804pt too wide) in paragraph at lines 360--360 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all.names = TRUE) # .Tcl.args put a ca llback ref in here[] [1846] [1847] Underfull \vbox (badness 10000) has occurred while \output is active [1848] Underfull \hbox (badness 1292) in paragraph at lines 671--678 []\T1/pcr/m/n/10 tcl []\T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-i ng any Tk or Tcl com-mand by sim-ply run-ning Underfull \vbox (badness 1603) has occurred while \output is active [1849] [1850] [1851] [1852] [1853] Underfull \vbox (badness 10000) has occurred while \output is active [1854] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1084--1084 []\T1/pcr/m/n/9 eval.txt <- function() eval(str2lang(tclvalue(tkget(txt.w, "0. 0", "end"))))[] [1855] [1856] [1857] [1858] [1859] Underfull \hbox (badness 1189) in paragraph at lines 1412--1415 [][][]\T1/pcr/m/n/10 select.list[][][] []\T1/ptm/m/n/10 (a text ver-sion ex-cep t on Win-dows and the ma-cOS GUI), [][][]\T1/pcr/m/n/10 menu[][][] []\T1/ptm/m/ n/10 (whose [1860]) (./tools-pkg.tex Chapter 13. [1861] Overfull \hbox (9.78043pt too wide) in paragraph at lines 69--69 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for new methods.[] [1862] Underfull \hbox (badness 1253) in paragraph at lines 167--170 []\T1/pcr/m/n/10 assertWarning() []\T1/ptm/m/n/10 as-serts that a warn-ing will be sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1863] Overfull \hbox (4.38043pt too wide) in paragraph at lines 218--218 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch ing warning)[] [1864] Underfull \hbox (badness 5147) in paragraph at lines 288--301 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 Underfull \hbox (badness 4792) in paragraph at lines 288--301 \T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][][]\T1/pcr/m/n /10 bibentry[][][] []\T1/ptm/m/n/10 as well as sev-eral other rou- Underfull \hbox (badness 2237) in paragraph at lines 288--301 \T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named []\T1/pcr/m/n /10 formatArticle[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 formatBook[]\T1/ptm/m/n/10 , [1865] Overfull \hbox (42.78088pt too wide) in paragraph at lines 373--373 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta ngle = TRUE, Underfull \hbox (badness 2460) in paragraph at lines 392--394 []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gin e to use. Over-rides any [1866] [1867] Underfull \hbox (badness 1142) in paragraph at lines 464--468 \T1/ptm/m/n/10 If given, vi-gnette source files are by de-fault looked for in s ub-di-rec-tory [1868] [1869] [1870] [1871] [1872] [1873] [1874] Overfull \hbox (0.78088pt too wide) in paragraph at lines 921--921 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", " xz"),[] [1875] Overfull \hbox (31.3804pt too wide) in paragraph at lines 976--976 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co mpress == "none")[] [1876] [1877] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1145--1145 [] \T1/pcr/m/n/10 outputs = FALSE, sources = FALS E, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1146--1146 []\T1/pcr/m/n/10 check_packages_in_dir_details(dir, logs = NULL, drop_ok = TRU E, ...)[] [1878] Underfull \hbox (badness 1014) in paragraph at lines 1188--1190 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1194--1196 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous [1879] Underfull \hbox (badness 10000) in paragraph at lines 1231--1234 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us- Underfull \hbox (badness 10000) in paragraph at lines 1231--1234 \T1/ptm/m/n/10 ing []\T1/pcr/m/n/10 summarize_check_packages_in_dir_results []\ T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 1239--1242 []\T1/pcr/m/n/10 check_packages_in_dir []\T1/ptm/m/n/10 re-turns an ob-ject in- her-it-ing from class [1880] [1881] Underfull \hbox (badness 10000) in paragraph at lines 1386--1389 []\T1/pcr/m/n/10 codocClasses []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 codocData [ ]\T1/ptm/m/n/10 re-turn ob-jects of class []\T1/pcr/m/n/10 "codocClasses" []\T1 /ptm/m/n/10 and [1882] [1883] Underfull \hbox (badness 4647) in paragraph at lines 1557--1562 []\T1/pcr/m/n/10 CRAN_package_db() []\T1/ptm/m/n/10 re-turns a data frame with char-ac-ter columns con-tain-ing most Underfull \hbox (badness 7869) in paragraph at lines 1557--1562 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' meta-data for the cu r-rent pack-ages in the CRAN pack-age repos-i- Underfull \hbox (badness 1681) in paragraph at lines 1557--1562 \T1/ptm/m/n/10 tory, in-clud-ing in par-tic-u-lar the De-scrip-tion and Main-ta iner in-for-ma-tion not pro-vided by [1884] Underfull \hbox (badness 2762) in paragraph at lines 1606--1609 []\T1/ptm/m/n/10 Internal func-tions []\T1/pcr/m/n/10 CRAN_aliases_db[]\T1/ptm/ m/n/10 , []\T1/pcr/m/n/10 CRAN_archive_db[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 CR AN_current_db []\T1/ptm/m/n/10 and [1885] [1886] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1718--1718 [] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En hances"))[] Underfull \hbox (badness 7981) in paragraph at lines 1725--1733 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 1725--1733 []\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", Underfull \hbox (badness 1558) in paragraph at lines 1725--1733 \T1/pcr/m/n/10 "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string []\T1/pcr/m/n/1 0 "all" []\T1/ptm/m/n/10 is short-hand for that vec-tor, [1887] [1888] [1889] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.GSC}) has been already used, duplicate ignored \relax l.1937 \aliasA{GSC}{find\_gs\_cmd}{GSC} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSC MD}) has been already used, duplicate ignored \relax l.1938 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1890] [1891] [1892] [1893] Underfull \hbox (badness 1142) in paragraph at lines 2207--2213 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 loadPkgRdMacros []\T1/ptm/m/n/10 func-tio n first looks for an []\T1/pcr/m/n/10 "RdMacros" []\T1/ptm/m/n/10 en-try in the pack-age [1894] Underfull \hbox (badness 2359) in paragraph at lines 2271--2278 []\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user and site spe-cific com-pi-la- Underfull \hbox (badness 1102) in paragraph at lines 2271--2278 \T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1 0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com- Underfull \hbox (badness 4168) in paragraph at lines 2271--2278 \T1/ptm/m/n/10 pi-la-tions in sub-di-rec-to-ries of `\T1/pcr/m/n/10 src\T1/ptm/ m/n/10 '), e.g., by adding con-fig-ure code call-ing \T1/phv/m/n/10 R \T1/ptm/m /n/10 with [1895] Underfull \hbox (badness 1342) in paragraph at lines 2323--2329 \T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in Underfull \hbox (badness 10000) in paragraph at lines 2348--2355 []\T1/pcr/m/n/10 matchConcordance []\T1/ptm/m/n/10 con-verts from out-put lo-ca -tions to source lo-ca-tions. 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[1897] [1898] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2537--2537 []\T1/pcr/m/n/10 package_dependencies(packages = NULL, db = NULL, which = "str ong", Underfull \hbox (badness 7981) in paragraph at lines 2552--2560 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 2552--2560 []\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", Underfull \hbox (badness 1558) in paragraph at lines 2552--2560 \T1/pcr/m/n/10 "Enhances")[]\T1/ptm/m/n/10 . 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Rd"),[] [1904] Underfull \hbox (badness 2486) in paragraph at lines 2950--2958 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion 3.2.0, User-d efined macros may be given in a sep-a-rate file us-ing [1905] [1906] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3162--3162 []\T1/pcr/m/n/10 checkDocFiles (package, dir, lib.loc = NULL, chkInternal = FALSE) [1907] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3166--3166 []\T1/pcr/m/n/10 checkRdContents (package, dir, lib.loc = NULL, chkInternal = FALSE)[] [1908] [1909] [1910] Underfull \hbox (badness 1072) in paragraph at lines 3358--3360 []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec- tor of links, as re-turned by [1911] [1912] [1913] [1914] [1915] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3706--3706 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro s", "system.Rd"))[] Underfull \hbox (badness 5417) in paragraph at lines 3744--3754 []\T1/ptm/m/n/10 By de-fault, the tags \T1/pcr/m/n/10 \S3method\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \S4method\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \command\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \docType\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \email\T1/ptm/m/n/10 , [1916] [1917] [1918] Underfull \hbox (badness 4108) in paragraph at lines 3960--3967 []\T1/ptm/m/n/10 This func-tion starts the in-ter-nal HTTP server, which runs o n the loop-back in-ter-face [1919] [1920] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4060--4060 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 4063--4063 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 4080--4082 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1921] Underfull \hbox (badness 2932) in paragraph at lines 4097--4103 []\T1/pcr/m/n/10 testInstalledBasic []\T1/ptm/m/n/10 runs the ba-sic tests, if in-stalled. This should be run with [1922] Underfull \hbox (badness 7832) in paragraph at lines 4219--4222 []\T1/ptm/m/n/10 Where sup-ported ([]\T1/pcr/m/n/10 texi2dvi []\T1/ptm/m/n/10 5 .0 and later; []\T1/pcr/m/n/10 texify.exe []\T1/ptm/m/n/10 from MiK-TeX), op-ti on [1923] [1924] [1925] [1926] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4454--4454 [] \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry run),[] [1927] [1928] Overfull \hbox (96.78088pt too wide) in paragraph at lines 4616--4616 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, mergeOpts = "", copyright, bugs) Underfull \hbox (badness 3118) in paragraph at lines 4627--4631 []\T1/ptm/m/n/10 a string, by de-fault empty, of op-tions to []\T1/pcr/m/n/10 m sgmerge []\T1/ptm/m/n/10 in ad-di-tion to Underfull \hbox (badness 10000) in paragraph at lines 4631--4634 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `[]\T1/pcr/m/n/10 Copyrig ht[]\T1/ptm/m/n/10 ' and [1929] Underfull \hbox (badness 6859) in paragraph at lines 4647--4652 []\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory []\T1/pcr/m/n/10 po []\T1/ ptm/m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\ T1/ptm/m/n/10 ' are up-dated from Underfull \hbox (badness 1184) in paragraph at lines 4655--4661 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po /\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T he Underfull \hbox (badness 2941) in paragraph at lines 4655--4661 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t he pack-age are ex-am-ined to cre-ate a file [1930] [1931] [1932] Underfull \hbox (badness 10000) in paragraph at lines 4889--4891 []\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 vignetteEngine[][][][]\T1/ptm/m/n/10 , such as []\T1/pcr/m/n/10 "utils::Sweave" []\T1/ptm/m/n/10 or [1933] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4918--4918 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4919--4919 [] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr ess = "xz",[] Underfull \hbox (badness 3240) in paragraph at lines 4932--4935 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T 1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ', Underfull \hbox (badness 1742) in paragraph at lines 4936--4946 []\T1/pcr/m/n/10 "Package"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Version"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "Priority"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Depe nds"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Imports"[]\T1/ptm/m/n/10 , [1934] Underfull \hbox (badness 1127) in paragraph at lines 4974--4980 []\T1/pcr/m/n/10 write_PACKAGES []\T1/ptm/m/n/10 scans the named di-rec-tory fo r R pack-ages, ex-tracts in-for-ma-tion from Underfull \hbox (badness 1635) in paragraph at lines 4974--4980 \T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file , and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1 0 ', Underfull \hbox (badness 1571) in paragraph at lines 5002--5006 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by Underfull \hbox (badness 2772) in paragraph at lines 5028--5033 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 PACKAGES.gz\T1/ptm/m/n/10 ' files. See [][][ ]\T1/pcr/m/n/10 update_PACKAGES[][][] []\T1/ptm/m/n/10 for ef-fi-ciently up-dat -ing ex-ist-ing [1935] [1936] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5170--5170 []\T1/pcr/m/n/9 xgettext(tmpPkg, asCall=TRUE )[[1]] # default; shows \TS1/pcr /m/n/9 ' \T1/pcr/m/n/9 sqrt(as.complex(x)) \TS1/pcr/m/n/9 '[] [1937]) (./utils-pkg.tex [1938] Chapter 14. Underfull \hbox (badness 1072) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[] \T1/pcr/m/n/10 insertions[]\T1/ptm/m/n/10 ', [1939] [1940] [1941] [1942] Overfull \hbox (4.38043pt too wide) in paragraph at lines 261--261 []\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with these names[] [1943] [1944] Underfull \hbox (badness 10000) in paragraph at lines 381--386 \T1/ptm/m/n/10 are []\T1/pcr/m/n/10 c("vertical", "horizontal", "cascade", "min imize", Underfull \hbox (badness 10000) in paragraph at lines 387--389 []\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 list[][][] []\T1/ptm/m/n/10 of win-dow han-dles, by de-fault pro-duced by [1945] Overfull \hbox (9.78043pt too wide) in paragraph at lines 453--453 []\T1/pcr/m/n/9 # This default is useful only in SDI mode: it will tile any F irefox window[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 455--455 []\T1/pcr/m/n/9 .arrangeWindowsDefaults <- list(c("R", "all"), pattern = c("", "Firefox"))[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 472--472 [] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No ", "Cancel"))),[] [1946] [1947] [1948] Overfull \hbox (0.78088pt too wide) in paragraph at lines 686--686 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc es"), Overfull \hbox (6.78088pt too wide) in paragraph at lines 692--692 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 693--693 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 694--694 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 695--695 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] [1949] Underfull \hbox (badness 10000) in paragraph at lines 729--735 []\T1/ptm/m/n/10 Functions []\T1/pcr/m/n/10 aspell_package_Rd_files[]\T1/ptm/m/ n/10 , []\T1/pcr/m/n/10 aspell_package_vignettes[]\T1/ptm/m/n/10 , Underfull \hbox (badness 4416) in paragraph at lines 729--735 []\T1/pcr/m/n/10 aspell_package_R_files []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 a spell_package_C_files []\T1/ptm/m/n/10 per-form spell check- [1950] [1951] [1952] [1953] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1053--1053 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL, [1954] Underfull \hbox (badness 7649) in paragraph at lines 1127--1133 [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 in-di-cat-ing if Bib-TeX co de should be given ad-di-tion-ally; Underfull \hbox (badness 5533) in paragraph at lines 1127--1133 \T1/ptm/m/n/10 cur-rently ap-plies only to []\T1/pcr/m/n/10 style = "citation"[ ]\T1/ptm/m/n/10 . The de-fault for Underfull \hbox (badness 4739) in paragraph at lines 1127--1133 \T1/ptm/m/n/10 the []\T1/pcr/m/n/10 print() []\T1/ptm/m/n/10 method de-pends on the num-ber of (bib) en-tries and Underfull \hbox (badness 1817) in paragraph at lines 1127--1133 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 1136--1138 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1955] [1956] Underfull \hbox (badness 10000) in paragraph at lines 1255--1258 []\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Digital _ Object _ [1957] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1338--1338 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] Underfull \vbox (badness 10000) has occurred while \output is active [1958] [1959] [1960] [1961] [1962] [1963] Underfull \hbox (badness 1859) in paragraph at lines 1747--1756 []\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b e quite large the com- Underfull \hbox (badness 2042) in paragraph at lines 1747--1756 \T1/ptm/m/n/10 mand []\T1/pcr/m/n/10 data.frame(x, y, z, monday, tuesday) []\T1 /ptm/m/n/10 never re-turns. Do not re-port that [1964] [1965] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1852--1852 [] \T1/pcr/m/n/9 data = infert, family = b inomial())))[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 1887--1887 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b efore$timestamp,[] [1966] [1967] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2033--2033 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp" ), md5sum=TRUE)[] [1968] Underfull \hbox (badness 2277) in paragraph at lines 2102--2107 []\T1/pcr/m/n/10 charClass []\T1/ptm/m/n/10 was added in \T1/phv/m/n/10 R \T1/p tm/m/n/10 4.1.0. A less di-rect way to ex-am-ine char-ac-ter classes [1969] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2134--2134 []\T1/pcr/m/n/9 cl <- c("alnum", "alpha", "blank", "digit", "graph", "punct", "upper", "xdigit")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2136--2136 []\T1/pcr/m/n/9 X <- as.data.frame(X); row.names(X) <- sQuote(intToUtf8(x, mul tiple = TRUE))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2144--2144 []\T1/pcr/m/n/9 ## How many printable characters are there? (Around 280,000 in Unicode 13.)[] [1970] [1971] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2292--2292 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind = NULL, [1972] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2344--2344 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind = NULL, [1973] Underfull \hbox (badness 1117) in paragraph at lines 2459--2466 []\T1/ptm/m/n/10 If the ob-ject re-turned by []\T1/pcr/m/n/10 citation() []\T1/ ptm/m/n/10 con-tains only one ref-er-ence, the as-so-ci-ated print Underfull \hbox (badness 1400) in paragraph at lines 2459--2466 \T1/ptm/m/n/10 method shows both a text ver-sion and a Bib-TeX en-try for it. I f a pack-age has more [1974] [1975] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2542--2542 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after = NULL,[] [1976] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2662--2662 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1977] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2702--2702 []\T1/pcr/m/n/10 citEntry(entry, textVersion = NULL, header = NULL, footer = N ULL, ...) Underfull \hbox (badness 1082) in paragraph at lines 2731--2735 [][][]\T1/pcr/m/n/10 citation[][][] []\T1/ptm/m/n/10 for more in-for-ma-tion ab out cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file s; [1978] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard }) has been already used, duplicate ignored \relax l.2736 ... the Clipboard in MS Windows}{clipboard} Underfull \hbox (badness 1163) in paragraph at lines 2767--2769 []\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats: see e.g. [][]$\T1/pcr/m/n/10 https : / / docs . [1979] [1980] Underfull \hbox (badness 10000) in paragraph at lines 2860--2862 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [1981] [1982] [1983] Underfull \hbox (badness 10000) in paragraph at lines 3078--3080 []\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see [1984] [1985] [1986] [1987] Underfull \hbox (badness 1762) in paragraph at lines 3371--3374 []\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re c-tory of the cur-rent work-ing di-rec-tory, set []\T1/pcr/m/n/10 package = [1988] Overfull \hbox (63.78036pt too wide) in paragraph at lines 3463--3463 []\T1/pcr/m/n/9 try(data(package = "rpart"), silent = TRUE) # list the data se ts in the rpart package[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3464--3464 []\T1/pcr/m/n/9 data(USArrests, "VADeaths") # load the data sets \TS1/pcr/m /n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] [1989] Underfull \hbox (badness 2452) in paragraph at lines 3538--3541 []\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class []\ T1/pcr/m/n/10 R_dataentry[]\T1/ptm/m/n/10 . Re-sources [1990] [1991] [1992] [1993] [1994] [1995] Overfull \hbox (74.58035pt too wide) in paragraph at lines 3967--3967 [] \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf orm$r_arch, "stats.dll"))[] [1996] Underfull \hbox (badness 4779) in paragraph at lines 4046--4051 []\T1/ptm/m/n/10 Support for method []\T1/pcr/m/n/10 "libcurl" []\T1/ptm/m/n/10 was op-tional on Win-dows prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0: use [1997] Underfull \hbox (badness 1072) in paragraph at lines 4109--4113 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the []\T1/pcr/m/n/10 quiet []\T1/ptm/m/n/10 ar-gu-ment and the [1998] Underfull \hbox (badness 7238) in paragraph at lines 4165--4170 []\T1/ptm/m/n/10 For the []\T1/pcr/m/n/10 "libcurl" []\T1/ptm/m/n/10 and []\T1/ pcr/m/n/10 "curl" []\T1/ptm/m/n/10 meth-ods, prox-ies can be set \T1/ptm/m/it/1 0 via \T1/ptm/m/n/10 the en-vi-ron- Underfull \hbox (badness 1337) in paragraph at lines 4165--4170 \T1/ptm/m/n/10 ment vari-ables []\T1/pcr/m/n/10 http_proxy []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 ftp_proxy[]\T1/ptm/m/n/10 . See [][]$\T1/pcr/m/n/10 https : / / curl . se / libcurl / c / Underfull \hbox (badness 1184) in paragraph at lines 4180--4196 \T1/ptm/m/n/10 string con-tain-ing `[]\T1/pcr/m/n/10 "Schannel"[]\T1/ptm/m/n/10 '. If it does not, for ver-i-fi-ca-tion to be on the en-vi-ron- [1999] [2000] Underfull \hbox (badness 4660) in paragraph at lines 4306--4309 \T1/ptm/m/n/10 able at the repos-i-to-ries, or []\T1/pcr/m/n/10 NULL []\T1/ptm/ m/n/10 which makes an in-ter-nal call to Underfull \hbox (badness 10000) in paragraph at lines 4330--4332 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][][]\T1/pcr/m/n/10 do wnload.file[][][] []\T1/ptm/m/n/10 and [2001] [2002] [2003] Underfull \hbox (badness 1565) in paragraph at lines 4517--4521 []\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of [2004] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4600--4600 [] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F ALSE,[] [2005] Underfull \hbox (badness 1910) in paragraph at lines 4634--4641 \T1/ptm/m/n/10 is saved, then ini-tial-ized to a spec-i-fied state, the ex-am-p le is run and Underfull \hbox (badness 1655) in paragraph at lines 4634--4641 \T1/ptm/m/n/10 the (saved) state is re-stored. []\T1/pcr/m/n/10 setRNG = TRUE [ ]\T1/ptm/m/n/10 sets the same state as Underfull \hbox (badness 2846) in paragraph at lines 4634--4641 []\T1/pcr/m/n/10 R CMD [][]check[][][] []\T1/ptm/m/n/10 does for run-ning a pac k-age's ex-am-ples. This is cur- Underfull \hbox (badness 3460) in paragraph at lines 4634--4641 \T1/ptm/m/n/10 rently equiv-a-lent to []\T1/pcr/m/n/10 setRNG = {RNGkind("defau lt", "default", Underfull \hbox (badness 1931) in paragraph at lines 4641--4648 []\T1/ptm/m/n/10 logical (or []\T1/pcr/m/n/10 "default"[]\T1/ptm/m/n/10 ) in-di -cat-ing if [][][]\T1/pcr/m/n/10 devAskNewPage[][][](ask = TRUE) [2006] [2007] [2008] Underfull \hbox (badness 5939) in paragraph at lines 4887--4889 []\T1/ptm/m/n/10 An en-try in []\T1/pcr/m/n/10 getOption("repos") []\T1/ptm/m/n /10 named `[]\T1/pcr/m/n/10 CRAN[]\T1/ptm/m/n/10 ' which is not the de-fault [2009] [2010] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5030--5030 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [2011] [2012] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.5101 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format.1} ) has been already used, duplicate ignored \relax l.5101 ...mat Unordered and Ordered Lists}{format} [2013] [2014] [2015] [2016] [2017] [2018] [2019] [2020] Underfull \hbox (badness 1622) in paragraph at lines 5624--5628 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [2021] [2022] [2023] [2024] [2025] Underfull \hbox (badness 1448) in paragraph at lines 6003--6008 []\T1/ptm/m/n/10 External pointer ob-jects are com-pared as ref-er-ence ob-ject s, cor-re-spond-ing to call-ing [2026] [2027] Overfull \hbox (96.78088pt too wide) in paragraph at lines 6153--6153 []\T1/pcr/m/n/10 ## NB: The methods for \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 data.f rame\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 and \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 array\ TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 are identical to the \TS1/pcr/m/n/10 '\T1/pcr/ m/n/10 matrix\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 one[] [2028] Overfull \hbox (66.78088pt too wide) in paragraph at lines 6165--6165 []\T1/pcr/m/n/10 tail(x, n = 6L, keepnums = TRUE, addrownums, ...) # exported as tail.matrix()[] [2029] [2030] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6299--6299 [] \T1/pcr/m/n/9 ## BUT if I use "useAttrib(.)", this is *not* ok, when n i s of length 2:[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 6300--6300 [] \T1/pcr/m/n/9 ## --- because [i,j]-indexing of data frames *also* drops "other" attributes ..[] [2031] [2032] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6510--6510 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h elp(dgamma):[] [2033] Underfull \hbox (badness 10000) in paragraph at lines 6594--6596 []\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 https : / / www . r-[] project . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also [2034] Underfull \hbox (badness 1502) in paragraph at lines 6643--6648 []\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words '. `Key- Underfull \hbox (badness 2103) in paragraph at lines 6643--6648 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2035] [2036] [2037] Underfull \hbox (badness 10000) in paragraph at lines 6816--6825 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, Underfull \hbox (badness 10000) in paragraph at lines 6816--6825 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10 ', which can be re-made by [2038] Underfull \hbox (badness 2150) in paragraph at lines 6880--6883 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See Underfull \hbox (badness 5175) in paragraph at lines 6896--6899 []\T1/pcr/m/n/10 hsearch_db() []\T1/ptm/m/n/10 builds and caches the help searc h database for sub-se-quent use by [2039] [2040] Underfull \hbox (badness 3118) in paragraph at lines 7019--7021 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for [2041] [2042] Underfull \hbox (badness 5091) in paragraph at lines 7194--7196 []\T1/ptm/m/n/10 download method, see [][][]\T1/pcr/m/n/10 download.file[][][][ ]\T1/ptm/m/n/10 . Un-used if a non-[]\T1/pcr/m/n/10 NULL Underfull \hbox (badness 10000) in paragraph at lines 7224--7231 []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 means to use []\T1/pcr/m/n/10 c("Depends ", "Imports", "LinkingTo", Underfull \hbox (badness 10000) in paragraph at lines 7224--7231 \T1/pcr/m/n/10 "Suggests") []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pkgs []\T1/ptm /m/n/10 and []\T1/pcr/m/n/10 c("Depends", "Imports", Underfull \hbox (badness 1270) in paragraph at lines 7224--7231 \T1/pcr/m/n/10 "LinkingTo") []\T1/ptm/m/n/10 for added de-pen-den-cies: this in -stalls all the pack-ages [2043] Underfull \hbox (badness 1270) in paragraph at lines 7239--7249 \T1/ptm/m/n/10 for the `[]\T1/pcr/m/n/10 --configure-args[]\T1/ptm/m/n/10 ' fla g in the call to []\T1/pcr/m/n/10 R CMD INSTALL[]\T1/ptm/m/n/10 . If Underfull \hbox (badness 4441) in paragraph at lines 7282--7285 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed to Underfull \hbox (badness 2837) in paragraph at lines 7282--7285 []\T1/pcr/m/n/10 R CMD INSTALL []\T1/ptm/m/n/10 for a source pack-age in-stall. E.g., []\T1/pcr/m/n/10 c("--html", Underfull \hbox (badness 1424) in paragraph at lines 7290--7293 []\T1/ptm/m/n/10 logical: if true, re-duce the amount of out-put. This is \T1/p tm/m/it/10 not \T1/ptm/m/n/10 passed to [2044] Underfull \hbox (badness 2376) in paragraph at lines 7361--7368 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is []\T1/pcr/m/n /10 "both" []\T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 7361--7368 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 7361--7368 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1087) in paragraph at lines 7369--7372 []\T1/ptm/m/n/10 Using pack-ages with []\T1/pcr/m/n/10 type = "source" []\T1/pt m/m/n/10 al-ways works pro-vided the pack-age con-tains no [2045] Underfull \hbox (badness 1314) in paragraph at lines 7449--7456 []\T1/pcr/m/n/10 install.packages []\T1/ptm/m/n/10 needs to be able to com-pute all the de-pen-den-cies of []\T1/pcr/m/n/10 pkgs []\T1/ptm/m/n/10 from [2046] Underfull \hbox (badness 10000) in paragraph at lines 7532--7537 [][][]\T1/pcr/m/n/10 update.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 download.pac kages[][][][]\T1/ptm/m/n/10 , Overfull \hbox (25.98041pt too wide) in paragraph at lines 7555--7555 [] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc lude/udunits2"))[] [2047] Underfull \hbox (badness 5133) in paragraph at lines 7591--7595 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each pack-age's Underfull \hbox (badness 1983) in paragraph at lines 7605--7608 []\T1/pcr/m/n/10 installed.packages []\T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along [2048] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7652--7652 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields = "License")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7657--7657 []\T1/pcr/m/n/9 ## Keep packages that come with R (priority="high") and all ot hers separate![] [2049] [2050] Underfull \hbox (badness 4132) in paragraph at lines 7783--7785 []\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion of []\T1/pcr/m/n/10 libtool []\T1/ptm/m/n/10 in-stalled at [2051] [2052] [2053] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7950--7950 []\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h ave defined?[] [2054] [2055] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8093--8093 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE) [2056] Underfull \hbox (badness 10000) in paragraph at lines 8133--8135 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [2057] Underfull \hbox (badness 10000) in paragraph at lines 8240--8242 []\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if Underfull \hbox (badness 10000) in paragraph at lines 8252--8254 []\T1/ptm/m/n/10 typically the re-sult of []\T1/pcr/m/n/10 methods(..)[]\T1/ptm /m/n/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of S3 class [2058] [2059] [2060] [2061] Underfull \hbox (badness 1859) in paragraph at lines 8482--8485 []\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br owser (by Underfull \hbox (badness 1052) in paragraph at lines 8501--8511 \T1/ptm/m/n/10 ac-cord-ing to ver-sion us-ing \T1/pcr/m/n/10 section \T1/ptm/m/ n/10 el-e-ments with names start-ing with a suit-able pre-fix [2062] Underfull \hbox (badness 1655) in paragraph at lines 8576--8579 []\T1/ptm/m/n/10 A data frame in-her-it-ing from class []\T1/pcr/m/n/10 "news_d b"[]\T1/ptm/m/n/10 , with [][][]\T1/pcr/m/n/10 attributes[][][] "package" []\T1 /ptm/m/n/10 (and Overfull \hbox (25.98041pt too wide) in paragraph at lines 8587--8587 []\T1/pcr/m/n/9 db4 <- news(Version == "4.0.0" & grepl("^BUG", Category) & gre pl("PR#", Text),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8595--8595 []\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[] [2063] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8603--8603 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st andardize a bit more[] [2064] Underfull \hbox (badness 1917) in paragraph at lines 8690--8692 []\T1/pcr/m/n/10 "B"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "KiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "MiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "GiB"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "TiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "PiB"[]\T1/ptm/m/ n/10 , [2065] [2066] [2067] [2068] Overfull \hbox (66.78088pt too wide) in paragraph at lines 8964--8964 [] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica tion", "Built"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8965--8965 [] \T1/pcr/m/n/10 tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%D", "%m/ %d/%y"),[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 8966--8966 [] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f ields=date.fields))[] [2069] Underfull \hbox (badness 10000) in paragraph at lines 8994--8996 []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 asDateBuilt()[]\T1/ptm/m/n/10 , a [][][]\ T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string as from Underfull \hbox (badness 10000) in paragraph at lines 9008--9010 []\T1/pcr/m/n/10 packageVersion() []\T1/ptm/m/n/10 is a con-ve-nience short-cut , al-low-ing things like []\T1/pcr/m/n/10 if Underfull \hbox (badness 1259) in paragraph at lines 9016--9021 []\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2070] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9060--9060 [] \T1/pcr/m/n/9 identical(pu, packageDate("stats"))) # as "utils" an d "stats" are[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9061--9061 [] \T1/pcr/m/n/9 # both \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 base R\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and "Built" at same time[] [2071] [2072] Underfull \hbox (badness 10000) in paragraph at lines 9189--9194 []\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 "Status"[]\T1/ptm/m/n/10 , a fac-tor wit h lev-els []\T1/pcr/m/n/10 c("ok", "upgrade", Underfull \hbox (badness 10000) in paragraph at lines 9196--9199 []\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 "Status"[]\T1/ptm/m/n/10 , a fac-tor wit h lev-els []\T1/pcr/m/n/10 c("installed", "not [2073] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9311--9311 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9312--9312 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [2074] [2075] [2076] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9492--9492 [] \T1/pcr/m/n/9 "S original, "),[] [2077] [2078] Underfull \hbox (badness 1789) in paragraph at lines 9662--9664 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [2079] [2080] [2081] [2082] Underfull \hbox (badness 2600) in paragraph at lines 9886--9889 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the name of the help topic; de-faults to [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] Overfull \hbox (30.78088pt too wide) in paragraph at lines 10499--10499 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", " no.loss"),[] [2091] [2092] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10660--10660 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr anspose = TRUE)[] [2093] [2094] [2095] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10841--10841 []\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23 456 98 76 54[] [2096] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10927--10927 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"),[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 10928--10928 [] \T1/pcr/m/n/10 row.names, col.names, as.is = !stringsAsFactors, t ryLogical = TRUE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10930--10930 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 10935--10935 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski pNul = FALSE)[] [2097] Underfull \hbox (badness 2027) in paragraph at lines 11007--11010 []\T1/ptm/m/n/10 Using []\T1/pcr/m/n/10 row.names = NULL []\T1/ptm/m/n/10 force s row num-ber-ing. Miss-ing or []\T1/pcr/m/n/10 NULL [2098] Underfull \hbox (badness 2435) in paragraph at lines 11030--11034 []\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 de-ter-m in-ing if columns con-sist-ing en-tirely of []\T1/pcr/m/n/10 "F"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1824) in paragraph at lines 11030--11034 []\T1/pcr/m/n/10 "FALSE"[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 "TRUE" []\T1/pt m/m/n/10 should be con-verted to [][][]\T1/pcr/m/n/10 logical[][][][]\T1/ptm/m/ n/10 ; passed to [2099] [2100] [2101] Overfull \hbox (12.78088pt too wide) in paragraph at lines 11291--11291 []\T1/pcr/m/n/10 readRegistry(key, hive = c("HLM", "HCR", "HCU", "HU", "HCC", "HPD"), Overfull \hbox (6.78088pt too wide) in paragraph at lines 11292--11292 [] \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64- bit"))[] Underfull \hbox (badness 10000) in paragraph at lines 11299--11304 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are Underfull \hbox (badness 10000) in paragraph at lines 11299--11304 \T1/ptm/m/n/10 for []\T1/pcr/m/n/10 HKEY_LOCAL_MACHINE[]\T1/ptm/m/n/10 , []\T1/ pcr/m/n/10 HKEY_CLASSES_ROOT[]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 11299--11304 []\T1/pcr/m/n/10 HKEY_CURRENT_USER[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 HKEY_USER S[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 HKEY_CURRENT_CONFIG [2102] [2103] [2104] [2105] Overfull \hbox (18.78088pt too wide) in paragraph at lines 11531--11531 [] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c (1, 0))) [2106] [2107] [2108] [2109] Underfull \hbox (badness 10000) in paragraph at lines 11797--11801 \T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral s & oldid = 78252134$[][]\T1/ptm/m/n/10 . Overfull \hbox (20.58041pt too wide) in paragraph at lines 11815--11815 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni ng for "IIIIII"[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11820--11820 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [2110] [2111] Overfull \hbox (18.78088pt too wide) in paragraph at lines 11956--11956 []\T1/pcr/m/n/10 4. | \-base:::tryCatchOne(expr, names, parentenv, handler s[[1L]])[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 11957--11957 []\T1/pcr/m/n/10 5. | \-base:::doTryCatch(return(expr), name, parentenv, handler)[] [2112] [2113] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12092--12092 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [2114] [2115] Underfull \hbox (badness 1917) in paragraph at lines 12224--12227 []\T1/ptm/m/n/10 If `[]\T1/pcr/m/n/10 --default-packages[]\T1/ptm/m/n/10 ' is n ot used, then []\T1/pcr/m/n/10 Rscript []\T1/ptm/m/n/10 checks the en-vi-ron-me nt vari- Underfull \hbox (badness 4328) in paragraph at lines 12224--12227 \T1/ptm/m/n/10 able []\T1/pcr/m/n/10 R_SCRIPT_DEFAULT_PACKAGES[]\T1/ptm/m/n/10 . If this is set, then it takes prece-dence over Overfull \hbox (106.98032pt too wide) in paragraph at lines 12247--12247 []\T1/pcr/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 sessionInfo()\TS1/pcr/m/n/9 '[] [2116] [2117] Overfull \hbox (54.78088pt too wide) in paragraph at lines 12339--12339 [] \T1/pcr/m/n/10 restrict = c("functions", "descriptions", "news", "Rfunctions",[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 12340--12340 [] \T1/pcr/m/n/10 "Rmanuals", "READMEs", "views", "vig nettes"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 12342--12342 [] \T1/pcr/m/n/10 sortby = c("score", "date:late", "date:early", "s ubject",[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 12343--12343 [] \T1/pcr/m/n/10 "subject:descending", "size", "size:de scending"),[] Underfull \hbox (badness 6725) in paragraph at lines 12366--12374 \T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 score[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 date: late []\T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first, Underfull \hbox (badness 2662) in paragraph at lines 12366--12374 \T1/ptm/m/n/10 der, []\T1/pcr/m/n/10 subject:descending []\T1/ptm/m/n/10 for re -verse al-pha-bet-i-cal or-der, []\T1/pcr/m/n/10 size []\T1/ptm/m/n/10 or [2118] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12411--12411 []\T1/pcr/m/n/9 fullquery <- RSiteSearch("lattice", restrict = c("vignettes"," Rfunctions"))[] [2119] Underfull \hbox (badness 1377) in paragraph at lines 12467--12470 []\T1/ptm/m/n/10 Character string spec-i-fy-ing whether emacs style ([]\T1/pcr/ m/n/10 "etags"[]\T1/ptm/m/n/10 ) or vi style Underfull \hbox (badness 3646) in paragraph at lines 12502--12504 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software / [2120] Overfull \hbox (30.78088pt too wide) in paragraph at lines 12540--12540 [] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F ALSE, ...)[] [2121] [2122] Underfull \hbox (badness 10000) in paragraph at lines 12722--12726 []\T1/ptm/m/n/10 The de-fault for []\T1/pcr/m/n/10 stylepath []\T1/ptm/m/n/10 i s now taken from the en-vi-ron-ment vari-able [2123] Underfull \hbox (badness 10000) in paragraph at lines 12755--12761 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a Underfull \hbox (badness 2027) in paragraph at lines 12770--12776 []\T1/ptm/m/n/10 The use of fancy quotes (see [][][]\T1/pcr/m/n/10 sQuote[][][] []\T1/ptm/m/n/10 ) can cause prob-lems when set-ting \T1/phv/m/n/10 R \T1/ptm/m /n/10 out-put in [2124] [2125] Overfull \hbox (6.78088pt too wide) in paragraph at lines 12927--12927 [] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa rent")[] Underfull \hbox (badness 1009) in paragraph at lines 12945--12957 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If [2126] Underfull \hbox (badness 2600) in paragraph at lines 12985--12987 []\T1/ptm/m/n/10 The file `\T1/pcr/m/n/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ures the R GUI ([]\T1/pcr/m/n/10 Rgui[]\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows and Underfull \hbox (badness 1043) in paragraph at lines 13028--13033 []\T1/ptm/m/n/10 At the time of writ-ing `\T1/pcr/m/n/10 Rdevga\T1/ptm/m/n/10 ' con-fig-ured the map-ping of font num-bers to fonts, and [2127] [2128] [2129] [2130] [2131] Underfull \hbox (badness 1888) in paragraph at lines 13330--13333 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form \T1/phv/m/n/10 R \T1/ptm/m/n/10 was built un-der. Where Underfull \hbox (badness 10000) in paragraph at lines 13347--13350 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g Underfull \hbox (badness 10000) in paragraph at lines 13350--13353 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g [2132] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13396--13396 []\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at end of report[] [2133] Underfull \hbox (badness 2158) in paragraph at lines 13455--13458 []\T1/ptm/m/n/10 Repository `[]\T1/pcr/m/n/10 CRAN[]\T1/ptm/m/n/10 ' is treated spe-cially: the value is taken from the cur-rent set-ting of Overfull \hbox (0.78088pt too wide) in paragraph at lines 13503--13503 []\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf fix)) [2134] [2135] [2136] Underfull \hbox (badness 2302) in paragraph at lines 13660--13662 []\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t o the Win-dows API call [2137] Underfull \hbox (badness 3333) in paragraph at lines 13768--13770 []\T1/pcr/m/n/10 getSrcFilename []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 getSrcDir ectory []\T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file- [2138] [2139] [2140] Overfull \hbox (42.78088pt too wide) in paragraph at lines 13935--13935 [] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing = TRUE, ...))[] Underfull \hbox (badness 2012) in paragraph at lines 13959--13964 []\T1/ptm/m/n/10 logical; if []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 (de-fault), [][][]\T1/pcr/m/n/10 deparse[][][](control = ) []\T1/ptm/m/n/10 will not ha ve Underfull \hbox (badness 5970) in paragraph at lines 13968--13971 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive Underfull \hbox (badness 2600) in paragraph at lines 13968--13971 [][][]\T1/pcr/m/n/10 options[][][]("width")[]\T1/ptm/m/n/10 ; note that this ha s only a weak ef-fect, un-less Underfull \hbox (badness 1052) in paragraph at lines 13979--13988 []\T1/ptm/m/n/10 (see [][][]\T1/pcr/m/n/10 options[][][][]\T1/ptm/m/n/10 ) whic h de-faults to []\T1/pcr/m/n/10 "no" []\T1/ptm/m/n/10 for back com-pat-i-bil-it y rea-sons; [2141] Underfull \hbox (badness 1442) in paragraph at lines 13995--13999 []\T1/ptm/m/n/10 numeric or []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 as by de-fau lt, de-ter-min-ing the []\T1/pcr/m/n/10 nlines []\T1/ptm/m/n/10 ar-gu-ment to Overfull \hbox (36.7804pt too wide) in paragraph at lines 14041--14041 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification of binary numbers[] [2142] Overfull \hbox (15.18042pt too wide) in paragraph at lines 14068--14068 []\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo ng" non-ASCII:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 14075--14075 []\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of 2 in order to se e 1 (in UTF-8!):[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 14077--14077 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) # "1 is 1" here[] [2143] [2144] [2145] Underfull \hbox (badness 10000) in paragraph at lines 14243--14245 []\T1/ptm/m/n/10 Options other than []\T1/pcr/m/n/10 memory = "none" []\T1/ptm/ m/n/10 ap-ply only to files pro-duced by [2146] Underfull \hbox (badness 10000) in paragraph at lines 14353--14356 []\T1/ptm/m/n/10 further ar-gu-ments passed to the driver's setup func-tion. Se e Underfull \hbox (badness 1389) in paragraph at lines 14353--14356 [][][]\T1/pcr/m/n/10 RweaveLatexSetup[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/ m/n/10 RtangleSetup[][][][]\T1/ptm/m/n/10 , re-spec-tively, for the ar-gu- [2147] Underfull \hbox (badness 6300) in paragraph at lines 14401--14408 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 syntax = NULL []\T1/ptm/m/n/10 (the de-fau lt) then the avail-able syn-tax ob-jects are con-sulted in Underfull \hbox (badness 6252) in paragraph at lines 14401--14408 \T1/ptm/m/n/10 turn, and se-lected if their []\T1/pcr/m/n/10 extension []\T1/pt m/m/n/10 com-po-nent matches (as a reg-exp) the file Underfull \hbox (badness 4556) in paragraph at lines 14401--14408 \T1/ptm/m/n/10 name. Ob-jects []\T1/pcr/m/n/10 SweaveSyntaxNoweb []\T1/ptm/m/n/ 10 (with []\T1/pcr/m/n/10 extension = "[.][rsRS]nw$"[]\T1/ptm/m/n/10 ) and [2148] [2149] Underfull \hbox (badness 2020) in paragraph at lines 14565--14573 \T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `[]\T1/pcr/m/n/10 -h[]\T1/ptm/m/ n/10 ' (fol-low sym-bolic links, also `[]\T1/pcr/m/n/10 -L[]\T1/ptm/m/n/10 ' on some plat-forms), Underfull \hbox (badness 1194) in paragraph at lines 14565--14573 \T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 --acls[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 -- exclude-backups[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 --exclude-vcs[]\T1/ptm/m/n /10 ' (and sim-i-lar) and on Win-dows [2150] Underfull \hbox (badness 1622) in paragraph at lines 14574--14581 []\T1/ptm/m/n/10 A con-ve-nient and ro-bust way to set op-tions for GNU []\T1/p cr/m/n/10 tar []\T1/ptm/m/n/10 is via en-vi-ron-ment vari-able [2151] Underfull \hbox (badness 5022) in paragraph at lines 14714--14718 []\T1/ptm/m/n/10 When ar-gu-ment []\T1/pcr/m/n/10 tar []\T1/ptm/m/n/10 is set t o the com-mand []\T1/pcr/m/n/10 tar []\T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 14721--14724 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / pubs . Underfull \hbox (badness 10000) in paragraph at lines 14721--14724 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht ml # tag _ 20 _ 92 _ [2152] [2153] [2154] [2155] [2156] [2157] [2158] [2159] [2160] Overfull \hbox (6.78088pt too wide) in paragraph at lines 15339--15339 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 15345--15345 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] [2161] Underfull \hbox (badness 4467) in paragraph at lines 15366--15368 []\T1/ptm/m/n/10 Download method, see [][][]\T1/pcr/m/n/10 download.file[][][][ ]\T1/ptm/m/n/10 . Un-used if a non-[]\T1/pcr/m/n/10 NULL Underfull \hbox (badness 4660) in paragraph at lines 15381--15385 \T1/ptm/m/n/10 able at the repos-i-to-ries, or []\T1/pcr/m/n/10 NULL []\T1/ptm/ m/n/10 which makes an in-ter-nal call to Underfull \hbox (badness 1694) in paragraph at lines 15395--15399 []\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][][]\T1/pcr/m/n/10 ins talled.packages[][][](lib.loc = Underfull \hbox (badness 10000) in paragraph at lines 15401--15406 []\T1/ptm/m/n/10 Arguments such as []\T1/pcr/m/n/10 destdir []\T1/ptm/m/n/10 an d []\T1/pcr/m/n/10 dependencies []\T1/ptm/m/n/10 to be Underfull \hbox (badness 10000) in paragraph at lines 15401--15406 \T1/ptm/m/n/10 passed to [][][]\T1/pcr/m/n/10 install.packages[][][] []\T1/ptm/ m/n/10 and []\T1/pcr/m/n/10 ignore_repo_cache[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 15401--15406 []\T1/pcr/m/n/10 max_repo_cache_age []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 noCac he []\T1/ptm/m/n/10 to [][][]\T1/pcr/m/n/10 available.packages[][][] Underfull \hbox (badness 1052) in paragraph at lines 15407--15409 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See [2162] Underfull \hbox (badness 10000) in paragraph at lines 15437--15442 []\T1/pcr/m/n/10 available = NULL []\T1/ptm/m/n/10 make a call to []\T1/pcr/m/n /10 available.packages(contriburl = Underfull \hbox (badness 1226) in paragraph at lines 15437--15442 \T1/pcr/m/n/10 contriburl, method = method) []\T1/ptm/m/n/10 and hence by de-fa ult fil-ters on \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion, OS type Underfull \hbox (badness 10000) in paragraph at lines 15458--15463 []\T1/ptm/m/n/10 Take care when us-ing []\T1/pcr/m/n/10 dependencies []\T1/ptm/ m/n/10 (passed to [][][]\T1/pcr/m/n/10 install.packages[][][][]\T1/ptm/m/n/10 ) with Underfull \hbox (badness 10000) in paragraph at lines 15466--15469 [][][]\T1/pcr/m/n/10 install.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n /10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 download.pa ckages[][][][]\T1/ptm/m/n/10 , [2163] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15543--15543 []\T1/pcr/m/n/9 ## Not run: url.show("https://www.stats.ox.ac.uk/pub/datasets/ csb/ch3a.txt") [2164] [2165] [2166] Underfull \hbox (badness 2293) in paragraph at lines 15750--15753 [][][]\T1/pcr/m/n/10 browseVignettes[][][] []\T1/ptm/m/n/10 for an HTML-based v i-gnette browser; [][][]\T1/pcr/m/n/10 RShowDoc[][][](, [2167] Overfull \hbox (42.18039pt too wide) in paragraph at lines 15766--15766 []\T1/pcr/m/n/9 ## Note that \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 package = *\TS1/pcr /m/n/9 ' \T1/pcr/m/n/9 is much faster in the case of many installed packages:[] [2168] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15833--15833 [] \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d ata = DAT)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 15855--15855 [] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal), data = DD)))[] [2169] [2170] Underfull \hbox (badness 1297) in paragraph at lines 15987--15989 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i s se-lected, or [2171] Underfull \hbox (badness 4036) in paragraph at lines 16034--16036 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 winMenuDel []\T1/ptm/m/n/10 func-tion wil l delete a menu and all of its items and sub-menus. [2172] [2173] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16154--16154 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", [2174] Underfull \hbox (badness 1715) in paragraph at lines 16206--16209 []\T1/ptm/m/n/10 arguments to []\T1/pcr/m/n/10 write.table[]\T1/ptm/m/n/10 : [] \T1/pcr/m/n/10 append[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 col.names[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 sep[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 dec []\T1/ptm/m/n /10 and Underfull \hbox (badness 10000) in paragraph at lines 16251--16253 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion e.g. []\T1/pcr/m/n/10 file = [2175] [2176] [2177]) [2178] [2179] [2180] (./KernSmooth-pkg.tex Chapter 15. [2181] Overfull \hbox (24.78088pt too wide) in paragraph at lines 123--123 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat e = TRUE) [2182] [2183] [2184] [2185] [2186] Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun = 0.05, [2187] [2188] [2189] [2190]) (./MASS-pkg.tex Chapter 16. [2191] [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] [2200] [2201] Overfull \hbox (20.58041pt too wide) in paragraph at lines 776--776 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b eav2$hours/24))[] [2202] [2203] [2204] [2205] [2206] [2207] [2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218] [2219] [2220] [2221] [2222] [2223] [2224] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2422--2422 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2426--2426 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] [2225] [2226] [2227] [2228] Underfull \hbox (badness 6559) in paragraph at lines 2707--2710 []\T1/ptm/m/n/10 further ar-gu-ments for []\T1/pcr/m/n/10 plot []\T1/ptm/m/n/10 and graph-i-cal pa-ram-e-ters. Note that [2229] [2230] [2231] Underfull \hbox (badness 10000) in paragraph at lines 2877--2882 []\T1/pcr/m/n/10 "gamma"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "geometric"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "log-normal"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lo gnormal"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2877--2882 []\T1/pcr/m/n/10 "logistic"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "negative binomi al"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "normal"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n /10 "Poisson"[]\T1/ptm/m/n/10 , [2232] [2233] Underfull \hbox (badness 4686) in paragraph at lines 3049--3051 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [2234] [2235] [2236] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3249--3249 [] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL SE, ...)[] [2237] [2238] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3381--3381 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist = "exponential")[] [2239] [2240] [2241] [2242] [2243] [2244] [2245] [2246] [2247] [2248] [2249] Underfull \hbox (badness 1845) in paragraph at lines 4183--4185 []\T1/ptm/m/n/10 The va-ri-ety of bar-ley ([]\T1/pcr/m/n/10 "manchuria"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "svansota"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "velv et"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "trebi" []\T1/ptm/m/n/10 and [2250] [2251] [2252] [2253] [2254] [2255] [2256] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4677--4677 [] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n", ...)[] [2257] [2258] [2259] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4899--4899 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model = FALSE, [2260] [2261] [2262] [2263] [2264] [2265] [2266] [2267] [2268] [2269] [2270] [2271] [2272] [2273] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5954--5954 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP ACK = FALSE) [2274] Overfull \hbox (48.78088pt too wide) in paragraph at lines 6015--6015 []\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/ 10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log") [2275] [2276] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.npk}) has been already used, duplicate ignored \relax l.6175 ...sical N, P, K Factorial Experiment}{npk} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.npk.1}) h as been already used, duplicate ignored \relax l.6175 ...sical N, P, K Factorial Experiment}{npk} [2277] [2278] [2279] [2280] [2281] [2282] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6595--6595 [] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb ose = TRUE)))[] [2283] Overfull \hbox (18.78088pt too wide) in paragraph at lines 6683--6683 [] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr ellis"))[] [2284] [2285] [2286] [2287] [2288] [2289] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7122--7122 []\T1/pcr/m/n/9 nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100 , A=10, B=1))[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7139--7139 [] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c auchit"))[] [2290] Underfull \hbox (badness 3138) in paragraph at lines 7217--7223 []\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c mr/m/n/10 ) = [2291] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7287--7287 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da ta = housing)[] [2292] [2293] Underfull \hbox (badness 1389) in paragraph at lines 7396--7399 []\T1/ptm/m/n/10 the di-men-sion of the space to be used. If this is less than []\T1/pcr/m/n/10 min(p, [2294] [2295] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7526--7526 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam p = "exact")[] [2296] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7591--7591 [] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC V"), ...)[] [2297] [2298] [2299] [2300] [2301] [2302] Underfull \hbox (badness 4686) in paragraph at lines 8029--8031 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [2303] [2304] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8148--8148 [] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control = NULL)[] Underfull \hbox (badness 1590) in paragraph at lines 8172--8176 []\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if []\T1/pcr/m /n/10 NA[]\T1/ptm/m/n/10 s are found. The [2305] [2306] [2307] [2308] [2309] [2310] [2311] [2312] [2313] [2314] [2315] [2316] [2317] [2318] [2319] [2320] [2321] [2322] [2323] [2324] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9554--9554 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS E, ...)[] [2325] Underfull \hbox (badness 2035) in paragraph at lines 9666--9668 []\T1/ptm/m/n/10 ``Fold your arms! Which is on top'' (Fac-tor, with lev-els []\ T1/pcr/m/n/10 "R on L"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "L on R"[]\T1/ptm/m/n /10 , Underfull \hbox (badness 1158) in paragraph at lines 9681--9684 []\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els []\T1/pcr/m/n/ 10 "Heavy"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Regul" []\T1/ptm/m/n/10 (reg-u-l arly), [2326] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9763--9763 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub le.eps^0.25) Overfull \hbox (30.78088pt too wide) in paragraph at lines 9765--9765 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double .eps^0.25,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9768--9768 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub le.eps^0.25)[] [2327] [2328] [2329] [2330] [2331] [2332] [2333] [2334] [2335] [2336] [2337] [2338] [2339]) (./Matrix-pkg.tex [2340] Chapter 17. Underfull \hbox (badness 10000) in paragraph at lines 35--38 []\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec t to change, and if you Underfull \hbox (badness 10000) in paragraph at lines 35--38 \T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack- age main-tain-ers [2341] Underfull \hbox (badness 1769) in paragraph at lines 89--92 []\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o wn code. Please con-tact us [2342] Underfull \hbox (badness 2229) in paragraph at lines 154--157 []\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm /m/n/10 ob-jects; here, when the first is Underfull \hbox (badness 1147) in paragraph at lines 154--157 \T1/ptm/m/n/10 an []\T1/pcr/m/n/10 "[][]abIndex[][][]" []\T1/ptm/m/n/10 vec-tor , these ar-gu-ments will be con-cate-nated to a new pdfTeX warning (ext4): destination with the same identifier (name{Rfn.all.equal }) has been already used, duplicate ignored \relax l.184 ...{all.equal}{all.equal-methods}{all.equal} Underfull \hbox (badness 10000) in paragraph at lines 211--214 []\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing Underfull \hbox (badness 10000) in paragraph at lines 217--219 []\T1/ptm/m/n/10 There are more meth-ods, no-tably also for []\T1/pcr/m/n/10 "[ ][]sparseVector[][][]"[]\T1/ptm/m/n/10 's, see [2343] Underfull \hbox (badness 3098) in paragraph at lines 266--268 []\T1/ptm/m/n/10 optional ar-gu-ments passed to the de-fault method for generic func-tion [2344] [2345] [2346] Overfull \hbox (15.18042pt too wide) in paragraph at lines 500--500 [] \T1/pcr/m/n/9 band(sm5, -1, 1)# "dsyMatrix": symmetric band preserves sym metry property[] [2347] Underfull \hbox (badness 5119) in paragraph at lines 543--547 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class Underfull \hbox (badness 1668) in paragraph at lines 547--552 [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/ m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse Overfull \hbox (4.38043pt too wide) in paragraph at lines 578--578 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 580--580 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] [2348] Overfull \hbox (36.7804pt too wide) in paragraph at lines 589--589 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20, 1), rpois(20, 3))[ c(1:3, 2:3, 3:2)],[] [2349] Overfull \hbox (52.98038pt too wide) in paragraph at lines 705--705 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd iag() -- for the case of *many* (k x k) matrices:[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 706--706 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(, , ....., ) where each mat_j is a k x k \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 matrix\TS1/pcr/m/n/9 '[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 707--707 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @return a sparse (N*k x N*k) matrix of class \code{"\linkS4class{dgCMatrix}"}.[] [2350] Overfull \hbox (31.3804pt too wide) in paragraph at lines 720--720 [] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \ T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri x indexing), but elegant?[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 721--721 [] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len( N), each=k)]),[] [2351] Overfull \hbox (9.78043pt too wide) in paragraph at lines 888--888 []\T1/pcr/m/n/9 L. <- L; L.[1:2,1] <- TRUE; L.@x[1:2] <- FALSE; L. # has "zero s" to drop0()[] [2352] Underfull \hbox (badness 1635) in paragraph at lines 970--975 []\T1/pcr/m/n/10 new("pBunchKaufman", ...)[]\T1/ptm/m/n/10 , but they are more typ-i-cally ob-tained as the value of Underfull \hbox (badness 10000) in paragraph at lines 980--983 []\T1/pcr/m/n/10 signature(from = "BunchKaufman", to = "dtrMatrix")[]\T1/ptm/m/ n/10 : re-turns a Underfull \hbox (badness 10000) in paragraph at lines 983--986 []\T1/pcr/m/n/10 signature(from = "pBunchKaufman", to = "dtpMatrix")[]\T1/ptm/m /n/10 : re-turns a Underfull \hbox (badness 10000) in paragraph at lines 986--989 []\T1/pcr/m/n/10 signature(from = "p?BunchKaufman", logarithm = [2353] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1059--1059 []\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m atrix"), ...)[] [2354] Underfull \hbox (badness 10000) in paragraph at lines 1132--1137 []\T1/ptm/m/n/10 An ob-ject rep-re-sent-ing the fac-tor-iza-tion, in-her-it-ing from vir-tual class [2355] Overfull \hbox (3.02814pt too wide) in paragraph at lines 1188--1188 []\T1/pcr/m/n/9 stopifnot(all.equal(as(A, "matrix"), as(Reduce(\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 %*%\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 , e.bk.A), "matrix")))[] [2356] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cbind2.Rd ash.methods}) has been already used, duplicate ignored \relax l.1236 ... on cbind2/rbind2}{cbind2.Rdash.methods} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cbind2}) has been already used, duplicate ignored \relax l.1237 \aliasA{cbind2}{cbind2-methods}{cbind2} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rbind2}) has been already used, duplicate ignored \relax l.1246 \aliasA{rbind2}{cbind2-methods}{rbind2} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rbind2.Rd ash.methods}) has been already used, duplicate ignored \relax l.1255 ...s}{cbind2-methods}{rbind2.Rdash.methods} [2357] Underfull \hbox (badness 10000) in paragraph at lines 1318--1323 []\T1/ptm/m/n/10 Our class def-i-ni-tion help pages men-tion-ing []\T1/pcr/m/n/ 10 cbind2() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 rbind2() []\T1/ptm/m/n/10 met h-ods: Underfull \hbox (badness 10000) in paragraph at lines 1373--1380 []\T1/ptm/m/n/10 The im-ple-men-ta-tion of class []\T1/pcr/m/n/10 CHMfactor []\ T1/ptm/m/n/10 is based on CHOLMOD's C-level [2358] [2359] Underfull \hbox (badness 5008) in paragraph at lines 1535--1550 []\T1/pcr/m/n/10 signature(from = "CHMfactor", logarithm = "logical")[]\T1/ptm/ m/n/10 : be- Underfull \hbox (badness 10000) in paragraph at lines 1585--1587 []\T1/pcr/m/n/10 signature(update = ., C = ., object = "CHMfactor")[]\T1/ptm/m/ n/10 : see [2360] Underfull \hbox (badness 1917) in paragraph at lines 1593--1597 []\T1/ptm/m/n/10 The CHOLMOD source code; see [][]$\T1/pcr/m/n/10 https : / / g ithub . com / DrTimothyAldenDavis / Underfull \hbox (badness 8132) in paragraph at lines 1593--1597 \T1/pcr/m/n/10 SuiteSparse$[][]\T1/ptm/m/n/10 , no-tably the header file `\T1/p cr/m/n/10 CHOLMOD/Include/cholmod.h\T1/ptm/m/n/10 ' defin-ing Overfull \hbox (9.78043pt too wide) in paragraph at lines 1643--1643 []\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m atrix"), ...)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1651--1651 [] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(list( NULL), dn[2L]),[] [2361] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1660--1660 [] \T1/pcr/m/n/9 ae2(A[ch.A@perm + 1L, ch.A@perm + 1L], with(e.ch.A, L1 %*% D %*% L1.))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1661--1661 [] \T1/pcr/m/n/9 ae2(A[ch.A@perm + 1L, ch.A@perm + 1L], with(E.ch.A, L %*% L. ))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1671--1671 []\T1/pcr/m/n/9 u2 <- update(ch.A, t(M), mult = sqrt(2)) # updating with cross prod(M), not M[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol}) ha s been already used, duplicate ignored \relax l.1676 \aliasA{chol}{chol-methods}{chol} [2362] Underfull \hbox (badness 10000) in paragraph at lines 1781--1785 \T1/pcr/m/n/10 double / dpstrf . f$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 htt ps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and Underfull \hbox (badness 1917) in paragraph at lines 1786--1790 []\T1/ptm/m/n/10 The CHOLMOD source code; see [][]$\T1/pcr/m/n/10 https : / / g ithub . com / DrTimothyAldenDavis / Underfull \hbox (badness 8132) in paragraph at lines 1786--1790 \T1/pcr/m/n/10 SuiteSparse$[][]\T1/ptm/m/n/10 , no-tably the header file `\T1/p cr/m/n/10 CHOLMOD/Include/cholmod.h\T1/ptm/m/n/10 ' defin-ing [2363] [2364] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol2inv} ) has been already used, duplicate ignored \relax l.1905 ...sA{chol2inv}{chol2inv-methods}{chol2inv} [2365] [2366] Underfull \hbox (badness 1931) in paragraph at lines 2041--2046 []\T1/ptm/m/n/10 a nu-meric vec-tor of length []\T1/pcr/m/n/10 n*n []\T1/ptm/m/ n/10 ([]\T1/pcr/m/n/10 Cholesky[]\T1/ptm/m/n/10 ) or []\T1/pcr/m/n/10 n*(n+1)/2 []\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 pCholesky[]\T1/ptm/m/n/10 ), where Underfull \hbox (badness 1226) in paragraph at lines 2056--2059 []\T1/ptm/m/n/10 Class [][][]\T1/pcr/m/n/10 CholeskyFactorization[][][][]\T1/pt m/m/n/10 , di-rectly. Class [][][]\T1/pcr/m/n/10 MatrixFactorization[][][][]\T1 /ptm/m/n/10 , by class Underfull \hbox (badness 3000) in paragraph at lines 2062--2070 []\T1/ptm/m/n/10 Objects can be gen-er-ated di-rectly by calls of the form []\T 1/pcr/m/n/10 new("Cholesky", ...) []\T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 2079--2083 []\T1/pcr/m/n/10 signature(from = "pCholesky", to = "dtpMatrix")[]\T1/ptm/m/n/1 0 : re-turns a Underfull \hbox (badness 10000) in paragraph at lines 2083--2086 []\T1/pcr/m/n/10 signature(from = "p?Cholesky", logarithm = "logical")[]\T1/ptm /m/n/10 : Underfull \hbox (badness 10000) in paragraph at lines 2117--2121 \T1/pcr/m/n/10 double / dpstrf . f$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 htt ps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and [2367] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2164--2164 []\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m atrix"), ...)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2172--2172 [] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(list( NULL), dn[2L]),[] [2368] [2369] Underfull \hbox (badness 10000) in paragraph at lines 2303--2310 []\T1/ptm/m/n/10 a [][]fi-nite[][][] num-ber. The ma-trix that is fac-tor-ized is []\T1/pcr/m/n/10 A + Imult * Underfull \hbox (badness 1946) in paragraph at lines 2303--2310 \T1/pcr/m/n/10 - diag(abs(A))) []\T1/ptm/m/n/10 en-sures that []\T1/pcr/m/n/10 A + Imult * diag(nrow(A)) []\T1/ptm/m/n/10 is di- [2370] Underfull \hbox (badness 10000) in paragraph at lines 2350--2363 []\T1/ptm/m/n/10 An ob-ject rep-re-sent-ing the fac-tor-iza-tion, in-her-it-ing from vir-tual class Underfull \hbox (badness 10000) in paragraph at lines 2366--2370 \T1/pcr/m/n/10 double / dpstrf . f$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 htt ps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and Underfull \hbox (badness 1917) in paragraph at lines 2371--2375 []\T1/ptm/m/n/10 The CHOLMOD source code; see [][]$\T1/pcr/m/n/10 https : / / g ithub . com / DrTimothyAldenDavis / Underfull \hbox (badness 8132) in paragraph at lines 2371--2375 \T1/pcr/m/n/10 SuiteSparse$[][]\T1/ptm/m/n/10 , no-tably the header file `\T1/p cr/m/n/10 CHOLMOD/Include/cholmod.h\T1/ptm/m/n/10 ' defin-ing [2371] Underfull \vbox (badness 10000) has occurred while \output is active [2372] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2488--2488 [] \T1/pcr/m/n/9 list(simpl1 = Cholesky(A4, perm = TRUE, super = FALSE, L DL = TRUE),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2489--2489 [] \T1/pcr/m/n/9 simpl0 = Cholesky(A4, perm = TRUE, super = FALSE, L DL = FALSE),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2490--2490 [] \T1/pcr/m/n/9 super0 = Cholesky(A4, perm = TRUE, super = TRUE )),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2492--2492 [] \T1/pcr/m/n/9 list(simpl1 = Cholesky(A4, perm = FALSE, super = FALSE, L DL = TRUE),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2493--2493 [] \T1/pcr/m/n/9 simpl0 = Cholesky(A4, perm = FALSE, super = FALSE, L DL = FALSE),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2494--2494 [] \T1/pcr/m/n/9 super0 = Cholesky(A4, perm = FALSE, super = TRUE )))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2498--2498 []\T1/pcr/m/n/9 rapply2 <- function(object, f, ...) rapply(object, f, , , how = "list", ...)[] Underfull \vbox (badness 10000) has occurred while \output is active [2373] Overfull \hbox (42.18039pt too wide) in paragraph at lines 2565--2565 [] \T1/pcr/m/n/9 x = c(1, 6, 38, 10, 60, 103, -4, 6, -32, -247, -2, - 16, -128, -2, -67))[] [2374] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2661--2661 [] \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4), j=c(2:4,1), x = 2, dimnames=dns))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2665--2665 [] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE, dimnames=dns))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2672--2672 [] \T1/pcr/m/n/9 a. <- sparseMatrix(i=4:1, j=1:4, dimnames=list(n4, n4), repr ="T") # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[] [2375] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colMeans} ) has been already used, duplicate ignored \relax l.2747 ...asA{colMeans}{colSums-methods}{colMeans} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colSums}) has been already used, duplicate ignored \relax l.2755 \aliasA{colSums}{colSums-methods}{colSums} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowMeans} ) has been already used, duplicate ignored \relax l.2762 ...asA{rowMeans}{colSums-methods}{rowMeans} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowSums}) has been already used, duplicate ignored \relax l.2770 \aliasA{rowSums}{colSums-methods}{rowSums} [2376] Underfull \hbox (badness 2922) in paragraph at lines 2822--2826 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i n-her-it-ing from Underfull \hbox (badness 1728) in paragraph at lines 2822--2826 \T1/ptm/m/n/10 class [][][]\T1/pcr/m/n/10 sparseVector[][][][]\T1/ptm/m/n/10 . Only ap-pli-ca-ble when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 is in-her-it-ing fr om a Underfull \hbox (badness 1237) in paragraph at lines 2833--2836 [][][]\T1/pcr/m/n/10 dimnames[][][](x) []\T1/ptm/m/n/10 are only kept (as [][][ ]\T1/pcr/m/n/10 names[][][](v)[]\T1/ptm/m/n/10 ) when the re-sult-ing []\T1/pcr /m/n/10 v []\T1/ptm/m/n/10 is [][][]\T1/pcr/m/n/10 numeric[][][][]\T1/ptm/m/n/1 0 , since [2377] [2378] Underfull \hbox (badness 3547) in paragraph at lines 2994--2997 []\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when [2379] [2380] [2381] [2382] [2383] Underfull \hbox (badness 10000) in paragraph at lines 3402--3405 []\T1/pcr/m/n/10 signature(from = "denseLU", logarithm = "logical")[]\T1/ptm/m/ n/10 : com- [2384] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3457--3457 []\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m atrix"), ...)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 3464--3464 [] \T1/pcr/m/n/9 new( "pMatrix", Dim = c(n, n), Dimnames = c(dn[ 1L], list(NULL)),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3467--3467 [] \T1/pcr/m/n/9 new("dtrMatrix", Dim = c(n, n), Dimnames = list( NULL, NULL),[] [2385] Overfull \hbox (31.3804pt too wide) in paragraph at lines 3470--3470 [] \T1/pcr/m/n/9 new("dtrMatrix", Dim = c(n, n), Dimnames = c(lis t(NULL), dn[2L]),[] [2386] Underfull \hbox (badness 7379) in paragraph at lines 3598--3600 []\T1/pcr/m/n/10 signature(x = "dgCMatrix")[]\T1/ptm/m/n/10 : com-putes the LU de-com-po-si-tion of a square [2387] [2388] [2389] Underfull \hbox (badness 4846) in paragraph at lines 3819--3823 []\T1/ptm/m/n/10 Note that both []\T1/pcr/m/n/10 new(.) []\T1/ptm/m/n/10 and [] [][]\T1/pcr/m/n/10 spMatrix[][][] []\T1/ptm/m/n/10 con-struc-tors for []\T1/pcr /m/n/10 "dgTMatrix" []\T1/ptm/m/n/10 (and other Underfull \hbox (badness 2717) in paragraph at lines 3824--3828 []\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can be stored in more than one pos-si-ble [2390] Underfull \hbox (badness 5231) in paragraph at lines 3869--3874 []\T1/ptm/m/n/10 Construct a for-mally di-ag-o-nal [][][]\T1/pcr/m/n/10 Matrix[ ][][][]\T1/ptm/m/n/10 , i.e., an ob-ject in-her-it-ing from vir-tual class Overfull \hbox (84.78088pt too wide) in paragraph at lines 3880--3880 []\T1/pcr/m/n/10 .sparseDiagonal(n, x = NULL, uplo = "U", shape = "t", unitri = TRUE, kind, cols)[] [2391] Underfull \hbox (badness 10000) in paragraph at lines 3936--3939 []\T1/pcr/m/n/10 .trDiagonal() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 .symDiagon al() []\T1/ptm/m/n/10 are sim-ple wrap-pers, for Underfull \hbox (badness 6792) in paragraph at lines 3936--3939 []\T1/pcr/m/n/10 .sparseDiagonal(shape = "t") []\T1/ptm/m/n/10 and []\T1/pcr/m/ n/10 .sparseDiagonal(shape = "s")[]\T1/ptm/m/n/10 , re-spec- [2392] Underfull \hbox (badness 3646) in paragraph at lines 4013--4016 []\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 dimnames[][][][]\T1/ptm/m/n/10 , a [] [][]\T1/pcr/m/n/10 list[][][][]\T1/ptm/m/n/10 , see the [][][]\T1/pcr/m/n/10 Ma trix[][][] []\T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally Underfull \hbox (badness 6542) in paragraph at lines 4048--4052 []\T1/pcr/m/n/10 signature(x = "diagonalMatrix")[]\T1/ptm/m/n/10 : all these gr oup meth-ods re-turn a Underfull \hbox (badness 4518) in paragraph at lines 4057--4063 []\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")[]\T1/ptm/m/n/10 : the re-sult is from class [2393] Underfull \hbox (badness 10000) in paragraph at lines 4064--4068 []\T1/pcr/m/n/10 (object = "diagonalMatrix")[]\T1/ptm/m/n/10 : Re-turns an ob-j ect of S3 class Underfull \hbox (badness 2318) in paragraph at lines 4074--4078 [][][]\T1/pcr/m/n/10 Diagonal[][][]() []\T1/ptm/m/n/10 as con-struc-tor of thes e ma-tri-ces, and [][][]\T1/pcr/m/n/10 isDiagonal[][][][]\T1/ptm/m/n/10 . [][][ ]\T1/pcr/m/n/10 ddiMatrix[][][] []\T1/ptm/m/n/10 and [2394] [2395] [2396] Underfull \hbox (badness 10000) in paragraph at lines 4331--4333 []\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")[]\T1/ptm/m/n/10 : this group con-tains [2397] [2398] Overfull \hbox (69.18036pt too wide) in paragraph at lines 4475--4475 []\T1/pcr/m/n/9 stopifnot(all.equal(S9p0, S9p))# same as as default, but diffe rent from the random one[] [2399] Underfull \hbox (badness 2469) in paragraph at lines 4590--4593 []\T1/pcr/m/n/10 signature(x = "dpoMatrix")[]\T1/ptm/m/n/10 : Re-turns the [][] []\T1/pcr/m/n/10 determinant[][][] []\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 x[]\T1/ ptm/m/n/10 , via [2400] Underfull \hbox (badness 10000) in paragraph at lines 4613--4618 []\T1/ptm/m/n/10 Currently the va-lid-ity meth-ods for these classes such as Underfull \hbox (badness 2020) in paragraph at lines 4613--4618 [][][]\T1/pcr/m/n/10 getValidity[][][](getClass("dpoMatrix")) []\T1/ptm/m/n/10 for ef-fi-ciency rea-sons only check the di- Underfull \hbox (badness 1748) in paragraph at lines 4619--4628 \T1/pcr/m/n/10 error=identity), "error") []\T1/ptm/m/n/10 . In-deed, when \T1/p tm/m/it/10 co-erc-ing \T1/ptm/m/n/10 to these classes, a ver-sion Underfull \hbox (badness 1590) in paragraph at lines 4619--4628 \T1/ptm/m/n/10 of [][][]\T1/pcr/m/n/10 Cholesky[][][]() []\T1/ptm/m/n/10 or [][ ][]\T1/pcr/m/n/10 chol[][][]() []\T1/ptm/m/n/10 is typ-i-cally used, e.g., see []\T1/pcr/m/n/10 selectMethod("coerce", Underfull \hbox (badness 6675) in paragraph at lines 4675--4682 []\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 Matrix[][][][]\T1/ptm/m/n/10 , typ-i-ca lly in-her-it-ing from vir-tual class [][][]\T1/pcr/m/n/10 sparseMatrix[][][][] \T1/ptm/m/n/10 . Underfull \hbox (badness 6493) in paragraph at lines 4675--4682 [][][]\T1/pcr/m/n/10 denseMatrix[][][] []\T1/ptm/m/n/10 and tra-di-tional vec-t ors and ma-tri-ces are co-erced to [2401] Underfull \hbox (badness 10000) in paragraph at lines 4690--4698 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing if the re-sult must in-herit from vi r-tual class Underfull \hbox (badness 1365) in paragraph at lines 4690--4698 [][][]\T1/pcr/m/n/10 CsparseMatrix[][][][]\T1/ptm/m/n/10 . If []\T1/pcr/m/n/10 FALSE []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 in-her-its from [][][]\T1/pcr/m/n/10 RsparseMatrix[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4713--4716 []\T1/ptm/m/n/10 Function [][][]\T1/pcr/m/n/10 sparseMatrix[][][][]\T1/ptm/m/n/ 10 , for con-struct-ing ob-jects in-her-it-ing from vir-tual class [2402] Underfull \hbox (badness 10000) in paragraph at lines 4757--4761 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10 new("dsCMatrix", ...) []\T1/ptm/m/n/10 or Underfull \hbox (badness 2103) in paragraph at lines 4757--4761 []\T1/pcr/m/n/10 new("dsTMatrix", ...)[]\T1/ptm/m/n/10 , or au-to-mat-i-cally v ia e.g., []\T1/pcr/m/n/10 as(*, "symmetricMatrix")[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1571) in paragraph at lines 4807--4810 []\T1/pcr/m/n/10 signature(x = "dsCMatrix", pivot = "logical")[]\T1/ptm/m/n/10 : Re-turns (and stores) the [2403] [2404] Underfull \hbox (badness 10000) in paragraph at lines 4949--4954 []\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "dMatrix"[]\T1/ptm/m/n/10 , by class [] \T1/pcr/m/n/10 "dsparseMatrix"[]\T1/ptm/m/n/10 , class []\T1/pcr/m/n/10 "sparse Matrix"[]\T1/ptm/m/n/10 , by Underfull \hbox (badness 6961) in paragraph at lines 4949--4954 \T1/ptm/m/n/10 class []\T1/pcr/m/n/10 "dsparseMatrix" []\T1/ptm/m/n/10 or []\T1 /pcr/m/n/10 "RsparseMatrix"[]\T1/ptm/m/n/10 ; class []\T1/pcr/m/n/10 "compMatri x" []\T1/ptm/m/n/10 by class Underfull \hbox (badness 1400) in paragraph at lines 4961--4964 []\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")[]\T1/ptm/m/n/10 : if []\T1/pcr/m/n/10 uplo == [2405] Underfull \hbox (badness 10000) in paragraph at lines 5013--5015 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10 new("dsyMatrix", ...) []\T1/ptm/m/n/10 or Underfull \hbox (badness 1365) in paragraph at lines 5049--5052 []\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")[]\T1/ptm/m/n/10 , or []\T1/pcr/m/n/10 x = "dsyMatrix" [2406] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5095--5095 []\T1/pcr/m/n/9 stopifnot(all(S1 == S2)) # equal "seen as matrix", but differ internally :[] [2407] [2408] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5201--5201 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim = c(5L, 5L),[] Underfull \hbox (badness 3635) in paragraph at lines 5256--5260 []\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ddenseMatrix"[]\T1/ptm/m/n/10 , di-rec tly. Class []\T1/pcr/m/n/10 "triangularMatrix"[]\T1/ptm/m/n/10 , di-rectly. Cla ss Underfull \hbox (badness 10000) in paragraph at lines 5265--5268 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")[]\T1/ptm/m/n/10 : Ma-trix mul-ti-pli-ca-tion; Underfull \hbox (badness 10000) in paragraph at lines 5268--5272 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")[]\T1/ptm/m/n /10 : the [2409] [2410] [2411] [2412] Underfull \hbox (badness 10000) in paragraph at lines 5524--5526 []\T1/ptm/m/n/10 a ma-trix fac-tor-iza-tion, typ-i-cally in-her-it-ing from vir -tual class Overfull \hbox (29.27832pt too wide) in paragraph at lines 5543--5543 [] \T1/pcr/m/n/10 all.equal(as(x, "matrix"), as(Reduce(\TS1/cmtt/m/n/10 `\T 1/pcr/m/n/10 %*%\TS1/cmtt/m/n/10 `\T1/pcr/m/n/10 , expand2(y)), "matrix")) Overfull \hbox (37.71342pt too wide) in alignment at lines 5574--5574 [] [] [2413] Underfull \hbox (badness 7064) in paragraph at lines 5602--5619 []\T1/pcr/m/n/10 signature(x = "p?BunchKaufman")[]\T1/ptm/m/n/10 : ex-pands the fac-tor-iza-tion $\OML/cmm/m/it/10 A \OT1/cmr/m/n/10 = Underfull \hbox (badness 3000) in paragraph at lines 5631--5638 []\T1/pcr/m/n/10 signature(x = "denseLU")[]\T1/ptm/m/n/10 : ex-pands the fac-to r-iza-tion $\OML/cmm/m/it/10 A \OT1/cmr/m/n/10 = \OML/cmm/m/it/10 P[]LU$ \T1/pt m/m/n/10 as Underfull \hbox (badness 2735) in paragraph at lines 5647--5654 []\T1/pcr/m/n/10 signature(x = "CHMfactor")[]\T1/ptm/m/n/10 : as []\T1/pcr/m/n/ 10 expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/pcr/m/n/10 list(P, L)[]\T1/p tm/m/n/10 . Underfull \hbox (badness 1337) in paragraph at lines 5654--5669 []\T1/pcr/m/n/10 signature(x = "sparseLU")[]\T1/ptm/m/n/10 : as []\T1/pcr/m/n/1 0 expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/pcr/m/n/10 list(P, L, U, Underfull \hbox (badness 2680) in paragraph at lines 5654--5669 \T1/pcr/m/n/10 Q)[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 expand(x)[["Q"]] []\T1/ptm /m/n/10 and []\T1/pcr/m/n/10 expand2(x)[["P2."]] []\T1/ptm/m/n/10 rep-re-sent t he same per- Underfull \hbox (badness 5374) in paragraph at lines 5654--5669 \T1/ptm/m/n/10 mu-ta-tion ma-trix $\OML/cmm/m/it/10 P[]$ \T1/ptm/m/n/10 but hav e op-po-site []\T1/pcr/m/n/10 margin []\T1/ptm/m/n/10 slots and in-verted []\T1 /pcr/m/n/10 perm []\T1/ptm/m/n/10 slots. Underfull \hbox (badness 2073) in paragraph at lines 5669--5674 []\T1/pcr/m/n/10 signature(x = "denseLU")[]\T1/ptm/m/n/10 : as []\T1/pcr/m/n/10 expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/pcr/m/n/10 list(L, U, P)[]\T1/ ptm/m/n/10 . [2414] [2415] [2416] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5881--5881 []\T1/pcr/m/n/9 str(pores <- readMM(system.file("external/pores_1.mtx", packag e = "Matrix")))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5882--5882 []\T1/pcr/m/n/9 str(utm <- readHB(system.file("external/utm300.rua" , packag e = "Matrix")))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5883--5883 []\T1/pcr/m/n/9 str(lundA <- readMM(system.file("external/lund_a.mtx" , packag e = "Matrix")))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5884--5884 []\T1/pcr/m/n/9 str(lundA <- readHB(system.file("external/lund_a.rsa" , packag e = "Matrix")))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5885--5885 []\T1/pcr/m/n/9 ## https://math.nist.gov/MatrixMarket/data/Harwell-Boeing/coun terx/counterx.htm[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5886--5886 []\T1/pcr/m/n/9 str(jgl <- readMM(system.file("external/jgl009.mtx" , packag e = "Matrix")))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5892--5892 []\T1/pcr/m/n/9 u. <- url("https://www.cise.ufl.edu/research/sparse/RB/Boeing/ msc00726.tar.gz")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5897--5897 []\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary dir./folder:[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5900--5900 []\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[] [2417] Overfull \hbox (58.38037pt too wide) in paragraph at lines 5910--5910 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume nts to sparseMatrix():[] [2418] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5972--5972 [] \T1/pcr/m/n/9 all.equal(facmul(x, nm, y, trans = TRUE, left = TRUE), crossprod(L, y))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5973--5973 [] \T1/pcr/m/n/9 all.equal(facmul(x, nm, y, trans = TRUE, left = FALSE), t crossprod(y, L))[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6052--6052 []\T1/pcr/m/n/10 .diag2dense(from, kind = ".", shape = "t", packed = FALSE, up lo = "U")[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 6054--6054 []\T1/pcr/m/n/10 .m2dense(from, class = ".ge", uplo = "U", diag = "N", trans = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6057--6057 []\T1/pcr/m/n/10 .diag2sparse(from, kind = ".", shape = "t", repr = "C", uplo = "U")[] [2419] Overfull \hbox (18.78088pt too wide) in paragraph at lines 6059--6059 []\T1/pcr/m/n/10 .m2sparse(from, class = ".gC", uplo = "U", diag = "N", trans = FALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 6131--6133 []\T1/ptm/m/n/10 a string in []\T1/pcr/m/n/10 c("trace", "sumLog", "prod", "min ", "max", [2420] Underfull \hbox (badness 10000) in paragraph at lines 6206--6212 [][]\T1/pcr/m/n/10 .solve.dgC.*(a, b)[]\T1/ptm/b/n/10 : []\T1/pcr/m/n/10 .solv e.dgC.lu(a, b) []\T1/ptm/m/n/10 needs a square ma-trix []\T1/pcr/m/n/10 a[]\T1/ ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 6206--6212 []\T1/pcr/m/n/10 .solve.dgC.qr(a, b) []\T1/ptm/m/n/10 needs a ``long'' ma-trix []\T1/pcr/m/n/10 a[]\T1/ptm/m/n/10 , with []\T1/pcr/m/n/10 nrow(a) >= ncol(a)[] \T1/ptm/m/n/10 . [2421] Underfull \hbox (badness 10000) in paragraph at lines 6220--6229 [][]\T1/pcr/m/n/10 .updateCHMfactor(object, parent, mult)[]\T1/ptm/b/n/10 : [] \T1/pcr/m/n/10 .updateCHMfactor []\T1/ptm/m/n/10 up- Underfull \hbox (badness 10000) in paragraph at lines 6220--6229 \T1/ptm/m/n/10 dates []\T1/pcr/m/n/10 object []\T1/ptm/m/n/10 with the re-sult of Cholesky fac-tor-iz-ing []\T1/pcr/m/n/10 F(parent) + mult[1] * Underfull \hbox (badness 2443) in paragraph at lines 6220--6229 \T1/pcr/m/n/10 diag(nrow(parent))[]\T1/ptm/m/n/10 , i.e., []\T1/pcr/m/n/10 F(pa rent) []\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 mult[1] []\T1/ptm/m/n/10 times the iden-tity ma-trix, [2422] [2423] [2424] Underfull \hbox (badness 10000) in paragraph at lines 6486--6491 []\T1/ptm/m/n/10 Classes [][][]\T1/pcr/m/n/10 compMatrix[][][][]\T1/ptm/m/n/10 , and the non-general vir-tual classes: [][][]\T1/pcr/m/n/10 symmetricMatrix[][ ][][]\T1/ptm/m/n/10 , [2425] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.image}) h as been already used, duplicate ignored \relax l.6529 \aliasA{image}{image-methods}{image} [2426] [2427] Underfull \hbox (badness 4120) in paragraph at lines 6625--6628 []\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][ ][]\T1/pcr/m/n/10 dgTMatrix[][][] []\T1/ptm/m/n/10 class. Use Overfull \hbox (47.58038pt too wide) in paragraph at lines 6644--6644 []\T1/pcr/m/n/9 stopifnot(!is.null(leg <- imgC$legend), is.list(leg$right)) # failed for 2 days ..[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6664--6664 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col /row) indices:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 6670--6670 [] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, border.col=NA)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 6671--6671 [] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd =2, border.col=NA)[] Overfull \hbox (144.78027pt too wide) in paragraph at lines 6675--6675 []\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor der.col = adjustcolor("skyblue", 1/2))[] [2428] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6683--6683 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a nti-aliasing[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 6686--6686 [] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi ly zoom in and out[] [2429] Underfull \hbox (badness 10000) in paragraph at lines 6820--6823 []\T1/pcr/m/n/10 signature(x = "indMatrix", y = "Matrix") []\T1/ptm/m/n/10 and oth-ers listed by Underfull \hbox (badness 1286) in paragraph at lines 6820--6823 []\T1/pcr/m/n/10 showMethods("%*%", classes = "indMatrix")[]\T1/ptm/m/n/10 : ma -trix prod-ucts im-ple-mented Underfull \hbox (badness 10000) in paragraph at lines 6823--6826 []\T1/pcr/m/n/10 signature(from = "numeric", to = "indMatrix")[]\T1/ptm/m/n/10 : sup-port-ing typ-i-cal Underfull \hbox (badness 3375) in paragraph at lines 6826--6831 []\T1/pcr/m/n/10 signature(from = "list", to = "indMatrix")[]\T1/ptm/m/n/10 : s up-port-ing []\T1/pcr/m/n/10 indMatrix [2430] Underfull \hbox (badness 4156) in paragraph at lines 6837--6839 []\T1/pcr/m/n/10 signature(x = "indMatrix")[]\T1/ptm/m/n/10 : row and Underfull \hbox (badness 1337) in paragraph at lines 6843--6847 []\T1/pcr/m/n/10 signature(X = "indMatrix", Y = "indMatrix")[]\T1/ptm/m/n/10 : Kro-necker prod-uct of Underfull \hbox (badness 1776) in paragraph at lines 6853--6862 []\T1/ptm/m/n/10 Fabian Scheipl at `\T1/pcr/m/n/10 uni-muenchen.de\T1/ptm/m/n/1 0 ', build-ing on the ex-ist-ing class [][][]\T1/pcr/m/n/10 pMatrix[][][] []\T1 /ptm/m/n/10 af-ter Underfull \hbox (badness 1253) in paragraph at lines 6853--6862 \T1/ptm/m/n/10 a nice hike's con-ver-sa-tion with Mar-tin Maech-ler. Meth-ods f or [][][]\T1/pcr/m/n/10 crossprod[][][](x, y) []\T1/ptm/m/n/10 and [2431] Underfull \hbox (badness 1509) in paragraph at lines 6946--6948 []\T1/ptm/m/n/10 an in-te-ger off-set, in-di-cat-ing that the re-sult should be a per-mu-ta-tion of Underfull \hbox (badness 10000) in paragraph at lines 6973--6977 []\T1/pcr/m/n/10 invertPerm(p) []\T1/ptm/m/n/10 re-turns an in-te-ger vec-tor o f length []\T1/pcr/m/n/10 length(p) []\T1/ptm/m/n/10 such that Underfull \hbox (badness 4441) in paragraph at lines 6973--6977 []\T1/pcr/m/n/10 p[invertPerm(p)] []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 invertP erm(p)[p] []\T1/ptm/m/n/10 are both []\T1/pcr/m/n/10 seq_along(p)[]\T1/ptm/m/n/ 10 , i.e., the [2432] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7010--7010 []\T1/pcr/m/n/9 ## Product of transpositions (1 2)(2 1)(4 3)(6 8)(10 1) = (3 4 )(6 8)(1 10)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.anyNA}) h as been already used, duplicate ignored \relax l.7024 \aliasA{anyNA}{is.na-methods}{anyNA} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.finite }) has been already used, duplicate ignored \relax l.7031 ...asA{is.finite}{is.na-methods}{is.finite} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.infini te}) has been already used, duplicate ignored \relax l.7039 ...is.infinite}{is.na-methods}{is.infinite} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.na}) h as been already used, duplicate ignored \relax l.7047 \aliasA{is.na}{is.na-methods}{is.na} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.nan}) has been already used, duplicate ignored \relax l.7054 \aliasA{is.nan}{is.na-methods}{is.nan} [2433] [2434] [2435] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.isSymmetr ic}) has been already used, duplicate ignored \relax l.7213 ...etric}{isSymmetric-methods}{isSymmetric} Overfull \hbox (138.78088pt too wide) in paragraph at lines 7260--7260 []\T1/pcr/m/n/10 isSymmetric(object, checkDN = TRUE, tol = 100 * .Machine$doub le.eps, tol1 = 8 * tol, ...)[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 7262--7262 []\T1/pcr/m/n/10 isSymmetric(object, checkDN = TRUE, tol = 100 * .Machine$doub le.eps, ...)[] [2436] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7317--7317 []\T1/pcr/m/n/9 isSymmetric(as(M, "generalMatrix")) # still symmetric, even if not "formally"[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7321--7321 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs = TRUE) # includes S3 g eneric from base[] [2437] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7404--7404 []\T1/pcr/m/n/9 isTriangular(as(M, "generalMatrix")) # still triangular, even if not "formally"[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 7431--7431 []\T1/pcr/m/n/10 KhatriRao(X, Y = X, FUN = "*", sparseY = TRUE, make.dimnames = FALSE) [2438] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7507--7507 []\T1/pcr/m/n/9 stopifnot(all(K1 <- KhatriRao(nd, zm) == 0), identical(dim(K1) , c(12L, 4L)),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7508--7508 [] \T1/pcr/m/n/9 all(K2 <- KhatriRao(zm, nd) == 0), identical(dim(K2) , c(12L, 4L)))[] [2439] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7515--7515 [] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di mnames(Kmd)))[] [2440] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.kronecker }) has been already used, duplicate ignored \relax l.7589 ...kronecker}{kronecker-methods}{kronecker} Underfull \hbox (badness 1062) in paragraph at lines 7686--7689 []\T1/pcr/m/n/10 ldenseMatrix []\T1/ptm/m/n/10 is the vir-tual class of all den se \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both [2441] Underfull \hbox (badness 6063) in paragraph at lines 7712--7715 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-call y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2442 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.*,ndiMatr ix,Matrix.Rdash.method}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.7826 C lass \code{"\LinkA{sparseMatrix}{sparseMatrix.Rdash.class}"}, by cla... ] Underfull \hbox (badness 2635) in paragraph at lines 7873--7878 []\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ldenseMatrix"[]\T1/ptm/m/n/10 , di-rec tly. Class []\T1/pcr/m/n/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/ 10 "ldenseMatrix"[]\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 7873--7878 \T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "denseMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/10 "ldenseMatrix"[]\T1/ptm/m/n/10 . Class []\T1/pcr/m/n/10 "Matri x"[]\T1/ptm/m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 7881--7884 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ); use, e.g., [2443] Underfull \hbox (badness 10000) in paragraph at lines 7938--7948 []\T1/pcr/m/n/10 lsTMatrix[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 ltTMatrix[]\T 1/ptm/m/n/10 ) or in com-pressed column-oriented form (class Underfull \hbox (badness 1242) in paragraph at lines 7938--7948 [][][]\T1/pcr/m/n/10 CsparseMatrix[][][][]\T1/ptm/m/n/10 , sub-classes []\T1/pc r/m/n/10 lgCMatrix[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lsCMatrix[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 ltCMatrix[]\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\ T1/ptm/m/n/10 --in [2444] Underfull \hbox (badness 3179) in paragraph at lines 8020--8023 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cal ly equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2445] Underfull \hbox (badness 10000) in paragraph at lines 8105--8108 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ; use, e.g., [2446] Underfull \hbox (badness 10000) in paragraph at lines 8166--8169 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ; use, e.g., [2447] [2448] [2449] Underfull \hbox (badness 10000) in paragraph at lines 8404--8407 []\T1/ptm/m/n/10 vector of all non-zero en-tries of []\T1/pcr/m/n/10 x[]\T1/ptm /m/n/10 ; ex-ists \T1/ptm/b/n/10 only \T1/ptm/m/n/10 when []\T1/pcr/m/n/10 as(x , Underfull \hbox (badness 1490) in paragraph at lines 8426--8428 []\T1/pcr/m/n/10 mat2triplet() []\T1/ptm/m/n/10 is con-cep-tu-ally the \T1/ptm/ m/it/10 in-verse \T1/ptm/m/n/10 func-tion of [][][]\T1/pcr/m/n/10 spMatrix[][][ ] []\T1/ptm/m/n/10 and (one case of) [2450] pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rpcent.* .Rpcent.}) has been already used, duplicate ignored \relax l.8447 ...*\%}{matmult-methods}{.Rpcent.*.Rpcent.} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.crossprod }) has been already used, duplicate ignored \relax l.8521 ...A{crossprod}{matmult-methods}{crossprod} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tcrosspro d}) has been already used, duplicate ignored \relax l.8597 ...tcrossprod}{matmult-methods}{tcrossprod} Underfull \hbox (badness 1881) in paragraph at lines 8683--8689 \T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][][]\T1/ pcr/m/n/10 t[][][](.)[]\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn [2451] Underfull \hbox (badness 10000) in paragraph at lines 8752--8755 []\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")[]\T1/ptm/m/n/10 : Ma-trix mul-ti-pli-ca-tion; Underfull \hbox (badness 10000) in paragraph at lines 8755--8760 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and other sig-na-tures (use Underfull \hbox (badness 3557) in paragraph at lines 8755--8760 []\T1/pcr/m/n/10 showMethods("%*%", class="dtrMatrix")[]\T1/ptm/m/n/10 ): ma-tr ix mul-ti-pli-ca-tion. Mul-ti- Underfull \hbox (badness 6608) in paragraph at lines 8760--8764 \T1/ptm/m/n/10 sig-na-tures, use []\T1/pcr/m/n/10 showMethods("crossprod", clas s = "dgeMatrix")[]\T1/ptm/m/n/10 , ma-trix Underfull \hbox (badness 1552) in paragraph at lines 8770--8771 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and other sig-na- [2452] [2453] [2454] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det}) has been already used, duplicate ignored \relax l.8995 \aliasA{det}{Matrix-class}{det} Underfull \hbox (badness 1337) in paragraph at lines 9069--9072 []\T1/pcr/m/n/10 signature(x = "Matrix", value = "list")[]\T1/ptm/m/n/10 : set the []\T1/pcr/m/n/10 dimnames []\T1/ptm/m/n/10 to a Underfull \hbox (badness 10000) in paragraph at lines 9082--9085 [2455] Underfull \hbox (badness 10000) in paragraph at lines 9091--9093 []\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")[]\T1/ptm/m/n/10 : This re-lies on a cor-rect [2456] [2457] Underfull \hbox (badness 10000) in paragraph at lines 9260--9264 []\T1/pcr/m/n/10 CholeskyFactorization[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Bunch KaufmanFactorization[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 9283--9285 []\T1/pcr/m/n/10 signature(x = "MatrixFactorization", logarithm = Underfull \hbox (badness 10000) in paragraph at lines 9300--9303 []\T1/pcr/m/n/10 signature(obj = "MatrixFactorization")[]\T1/ptm/m/n/10 : re-tu rns []\T1/pcr/m/n/10 obj []\T1/ptm/m/n/10 with [2458] Underfull \hbox (badness 3019) in paragraph at lines 9312--9315 []\T1/ptm/m/n/10 Classes ex-tend-ing []\T1/pcr/m/n/10 CholeskyFactorization[]\T 1/ptm/m/n/10 , namely [][][]\T1/pcr/m/n/10 Cholesky[][][][]\T1/ptm/m/n/10 , [][ ][]\T1/pcr/m/n/10 pCholesky[][][][]\T1/ptm/m/n/10 , and Underfull \hbox (badness 10000) in paragraph at lines 9316--9318 []\T1/ptm/m/n/10 Classes ex-tend-ing []\T1/pcr/m/n/10 BunchKaufmanFactorization []\T1/ptm/m/n/10 , namely [][][]\T1/pcr/m/n/10 BunchKaufman[][][] []\T1/ptm/m/n /10 and Underfull \hbox (badness 10000) in paragraph at lines 9331--9334 []\T1/ptm/m/n/10 Generic func-tions [][][]\T1/pcr/m/n/10 expand1[][][] []\T1/pt m/m/n/10 and [][][]\T1/pcr/m/n/10 expand2[][][] []\T1/ptm/m/n/10 for con-struct -ing ma-trix fac-tors from Underfull \hbox (badness 1062) in paragraph at lines 9360--9363 []\T1/pcr/m/n/10 ndenseMatrix []\T1/ptm/m/n/10 is the vir-tual class of all den se \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both Underfull \hbox (badness 6063) in paragraph at lines 9392--9395 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-call y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2459] Underfull \hbox (badness 3312) in paragraph at lines 9449--9451 []\T1/ptm/m/n/10 logical in-di-cat-ing if []\T1/pcr/m/n/10 X <- (X + t(X))/2 [] \T1/ptm/m/n/10 should be done, af-ter []\T1/pcr/m/n/10 X <- [2460] [2461] Overfull \hbox (85.38034pt too wide) in paragraph at lines 9552--9552 [] \T1/pcr/m/n/9 all.equal(n.A.m, unname(as.matrix(n.A$mat)), tolerance = 1e -15)# seen rel.d.= 1.46e-16[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 9592--9592 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a ll in this example[] [2462] Underfull \hbox (badness 2635) in paragraph at lines 9645--9650 []\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ndenseMatrix"[]\T1/ptm/m/n/10 , di-rec tly. Class []\T1/pcr/m/n/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/ 10 "ndenseMatrix"[]\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 9645--9650 \T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "denseMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/10 "ndenseMatrix"[]\T1/ptm/m/n/10 . Class []\T1/pcr/m/n/10 "Matri x"[]\T1/ptm/m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 9653--9656 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ); use, e.g., [2463] Underfull \hbox (badness 2521) in paragraph at lines 9721--9727 []\T1/pcr/m/n/10 signature(from = "matrix", to = "nMatrix")[]\T1/ptm/m/n/10 : N ote that these co-er-cions [2464] Underfull \hbox (badness 1867) in paragraph at lines 9834--9836 []\T1/ptm/m/n/10 fast sim- [2465] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.norm}) ha s been already used, duplicate ignored \relax l.9876 \aliasA{norm}{norm-methods}{norm} [2466] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9971--9971 []\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9972--9972 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9973--9973 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Underfull \hbox (badness 2401) in paragraph at lines 10018--10028 []\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][][]\T1/pcr/m/n /10 TsparseMatrix[][][][]\T1/ptm/m/n/10 , sub-classes []\T1/pcr/m/n/10 ngTMatri x[]\T1/ptm/m/n/10 , [2467] Underfull \hbox (badness 3179) in paragraph at lines 10089--10092 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cal ly equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2468] Underfull \hbox (badness 10000) in paragraph at lines 10169--10172 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ; use, e.g., [2469] Underfull \hbox (badness 10000) in paragraph at lines 10233--10236 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ; use, e.g., [2470] [2471] Underfull \hbox (badness 10000) in paragraph at lines 10330--10332 []\T1/ptm/m/n/10 typically a []\T1/pcr/m/n/10 "packedMatrix"[]\T1/ptm/m/n/10 , though [2472] [2473] Underfull \hbox (badness 10000) in paragraph at lines 10547--10550 []\T1/pcr/m/n/10 signature(x = "pMatrix", y = "Matrix") []\T1/ptm/m/n/10 and ot h-ers listed by Underfull \hbox (badness 8189) in paragraph at lines 10547--10550 []\T1/pcr/m/n/10 showMethods("%*%", classes = "pMatrix")[]\T1/ptm/m/n/10 : ma-t rix prod-ucts im-ple-mented [2474] Underfull \hbox (badness 10000) in paragraph at lines 10550--10554 []\T1/pcr/m/n/10 signature(from = "numeric", to = "pMatrix")[]\T1/ptm/m/n/10 : sup-port-ing typ-i-cal Underfull \hbox (badness 2460) in paragraph at lines 10558--10564 []\T1/pcr/m/n/10 signature(a = "pMatrix", b = "missing")[]\T1/ptm/m/n/10 : the in-verse per-mu-ta-tion ma-trix, [2475] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10628--10628 [] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD iag = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10631--10631 []\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m ax.print")),[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10633--10633 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 10637--10637 []\T1/pcr/m/n/10 printSpMatrix2(x, digits = NULL, maxp = max(100L, getOption(" max.print")),[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10638--10638 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Underfull \hbox (badness 3989) in paragraph at lines 10663--10673 []\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of [] \T1/pcr/m/n/10 x []\T1/ptm/m/n/10 should Underfull \hbox (badness 10000) in paragraph at lines 10663--10673 \T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro m [2476] [2477] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr}) has been already used, duplicate ignored \relax l.10764 \aliasA{qr}{qr-methods}{qr} [2478] [2479] Overfull \hbox (25.98041pt too wide) in paragraph at lines 10896--10896 [] \T1/pcr/m/n/9 all.equal(qr.coef(qr.A1, b), drop(solve(crossprod(A1), cro ssprod(A1, b))))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10912--10912 [] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 qr.coef\TS1/pcr/m/n/9 ' \ T1/pcr/m/n/9 computes unique least squares solution of "nearby" problem[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10913--10913 [] \T1/pcr/m/n/9 ## Z x = b for some full rank Z ~ A, currently without war ning {FIXME} ![] Underfull \vbox (badness 10000) has occurred while \output is active [2480] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10956--10956 []\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m atrix"), ...)[] [2481] Underfull \hbox (badness 2005) in paragraph at lines 11008--11014 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of [][][]\T1/pcr/m/n/10 qr[][][](x, tol, Underfull \hbox (badness 10000) in paragraph at lines 11025--11028 []\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense []\T1/pcr/m/n/10 x[]\ T1/ptm/m/n/10 , it cor-re-sponds to [2482] Overfull \hbox (85.38034pt too wide) in paragraph at lines 11124--11124 []\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/ n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale free"[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 11140--11140 []\T1/pcr/m/n/9 sapply(meths, function(.m.) rankMatrix(M15, method = .m., tol = 1e-7)) # all 14[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 11147--11147 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # war ning+ ~1.5 sec (2013)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 11148--11148 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con siderably faster![] [2483] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h as been already used, duplicate ignored \relax l.11167 \aliasA{rcond}{rcond-methods}{rcond} [2484] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11283--11283 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not have full rank[] [2485] [2486] [2487] Underfull \hbox (badness 2150) in paragraph at lines 11476--11484 \T1/ptm/m/n/10 dices, if not []\T1/pcr/m/n/10 symmetric [][]sample.int[][][](nr ow*ncol, nnz)[]\T1/ptm/m/n/10 , then---if []\T1/pcr/m/n/10 rand.x []\T1/ptm/m/n /10 is not [2488] [2489] Underfull \hbox (badness 5147) in paragraph at lines 11633--11636 []\T1/ptm/m/n/10 Class [][][]\T1/pcr/m/n/10 SchurFactorization[][][][]\T1/ptm/m /n/10 , di-rectly. Class [][][]\T1/pcr/m/n/10 MatrixFactorization[][][][]\T1/pt m/m/n/10 , by class [2490] Underfull \hbox (badness 3179) in paragraph at lines 11648--11651 []\T1/pcr/m/n/10 signature(from = "Schur", logarithm = "logical")[]\T1/ptm/m/n/ 10 : com-putes [2491] [2492] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11813--11813 [] \T1/pcr/m/n/9 all.equal(e1, e3[order(Mod(e3), decreasing = TRUE)], toler ance = 1e-13)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solve}) h as been already used, duplicate ignored \relax l.11823 \aliasA{solve}{solve-methods}{solve} [2493] Overfull \hbox (90.78088pt too wide) in paragraph at lines 11947--11947 []\T1/pcr/m/n/10 solve(a, b, system = c("A", "LDLt", "LD", "DLt", "L", "Lt", " D", "P", "Pt"), ...)[] Underfull \hbox (badness 1147) in paragraph at lines 11959--11965 []\T1/ptm/m/n/10 a vec-tor, [][][]\T1/pcr/m/n/10 sparseVector[][][][]\T1/ptm/m/ n/10 , ma-trix, or [][][]\T1/pcr/m/n/10 Matrix[][][] []\T1/ptm/m/n/10 sat-is-fy -ing []\T1/pcr/m/n/10 NROW(b) == Underfull \hbox (badness 3460) in paragraph at lines 12009--12014 []\T1/ptm/m/n/10 Methods for dense []\T1/pcr/m/n/10 a []\T1/ptm/m/n/10 are buil t on 14 LA-PACK rou-tines: class []\T1/pcr/m/n/10 d..Matrix[]\T1/ptm/m/n/10 , w here [2494] Overfull \hbox (52.98038pt too wide) in paragraph at lines 12082--12082 []\T1/pcr/m/n/9 image(ia0 <- solve(a, tol = 0)) # checker board, dense [but re ally, a is singular!][] Overfull \hbox (25.98041pt too wide) in paragraph at lines 12086--12086 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] [2495] Underfull \hbox (badness 10000) in paragraph at lines 12109--12112 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, from a for-mu la and data frame Overfull \hbox (6.78088pt too wide) in paragraph at lines 12126--12126 [] \T1/pcr/m/n/10 drop.unused.levels = TRUE, repr = c("C", "R", "T"), giveCs parse)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 12128--12128 [] \T1/pcr/m/n/10 drop.unused.levels = TRUE, repr = c("C", "R", "T"), giveCs parse,[] Underfull \hbox (badness 1648) in paragraph at lines 12137--12139 []\T1/ptm/m/n/10 a data frame cre-ated with [][][]\T1/pcr/m/n/10 model.frame[][ ][][]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 10000) in paragraph at lines 12145--12148 []\T1/ptm/m/n/10 character string or []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or (co-er-ca-ble to) Underfull \hbox (badness 2591) in paragraph at lines 12145--12148 []\T1/pcr/m/n/10 "[][]sparseMatrix[][][]"[]\T1/ptm/m/n/10 , spec-i-fy-ing the c on-trasts to be ap-plied to the Underfull \hbox (badness 10000) in paragraph at lines 12156--12160 []\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for Underfull \hbox (badness 2828) in paragraph at lines 12156--12160 []\T1/pcr/m/n/10 sparse.model.matrix []\T1/ptm/m/n/10 has been changed to []\T1 /pcr/m/n/10 FALSE[]\T1/ptm/m/n/10 , 2010-07, for [2496] Underfull \hbox (badness 1668) in paragraph at lines 12171--12176 [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/ m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse Underfull \hbox (badness 3291) in paragraph at lines 12198--12203 []\T1/pcr/m/n/10 model.Matrix(sparse = TRUE) []\T1/ptm/m/n/10 from pack-age [][ ]\T1/ptm/b/n/10 Ma-trix-Mod-els[][] \T1/ptm/m/n/10 may be nowa-days be Underfull \hbox (badness 2073) in paragraph at lines 12198--12203 \T1/ptm/m/n/10 prefer-able to []\T1/pcr/m/n/10 sparse.model.matrix[]\T1/ptm/m/n /10 , as []\T1/pcr/m/n/10 model.Matrix []\T1/ptm/m/n/10 re-turns an ob-ject of class [2497] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12252--12252 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M) == c(0, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12253--12253 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M) == c(3, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12254--12254 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2498] Underfull \hbox (badness 2961) in paragraph at lines 12316--12319 []\T1/pcr/m/n/10 signature(from = "sparseLU", logarithm = "logical")[]\T1/ptm/m /n/10 : com- Overfull \hbox (9.78043pt too wide) in paragraph at lines 12359--12359 []\T1/pcr/m/n/9 A <- as(readMM(system.file("external", "pores_1.mtx", package = "Matrix")),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12370--12370 []\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m atrix"), ...)[] [2499] Overfull \hbox (20.58041pt too wide) in paragraph at lines 12377--12377 [] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(dn[1L ], list(NULL)),[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 12380--12380 [] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(list( NULL), dn[2L]),[] Underfull \hbox (badness 10000) in paragraph at lines 12405--12407 []\T1/ptm/m/n/10 This in-ter-face is rec-om-mended over di-rect con-struc-tion via calls such as Overfull \hbox (0.78088pt too wide) in paragraph at lines 12412--12412 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] [2500] Underfull \hbox (badness 2261) in paragraph at lines 12450--12456 \T1/ptm/m/n/10 of the sparse ma-trix re-sult, i.e., spec-i-fy-ing one of the vi r-tual classes [2501] Underfull \hbox (badness 10000) in paragraph at lines 12539--12542 []\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][][]\T1/pcr/m/n/10 xtabs[][][ ](*, sparse=TRUE)[]\T1/ptm/m/n/10 , for sparse ta-bles and Overfull \hbox (4.38043pt too wide) in paragraph at lines 12552--12552 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12556--12556 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12557--12557 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12562--12562 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims = c(10,20)))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12565--12565 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar e consistent[] [2502] Overfull \hbox (15.18042pt too wide) in paragraph at lines 12588--12588 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 12589--12589 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12615--12615 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep resentations.[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 12618--12618 [] \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack age = "SparseM"))) {[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12620--12620 [] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims = X@dimension)[] [2503] Underfull \hbox (badness 6842) in paragraph at lines 12710--12713 []\T1/pcr/m/n/10 (x = "sparseMatrix", logarithm=TRUE)[]\T1/ptm/m/n/10 : [][][]\ T1/pcr/m/n/10 determinant[][][]() []\T1/ptm/m/n/10 meth-ods Underfull \hbox (badness 10000) in paragraph at lines 12745--12749 [][][]\T1/pcr/m/n/10 sparseMatrix[][][][]\T1/ptm/m/n/10 , and its ref-er-ences, such as [][][]\T1/pcr/m/n/10 xtabs[][][](*, sparse=TRUE)[]\T1/ptm/m/n/10 , or [2504] [2505] Underfull \hbox (badness 2961) in paragraph at lines 12929--12932 []\T1/pcr/m/n/10 signature(from = "sparseQR", logarithm = "logical")[]\T1/ptm/m /n/10 : com- [2506] Underfull \hbox (badness 3229) in paragraph at lines 13007--13011 []\T1/ptm/m/n/10 The many aux-il-iary func-tions for QR fac-tor-iza-tions: [][] []\T1/pcr/m/n/10 qr.Q[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 qr.R[][][][] \T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 qr.X[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc r/m/n/10 qr.coef[][][][]\T1/ptm/m/n/10 , [2507] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13047--13047 []\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m atrix"), ...)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 13055--13055 [] \T1/pcr/m/n/9 new("pMatrix", Dim = c(m, m), Dimnames = c(dn[1L ], list(NULL)),[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 13058--13058 [] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(list( NULL), dn[2L]),[] Underfull \vbox (badness 10000) has occurred while \output is active [2508] Overfull \hbox (42.18039pt too wide) in paragraph at lines 13077--13077 [] \T1/pcr/m/n/9 ae2(qrc <- qr.coef (qr.A, b), with(e.qr.A, solve(R1 %*% P 2., t(qrQ)) %*% b))[] Underfull \hbox (badness 5036) in paragraph at lines 13112--13114 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a [2509] Underfull \hbox (badness 2970) in paragraph at lines 13232--13238 []\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class []\T1/pcr/m/ n/10 "sparseVector" []\T1/ptm/m/n/10 has the five ac- Underfull \hbox (badness 3679) in paragraph at lines 13232--13238 \T1/ptm/m/n/10 tual daugh-ter classes []\T1/pcr/m/n/10 "dsparseVector"[]\T1/ptm /m/n/10 , []\T1/pcr/m/n/10 "isparseVector"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 " lsparseVector"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13277--13280 []\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") []\T1/ptm/m/ n/10 co-erces sparse [2510] Underfull \hbox (badness 10000) in paragraph at lines 13317--13322 []\T1/pcr/m/n/10 (x = "nsparseVector")[]\T1/ptm/m/n/10 : re-turn [][][]\T1/pcr/ m/n/10 logical[][][] []\T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 13332--13334 [][][]\T1/pcr/m/n/10 sparseVector[][][]() []\T1/ptm/m/n/10 for friendly con-str uc-tion of sparse vec-tors (apart from []\T1/pcr/m/n/10 as(*, [2511] Underfull \vbox (badness 10000) has occurred while \output is active [2512] Overfull \hbox (24.78088pt too wide) in paragraph at lines 13432--13432 []\T1/pcr/m/n/10 spMatrix(nrow, ncol, i = integer(0L), j = integer(0L), x = do uble(0L)) Underfull \hbox (badness 2310) in paragraph at lines 13459--13465 [][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) []\T1/ptm/m/n/10 for the more usual con-struc-tor of such ma-tri-ces. Then, [2513] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.[<.Rdash. }) has been already used, duplicate ignored \relax l.13511 ...\Rdash{}}{Subassign-methods}{[<.Rdash.} Underfull \hbox (badness 6910) in paragraph at lines 13598--13600 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2514] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.[}) has b een already used, duplicate ignored \relax l.13647 \aliasA{[}{Subscript-methods}{[} [2515] [2516] Underfull \hbox (badness 2591) in paragraph at lines 13780--13785 \T1/ptm/m/n/10 Classes [][][]\T1/pcr/m/n/10 triangularMatrix[][][][]\T1/ptm/m/n /10 , and, e.g., [][][]\T1/pcr/m/n/10 dsyMatrix[][][] []\T1/ptm/m/n/10 for nu-m eric \T1/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or [2517] Underfull \hbox (badness 2057) in paragraph at lines 13856--13858 []\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe r-ent ma-trix classes, use e.g., Underfull \hbox (badness 6396) in paragraph at lines 13865--13869 []\T1/pcr/m/n/10 symmpart(x) []\T1/ptm/m/n/10 re-turns a sym-met-ric ma-trix, i n-her-it-ing from [][][]\T1/pcr/m/n/10 symmetricMatrix[][][] []\T1/ptm/m/n/10 o r Underfull \hbox (badness 7722) in paragraph at lines 13870--13875 []\T1/pcr/m/n/10 skewpart(x) []\T1/ptm/m/n/10 re-turns a skew-symmetric ma-trix , in-her-it-ing from [][][]\T1/pcr/m/n/10 generalMatrix[][][][]\T1/ptm/m/n/10 , [2518] Underfull \hbox (badness 6641) in paragraph at lines 13947--13950 []\T1/ptm/m/n/10 Currently, [][][]\T1/pcr/m/n/10 Schur[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 isSymmetric[][][] []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 as () []\T1/ptm/m/n/10 (i.e. [][][]\T1/pcr/m/n/10 coerce[][][][]\T1/ptm/m/n/10 ) h ave meth-ods with [2519] Underfull \hbox (badness 5133) in paragraph at lines 13983--13987 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 "TsparseMatrix" []\T1/ptm/m/n/10 class is the vir-tual class of all sparse ma-tri-ces coded in Underfull \hbox (badness 2818) in paragraph at lines 13983--13987 \T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c re-ated from it. See [2520] Underfull \hbox (badness 1668) in paragraph at lines 14113--14116 [][][]\T1/pcr/m/n/10 pack[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 unpac k[][][][]\T1/ptm/m/n/10 ; its vir-tual "com-ple-ment" []\T1/pcr/m/n/10 "[][]pac kedMatrix[][][]"[]\T1/ptm/m/n/10 ; its proper sub-classes [2521] [2522] Underfull \hbox (badness 10000) in paragraph at lines 14224--14230 []\T1/ptm/m/n/10 GAL lat-tice file `\T1/pcr/m/n/10 usc_q.GAL\T1/ptm/m/n/10 ' (r e-trieved in 2008 from [2523] [2524] [2525]) (./boot-pkg.tex [2526] Chapter 18. [2527] [2528] [2529] [2530] [2531] [2532] [2533] Overfull \hbox (12.78088pt too wide) in paragraph at lines 532--532 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f" , "w"), [2534] Underfull \hbox (badness 1325) in paragraph at lines 570--577 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r e-quired. Pos-si-ble Underfull \hbox (badness 1275) in paragraph at lines 585--590 []\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m ulti-sample prob- [2535] [2536] [2537] Underfull \hbox (badness 1881) in paragraph at lines 826--828 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 6493) in paragraph at lines 853--857 [][][]\T1/pcr/m/n/10 boot.array[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 bo ot.ci[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 censboot[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 empinf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 j ack.after.boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 tilt.boot[][][][]\T 1/ptm/m/n/10 , [2538] Overfull \hbox (4.38043pt too wide) in paragraph at lines 887--887 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, data = nuke)[] Underfull \vbox (badness 10000) has occurred while \output is active [2539] [2540] [2541] Underfull \hbox (badness 1496) in paragraph at lines 1084--1093 []\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari- ance of the Underfull \hbox (badness 2005) in paragraph at lines 1084--1093 \T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i n-ter-vals. If it Underfull \hbox (badness 2343) in paragraph at lines 1084--1093 \T1/ptm/m/n/10 is not sup-plied and []\T1/pcr/m/n/10 length(index) []\T1/ptm/m/ n/10 is 2 then []\T1/pcr/m/n/10 var.t0 []\T1/ptm/m/n/10 de-faults to Underfull \hbox (badness 2150) in paragraph at lines 1105--1111 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa ult value is [2542] [2543] [2544] [2545] Underfull \hbox (badness 1571) in paragraph at lines 1445--1447 []\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis- [2546] [2547] [2548] [2549] [2550] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1738--1738 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix( 1,n,2), [2551] [2552] [2553] Underfull \vbox (badness 10000) has occurred while \output is active [2554] Overfull \hbox (31.3804pt too wide) in paragraph at lines 2013--2013 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4) + strata(ulcer),[] [2555] Underfull \hbox (badness 6268) in paragraph at lines 2084--2086 []\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch an-ning House. [2556] [2557] [2558] Underfull \hbox (badness 1565) in paragraph at lines 2338--2343 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori g-i-nal data set [2559] Underfull \hbox (badness 4595) in paragraph at lines 2363--2368 \T1/ptm/m/n/10 are passed un-changed ev-ery time []\T1/pcr/m/n/10 boot.out$stat istic []\T1/ptm/m/n/10 is called. Underfull \hbox (badness 1881) in paragraph at lines 2432--2434 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 2057) in paragraph at lines 2440--2441 [][][]\T1/pcr/m/n/10 boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 empinf[] [][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 k3.linear[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 linear.approx[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 saddle.distn[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 smooth.spline[][][][] \T1/ptm/m/n/10 , [2560] [2561] Underfull \hbox (badness 1077) in paragraph at lines 2536--2540 []\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of []\T1/pcr/m /n/10 n/((n-1)*(n-2)) []\T1/ptm/m/n/10 where []\T1/pcr/m/n/10 n []\T1/ptm/m/n/1 0 is the sam-ple Underfull \hbox (badness 1112) in paragraph at lines 2536--2540 \T1/ptm/m/n/10 size, if []\T1/pcr/m/n/10 unbiased []\T1/ptm/m/n/10 is []\T1/pcr /m/n/10 FALSE []\T1/ptm/m/n/10 then a mul-ti-plier of []\T1/pcr/m/n/10 1/n []\T 1/ptm/m/n/10 is used. This is mul-ti-plied by [2562] [2563] [2564] [2565] [2566] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2895--2895 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25, Overfull \hbox (18.78088pt too wide) in paragraph at lines 2897--2897 []\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25,[] [2567] [2568] [2569] Underfull \hbox (badness 3861) in paragraph at lines 3105--3108 [][][]\T1/pcr/m/n/10 boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 boot.arr ay[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 boot.ci[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 control[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 jack .after.boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 linear.approx[][][][]\ T1/ptm/m/n/10 , [2570] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3158--3158 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1 :ncol(mat)) [2571] [2572] [2573] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3378--3378 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling [2574] [2575] [2576] [2577] [2578] [2579] [2580] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3838--3838 [] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q = NULL)[] [2581] [2582] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3977--3977 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 = grav.z0[3])[] [2583] [2584] [2585] [2586] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4259--4259 []\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz e data as in [2587] [2588] Underfull \hbox (badness 10000) in paragraph at lines 4362--4364 []\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o f Underfull \hbox (badness 1430) in paragraph at lines 4371--4375 \T1/ptm/m/n/10 If []\T1/pcr/m/n/10 t0 []\T1/ptm/m/n/10 is sup-plied but nei-the r []\T1/pcr/m/n/10 t []\T1/ptm/m/n/10 nor []\T1/pcr/m/n/10 L []\T1/ptm/m/n/10 a re sup-plied then []\T1/pcr/m/n/10 t0 []\T1/ptm/m/n/10 is set to [2589] [2590] [2591] [2592] [2593] [2594] [2595] [2596] [2597] Underfull \hbox (badness 3000) in paragraph at lines 4959--4962 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2598] [2599] [2600] [2601] Underfull \hbox (badness 2293) in paragraph at lines 5238--5241 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5238--5241 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2602] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5317--5317 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat a = grav1[, 2])[] [2603] [2604] [2605] [2606] [2607] [2608] [2609] [2610] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5866--5866 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c ity.sp1$spa[1][] [2611] Underfull \hbox (badness 1127) in paragraph at lines 5988--6006 []\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less than []\T1/pcr/m/n/10 min(alpha)/10[]\T1/ptm/m/n/10 , then [2612] Underfull \hbox (badness 2837) in paragraph at lines 6021--6024 []\T1/ptm/m/n/10 The re-turned value is an ob-ject of class []\T1/pcr/m/n/10 "s addle.distn"[]\T1/ptm/m/n/10 . See the help file for [2613] [2614] [2615] [2616] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6306--6306 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and Wright (1991). [2617] [2618] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6495--6495 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling Overfull \hbox (20.58041pt too wide) in paragraph at lines 6497--6497 []\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t ilting was used[] [2619] [2620] [2621] Underfull \hbox (badness 1596) in paragraph at lines 6742--6746 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m ent ex-pected by [2622] [2623] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6902--6902 [] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha = c(0.05, 0.95),[] [2624] [2625] [2626] [2627] [2628] [2629] [2630] [2631]) (./class-pkg.tex [2632] Chapter 19. [2633] [2634] [2635] [2636] [2637] [2638] [2639] [2640] [2641] [2642] [2643] [2644] [2645] [2646] Overfull \hbox (42.18039pt too wide) in paragraph at lines 1006--1006 [] \T1/pcr/m/n/9 alpha = list(seq(0.05, 0, length.out = 1e4), seq(0.02, 0, length.out = 1e5)),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1007--1007 [] \T1/pcr/m/n/9 radii = list(seq(8, 1, length.out = 1e4), seq(4, 1, length .out = 1e5)))[] [2647] [2648]) (./cluster-pkg.tex Chapter 20. [2649] [2650] [2651] Overfull \hbox (42.18039pt too wide) in paragraph at lines 253--253 [] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met hod = 0.5)[iC]) ,[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 254--254 [] \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, -.5))[iC]),[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 255--255 [] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, +.5))[iC]))[] [2652] [2653] [2654] [2655] Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519 [] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot = axes,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 523--523 [] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5, ...)[] [2656] [2657] Overfull \hbox (66.78088pt too wide) in paragraph at lines 638--638 [] \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c orrect.d = TRUE)[] [2658] Underfull \hbox (badness 3078) in paragraph at lines 692--695 []\T1/ptm/m/n/10 Setting this to []\T1/pcr/m/n/10 FALSE []\T1/ptm/m/n/10 saves mem-ory (and hence time), but dis-ables [2659] [2660] Underfull \hbox (badness 2941) in paragraph at lines 795--798 [][][]\T1/pcr/m/n/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-en ces; [][][]\T1/pcr/m/n/10 clara.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 pam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 partition.object[][][][]\ T1/ptm/m/n/10 , [2661] Overfull \hbox (9.78043pt too wide) in paragraph at lines 838--838 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo r this seed):[] Underfull \hbox (badness 10000) in paragraph at lines 885--887 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2662] Overfull \hbox (24.78088pt too wide) in paragraph at lines 950--950 [] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code =3), ...)[] [2663] Underfull \hbox (badness 4872) in paragraph at lines 996--998 []\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is Underfull \hbox (badness 1342) in paragraph at lines 1010--1014 []\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in 2012, [2664] Underfull \hbox (badness 10000) in paragraph at lines 1102--1104 [][][]$\T1/pcr/m/n/10 https : / / bioconductor . org / packages / 3 . 12 / bioc / html / SAGx . html$[][] \T1/ptm/m/n/10 Dep-re- [2665] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1126--1126 [] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE. factor = SEf)))[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 1143--1143 []\T1/pcr/m/n/9 ## You can manually set it before running this : doExtras < - TRUE # or FALSE[] Underfull \vbox (badness 10000) has occurred while \output is active [2666] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1181--1181 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap() ==> k = 1 clust er is optimal")[] Underfull \hbox (badness 4144) in paragraph at lines 1213--1217 []\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 does not have a []\T1 /pcr/m/n/10 diss []\T1/ptm/m/n/10 nor a []\T1/pcr/m/n/10 data []\T1/ptm/m/n/10 com-po-nent, e.g., for [2667] Overfull \hbox (60.78088pt too wide) in paragraph at lines 1289--1289 [] \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1, cex.txt = cex,[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1295--1295 [] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin t variability."),[] [2668] [2669] [2670] Underfull \hbox (badness 10000) in paragraph at lines 1482--1485 Underfull \hbox (badness 10000) in paragraph at lines 1499--1503 [][][]\T1/pcr/m/n/10 princomp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cmds cale[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pam[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 clara[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 daisy[][ ][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 par[][][][]\T1/ptm/m/n/10 , [][][]\T 1/pcr/m/n/10 identify[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cov.mve[][][ ][]\T1/ptm/m/n/10 , Overfull \hbox (31.3804pt too wide) in paragraph at lines 1523--1523 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a nd label ellipses[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1533--1533 [] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i dent. only points[] [2671] Underfull \hbox (badness 5741) in paragraph at lines 1573--1576 []\T1/pcr/m/n/10 coefHier() []\T1/ptm/m/n/10 di-rectly in-ter-faces to the un-d er-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only [2672] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1642--1642 [] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa rnType,[] [2673] Underfull \hbox (badness 1552) in paragraph at lines 1691--1693 []\T1/ptm/b/n/10 A\T1/ptm/m/n/10 symmetric bi-nary vari-able, aka []\T1/pcr/m/n /10 "A" []\T1/ptm/m/n/10 in re-sult []\T1/pcr/m/n/10 Types[]\T1/ptm/m/n/10 , se e Underfull \hbox (badness 1629) in paragraph at lines 1705--1709 []\T1/ptm/b/n/10 I\T1/ptm/m/n/10 nterval scaled -- the \T1/ptm/b/n/10 de-fault \T1/ptm/m/n/10 for all nu-meric Underfull \hbox (badness 3746) in paragraph at lines 1705--1709 \T1/ptm/m/n/10 (incl []\T1/pcr/m/n/10 integer[]\T1/ptm/m/n/10 ) columns of []\T 1/pcr/m/n/10 x[]\T1/ptm/m/n/10 , aka []\T1/pcr/m/n/10 "I" []\T1/ptm/m/n/10 in r e-sult []\T1/pcr/m/n/10 Types[]\T1/ptm/m/n/10 , see [2674] Underfull \hbox (badness 1540) in paragraph at lines 1781--1789 \T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1 0 w[]^^N[]$\T1/ptm/m/n/10 , where $\OML/cmm/m/it/10 w[]$[]\T1/pcr/m/n/10 = [2675] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1870--1870 []\T1/pcr/m/n/9 ## Example 2 in reference, extended --- different ways of "m ixed" / "gower":[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1874--1874 []\T1/pcr/m/n/9 summary(d0 <- daisy(flower)) # -> the first 3 {0,1} treate d as *N*ominal[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 1875--1875 []\T1/pcr/m/n/9 summary(dS123 <- daisy(flower, type = list(symm = 1:3))) # fi rst 3 treated as *S*ymmetric[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1876--1876 []\T1/pcr/m/n/9 stopifnot(dS123 == d0) # i.e., *S*ymmetric <==> *N*ominal {fo r 2-level factor}[] Overfull \hbox (106.98032pt too wide) in paragraph at lines 1880--1880 []\T1/pcr/m/n/9 summary(dA123 <- daisy(flowerN)) # .. all 3 logicals treated * A*symmetric binary (w/ warning)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1882--1882 []\T1/pcr/m/n/9 summary(dA13 <- daisy(flower, type = list(asymm = c(1, 3), ord ratio = 7)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1890--1890 []\T1/pcr/m/n/9 summary(dN <- daisy(Nflow)) # w/ warning: treated binary .. 1: 3 as interval[] Overfull \hbox (117.7803pt too wide) in paragraph at lines 1891--1891 []\T1/pcr/m/n/9 ## Still, using Euclidean/Manhattan distance for {0-1} *is* id entical to treating them as "N" :[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 1907--1907 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st and = FALSE, [2676] [2677] [2678] [2679] [2680] Underfull \hbox (badness 10000) in paragraph at lines 2228--2231 Underfull \hbox (badness 3179) in paragraph at lines 2242--2248 [][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] []\T1/ptm/m/n/10 which is also the [][][]\T1/pcr/m/n/10 predict[][][] []\T1/ptm/m/n/10 method for []\T1/pcr/m/n/1 0 ellipsoid []\T1/ptm/m/n/10 ob-jects. [2681] [2682] Underfull \hbox (badness 10000) in paragraph at lines 2400--2403 [][][]\T1/pcr/m/n/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-en ces; [][][]\T1/pcr/m/n/10 fanny.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 partition.object[][][][]\T1/ptm/m/n/10 , [2683] Underfull \hbox (badness 1292) in paragraph at lines 2468--2471 []\T1/ptm/m/n/10 named vec-tor with []\T1/pcr/m/n/10 iterations[]\T1/ptm/m/n/10 , the num-ber of it-er-a-tions needed and [2684] Underfull \hbox (badness 6675) in paragraph at lines 2477--2479 []\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl us-ter-ing, see Underfull \hbox (badness 10000) in paragraph at lines 2500--2503 [][][]\T1/pcr/m/n/10 fanny[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.f anny[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 dissimilarity.object[][][][]\ T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 partition.object[][][][]\T1/ptm/m/n/10 , [2685] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2575--2575 [] \T1/pcr/m/n/9 "4" = "red", "5" = "blue")[levels(f lowerN$color)][] Overfull \hbox (90.78033pt too wide) in paragraph at lines 2576--2576 []\T1/pcr/m/n/9 levels(flowerN$soil) <- c("1" = "dry", "2" = "normal", "3" = "wet")[levels(flowerN$soil)][] [2686] Overfull \hbox (48.78088pt too wide) in paragraph at lines 2639--2639 []\T1/pcr/m/n/10 medoids(x, clustering, diss = inherits(x, "dist"), USE.NAMES = FALSE, ...) [2687] Overfull \hbox (69.18036pt too wide) in paragraph at lines 2686--2686 [] \T1/pcr/m/n/9 stopifnot(length(cl.k) == nrow(votes.repub), 1 <= cl.k, cl.k <= k, table(cl.k) >= 2)[] [2688] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2791--2791 []\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/ 9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[] [2689] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2870--2870 [] \T1/pcr/m/n/10 variant = c("original", "o_1", "o_2", "f_3", "f_4", "f_5" , "faster"),[] [2690] [2691] [2692] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3099--3099 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro und (1, 16):[] [2693] [2694] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3202--3202 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co l.axis = "red")[] [2695] [2696] [2697] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3398--3398 [] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x $ac, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3399--3399 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2698] Underfull \hbox (badness 10000) in paragraph at lines 3466--3469 []\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via []\T1/pcr/m /n/10 pltree() []\T1/ptm/m/n/10 is pro-vided by []\T1/pcr/m/n/10 dg <- [2699] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3516--3516 [] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3517--3517 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2700] [2701] [2702] Underfull \hbox (badness 10000) in paragraph at lines 3702--3705 []\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 does not have a []\T1 /pcr/m/n/10 diss []\T1/ptm/m/n/10 com-po-nent as for [][][]\T1/pcr/m/n/10 pam[] [][](*, Underfull \hbox (badness 1448) in paragraph at lines 3702--3705 \T1/pcr/m/n/10 keep.diss=FALSE)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 dist []\T1/p tm/m/n/10 must be the dis-sim-i-lar-ity if a clus-plot is [2703] Underfull \hbox (badness 10000) in paragraph at lines 3765--3770 [][][]\T1/pcr/m/n/10 partition.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n /10 clusplot.partition[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 clusplot.de fault[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pam[][][][]\T1/ptm/m/n/10 , [2704] Underfull \hbox (badness 1748) in paragraph at lines 3827--3832 \T1/ptm/m/n/10 dis-patches to [][][]\T1/pcr/m/n/10 plot.hclust[][][](..)[]\T1/p tm/m/n/10 . If more flex-i-ble plots are needed, con-sider []\T1/pcr/m/n/10 xx <- Underfull \hbox (badness 6268) in paragraph at lines 3839--3842 [][][]\T1/pcr/m/n/10 agnes[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 agnes.o bject[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 diana[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 diana.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/1 0 hclust[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 par[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.agnes[][][][]\T1/ptm/m/n/10 , [2705] [2706] [2707] Underfull \hbox (badness 10000) in paragraph at lines 4024--4027 [][][]\T1/pcr/m/n/10 summary.agnes[][][] []\T1/ptm/m/n/10 pro-duc-ing more out- put; [][][]\T1/pcr/m/n/10 agnes[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 ag nes.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/ n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4055--4058 [][][]\T1/pcr/m/n/10 summary.clara[][][] []\T1/ptm/m/n/10 pro-duc-ing more out- put; [][][]\T1/pcr/m/n/10 clara[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cl ara.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/ n/10 , [2708] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4108--4108 [] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right = TRUE, ...)[] [2709] Underfull \hbox (badness 2035) in paragraph at lines 4119--4121 []\T1/ptm/m/n/10 a []\T1/pcr/m/n/10 dissimilarity []\T1/ptm/m/n/10 ob-ject or a []\T1/pcr/m/n/10 summary.dissimilarity []\T1/ptm/m/n/10 one for [2710] [2711] [2712] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4312--4312 [] \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w idth "* s[i]),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 4314--4314 [] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat = TRUE, ...)[] [2713] [2714] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4456--4456 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus ter-wise coloring[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4465--4465 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4467--4467 [] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma in")); frame()[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 4470--4470 []\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol denrod4", "gray20")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4472--4472 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE,[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4479--4479 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro wnames == indices[] [2715] [2716] [2717] [2718] [2719] [2720] [2721] Underfull \hbox (badness 10000) in paragraph at lines 4853--4859 []\T1/ptm/m/n/10 Our ver-sion of the []\T1/pcr/m/n/10 xclara []\T1/ptm/m/n/10 i s slightly more rounded than the one from Underfull \hbox (badness 10000) in paragraph at lines 4869--4871 []\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file `\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side Overfull \hbox (52.98038pt too wide) in paragraph at lines 4882--4882 []\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10 01:2000}, {2001:3000} Overfull \hbox (9.78043pt too wide) in paragraph at lines 4884--4884 []\T1/pcr/m/n/9 p.ID <- c(78, 1411, 2535) ## PAM\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s medoid indices == pam(xclara, 3)$id.med[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4894--4894 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o bservations:[] [2722] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4898--4898 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? - - Robust range:[] [2723]) (./codetools-pkg.tex [2724] Chapter 21. Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16 [] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17 [] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = !all,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18 [] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress Undefined,[] [2725] Underfull \hbox (badness 10000) in paragraph at lines 65--70 []\T1/pcr/m/n/10 checkUsageEnv []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 checkUsage Package []\T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply [2726] Overfull \hbox (18.78088pt too wide) in paragraph at lines 118--118 []\T1/pcr/m/n/10 makeConstantFolder(..., leaf, handler, call, exit, isLocal, f oldable,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 121--121 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e nterInternal,[] [2727] [2728] [2729]) (./foreign-pkg.tex [2730] Chapter 22. Underfull \hbox (badness 10000) in paragraph at lines 33--37 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of a Data Underfull \hbox (badness 10000) in paragraph at lines 33--37 \T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able as [][]$\T1/p cr/m/n/10 https : / / support . Underfull \hbox (badness 10000) in paragraph at lines 33--37 \T1/pcr/m/n/10 sas . com / content / dam / SAS / support / en / technical-[]pap ers / Overfull \hbox (74.28088pt too wide) in paragraph at lines 33--37 \T1/pcr/m/n/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[]s et-[]in-[]sas-[]transport-[]xport-[]format . [2731] Underfull \hbox (badness 1231) in paragraph at lines 67--70 []\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr om, or a [2732] [2733] Underfull \hbox (badness 3601) in paragraph at lines 237--245 []\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude []\T1/pcr/m /n/10 "datalabel"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "time.stamp"[]\T1/ptm/m/n/ 10 , [2734] Overfull \hbox (12.78088pt too wide) in paragraph at lines 295--295 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates = FALSE, [2735] [2736] [2737] Overfull \hbox (48.78088pt too wide) in paragraph at lines 461--461 [] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t o.data.frame,[] [2738] Overfull \hbox (30.78088pt too wide) in paragraph at lines 462--462 [] \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen d", "no"),[] Underfull \hbox (badness 2846) in paragraph at lines 505--514 []\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif- fer-ent lev- Underfull \hbox (badness 3746) in paragraph at lines 505--514 \T1/ptm/m/n/10 els. For []\T1/pcr/m/n/10 "append" []\T1/ptm/m/n/10 (the de-faul t), the first orig-i-nal value la-bel is Underfull \hbox (badness 2269) in paragraph at lines 505--514 \T1/ptm/m/n/10 kept while fur-ther du-pli-cated la-bels are re-named to []\T1/p cr/m/n/10 paste0(label, Underfull \hbox (badness 10000) in paragraph at lines 515--518 []\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with du- Underfull \hbox (badness 10000) in paragraph at lines 515--518 \T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault []\T1/pcr/m/n/10 "_dup licated_"[]\T1/ptm/m/n/10 ) if [2739] Underfull \hbox (badness 10000) in paragraph at lines 549--557 []\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 https : / / learn . microsoft . com / en-[]us / windows / win32 / intl / Underfull \hbox (badness 7613) in paragraph at lines 567--573 []\T1/ptm/m/n/10 There may be at-tributes []\T1/pcr/m/n/10 "label.table" []\T1/ ptm/m/n/10 and []\T1/pcr/m/n/10 "variable.labels"[]\T1/ptm/m/n/10 . At-tribute [2740] Overfull \hbox (20.58041pt too wide) in paragraph at lines 622--622 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg ument settings.[] Overfull \hbox (112.38031pt too wide) in paragraph at lines 623--623 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to R factor labels) are uncomplete,[] [2741] Overfull \hbox (9.78043pt too wide) in paragraph at lines 656--656 []\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ ate variables[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 660--660 []\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt h=w), "\n"))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 667--667 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, collapse="")[] [2742] [2743] Underfull \hbox (badness 10000) in paragraph at lines 811--812 Overfull \hbox (4.38043pt too wide) in paragraph at lines 821--821 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f oreign")[1])[] [2744] Underfull \hbox (badness 10000) in paragraph at lines 868--872 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of a Data Underfull \hbox (badness 10000) in paragraph at lines 868--872 \T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able at [][]$\T1/p cr/m/n/10 https : / / support . Underfull \hbox (badness 10000) in paragraph at lines 868--872 \T1/pcr/m/n/10 sas . com / content / dam / SAS / support / en / technical-[]pap ers / Overfull \hbox (74.28088pt too wide) in paragraph at lines 868--872 \T1/pcr/m/n/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[]s et-[]in-[]sas-[]transport-[]xport-[]format . [2745] Overfull \hbox (24.78088pt too wide) in paragraph at lines 899--899 [] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G lobalEnv) [2746] Overfull \hbox (0.78088pt too wide) in paragraph at lines 963--963 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute (x))) [2747] [2748] Underfull \hbox (badness 10000) in paragraph at lines 1075--1076 [][][]$\T1/pcr/m/n/10 https : / / www . clicketyclick . dk / databases / xbase / format / data _ types . Overfull \hbox (24.78088pt too wide) in paragraph at lines 1111--1111 [] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", "codes"))[] [2749] [2750] Underfull \hbox (badness 10000) in paragraph at lines 1268--1274 []\T1/ptm/m/n/10 The work for this func-tion is done by []\T1/pcr/m/n/10 foreig n:::writeForeignStata[]\T1/ptm/m/n/10 , [2751] Underfull \hbox (badness 2088) in paragraph at lines 1294--1297 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 package="SPSS"[]\T1/ptm/m/n/10 , as a sid e ef-fect, the dec-i-mal in-di-ca-tor is al-ways set by []\T1/pcr/m/n/10 SET [2752]) (./lattice-pkg.tex Chapter 23. [2753] Underfull \hbox (badness 2073) in paragraph at lines 117--121 \T1/ptm/m/n/10 pro-vide a holis-tic in-tro-duc-tion to the Trel-lis paradigm: [ ][]$\T1/pcr/m/n/10 http : / / web . archive . org / Underfull \hbox (badness 10000) in paragraph at lines 117--121 \T1/pcr/m/n/10 web / 20081020164041 / http : / / cm . bell-[]labs . com / cm / ms / departments / sia / [2754] [2755] Overfull \hbox (12.78088pt too wide) in paragraph at lines 291--291 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 295--295 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .xyplot"),[] [2756] Overfull \hbox (42.78088pt too wide) in paragraph at lines 306--306 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul t.dotplot"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 316--316 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.barchart"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 327--327 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.stripplot"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 351--351 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Underfull \vbox (badness 10000) has occurred while \output is active [2757] Overfull \hbox (30.78088pt too wide) in paragraph at lines 355--355 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .bwplot"),[] [2758] [2759] [2760] Underfull \hbox (badness 1221) in paragraph at lines 676--679 []\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as ar-gu-ments to [2761] [2762] [2763] [2764] Underfull \hbox (badness 2005) in paragraph at lines 1014--1026 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of fac-tors will be Underfull \hbox (badness 1199) in paragraph at lines 1014--1026 \T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a use-ful lay-out. [2765] [2766] Underfull \hbox (badness 1661) in paragraph at lines 1127--1133 []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 y []\T1/ptm/m/n/10 sho uld be num-bers be-tween 0 and 1, giv-ing co-or-di-nates [2767] Underfull \hbox (badness 1097) in paragraph at lines 1253--1255 []\T1/ptm/m/n/10 Logical flag, whether leg-end should have a Underfull \hbox (badness 1917) in paragraph at lines 1267--1268 []\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to [2768] [2769] [2770] Underfull \hbox (badness 1540) in paragraph at lines 1507--1513 []\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][][]\T1/pcr/m/ n/10 plot.trellis[][][][]\T1/ptm/m/n/10 , [2771] Underfull \hbox (badness 10000) in paragraph at lines 1594--1611 [][][]\T1/pcr/m/n/10 panel.dotplot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.stripplot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.superpose[] [][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.loess[][][][]\T1/ptm/m/n/10 , [2772] Underfull \vbox (badness 10000) has occurred while \output is active [2773] Overfull \hbox (36.7804pt too wide) in paragraph at lines 1682--1682 [] \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar dSprays$rowpos))),[] [2774] Underfull \hbox (badness 2012) in paragraph at lines 1736--1738 []\T1/ptm/m/n/10 additional ar-gu-ments passed to [][][]\T1/pcr/m/n/10 xyplot[] [][][]\T1/ptm/m/n/10 , which may pass them on to Underfull \hbox (badness 6808) in paragraph at lines 1766--1770 []\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p assed to Underfull \hbox (badness 10000) in paragraph at lines 1783--1786 []\T1/ptm/m/n/10 style set-tings be-yond the stan-dard []\T1/pcr/m/n/10 col[]\T 1/ptm/m/n/10 , []\T1/pcr/m/n/10 lty[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lwd[]\T1 /ptm/m/n/10 , etc; see [2775] Underfull \hbox (badness 10000) in paragraph at lines 1836--1838 []\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix An-drews [2776] [2777] [2778] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2077--2077 [] \T1/pcr/m/n/10 auto.key = lattice.getOption("default.args")$auto .key,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2090--2090 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl ot"),[] Underfull \vbox (badness 10000) has occurred while \output is active [2779] Underfull \hbox (badness 10000) in paragraph at lines 2169--2172 []\T1/ptm/m/n/10 When []\T1/pcr/m/n/10 breaks []\T1/ptm/m/n/10 is un-spec-i-fie d, the value of Underfull \hbox (badness 1320) in paragraph at lines 2169--2172 []\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") []\T1/ptm/m/n/10 is firs t checked. If [2780] [2781] [2782] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2374--2374 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2378--2378 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .qqmath"),[] [2783] [2784] [2785] [2786] [2787] Overfull \hbox (60.78088pt too wide) in paragraph at lines 2737--2737 [] \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev elplot.raster")[] [2788] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2769--2769 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl ot"),[] Underfull \vbox (badness 10000) has occurred while \output is active [2789] Underfull \hbox (badness 2913) in paragraph at lines 2848--2853 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when []\T1/ pcr/m/n/10 x []\T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 2848--2853 []\T1/pcr/m/n/10 row.values []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 column.values []\T1/ptm/m/n/10 must have the same lengths as [2790] [2791] Underfull \hbox (badness 6758) in paragraph at lines 2976--2980 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be Underfull \hbox (badness 7576) in paragraph at lines 2976--2980 \T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][][]\T1/pcr/m/n/10 grid.ra ster[][][][]\T1/ptm/m/n/10 . See also Underfull \hbox (badness 10000) in paragraph at lines 2982--2984 []\T1/ptm/m/n/10 Logical flag, passed to [][][]\T1/pcr/m/n/10 rasterGrob[][][] []\T1/ptm/m/n/10 when Underfull \hbox (badness 1609) in paragraph at lines 3034--3040 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti ons should be used, Underfull \hbox (badness 2772) in paragraph at lines 3034--3040 \T1/ptm/m/n/10 both for the false color im-age and the color key (if present). Ef- Underfull \hbox (badness 1400) in paragraph at lines 3034--3040 \T1/ptm/m/n/10 fec-tively, set-ting this to []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n /10 changes the de-fault panel func-tion from Underfull \hbox (badness 2486) in paragraph at lines 3058--3062 []\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for the de-fault panel func-tion [2792] [2793] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3163--3163 [] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3164--3164 [] \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3165--3165 [] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite = TRUE),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3176--3176 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. cloud"),[] [2794] Overfull \hbox (66.78088pt too wide) in paragraph at lines 3191--3191 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.wireframe"),[] [2795] Underfull \hbox (badness 2913) in paragraph at lines 3256--3261 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when []\T1/ pcr/m/n/10 x []\T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 3256--3261 []\T1/pcr/m/n/10 row.values []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 column.values []\T1/ptm/m/n/10 must have the same lengths as [2796] [2797] [2798] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.parallel} ) has been already used, duplicate ignored \relax l.3545 \aliasA{parallel}{B\_08\_splom}{parallel} [2799] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3587--3587 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. splom"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3610--3610 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.parallel"),[] Underfull \vbox (badness 10000) has occurred while \output is active [2800] [2801] [2802] [2803] [2804] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3947--3947 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt( var(x))) [2805] Underfull \hbox (badness 2277) in paragraph at lines 4033--4037 []\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault set-tings by Underfull \hbox (badness 2435) in paragraph at lines 4033--4037 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2806] [2807] Overfull \hbox (120.78088pt too wide) in paragraph at lines 4130--4130 [] \T1/pcr/m/n/10 symbol = palette.colors(palette = "Okabe-Ito") [c(6, 2, 4, 7, 3, 5, 8)],[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 4132--4132 [] \T1/pcr/m/n/10 region = hcl.colors(14, palette = "YlGnBu", re v = TRUE),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4139--4139 [] \T1/pcr/m/n/10 reference = "gray90", bg = "transparent", fg = " black",[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 4140--4140 [] \T1/pcr/m/n/10 strip.bg = rep("gray95", 7), strip.fg = rep("gra y70", 7),[] [2808] [2809] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4283--4283 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict = FALSE) Underfull \hbox (badness 1173) in paragraph at lines 4292--4296 []\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un- spec-i-fied in Underfull \hbox (badness 3219) in paragraph at lines 4319--4321 []\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i s-sued when Underfull \hbox (badness 1728) in paragraph at lines 4336--4340 []\T1/pcr/m/n/10 theme[]\T1/ptm/m/n/10 ). These are used to mod-ify the cur-ren t set-tings (ob-tained by [2810] Underfull \hbox (badness 5161) in paragraph at lines 4401--4405 []\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in []\T1/pcr/m/n/10 trell is.settings []\T1/ptm/m/n/10 has not been fi-nal-ized, Underfull \hbox (badness 4913) in paragraph at lines 4401--4405 \T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca n be ob-tained by [2811] [2812] Underfull \hbox (badness 1067) in paragraph at lines 4519--4529 []\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. []\T1/pcr/m/n/10 col []\T1/ptm/m/n/ 10 is used for com-po-nents []\T1/pcr/m/n/10 "plot.symbol"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4519--4529 []\T1/pcr/m/n/10 "plot.line"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "plot.polygon"[ ]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "superpose.symbol"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1735) in paragraph at lines 4519--4529 []\T1/pcr/m/n/10 "superpose.line"[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 "super pose.polygon"[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 col.points Underfull \hbox (badness 10000) in paragraph at lines 4519--4529 []\T1/ptm/m/n/10 over-rides []\T1/pcr/m/n/10 col[]\T1/ptm/m/n/10 , but is used only for []\T1/pcr/m/n/10 "plot.symbol" []\T1/ptm/m/n/10 and Underfull \hbox (badness 5231) in paragraph at lines 4519--4529 []\T1/pcr/m/n/10 "superpose.symbol"[]\T1/ptm/m/n/10 . Sim-i-larly, []\T1/pcr/m/ n/10 col.line []\T1/ptm/m/n/10 over-rides []\T1/pcr/m/n/10 col []\T1/ptm/m/n/10 for Underfull \hbox (badness 1701) in paragraph at lines 4544--4547 []\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents []\T1/pcr/m/n/10 pl ot.symbol[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 plot.polygon[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4547--4549 []\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents []\T1/pcr/m/n/10 plot.polygon []\T1/ptm/m/n/10 and [2813] [2814] Underfull \hbox (badness 2932) in paragraph at lines 4690--4695 []\T1/pcr/m/n/10 auto.key[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 aspect[]\T1/ptm/m/ n/10 , []\T1/pcr/m/n/10 between[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 grid[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 skip[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 strip[]\T1/ ptm/m/n/10 , []\T1/pcr/m/n/10 xscale.components[]\T1/ptm/m/n/10 , [2815] [2816] [2817] [2818] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4966--4966 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab = "Height")[] [2819] [2820] [2821] Underfull \hbox (badness 10000) in paragraph at lines 5153--5156 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 trellis[]\T1/ptm/m/n/10 , by de-fault plot-ted by []\T1/pcr/m/n/10 print.trellis[]\T1/ptm/m/n/10 . [2822] Underfull \hbox (badness 1442) in paragraph at lines 5285--5288 []\T1/pcr/m/n/10 plot.shingle []\T1/ptm/m/n/10 dis-plays the ranges of shin-gle s via rect-an-gles. []\T1/pcr/m/n/10 print.shingle []\T1/ptm/m/n/10 and [2823] [2824] [2825] [2826] [2827] [2828] Underfull \hbox (badness 3646) in paragraph at lines 5624--5627 [][][]\T1/pcr/m/n/10 Lattice[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 draw. key[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 trellis.par.get[][][][]\T1/ptm /m/n/10 , and [][][]\T1/pcr/m/n/10 xyplot[][][][]\T1/ptm/m/n/10 , specif-i-call y the en-try for Overfull \hbox (36.78088pt too wide) in paragraph at lines 5654--5654 [] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh ich.given],[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5655--5655 [] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which .given],[] [2829] Underfull \hbox (badness 10000) in paragraph at lines 5743--5746 []\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i -zon-tal. Underfull \hbox (badness 2103) in paragraph at lines 5743--5746 []\T1/pcr/m/n/10 horizontal=FALSE []\T1/ptm/m/n/10 is use-ful for strips on the left of pan-els us-ing [2830] Underfull \hbox (badness 1635) in paragraph at lines 5769--5774 []\T1/pcr/m/n/10 strip.default []\T1/ptm/m/n/10 is called for its side-effect, which is to draw a strip ap-pro-pri-ate for [2831] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5920--5920 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la bels,[] [2832] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5934--5934 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose "), ...)[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5935--5935 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos e"), ...)[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5938--5938 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location" , "toplevel",[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5941--5941 [] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig ht", "page"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 5943--5943 [] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in side"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5949--5949 [] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi ch.given",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5950--5950 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5951--5951 [] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi ch.panel",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5952--5952 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5953--5953 [] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co lumn",[] Underfull \hbox (badness 10000) in paragraph at lines 5969--5971 []\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of Underfull \hbox (badness 2376) in paragraph at lines 5980--5982 []\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point. De-faults to [2833] [2834] Underfull \hbox (badness 2538) in paragraph at lines 6105--6109 \T1/ptm/m/n/10 For []\T1/pcr/m/n/10 trellis.focus[]\T1/ptm/m/n/10 , the de-faul t is []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 in in-ter-ac-tive mode, and Underfull \hbox (badness 4205) in paragraph at lines 6116--6123 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 panel.identify.qqmath[]\T1/ptm/m/n/10 , e x-tra pa-ram-e-ters are passed on to Underfull \hbox (badness 4792) in paragraph at lines 6116--6123 []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 trellis.switchFocus[]\T1/ptm/m/n/10 , the se are used (in com-bi-na-tion with [2835] [2836] Underfull \hbox (badness 10000) in paragraph at lines 6269--6273 [][][]\T1/pcr/m/n/10 identify[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Latt ice[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.trellis[][][][]\T1/ptm/m /n/10 , [][][]\T1/pcr/m/n/10 trellis.currentLayout[][][][]\T1/ptm/m/n/10 , [2837] [2838] Underfull \hbox (badness 4242) in paragraph at lines 6416--6421 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- [2839] [2840] Underfull \hbox (badness 3601) in paragraph at lines 6532--6537 []\T1/ptm/m/n/10 Creates Box and Whisker plot of []\T1/pcr/m/n/10 x []\T1/ptm/m /n/10 for ev-ery level of []\T1/pcr/m/n/10 y []\T1/ptm/m/n/10 (or the other way round Underfull \hbox (badness 2486) in paragraph at lines 6532--6537 \T1/ptm/m/n/10 if []\T1/pcr/m/n/10 horizontal=FALSE[]\T1/ptm/m/n/10 ). By de-fa ult, the ac-tual box-plot statis-tics are cal-cu-lated us-ing [2841] Overfull \hbox (60.78088pt too wide) in paragraph at lines 6620--6620 [] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co lors")$palette,[] [2842] [2843] [2844] Underfull \hbox (badness 10000) in paragraph at lines 6819--6823 []\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The Underfull \hbox (badness 10000) in paragraph at lines 6824--6826 []\T1/ptm/m/n/10 numeric, be-tween 0 and 1, giv-ing a min-i-mum sat-u-ra-tion i n [2845] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6920--6920 [] \T1/pcr/m/n/9 shade.colors.palette = makeShadePalette(hcl.colors(1 0, "Inferno"),[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6923--6923 [] \T1/pcr/m/n/9 shade.colors.palette = makeShadePalette(hcl.colors(1 0, "Dark Mint"),[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6926--6926 [] \T1/pcr/m/n/9 shade.colors.palette = makeShadePalette(hcl.colors(1 0, "Harmonic"),[] [2846] [2847] [2848] [2849] [2850] [2851] Underfull \hbox (badness 1320) in paragraph at lines 7288--7295 []\T1/pcr/m/n/10 panel.levelplot.raster []\T1/ptm/m/n/10 is an al-ter-na-tive p anel func-tion that uses the raster draw- Underfull \hbox (badness 1715) in paragraph at lines 7288--7295 \T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more ef-fi-cient. When us-ing [2852] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7363--7363 [] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = NULL,[] [2853] Underfull \hbox (badness 10000) in paragraph at lines 7393--7397 []\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments to Underfull \hbox (badness 1584) in paragraph at lines 7393--7397 []\T1/pcr/m/n/10 diag.panel.splom []\T1/ptm/m/n/10 to know what ar-gu-ments thi s func-tion is passed [2854] Underfull \hbox (badness 10000) in paragraph at lines 7498--7501 \T1/ptm/m/n/10 and []\T1/pcr/m/n/10 diag.panel []\T1/ptm/m/n/10 from []\T1/pcr/ m/n/10 panel.pairs[]\T1/ptm/m/n/10 . Cur-rently ig-nored by Overfull \hbox (101.58032pt too wide) in paragraph at lines 7523--7523 [] \T1/pcr/m/n/9 function(i,j) hcl.colors(11)[i+j-1]) ## rainbow( 11, start=.12, end=.5)[i+j-1])[] [2855] [2856] Underfull \hbox (badness 2012) in paragraph at lines 7664--7667 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2857] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7710--7710 [] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta ils.n = 50))[] [2858] [2859] [2860] Underfull \hbox (badness 1939) in paragraph at lines 7899--7907 []\T1/pcr/m/n/10 "lm" []\T1/ptm/m/n/10 adds a lin-ear re-gres-sion line (same a s [][][]\T1/pcr/m/n/10 panel.lmline[][][][]\T1/ptm/m/n/10 , ex-cept Underfull \hbox (badness 1163) in paragraph at lines 7899--7907 \T1/ptm/m/n/10 for de-fault graph-i-cal pa-ram-e-ters). []\T1/pcr/m/n/10 "loess " []\T1/ptm/m/n/10 adds a loess fit (same as Underfull \hbox (badness 2772) in paragraph at lines 7922--7925 []\T1/ptm/m/n/10 Most gen-er-ally, []\T1/pcr/m/n/10 grid []\T1/ptm/m/n/10 can b e a list of ar-gu-ments to be sup-plied to [2861] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7993--7993 [] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y = c(1/6, 4/6)),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8003--8003 [] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d raw = FALSE),[] [2862] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8088--8088 [] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam e.type)[] [2863] Overfull \hbox (84.78088pt too wide) in paragraph at lines 8107--8107 [] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ide ntifier, name.type)[] [2864] [2865] Overfull \hbox (63.78036pt too wide) in paragraph at lines 8246--8246 []\T1/pcr/m/n/9 xyplot(y ~ x, d, panel = panel.rect, col = 4, alpha = 0.5, wid th = 0.1, height = 0.1)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8253--8253 []\T1/pcr/m/n/9 xyplot(y ~ x, d, panel = panel.polygon, col = 4, alpha = 0.5, rule = "evenodd")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8255--8255 []\T1/pcr/m/n/9 ## Example adapted from https://journal.r-project.org/articles /RJ-2012-017/[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8259--8259 []\T1/pcr/m/n/9 xyplot(y ~ x, data = d, panel = panel.polygon, rule = "none", col = "grey")[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8260--8260 []\T1/pcr/m/n/9 xyplot(y ~ x, data = d, panel = panel.polypath, rule = "windin g", col = "grey")[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8261--8261 []\T1/pcr/m/n/9 xyplot(y ~ x, data = d, panel = panel.polypath, rule = "evenod d", col = "grey")[] [2866] Overfull \hbox (66.78088pt too wide) in paragraph at lines 8324--8324 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden tifier = "grid")[] [2867] Underfull \hbox (badness 1436) in paragraph at lines 8379--8385 []\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c al pa-ram-e-ters for [2868] Overfull \hbox (42.18039pt too wide) in paragraph at lines 8509--8509 [] \T1/pcr/m/n/9 panel.superpose(x, y, ..., panel.groups = panel.ave rage, grid = FALSE,[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8523--8523 [] \T1/pcr/m/n/9 args = list(mean = mean(x), sd = sd(x)), ...)[] [2869] [2870] [2871] [2872] [2873] [2874] [2875] Underfull \hbox (badness 10000) in paragraph at lines 8948--8951 []\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to []\T1/pcr/m/n/10 panel.super pose Underfull \hbox (badness 10000) in paragraph at lines 8948--8951 []\T1/ptm/m/n/10 from []\T1/pcr/m/n/10 panel.superpose.2[]\T1/ptm/m/n/10 , and to []\T1/pcr/m/n/10 panel.groups []\T1/ptm/m/n/10 from [2876] [2877] Overfull \hbox (24.78088pt too wide) in paragraph at lines 9123--9123 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st ack, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9124--9124 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin t, ...)[] [2878] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9136--9136 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr ipts, ...)[] Underfull \hbox (badness 3118) in paragraph at lines 9155--9158 []\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. []\T1/pcr/m/n/10 type [ ]\T1/ptm/m/n/10 has a dif-fer-ent mean-ing in [2879] Underfull \hbox (badness 1515) in paragraph at lines 9231--9235 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2880] [2881] Underfull \hbox (badness 6316) in paragraph at lines 9337--9342 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in [2882] Overfull \hbox (47.58038pt too wide) in paragraph at lines 9447--9447 [] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b ottom$labels$labels)[] [2883] [2884] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9586--9586 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su nspot.year)),[] [2885] Underfull \hbox (badness 1028) in paragraph at lines 9645--9649 \T1/pcr/m/n/10 condition []\T1/ptm/m/n/10 for 2-D, and []\T1/pcr/m/n/10 left, r ight.x, right.y, left.name, right.x.name, [2886] [2887] [2888] [2889] [2890] [2891] [2892] Underfull \hbox (badness 7238) in paragraph at lines 10109--10113 []\T1/ptm/m/n/10 Factor with lev-els []\T1/pcr/m/n/10 "Svansota"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "No. 462"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Manchuria"[] \T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "No. 475"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10109--10113 []\T1/pcr/m/n/10 "Velvet"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Peatland"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "Glabron"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "No. 4 57"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Wisconsin No. 38"[]\T1/ptm/m/n/10 , [2893] [2894] [2895] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma} ) has been already used, duplicate ignored \relax l.10340 \aliasA{melanoma}{H\_melanoma}{melanoma} [2896] [2897] [2898] Underfull \hbox (badness 10000) in paragraph at lines 10502--10507 \T1/pcr/m/n/10 diseases[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Diabetes[]\T1/ptm/m/ n/10 , []\T1/pcr/m/n/10 Flu and pneumonia[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 He art disease[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Lower Overfull \hbox (9.78043pt too wide) in paragraph at lines 10575--10575 [] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list( columns = 2),[] [2899] [2900]) (./mgcv-pkg.tex Chapter 24. [2901] [2902] Overfull \hbox (6.78088pt too wide) in paragraph at lines 160--160 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL, Overfull \hbox (18.78088pt too wide) in paragraph at lines 163--163 [] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret e=FALSE,[] [2903] Overfull \hbox (48.78088pt too wide) in paragraph at lines 165--165 [] \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in tercept=NULL,[] Underfull \hbox (badness 1142) in paragraph at lines 185--189 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 210--215 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2904] [2905] [2906] [2907] Underfull \hbox (badness 10000) in paragraph at lines 379--386 [][][]\T1/pcr/m/n/10 mgcv.parallel[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gamObject[][][][]\T1 /ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/ptm/m/n/10 , [][][]\T1 /pcr/m/n/10 smooth.terms[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 379--386 [][][]\T1/pcr/m/n/10 linear.functional.terms[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][] [][]predict. gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 379--386 [][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 g am.side[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.selection[][][][]\T1/p tm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][][]\T1/ptm /m/n/10 , [2908] Overfull \hbox (4.38043pt too wide) in paragraph at lines 422--422 []\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2 ,bs=bs,k=k)+[] [2909] [2910] [2911] Underfull \hbox (badness 2922) in paragraph at lines 634--635 []\T1/ptm/m/n/10 The link func-tion: one of []\T1/pcr/m/n/10 "logit"[]\T1/ptm/m /n/10 , []\T1/pcr/m/n/10 "probit"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cloglog" []\T1/ptm/m/n/10 and [2912] [2913] Underfull \hbox (badness 1406) in paragraph at lines 704--705 []\T1/ptm/m/n/10 The MKL BLAS is mut-lithreaded by de-fault. Un-der linux set-t ing en-vi-ron-ment vari-able [2914] [2915] Underfull \hbox (badness 1158) in paragraph at lines 814--816 []\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe n us-ing pe-nal-ized re-gres-sion [2916] Underfull \hbox (badness 1259) in paragraph at lines 877--878 []\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro -duc-tion with R (2nd edi-tion). [2917] Underfull \vbox (badness 10000) has occurred while \output is active [2918] [2919] [2920] [2921] [2922] [2923] [2924] [2925] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1337--1337 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1338--1338 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1355--1355 [] \T1/pcr/m/n/9 plot(b$y[oy],rs[oy,ii[1]],ylim=c(-3,3),type="l",ylab="scor e residuals",[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1367--1367 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor +rx+obstruct[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1376--1376 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in d]),type="l",[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1378--1378 [] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind]) ,lwd=2,col=i)[] Underfull \vbox (badness 10000) has occurred while \output is active [2926] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1409--1409 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights= d,data=surv)[] Underfull \vbox (badness 10000) has occurred while \output is active [2927] [2928] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1492--1492 [] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid), initial = 0,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1503--1503 [] \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][ nrow(um)] <- 1[] Underfull \vbox (badness 10000) has occurred while \output is active [2929] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1542--1542 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter polate to te[] [2930] [2931] [2932] [2933] [2934] [2935] [2936] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1939--1939 []\T1/pcr/m/n/9 bd <- bam(y~s(x0)+ s(x1) + s(x1,fac,bs="sz",k=5)+s(x2,k=20),di screte=TRUE)[] [2937] [2938] [2939] [2940] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2174--2174 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str ict=FALSE) [2941] [2942] [2943] [2944] [2945] [2946] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2579--2579 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL,[] Underfull \hbox (badness 1728) in paragraph at lines 2591--2594 []\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][][]\T1/pcr/m/n /10 formula.gam[][][] []\T1/ptm/m/n/10 and also Underfull \hbox (badness 1142) in paragraph at lines 2604--2608 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2947] Underfull \hbox (badness 1043) in paragraph at lines 2630--2636 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2948] [2949] [2950] Underfull \hbox (badness 1043) in paragraph at lines 2795--2801 \T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v en-tion mech-a-nism de-scribed in [2951] [2952] Underfull \hbox (badness 10000) in paragraph at lines 2933--2939 [][][]\T1/pcr/m/n/10 mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gamObject[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/pt m/m/n/10 , [][][]\T1/pcr/m/n/10 smooth.terms[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2933--2939 [][][]\T1/pcr/m/n/10 linear.functional.terms[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][] [][]predict. gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2933--2939 [][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 g am.side[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.selection[][][][]\T1/p tm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][][]\T1/ptm /m/n/10 , [2953] Underfull \vbox (badness 10000) has occurred while \output is active [2954] Underfull \vbox (badness 10000) has occurred while \output is active [2955] [2956] [2957] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3250--3250 []\T1/pcr/m/n/10 gam.control(nthreads=1,ncv.threads=1,irls.reg=0.0,epsilon = 1 e-07, [2958] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3251--3251 [] \T1/pcr/m/n/10 maxit = 200,mgcv.tol=1e-7,mgcv.half=15, trace = F ALSE,[] [2959] [2960] [2961] [2962] [2963] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3591--3591 [] \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco l(x)),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3594--3594 [] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol (x)),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3595--3595 [] \T1/pcr/m/n/10 pearson.extra=0,dev.extra=0,n.true=-1,Sl=NULL,nei=NU LL,...)[] [2964] [2965] [2966] [2967] [2968] [2969] [2970] [2971] Underfull \hbox (badness 5189) in paragraph at lines 4073--4077 []\T1/ptm/m/n/10 Random ef-fects can be added to []\T1/pcr/m/n/10 gam []\T1/ptm /m/n/10 mod-els us-ing []\T1/pcr/m/n/10 s(...,bs="re") []\T1/ptm/m/n/10 terms ( see [2972] [2973] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4190--4190 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Underfull \vbox (badness 10000) has occurred while \output is active [2974] [2975] [2976] Underfull \hbox (badness 1184) in paragraph at lines 4360--4364 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2977] [2978] [2979] [2980] [2981] [2982] [2983] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4806--4806 [] \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i d=1)+s(x1,id=1)+[] [2984] [2985] [2986] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4956--4956 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, d1b = 0, [2987] [2988] Underfull \hbox (badness 1142) in paragraph at lines 5083--5087 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2989] Underfull \hbox (badness 10000) in paragraph at lines 5155--5164 []\T1/ptm/m/n/10 In the event of []\T1/pcr/m/n/10 lme []\T1/ptm/m/n/10 con-ver- gence fail-ures, con-sider mod-i-fy-ing [2990] [2991] Underfull \hbox (badness 5970) in paragraph at lines 5272--5278 [][][]\T1/pcr/m/n/10 magic[][][] []\T1/ptm/m/n/10 for an al-ter-na-tive for cor -re-lated data, [][][]\T1/pcr/m/n/10 te[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.gam[][][][]\T1/ptm /m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 1418) in paragraph at lines 5272--5278 [][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 n egbin[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 vis.gam[][][][]\T1/ptm/m/n/1 0 ,[][][]\T1/pcr/m/n/10 pdTens[][][][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 gamm4 [ ]\T1/ptm/m/n/10 ( [][]$\T1/pcr/m/n/10 https : / / cran . r-[]project . [2992] Underfull \vbox (badness 10000) has occurred while \output is active [2993] [2994] [2995] [2996] Underfull \hbox (badness 1577) in paragraph at lines 5622--5625 []\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see [] [][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 ar-gu-ment Underfull \hbox (badness 2181) in paragraph at lines 5629--5630 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2997] [2998] [2999] [3000] [3001] [3002] [3003] [3004] [3005] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6127--6127 []\T1/pcr/m/n/10 ginla(G,A=NULL,nk=16,nb=100,J=1,interactive=FALSE,integ=0,app rox=0) Underfull \hbox (badness 6708) in paragraph at lines 6133--6134 []\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by []\T1/pcr/m/n/10 gam(.. .,fit=FALSE) []\T1/ptm/m/n/10 or [3006] [3007] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6182--6182 [] \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d ata. A simple[] [3008] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6207--6207 [] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j] ,lty=lty[j])[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6236--6236 [] \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo r comparison[] [3009] [3010] [3011] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6358--6358 [] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r norm(100)*.4[] [3012] [3013] [3014] [3015] [3016] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6695--6695 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n a.action, Overfull \hbox (36.78088pt too wide) in paragraph at lines 6697--6697 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona lize=FALSE)[] Underfull \hbox (badness 1142) in paragraph at lines 6718--6722 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [3017] [3018] [3019] [3020] [3021] [3022] [3023] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7037--7037 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999, all.derivs=FALSE) [3024] [3025] [3026] Underfull \vbox (badness 10000) has occurred while \output is active [3027] Underfull \vbox (badness 10000) has occurred while \output is active [3028] [3029] [3030] Overfull \hbox (52.98038pt too wide) in paragraph at lines 7469--7469 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want to rule the world.",[] [3031] Overfull \hbox (36.78088pt too wide) in paragraph at lines 7496--7496 [] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y), nthreads=1)[] [3032] [3033] [3034] [3035] [3036] [3037] Underfull \vbox (badness 4805) has occurred while \output is active [3038] [3039] [3040] Underfull \hbox (badness 1242) in paragraph at lines 8050--8051 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [3041] [3042] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8137--8137 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt ion with bam...[] [3043] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8200--8200 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate d covariates[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8219--8219 [] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]] ,na.rm=TRUE)[] [3044] [3045] [3046] [3047] [3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055] [3056] [3057] [3058] [3059] [3060] [3061] [3062] [3063] [3064] Underfull \vbox (badness 10000) has occurred while \output is active [3065] [3066] Underfull \hbox (badness 10000) in paragraph at lines 9538--9541 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: []\T1/pcr/m/n/10 Dim .pdIndot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 coef.pdIdnot[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 9538--9541 []\T1/pcr/m/n/10 corMatrix.pdIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 logDet.pd Idnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdConstruct.pdIdnot[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3118) in paragraph at lines 9538--9541 []\T1/pcr/m/n/10 pdFactor.pdIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdMatrix.p dIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 solve.pdIdnot[]\T1/ptm/m/n/10 , []\T1 /pcr/m/n/10 summary.pdIdnot[]\T1/ptm/m/n/10 . [3067] Underfull \hbox (badness 10000) in paragraph at lines 9594--9597 []\T1/ptm/m/n/10 These func-tions ([]\T1/pcr/m/n/10 pdTens[]\T1/ptm/m/n/10 , [] \T1/pcr/m/n/10 pdConstruct.pdTens[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdFactor.p dTens[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3108) in paragraph at lines 9594--9597 []\T1/pcr/m/n/10 pdMatrix.pdTens[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 coef.pdTens []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 summary.pdTens[]\T1/ptm/m/n/10 ) would n ot nor-mally be [3068] [3069] [3070] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9814--9814 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s cale=-1,[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 9818--9818 [] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi ds=FALSE,[] [3071] [3072] [3073] Underfull \hbox (badness 1629) in paragraph at lines 9974--9979 []\T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is some-times to clone the [3074] [3075] [3076] [3077] Overfull \hbox (84.78088pt too wide) in paragraph at lines 10186--10186 [] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread s=1,gc.level=0,...)[] Underfull \hbox (badness 1062) in paragraph at lines 10223--10227 []\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 type=="terms" []\T1/ptm/m/n/10 or []\T1/pc r/m/n/10 type="iterms" []\T1/ptm/m/n/10 then terms (smooth or para- [3078] [3079] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10356--10356 [] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL L,...)[] [3080] [3081] [3082] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10517--10517 []\T1/pcr/m/n/9 x1 <- seq(.2,.8,length=m1);x2 <- seq(.2,.8,length=m2) ## margi nal grid points[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10518--10518 []\T1/pcr/m/n/9 df <- data.frame(x0=rep(.5,n),x1=rep(x1,m2),x2=rep(x2,each=m1) ,x3=rep(0,n))[] [3083] Underfull \vbox (badness 10000) has occurred while \output is active [3084] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10637--10637 [] \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s mooth deriv i[] [3085] Underfull \hbox (badness 1205) in paragraph at lines 10675--10676 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 10675--10676 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for Underfull \hbox (badness 1975) in paragraph at lines 10681--10686 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [3086] Underfull \hbox (badness 1205) in paragraph at lines 10765--10766 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 10765--10766 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [3087] Underfull \hbox (badness 10000) in paragraph at lines 10834--10837 []\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from Underfull \hbox (badness 2057) in paragraph at lines 10834--10837 [][][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][][]\T1/ptm/m/n/10 , al -though el-e-ments []\T1/pcr/m/n/10 X []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 S [ ]\T1/ptm/m/n/10 are not needed, [3088] [3089] [3090] Underfull \hbox (badness 1253) in paragraph at lines 10964--10966 []\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion cri-te-rion re-ported is one of GCV, [3091] [3092] [3093] [3094] [3095] Underfull \hbox (badness 1946) in paragraph at lines 11217--11224 []\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef- fects in a GAM in the same Underfull \hbox (badness 2221) in paragraph at lines 11217--11224 \T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre s-sion terms. This method Underfull \hbox (badness 2042) in paragraph at lines 11217--11224 \T1/ptm/m/n/10 can be used with [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 by mak-ing use of []\T1/pcr/m/n/10 s(...,bs="re") []\T1/ptm/m/n/10 terms in a model: see Underfull \hbox (badness 2846) in paragraph at lines 11225--11228 []\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the []\T1/pcr/m/n /10 paraPen []\T1/ptm/m/n/10 ar-gu-ment to [][][]\T1/pcr/m/n/10 gam[][][] []\T1 /ptm/m/n/10 can be used: Underfull \hbox (badness 5862) in paragraph at lines 11225--11228 \T1/ptm/m/n/10 see [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/ptm/m/n/10 . If s mooth-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g. [3096] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11291--11291 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11301--11301 []\T1/pcr/m/n/9 ## The effect of the new factor levels (or any interaction inv olving them)[] [3097] Underfull \hbox (badness 10000) in paragraph at lines 11332--11335 []\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of []\T1/pcr/m/n/ 10 "deviance"[]\T1/ptm/m/n/10 , [3098] [3099] [3100] [3101] [3102] Overfull \hbox (36.78088pt too wide) in paragraph at lines 11634--11634 []\T1/pcr/m/n/10 s(..., k=-1,fx=FALSE,bs="tp",m=NA,by=NA,xt=NULL,id=NULL,sp=NU LL,pc=NULL) [3103] [3104] [3105] [3106] [3107] [3108] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12007--12007 [] \T1/pcr/m/n/9 true <- mu + (del * sigma) * sinh((1/del) * asinh(qnorm(qq)) + (eps/del))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12021--12021 []\T1/pcr/m/n/9 b <- gam(list(accel~s(times, k=20, bs = "ad"), ~s(times, k = 1 0), ~1, ~1),[] Underfull \vbox (badness 10000) has occurred while \output is active [3109] [3110] Underfull \hbox (badness 3861) in paragraph at lines 12123--12126 []\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to model ma-trix X, or, if Overfull \hbox (36.78088pt too wide) in paragraph at lines 12132--12132 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, cov = TRUE,[] [3111] Underfull \hbox (badness 10000) in paragraph at lines 12149--12153 []\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 inverse==TRUE []\T1/ptm/m/n/10 and []\T1/p cr/m/n/10 both.sides==FALSE []\T1/ptm/m/n/10 then the re- Underfull \hbox (badness 10000) in paragraph at lines 12189--12193 []\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 inverse==TRUE []\T1/ptm/m/n/10 and []\T1/p cr/m/n/10 both.sides==FALSE []\T1/ptm/m/n/10 then the re- [3112] [3113] [3114] Overfull \hbox (20.58041pt too wide) in paragraph at lines 12333--12333 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$ vectors[,ind]))[] Underfull \hbox (badness 1975) in paragraph at lines 12344--12349 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [3115] Underfull \hbox (badness 1803) in paragraph at lines 12421--12425 \T1/ptm/m/n/10 The last en-try will be the []\T1/pcr/m/n/10 by []\T1/ptm/m/n/10 vari-able, if []\T1/pcr/m/n/10 object$by []\T1/ptm/m/n/10 is not []\T1/pcr/m/n /10 "NA"[]\T1/ptm/m/n/10 . Underfull \hbox (badness 1502) in paragraph at lines 12433--12445 []\T1/pcr/m/n/10 cs.smooth.spec []\T1/ptm/m/n/10 (cu-bic re-gres-sion splines w ith shrinkage-to-zero); []\T1/pcr/m/n/10 cc.smooth.spec [3116] Underfull \hbox (badness 2401) in paragraph at lines 12450--12454 []\T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able . Plot meth-ods can be Underfull \hbox (badness 2970) in paragraph at lines 12450--12454 \T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for []\T1/pc r/m/n/10 mgcv:::plot.sos.smooth[]\T1/ptm/m/n/10 , [3117] [3118] [3119] Underfull \hbox (badness 6876) in paragraph at lines 12645--12651 [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use adap-tive smooths of on e or two vari-ables, spec-i-fied via terms like [3120] Underfull \hbox (badness 10000) in paragraph at lines 12686--12687 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3121] [3122] Underfull \hbox (badness 10000) in paragraph at lines 12804--12805 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3123] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12858--12858 [] \T1/pcr/m/n/9 b <- gam(y~s(x0,bs=bs,m=c(4,2))+s(x1,bs=bs)+s(x2,k=15,bs=bs, m=c(4,3,0))+[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12870--12870 [] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5, 1.5) (black)[] [3124] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12882--12882 [] \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions and intervals[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12887--12887 [] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i ntervals away[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12893--12893 [] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w ild and wide[] Overfull \hbox (3.70428pt too wide) in paragraph at lines 12894--12894 [] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/cmtt/m/n/9 `\T1 /pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] [3125] Underfull \hbox (badness 10000) in paragraph at lines 12963--12965 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a Underfull \hbox (badness 10000) in paragraph at lines 12963--12965 \T1/ptm/m/n/10 term []\T1/pcr/m/n/10 s(...,bs="cr",...)[]\T1/ptm/m/n/10 , []\T1 /pcr/m/n/10 s(...,bs="cs",...) []\T1/ptm/m/n/10 or [3126] [3127] Underfull \hbox (badness 10000) in paragraph at lines 13093--13094 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3128] [3129] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13174--13174 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first deriv penalty[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13175--13175 []\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi ed 2nd deriv[] [3130] [3131] Underfull \hbox (badness 10000) in paragraph at lines 13328--13329 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3132] [3133] [3134] [3135] [3136] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13578--13578 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m ethod="REML")[] [3137] Underfull \hbox (badness 10000) in paragraph at lines 13639--13641 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3138] [3139] Underfull \hbox (badness 10000) in paragraph at lines 13798--13801 []\T1/ptm/m/n/10 For the []\T1/pcr/m/n/10 smooth.construct []\T1/ptm/m/n/10 met hod a smooth spec-i-fi-ca-tion ob- Underfull \hbox (badness 3312) in paragraph at lines 13798--13801 \T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term []\T1/pcr/m/n/10 s(x,...,bs ="re",)[]\T1/ptm/m/n/10 . For the Underfull \hbox (badness 7099) in paragraph at lines 13798--13801 []\T1/pcr/m/n/10 predict.Matrix []\T1/ptm/m/n/10 method an ob-ject of class []\ T1/pcr/m/n/10 "random.effect" [3140] [3141] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13884--13884 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with 2 variances[] [3142] Underfull \hbox (badness 10000) in paragraph at lines 13929--13935 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a Underfull \hbox (badness 7832) in paragraph at lines 13929--13935 []\T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) []\T1/ptm/m/n/10 term in a []\T1/pcr/m/n/10 gam []\T1/ptm/m/n/10 for- [3143] [3144] [3145] Overfull \hbox (36.7804pt too wide) in paragraph at lines 14144--14144 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] Underfull \vbox (badness 10000) has occurred while \output is active [3146] Underfull \vbox (badness 10000) has occurred while \output is active [3147] Underfull \hbox (badness 10000) in paragraph at lines 14247--14255 [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths on th e sphere, via terms like Underfull \hbox (badness 10000) in paragraph at lines 14273--14274 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3148] [3149] [3150] Underfull \hbox (badness 7613) in paragraph at lines 14418--14421 []\T1/ptm/m/n/10 method an ob-ject of class []\T1/pcr/m/n/10 "sz.interaction" [ ]\T1/ptm/m/n/10 pro-duced by the [3151] Underfull \hbox (badness 1546) in paragraph at lines 14439--14440 []\T1/ptm/m/n/10 The terms can have a smooth-ing pa-ram-e-ter per smooth, or a sin-gle smooth-ing pa-ram-e- Overfull \hbox (128.58029pt too wide) in paragraph at lines 14485--14485 []\T1/pcr/m/n/9 b <- gam(y ~ s(x)+s(f1,x,bs="sz")+s(f2,x,bs="sz")+s(f1,f2,x,bs ="sz",id=1),data=dat,method="REML")[] [3152] [3153] [3154] Underfull \hbox (badness 3396) in paragraph at lines 14631--14634 [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths of an y num-ber of vari-ables, spec-i-fied via terms like Underfull \hbox (badness 10000) in paragraph at lines 14676--14678 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3155] [3156] [3157] [3158] [3159] [3160] Underfull \hbox (badness 10000) in paragraph at lines 14967--14969 []\T1/pcr/m/n/10 bs="fs" []\T1/ptm/m/n/10 A spe-cial smoother class (see [3161] Underfull \hbox (badness 10000) in paragraph at lines 15001--15005 [][][]\T1/pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][][]\ T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 t2[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 tprs[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Duchon.spline[][][][]\T 1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cubic.regression.spline[][][][]\T1/ptm/m/n/ 10 , Underfull \hbox (badness 10000) in paragraph at lines 15001--15005 [][][]\T1/pcr/m/n/10 p.spline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 d.sp line[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 mrf[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 soap[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Spherical .Spline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 adaptive.smooth[][][][]\T1 /ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 15001--15005 [][][]\T1/pcr/m/n/10 user.defined.smooth[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/ m/n/10 smooth.construct.re.smooth.spec[][][][]\T1/ptm/m/n/10 , [3162] [3163] [3164] [3165] [3166] Underfull \hbox (badness 2158) in paragraph at lines 15291--15291 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [3167] Overfull \hbox (48.78088pt too wide) in paragraph at lines 15370--15370 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0, centre=FALSE)[] [3168] [3169] Overfull \hbox (12.78088pt too wide) in paragraph at lines 15504--15504 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars "),...)[] [3170] [3171] Underfull \hbox (badness 4846) in paragraph at lines 15635--15638 []\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or es-ti-ma-tors if [3172] [3173] [3174] [3175] [3176] [3177] [3178] [3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186] [3187] [3188] [3189] [3190] [3191] Overfull \hbox (120.78088pt too wide) in paragraph at lines 16853--16853 []\T1/pcr/m/n/10 vcov(object, sandwich=FALSE, freq = FALSE, dispersion = NULL, unconditional=FALSE, ...)[] [3192] Underfull \hbox (badness 1715) in paragraph at lines 16875--16876 []\T1/ptm/m/n/10 Basically, just ex-tracts []\T1/pcr/m/n/10 object$Ve[]\T1/ptm/ m/n/10 , []\T1/pcr/m/n/10 object$Vp []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 object $Vc []\T1/ptm/m/n/10 (if avail-able) from a [3193] [3194] [3195] Overfull \hbox (54.78088pt too wide) in paragraph at lines 17065--17065 []\T1/pcr/m/n/10 XWXd(X,w,k,ks,ts,dt,v,qc,nthreads=1,drop=NULL,ar.stop=-1,ar.r ow=-1,ar.w=-1, Overfull \hbox (48.78088pt too wide) in paragraph at lines 17067--17067 []\T1/pcr/m/n/10 XWyd(X,w,y,k,ks,ts,dt,v,qc,drop=NULL,ar.stop=-1,ar.row=-1,ar. w=-1,lt=NULL)[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17069--17069 []\T1/pcr/m/n/10 diagXVXd(X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,rt= NULL)[] [3196] Underfull \hbox (badness 10000) in paragraph at lines 17089--17090 []\T1/ptm/m/n/10 Negative to ig-nore. Oth-er-wise sum rows Underfull \hbox (badness 1668) in paragraph at lines 17089--17090 []\T1/pcr/m/n/10 (ar.stop[i-1]+1):ar.stop[i] []\T1/ptm/m/n/10 of the rows se-le cted by []\T1/pcr/m/n/10 ar.row [3197] Underfull \vbox (badness 10000) has occurred while \output is active [3198] [3199] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17277--17277 []\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li near predictor,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17278--17278 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun ded in regions[] [3200] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17290--17290 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val ues, to check we[] [3201] [3202] [3203]) (./nlme-pkg.tex [3204] Chapter 25. [3205] Underfull \hbox (badness 1009) in paragraph at lines 84--93 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3206] Underfull \hbox (badness 1009) in paragraph at lines 174--183 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3207] [3208] [3209] [3210] [3211] Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454 [] \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [3212] [3213] Overfull \hbox (20.58041pt too wide) in paragraph at lines 595--595 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 --------------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 611--611 []\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n on-sensical!)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 614--614 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 --------------------------- ---------------[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 621--621 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 --------------------------- ---------------[] [3214] [3215] [3216] [3217] [3218] [3219] [3220] [3221] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1085--1085 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil lary fissure"),[] [3222] Underfull \hbox (badness 5446) in paragraph at lines 1147--1149 []\T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel .htm[]\T1/ptm/m/n/10 ', the first edi-tion of [3223] [3224] [3225] [3226] [3227] [3228] [3229] Underfull \hbox (badness 10000) in paragraph at lines 1626--1629 [][][]\T1/pcr/m/n/10 lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fixed. effects.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 ranef.lmList[][][][ ]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.ranef.lmList[][][][]\T1/ptm/m/n/10 , [3230] Underfull \hbox (badness 3780) in paragraph at lines 1643--1645 []\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a ted with each com-po-nent of the [3231] [3232] [3233] [3234] [3235] Underfull \hbox (badness 2042) in paragraph at lines 1992--1998 \T1/ptm/m/n/10 is in-ner to the []\T1/pcr/m/n/10 displayLevel []\T1/ptm/m/n/10 group-ing fac-tor. If equal to []\T1/pcr/m/n/10 TRUE[]\T1/ptm/m/n/10 , [3236] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2054--2054 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla pse = "Dog")[] [3237] Underfull \hbox (badness 1132) in paragraph at lines 2143--2145 []\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac ted us-ing the [3238] [3239] Underfull \hbox (badness 4168) in paragraph at lines 2254--2260 [][][]\T1/pcr/m/n/10 ACF.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corAR MA[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/pcr/m/n/10 Dim.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 , [3240] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2279--2279 [] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [3241] [3242] [3243] [3244] [3245] [3246] [3247] [3248] Underfull \hbox (badness 10000) in paragraph at lines 2845--2849 [][][]\T1/pcr/m/n/10 corFactor[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cor Matrix.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 recalc.corStruct[ ][][][]\T1/ptm/m/n/10 , [3249] [3250] [3251] [3252] [3253] [3254 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.corMatrix .corCompSymm}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.3188 ...trix(cs1, covariate = 1:4, corr = FALSE) ] [3255] [3256] [3257] [3258] [3259] [3260] Underfull \hbox (badness 6493) in paragraph at lines 3580--3588 [][][]\T1/pcr/m/n/10 corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corGau s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corLin[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 corRatio[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corSp her[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][][]\T 1/ptm/m/n/10 , [3261] [3262] [3263] [3264] [3265] [3266] [3267] [3268] [3269] [3270] [3271] [3272] [3273] [3274] [3275] [3276] [3277] [3278] [3279] [3280] [3281] [3282] [3283] [3284] Underfull \hbox (badness 10000) in paragraph at lines 5160--5164 [][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/p cr/m/n/10 getCovariate.data.frame[][][][]\T1/ptm/m/n/10 , [3285] [3286] [3287] [3288] [3289] [3290] [3291] Underfull \hbox (badness 10000) in paragraph at lines 5592--5595 [][][]\T1/pcr/m/n/10 getGroupsFormula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n /10 getGroups.data.frame[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 getGroups .gls[][][][]\T1/ptm/m/n/10 , [3292] [3293] [3294] [3295] [3296] [3297] [3298] [3299] [3300] Underfull \hbox (badness 2799) in paragraph at lines 6098--6104 \T1/ptm/m/n/10 covariance ma-trix, ei-ther []\T1/pcr/m/n/10 "random.effects" [] \T1/ptm/m/n/10 for the random-effects [3301] Underfull \hbox (badness 7133) in paragraph at lines 6159--6163 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in [ ]\T1/pcr/m/n/10 model[]\T1/ptm/m/n/10 , [3302] Underfull \hbox (badness 2057) in paragraph at lines 6248--6259 [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gl sControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 glsObject[][][][]\T1/ptm/ m/n/10 , [][][]\T1/pcr/m/n/10 glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 plot.gls[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.gls[][][][] \T1/ptm/m/n/10 , [3303] Underfull \hbox (badness 10000) in paragraph at lines 6312--6314 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3304] [3305] [3306] [3307] Underfull \hbox (badness 7133) in paragraph at lines 6560--6564 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in [ ]\T1/pcr/m/n/10 model[]\T1/ptm/m/n/10 , [3308] Underfull \hbox (badness 10000) in paragraph at lines 6659--6665 [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gn lsControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gnlsObject[][][][]\T1/pt m/m/n/10 , [][][]\T1/pcr/m/n/10 gnlsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc r/m/n/10 predict.gnls[][][][]\T1/ptm/m/n/10 , Overfull \hbox (54.78088pt too wide) in paragraph at lines 6686--6686 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min Scale = 0.001, [3309] Underfull \hbox (badness 10000) in paragraph at lines 6724--6726 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3310] [3311] [3312] [3313] Underfull \hbox (badness 10000) in paragraph at lines 6995--7002 [][][]\T1/pcr/m/n/10 formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gappl y[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gsummary[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.nff GroupedData[][][][]\T1/ptm/m/n/10 , [3314] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7013--7013 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla ry fissure" ),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7018--7018 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted from object[] Underfull \hbox (badness 2875) in paragraph at lines 7040--7042 []\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a []\T1/pcr/m/n/10 gr oupedData []\T1/ptm/m/n/10 ob-ject or a [3315] [3316] [3317] Underfull \hbox (badness 10000) in paragraph at lines 7255--7260 [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr /m/n/10 Initialize.lmeStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initi alize.glsStruct[][][][]\T1/ptm/m/n/10 , [3318] [3319] [3320] Underfull \hbox (badness 1997) in paragraph at lines 7406--7414 []\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial -iza-tion and op-ti- Underfull \hbox (badness 2205) in paragraph at lines 7406--7414 \T1/ptm/m/n/10 miza-tion al-go-rithms used in []\T1/pcr/m/n/10 lme[]\T1/ptm/m/n /10 . De-faults to []\T1/pcr/m/n/10 list(niterEM=20, Underfull \hbox (badness 3118) in paragraph at lines 7429--7432 [][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initializ e.reStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.corStruct[][ ][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.varFunc[][][][]\T1/ptm/m/ n/10 , [3321] [3322] [3323] Underfull \hbox (badness 3354) in paragraph at lines 7645--7647 []\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when []\T1/pcr/m/n/ 10 which []\T1/ptm/m/n/10 is not equal to [3324] [3325] [3326] [3327] [3328] [3329] [3330] [3331] Underfull \hbox (badness 10000) in paragraph at lines 8173--8190 [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lm e.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lme.groupedData[][][][]\T 1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lmeControl[][][][]\T1/ptm/m/n/10 , [][][]\T 1/pcr/m/n/10 lmeObject[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8173--8190 [][][]\T1/pcr/m/n/10 lmeStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lmL ist[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/pcr/m/n/10 plot.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 qqnorm.lme[][][][]\T1/ ptm/m/n/10 , [3332] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8216--8216 [] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data = TRUE)[] Underfull \hbox (badness 1642) in paragraph at lines 8225--8247 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3333] [3334] [3335] [3336] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8490--8490 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni terEM = 25, [3337] Underfull \hbox (badness 10000) in paragraph at lines 8538--8540 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Overfull \hbox (9.78043pt too wide) in paragraph at lines 8582--8582 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3338] [3339] [3340] [3341] [3342] [3343] [3344] [3345] [3346] [3347] [3348] [3349] Underfull \hbox (badness 10000) in paragraph at lines 9345--9352 [][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 ,[][][]\T1/pcr/m/n/10 gls[][][][ ]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logLik.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logLik.glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 logLik.lmeStruct[][][][]\T1/ptm/m/n/10 , Overfull \hbox (4.38043pt too wide) in paragraph at lines 9356--9356 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me thod = "ML") [3350] [3351] [3352] [3353] [3354] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9707 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Matrix.1} ) has been already used, duplicate ignored \relax l.9707 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3355] Underfull \hbox (badness 10000) in paragraph at lines 9727--9730 []\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a s Underfull \hbox (badness 3108) in paragraph at lines 9771--9774 []\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive -definite Underfull \hbox (badness 2521) in paragraph at lines 9771--9774 \T1/ptm/m/n/10 ma-trix rep-re-sented by []\T1/pcr/m/n/10 object[]\T1/ptm/m/n/10 . Must have the same di-men-sions as [3356] [3357] [3358] [3359] [3360] [3361] [3362] [3363] [3364] [3365] [3366] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10451--10451 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights, [3367] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10455--10455 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights,[] Underfull \hbox (badness 1596) in paragraph at lines 10484--10510 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3368] [3369] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10638--10638 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights,[] [3370] [3371] [3372] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10789--10789 [] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma = NULL, ...)[] Underfull \hbox (badness 2213) in paragraph at lines 10800--10805 []\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][][]\T1/pcr/m/n/10 nlmi nb[][][] []\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 iter.max[]\T1/ptm/m/n/10 ) or the [ ][][]\T1/pcr/m/n/10 nlm[][][] Underfull \hbox (badness 6961) in paragraph at lines 10822--10826 []\T1/ptm/m/n/10 a log-i-cal value passed as the []\T1/pcr/m/n/10 trace []\T1/p tm/m/n/10 to [][][]\T1/pcr/m/n/10 nlminb[][][](.., control= [3373] Underfull \hbox (badness 10000) in paragraph at lines 10841--10843 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3374] [3375] [3376] [3377] Overfull \hbox (96.18033pt too wide) in paragraph at lines 11137--11137 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* message instead of one *each*[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 11138--11138 []\T1/pcr/m/n/9 mat.class <- class(matrix(1)) # ("matrix", "array") for R >= 4 .0.0; ("matrix" in older R)[] [3378] [3379] [3380] [3381] [3382] [3383] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11528--11528 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo nt)), .. lme(*)) [3384] [3385] [3386] [3387] [3388] [3389] Underfull \hbox (badness 6268) in paragraph at lines 11915--11925 [][][]\T1/pcr/m/n/10 pdBlocked[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdC ompSymm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdDiag[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 pdFactor[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdIdent[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 pdMatrix[][][][]\T1/ptm/m/n/10 , [3390] [3391] [3392] [3393] Underfull \hbox (badness 10000) in paragraph at lines 12176--12182 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 coef.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdBlocked[][][][]\T1 /ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 pdConstruct[][][][]\T1/ptm/m/n/10 , [3394] [3395] [3396] [3397] [3398] Underfull \hbox (badness 6876) in paragraph at lines 12498--12500 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 value []\T1/ptm/m/n/10 is an \T1/ptm/m/it/ 10 ini-tial-ized []\T1/pcr/m/n/10 pdMat []\T1/ptm/m/n/10 ob-ject, []\T1/pcr/m/n /10 object []\T1/ptm/m/n/10 will be con-structed from [3399] [3400] Underfull \hbox (badness 2452) in paragraph at lines 12654--12661 [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdC ompSymm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdDiag[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 pdIdent[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdNatural[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdSymm[][][][]\T1/ptm/m/ n/10 , [][][]\T1/pcr/m/n/10 reStruct[][][][]\T1/ptm/m/n/10 , [3401] Underfull \hbox (badness 10000) in paragraph at lines 12720--12726 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdFactor[][][][]\T1/p tm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 pdMatrix.reStruct[][][][]\T1/ptm/m/n/10 , [3402] [3403] [3404] [3405] [3406] [3407] [3408] [3409] [3410] Overfull \hbox (25.98041pt too wide) in paragraph at lines 13309--13309 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo nt)), .. lme(*)) [3411] [3412] [3413] [3414] [3415] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13674--13674 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 0, id = 0.05)[] [3416] Underfull \hbox (badness 10000) in paragraph at lines 13701--13704 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nffGroupe dData[]\T1/ptm/m/n/10 , rep-re-sent-ing a [3417] Underfull \hbox (badness 1838) in paragraph at lines 13744--13751 []\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If []\T1/pcr/m/ n/10 TRUE []\T1/ptm/m/n/10 and ei-ther []\T1/pcr/m/n/10 inner Underfull \hbox (badness 3713) in paragraph at lines 13744--13751 []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 innerGroups []\T1/ptm/m/n/10 are non-[]\T1 /pcr/m/n/10 NULL[]\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent []\T1/pcr/m/n/ 10 inner Overfull \hbox (12.78088pt too wide) in paragraph at lines 13801--13801 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect, panel,[] [3418] Underfull \hbox (badness 10000) in paragraph at lines 13808--13811 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nfnGroupe dData[]\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 2469) in paragraph at lines 13808--13811 []\T1/pcr/m/n/10 groupedData []\T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-vari-ate and a sin-gle [3419] Underfull \hbox (badness 10000) in paragraph at lines 13916--13919 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nmGrouped Data[]\T1/ptm/m/n/10 , rep-re-sent-ing a [3420] [3421] Underfull \hbox (badness 10000) in paragraph at lines 14010--14012 [][][]\T1/pcr/m/n/10 groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 c ollapse.groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.nfnGroupe dData[][][][]\T1/ptm/m/n/10 , [3422] [3423] [3424] [3425] [3426] [3427] [3428] [3429] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14534--14534 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female", "Male","Male"),[] [3430] [3431] [3432] [3433] [3434] [3435] [3436] [3437] [3438] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.random.ef fects}) has been already used, duplicate ignored \relax l.15187 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.random.ef fects.1}) has been already used, duplicate ignored \relax l.15187 ...Extract Random Effects}{random.effects} [3439] [3440] [3441] [3442] [3443] [3444] [3445] [3446] [3447] [3448] Underfull \hbox (badness 2126) in paragraph at lines 15826--15830 []\T1/ptm/m/n/10 Charles F. Minto, Thomas W. Schnider and Steven L. Shafer (199 7). Phar-ma-coki-net- [3449] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15834--15834 []\T1/pcr/m/n/9 plot(Remifentanil, type = "l", lwd = 2) # shows the 65 patient s\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 remi profiles Overfull \hbox (31.3804pt too wide) in paragraph at lines 15853--15853 [] \T1/pcr/m/n/9 stopifnot(all.equal(BSA, Wt^{0.425} * Ht^{0.725} * 0.00718 4, tol = 1.5e-5),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15854--15854 [] \T1/pcr/m/n/9 all.equal(LBM, LBMfn(Wt, Ht, Sex), tol = 7e-7)[] [3450] Underfull \hbox (badness 1009) in paragraph at lines 15884--15893 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3451] [3452] Overfull \hbox (66.78088pt too wide) in paragraph at lines 16031--16031 [] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi st = FALSE, ...)[] [3453] [3454] [3455] [3456] [3457] Underfull \hbox (badness 10000) in paragraph at lines 16366--16372 [][][]\T1/pcr/m/n/10 groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 l me[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 solve.reStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 summary.reStruct[][][][]\T1/ptm/m/n/10 , [3458] Overfull \hbox (18.78088pt too wide) in paragraph at lines 16398--16398 [] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG en, ...)[] [3459] [3460] [3461] [3462] [3463] [3464] [3465] Underfull \hbox (badness 1728) in paragraph at lines 16885--16888 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3466] [3467] [3468] [3469] [3470] Underfull \hbox (badness 1803) in paragraph at lines 17219--17228 \T1/pcr/m/n/10 of an Identity" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pdIdent[]\ T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "General Positive-Definite, Underfull \hbox (badness 10000) in paragraph at lines 17219--17228 \T1/pcr/m/n/10 Natural Parametrization" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 p dNatural[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "General Underfull \hbox (badness 7888) in paragraph at lines 17219--17228 \T1/pcr/m/n/10 Positive-Definite" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pdSymm[ ]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 data.class(object) [3471] Underfull \hbox (badness 10000) in paragraph at lines 17290--17291 []\T1/pcr/m/n/10 "Constant plus power of variance Underfull \hbox (badness 10000) in paragraph at lines 17291--17292 []\T1/pcr/m/n/10 "Constant plus proportion of variance [3472] [3473] [3474] [3475] Underfull \hbox (badness 10000) in paragraph at lines 17541--17549 [][][]\T1/pcr/m/n/10 varComb[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varCo nstPower[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varConstProp[][][][]\T1/p tm/m/n/10 , [][][]\T1/pcr/m/n/10 varExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 varFixed[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varIdent[][][][]\T1 /ptm/m/n/10 , [3476] [3477] [3478] [3479] Overfull \hbox (4.38043pt too wide) in paragraph at lines 17813--17813 []\T1/pcr/m/n/9 # Generate some synthetic data using the two-component error m odel and use Overfull \hbox (25.98041pt too wide) in paragraph at lines 17815--17815 []\T1/pcr/m/n/9 # overparameterisation in the case of a constant term in the v ariance function[] [3480] [3481] [3482] [3483] [3484] [3485] Underfull \hbox (badness 10000) in paragraph at lines 18251--18261 [][][]\T1/pcr/m/n/10 Variogram.corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n /10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.co rLin[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18251--18261 [][][]\T1/pcr/m/n/10 Variogram.corRatio[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 Variogram.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogr am.corSpher[][][][]\T1/ptm/m/n/10 , [3486] Underfull \hbox (badness 3579) in paragraph at lines 18289--18294 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3487] Underfull \hbox (badness 3579) in paragraph at lines 18353--18358 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3488] Underfull \hbox (badness 3579) in paragraph at lines 18416--18421 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3489] Underfull \hbox (badness 1577) in paragraph at lines 18477--18479 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 "[][]corR atio[][][]"[]\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal Underfull \hbox (badness 3579) in paragraph at lines 18479--18484 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3490] Underfull \hbox (badness 3579) in paragraph at lines 18542--18547 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence Underfull \hbox (badness 10000) in paragraph at lines 18575--18584 [][][]\T1/pcr/m/n/10 corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Va riogram[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.default[][][][]\ T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.corExp[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18575--18584 [][][]\T1/pcr/m/n/10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 Variogram.corLin[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.co rRatio[][][][]\T1/ptm/m/n/10 , [3491] Underfull \hbox (badness 3579) in paragraph at lines 18614--18619 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3492] [3493] Underfull \hbox (badness 1009) in paragraph at lines 18760--18769 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3494] [3495] Underfull \hbox (badness 1009) in paragraph at lines 18892--18901 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3496] [3497] [3498] [3499] [3500] [3501] [3502] [3503] [3504]) (./nnet-pkg.tex Chapter 26. pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom} ) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom. 1}) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} [3505] Overfull \hbox (12.78088pt too wide) in paragraph at lines 71--71 [] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored = FALSE,[] [3506] [3507] [3508] Overfull \hbox (15.18042pt too wide) in paragraph at lines 371--371 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3509] Overfull \hbox (4.38043pt too wide) in paragraph at lines 428--428 []\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c( 0,0,1),50)),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 431--431 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay =5e-4, maxit=200)[] [3510] [3511] Overfull \hbox (15.18042pt too wide) in paragraph at lines 511--511 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3512]) (./rpart-pkg.tex Chapter 27. [3513] [3514] [3515] [3516] Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse = TRUE, ...)[] [3517] Underfull \hbox (badness 2351) in paragraph at lines 349--353 \T1/ptm/m/n/10 age: []\T1/pcr/m/n/10 pretty = 0 []\T1/ptm/m/n/10 im-plies []\T1 /pcr/m/n/10 minlength = 0L[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pretty = NULL []\ T1/ptm/m/n/10 im-plies [3518] [3519] [3520] Underfull \hbox (badness 1442) in paragraph at lines 592--598 []\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 FALSE[]\T1/ptm/m/n/10 , the leaf nodes wil l be at the hor-i-zon-tal plot co-or-di-nates of [3521] [3522] Overfull \hbox (0.78088pt too wide) in paragraph at lines 738--738 [] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep = ""),[] Underfull \hbox (badness 10000) in paragraph at lines 771--775 []\T1/ptm/m/n/10 Logical. If []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 (de-fault), adds to the la-bel Underfull \hbox (badness 1142) in paragraph at lines 771--775 \T1/pcr/m/n/10 #events level1/ #events level2/ \T1/ptm/m/n/10 etc. for method [ ]\T1/pcr/m/n/10 class[]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 n [3523] [3524] [3525] Overfull \hbox (25.98041pt too wide) in paragraph at lines 915--915 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie s, probabilities[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 934--934 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d igits"),[] [3526] [3527] [3528] [3529] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1180--1180 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m ethod, Overfull \hbox (12.78088pt too wide) in paragraph at lines 1181--1181 [] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos t, ...)[] Underfull \hbox (badness 2846) in paragraph at lines 1243--1245 []\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the []\T1/pcr/m/n /10 rpart []\T1/ptm/m/n/10 al-go-rithm. See [3530] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1287--1287 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the text is clipped[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1303--1303 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c p = 0.01, Overfull \hbox (60.78088pt too wide) in paragraph at lines 1304--1304 [] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,[] [3531] [3532] [3533] [3534] [3535] [3536] [3537] Underfull \hbox (badness 1565) in paragraph at lines 1760--1763 []\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val- ues are `[]\T1/pcr/m/n/10 diploid[]\T1/ptm/m/n/10 ', [3538] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1854--1854 [] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,[] [3539] [3540] [3541]) (./spatial-pkg.tex [3542] Chapter 28. [3543] [3544] [3545] [3546] [3547] [3548] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3549] [3550] [3551] [3552] [3553] [3554] [3555] [3556] [3557] [3558] [3559] [3560] [3561]) (./survival-pkg.tex [3562] Chapter 29. [3563] [3564] Overfull \hbox (31.3804pt too wide) in paragraph at lines 173--173 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data = lung, nmin = 1[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 192--192 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t he last point[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 195--195 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a nd Grambsch.[] [3565] [3566] Underfull \hbox (badness 6412) in paragraph at lines 284--286 []\T1/ptm/m/n/10 an op-tional list or vec-tor of group-ing el-e-ments, each as long as [3567] [3568] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has been already used, duplicate ignored \relax l.384 ... Myelogenous Leukemia survival data}{aml} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml.1}) h as been already used, duplicate ignored \relax l.384 ... Myelogenous Leukemia survival data}{aml} [3569] Overfull \hbox (9.78043pt too wide) in paragraph at lines 485--485 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da ta = ovarian) Overfull \hbox (4.38043pt too wide) in paragraph at lines 487--487 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d ata=ovarian)[] [3570] Overfull \hbox (6.78088pt too wide) in paragraph at lines 525--525 [] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog), lung)[] [3571] [3572] [3573] [3574] Overfull \hbox (20.58041pt too wide) in paragraph at lines 773--773 []\T1/pcr/m/n/9 py <- pseudo(survfit(Surv(time, status) ~1, lung), time=730) # 2 year survival Overfull \hbox (30.78088pt too wide) in paragraph at lines 789--789 []\T1/pcr/m/n/10 brier(fit, times, newdata, ties = TRUE, detail = FALSE, timef ix = TRUE, [3575] [3576] Overfull \hbox (48.78088pt too wide) in paragraph at lines 872--872 [] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan", "II.Borgan"),[] [3577] [3578] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1015--1015 [] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz e=stratsizes,[] [3579] [3580] Underfull \hbox (badness 1097) in paragraph at lines 1186--1188 []\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi al and negative-binomial data. [3581] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1206--1206 []\T1/pcr/m/n/9 ppois(4, 10.24153) #chance of seeing 4 or fewer events wit h large rate[] [3582] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1321--1321 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat um), data=infert) [3583] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1382--1382 []\T1/pcr/m/n/9 marginal.model <- coxph(Surv(time, status) ~ rx, data= rats, c luster=litter, pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colon}) h as been already used, duplicate ignored \relax l.1388 ...erapy for Stage B/C colon cancer}{colon} [3584] [3585] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1488--1488 [] \T1/pcr/m/n/10 influence=0, ranks = FALSE, reverse=FALSE, timefix=TRUE, ke epstrata=10, ...)[] [3586] [3587] [3588] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1714--1714 []\T1/pcr/m/n/9 options(na.action = na.exclude) # predict all 1384 obs, incl uding missing[] [3589] [3590] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1808--1808 []\T1/pcr/m/n/10 cox.zph(fit, transform="km", terms=TRUE, singledf=FALSE, glob al=TRUE) [3591] [3592] [3593] [3594] Underfull \hbox (badness 10000) in paragraph at lines 2124--2139 []\T1/ptm/m/n/10 One user mis-take that has re-cently arisen is to slav-ishly f ol-low the ad-vice of Underfull \hbox (badness 7486) in paragraph at lines 2124--2139 \T1/ptm/m/n/10 some cod-ing guides and prepend []\T1/pcr/m/n/10 survival:: []\T 1/ptm/m/n/10 onto ev-er-thing, in-clud-ing the spe- Underfull \hbox (badness 10000) in paragraph at lines 2124--2139 \T1/ptm/m/n/10 cial terms, e.g., []\T1/pcr/m/n/10 survival::coxph(survival:Surv (time, status) ~ age + [3595] Underfull \hbox (badness 3861) in paragraph at lines 2219--2223 [][][]\T1/pcr/m/n/10 coxph.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 coxphms.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 coxph.control[][][] []\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cluster[][][][]\T1/ptm/m/n/10 , [][][]\ T1/pcr/m/n/10 strata[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Surv[][][][]\ T1/ptm/m/n/10 , [3596] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2274--2274 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix =TRUE)[] [3597] [3598] [3599] [3600] [3601] [3602] [3603] [3604] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2902--2902 [] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" " exponential"[] [3605] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2943--2943 []\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass, etype, [3606] [3607] [3608] [3609] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3187--3187 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t df = 5,[] [3610] [3611] [3612] [3613] Underfull \hbox (badness 1019) in paragraph at lines 3449--3451 []\T1/ptm/m/n/10 outcome: []\T1/pcr/m/n/10 censor[]\T1/ptm/m/n/10 , []\T1/pcr/m /n/10 thymic lymphoma[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 reticulum cell sarcoma other [3614] [3615] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3593--3593 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt y(id), kidney) [3616] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3628--3628 [] \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre ssion", "death")))[] Underfull \hbox (badness 1389) in paragraph at lines 3642--3644 []\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan -Meier plot gen-er-ated with Overfull \hbox (12.78088pt too wide) in paragraph at lines 3653--3653 [] \T1/pcr/m/n/10 conf.type = c("log", "log-log", "plain", "logit", "ar csin"),[] [3617] [3618] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3787--3787 [] \T1/pcr/m/n/9 rmap=list(sex=sex, age=age*365.35, year=as.Da te(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/01/01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3619] [3620] Overfull \hbox (467.89665pt too wide) in alignment at lines 3928--3928 [] [] [3621] [3622] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4050--4050 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential ly the same.[] [3623] [3624] [3625] [3626] [3627] [3628] [3629] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4496--4496 [] \T1/pcr/m/n/9 entry.dt = as.Date(paste("2011", 1:10, "5" , sep=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 -\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3630] [3631] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4646--4646 []\T1/pcr/m/n/9 tdata <- data.frame(x= lung$age, y = 10*log(lung$age-35) + rno rm(228, 0, 2))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4651--4651 []\T1/pcr/m/n/9 knots <- unlist(attributes(fit1$model[[2]])[c(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Boundary.knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )])[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4655--4655 []\T1/pcr/m/n/9 unname(coef(fit1)[-1] - coef(fit1)[1]) # differences: yhat[2: 4] - yhat[1][] [3632] [3633] [3634] [3635] [3636] [3637] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4986--4986 [] \T1/pcr/m/n/10 xlab="Time", ylab, lty=1:2, col=1, lwd=1, hr=FALSE, p lot=TRUE, ...)[] [3638] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5075--5075 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca le=1,[] [3639] [3640] [3641] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5305--5305 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), collapse,[] [3642] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5431--5431 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] [3643] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5439--5439 [] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means , na.rm=TRUE)[] [3644] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5525--5525 []\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival is at +infinity[] [3645] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5603--5603 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars"), expand=FALSE , ...)[] [3646] Underfull \hbox (badness 1852) in paragraph at lines 5675--5677 []\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.survfit"[]\T1/pt m/m/n/10 , which is the re-sult of the [3647] [3648] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5801--5801 []\T1/pcr/m/n/10 pseudo(fit, times, type, addNA=TRUE, data.frame=FALSE, minus1 =FALSE, ...) [3649] [3650] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5912--5912 []\T1/pcr/m/n/9 rhat <- predict(rfit, newdata=expand.grid(ph.ecog=0:3, sex=1:2 ), se.fit=TRUE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5924--5924 []\T1/pcr/m/n/9 # the estimate for ph.ecog=3 is very unstable (n=1), pseudoval ues smooth it.[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5926--5926 []\T1/pcr/m/n/9 # In all the above we should be using the robust variance, e.g ., svyglm, but[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5950--5950 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me thod, Overfull \hbox (36.78088pt too wide) in paragraph at lines 5951--5951 [] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co mbine, ...)[] [3651] [3652] [3653] Overfull \hbox (30.78088pt too wide) in paragraph at lines 6114--6114 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] [3654] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6216--6216 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age + sex, mgus,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6237--6237 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50 ,60,70,100)) +[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6239--6239 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5 0,60,70,100)) +[] [3655] [3656] [3657] [3658] [3659] [3660] [3661] Overfull \hbox (42.78088pt too wide) in paragraph at lines 6705--6705 [] \T1/pcr/m/n/10 collapse=FALSE, weighted= (type %in% c("dfbeta", "dfbe tas")), ...)[] [3662] [3663] [3664] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6887--6887 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb etas",[] Underfull \hbox (badness 1043) in paragraph at lines 6899--6902 []\T1/pcr/m/n/10 "dfbetas"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "working"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "ldcase"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lsresp "[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ldshape"[]\T1/ptm/m/n/10 , and [3665] [3666] [3667] [3668] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7206--7206 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the ta=5), lung)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7207--7207 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog , theta=1), lung)[] [3669] [3670] [3671] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7391--7391 []\T1/pcr/m/n/10 rttright(formula, data, weights, subset, na.action, times, id , timefix = TRUE, [3672] Overfull \hbox (42.18039pt too wide) in paragraph at lines 7474--7474 []\T1/pcr/m/n/9 cdf <- cdf[!duplicated(aml$time[index], fromLast=TRUE)] # rem ove duplicate times[] [3673] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7478--7478 []\T1/pcr/m/n/9 wt2 <- rttright(Surv(dtime, death) ~ hormon, rotterdam, times= 365*c(3, 5))[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) has been already used, duplicate ignored \relax l.7482 ...ata from a soldering experiment}{solder} [3674] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7588--7588 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1, col = 1, [3675] [3676] [3677] [3678] [3679] [3680] Overfull \hbox (42.78088pt too wide) in paragraph at lines 7954--7954 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r r =expected,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 7955--7955 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli ne = FALSE,[] [3681] [3682] [3683] [3684] Overfull \hbox (54.78088pt too wide) in paragraph at lines 8272--8272 [] \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/ 10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/ n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[] [3685] [3686] [3687] [3688] Underfull \hbox (badness 1253) in paragraph at lines 8561--8564 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 median[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 quantile []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 plot []\T1/ptm/m/n/10 meth-ods first con-struct a sur-vival curve us-ing [3689] [3690] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8691--8691 []\T1/pcr/m/n/10 survcheck(formula, data, subset, na.action, id, istate, istat e0="(s0)", [3691] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8814--8814 []\T1/pcr/m/n/10 survcondense(formula, data, subset, weights, na.action= na.pa ss, id, [3692] [3693] [3694] Overfull \hbox (36.7804pt too wide) in paragraph at lines 9013--9013 [] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1 , year=accept.dt),[] [3695] Overfull \hbox (24.78088pt too wide) in paragraph at lines 9038--9038 [] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv idual.h",[] Underfull \hbox (badness 1038) in paragraph at lines 9080--9086 []\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre -dicted sur-vival [3696] Overfull \hbox (48.78088pt too wide) in paragraph at lines 9132--9132 [] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d t-entry.dt)),[] [3697] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9218--9218 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival by 1/2 years[] [3698] [3699] [3700] Underfull \hbox (badness 10000) in paragraph at lines 9438--9443 [][][]\T1/pcr/m/n/10 survfit.formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 survfit.coxph[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 survfit.object[][ ][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.survfit[][][][]\T1/ptm/m/n/10 , Overfull \hbox (12.78088pt too wide) in paragraph at lines 9458--9458 [] \T1/pcr/m/n/10 se.fit=TRUE, conf.int=.95, individual=FALSE, stype=2, ctype,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9459--9459 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] [3701] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9464--9464 [] \T1/pcr/m/n/10 se.fit=FALSE, conf.int=.95, individual=FALSE, stype=2 , ctype,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9465--9465 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] [3702] [3703] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9688--9688 [] \T1/pcr/m/n/10 stype=1, ctype=1, id, cluster, robust, istate, timefi x=TRUE,[] [3704] [3705] Underfull \hbox (badness 2653) in paragraph at lines 9822--9827 \T1/pcr/m/n/10 ctype=1[]\T1/ptm/m/n/10 , "fleming-harrington" which is equiv-a- lent to []\T1/pcr/m/n/10 stype=2, [3706] [3707] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9962--9962 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3708] [3709] [3710] [3711] [3712] Overfull \hbox (30.78088pt too wide) in paragraph at lines 10349--10349 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, Underfull \hbox (badness 1354) in paragraph at lines 10390--10394 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3713] Overfull \hbox (60.78088pt too wide) in paragraph at lines 10436--10436 []\T1/pcr/m/n/10 survConcordance(formula, data, weights, subset, na.action) # use concordance [3714] [3715] Underfull \hbox (badness 2035) in paragraph at lines 10600--10607 \T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][][]\T1/pcr/m/n/10 su rvreg.distributions[][][][]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 10600--10607 \T1/ptm/m/n/10 These in-clude []\T1/pcr/m/n/10 "weibull"[]\T1/ptm/m/n/10 , []\T 1/pcr/m/n/10 "exponential"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "gaussian"[]\T1/p tm/m/n/10 , Underfull \hbox (badness 1297) in paragraph at lines 10600--10607 []\T1/pcr/m/n/10 "logistic"[]\T1/ptm/m/n/10 ,[]\T1/pcr/m/n/10 "lognormal" []\T1 /ptm/m/n/10 and []\T1/pcr/m/n/10 "loglogistic"[]\T1/ptm/m/n/10 . Oth-er-wise, i t is [3716] [3717] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10690--10690 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3718] [3719] Overfull \hbox (31.3804pt too wide) in paragraph at lines 10847--10847 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3720] [3721] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10979--10979 [] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x ^2*temp -1))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 10982--10982 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3722] [3723] [3724] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11158--11158 []\T1/pcr/m/n/9 pfit2 <- pyears(Surv(years, death) ~ fgrp + agegrp, scale =100 0, data=test)[] [3725] [3726] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11316--11316 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic al trial plus[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11317--11317 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11323--11323 [] \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day , alk.phos))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 11325--11325 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil i), data=pbc2)[] [3727] [3728] [3729] [3730] [3731] [3732] [3733] Overfull \hbox (12.78088pt too wide) in paragraph at lines 11766--11766 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l inear",[] [3734] [3735] [3736]) No file fullrefman.ind. 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Transcript written on fullrefman.log. This is makeindex, version 2.17 [TeX Live 2023] (kpathsea + Thai support). Scanning input file fullrefman.idx.............................done (25505 entries accepted, 111 rejected). Sorting entries..................................................................................................................................................................................................................................................................................................done (430077 comparisons). Generating output file fullrefman.ind...........................done (26020 lines written, 109 warnings). Output written in fullrefman.ind. Transcript written in fullrefman.ilg. This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Arch Linux) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./fullrefman.tex LaTeX2e <2022-11-01> patch level 1 L3 programming layer <2023-02-22> (/usr/share/texmf-dist/tex/latex/base/book.cls Document Class: book 2022/07/02 v1.4n Standard LaTeX document class (/usr/share/texmf-dist/tex/latex/base/bk10.clo)) (../../share/texmf/tex/latex/Rd.sty (/usr/share/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texmf-dist/tex/latex/tools/bm.sty) (/usr/share/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texmf-dist/tex/latex/url/url.sty) (/usr/share/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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[3] [4] Underfull \hbox (badness 6741) in paragraph at lines 137--143 []\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber []\T1/pcr/m/n/ 10 x []\T1/ptm/m/n/10 such that []\T1/pcr/m/n/10 1 + x != 1[]\T1/ptm/m/n/10 . Underfull \hbox (badness 4805) in paragraph at lines 137--143 \T1/ptm/m/n/10 It equals []\T1/pcr/m/n/10 double.base ^ ulp.digits []\T1/ptm/m/ n/10 if ei-ther []\T1/pcr/m/n/10 double.base []\T1/ptm/m/n/10 is Underfull \hbox (badness 4316) in paragraph at lines 137--143 \T1/ptm/m/n/10 2 or []\T1/pcr/m/n/10 double.rounding []\T1/ptm/m/n/10 is 0; oth -er-wise, it is []\T1/pcr/m/n/10 (double.base ^ Underfull \hbox (badness 4454) in paragraph at lines 143--151 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber []\T1/pcr/m/n/10 x [ ]\T1/ptm/m/n/10 such that []\T1/pcr/m/n/10 1 - x != 1[]\T1/ptm/m/n/10 . It Underfull \hbox (badness 1028) in paragraph at lines 143--151 \T1/ptm/m/n/10 equals []\T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits []\T 1/ptm/m/n/10 if []\T1/pcr/m/n/10 double.base Underfull \hbox (badness 2980) in paragraph at lines 143--151 []\T1/ptm/m/n/10 is 2 or []\T1/pcr/m/n/10 double.rounding []\T1/ptm/m/n/10 is 0 ; oth-er-wise, it is []\T1/pcr/m/n/10 (double.base Underfull \hbox (badness 1394) in paragraph at lines 143--151 \T1/pcr/m/n/10 ^ double.neg.ulp.digits) / 2[]\T1/ptm/m/n/10 . Nor-mally []\T1/p cr/m/n/10 1.110223e-16[]\T1/ptm/m/n/10 . As [5] Underfull \hbox (badness 1142) in paragraph at lines 215--220 []\T1/ptm/m/n/10 the num-ber of \T1/ptm/m/it/10 bytes \T1/ptm/m/n/10 in the C [ ]\T1/pcr/m/n/10 time_t []\T1/ptm/m/n/10 type: a 64-bit []\T1/pcr/m/n/10 time_t []\T1/ptm/m/n/10 (value Underfull \hbox (badness 1478) in paragraph at lines 215--220 []\T1/pcr/m/n/10 8[]\T1/ptm/m/n/10 ) is much pre-ferred these days. Note that t his is the type used by Underfull \hbox (badness 3009) in paragraph at lines 231--243 []\T1/pcr/m/n/10 *.exponent[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 *.min.exp[]\T1/p tm/m/n/10 , and []\T1/pcr/m/n/10 *.max.exp[]\T1/ptm/m/n/10 , com-puted en-tirel y anal-o-gously to their [6] [7] Underfull \hbox (badness 10000) in paragraph at lines 374--378 [][][]\T1/pcr/m/n/10 R.version[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 Sys.info[][][] []\T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-l ar, [8] [9] [10] Underfull \hbox (badness 1072) in paragraph at lines 571--577 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[] \T1/pcr/m/n/10 insertions[]\T1/ptm/m/n/10 ', [11] Overfull \hbox (4.38043pt too wide) in paragraph at lines 639--639 []\T1/pcr/m/n/9 agrep("laysy", c("1 lazy", "1", "1 LAZY"), max.distance = 2, v alue = TRUE)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 640--640 []\T1/pcr/m/n/9 agrep("laysy", c("1 lazy", "1", "1 LAZY"), max.distance = 2, i gnore.case = TRUE)[] [12] [13] (/usr/share/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [14] [15] Overfull \hbox (4.38043pt too wide) in paragraph at lines 920--920 []\T1/pcr/m/n/9 all.equal(tan(d45), one, tolerance = 0, scale = 1+(-2:2)/1e9) # "absolute"[] [16] Overfull \hbox (4.38043pt too wide) in paragraph at lines 941--941 []\T1/pcr/m/n/9 mtext(paste("mean(all.equal(x1, x2*(1 + eps_k))) {100 x} Mean rel.diff.=",[] [17] Overfull \hbox (0.78088pt too wide) in paragraph at lines 990--990 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE) [18] [19] [20] [21] [22] [23] [24] (/usr/share/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texmf-dist/tex/latex/base/ts1cmtt.fd) [25{/usr/share/texmf-dist/fon ts/enc/dvips/cm-super/cm-super-ts1.enc}] Underfull \hbox (badness 1221) in paragraph at lines 1523--1529 []\T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion, where \T1/phv/m/n/10 R \T1/p tm/m/n/10 uses ``floored'' in-te-ger di-vi-sion, i.e., []\T1/pcr/m/n/10 q <- x %/% y := [26] Underfull \hbox (badness 10000) in paragraph at lines 1611--1617 Underfull \hbox (badness 10000) in paragraph at lines 1624--1626 []\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac le . com / cd / E19957-[]01 / 806-[]3568 / ncg _ [27] [28] [29] [30] Underfull \vbox (badness 10000) has occurred while \output is active [31] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1966--1966 [] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em pty.names = TRUE,[] Underfull \hbox (badness 1303) in paragraph at lines 1998--2001 []\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more than 256 (or [32] Underfull \hbox (badness 1325) in paragraph at lines 2027--2031 []\T1/ptm/m/n/10 Direct calls to []\T1/pcr/m/n/10 as.data.frame.() []\T1 /ptm/m/n/10 are still pos-si-ble (base pack-age!), for 12 Underfull \hbox (badness 3568) in paragraph at lines 2027--2031 \T1/ptm/m/n/10 atomic base classes, but will dep-re-cated (al-ready vis-i-bly b y set-ting en-vi-ron-ment vari- Underfull \hbox (badness 4144) in paragraph at lines 2027--2031 \T1/ptm/m/n/10 able []\T1/pcr/m/n/10 _R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_ [] \T1/ptm/m/n/10 to non-empty) where call-ing [33] [34] [35] Overfull \hbox (112.38031pt too wide) in paragraph at lines 2267--2267 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [36] Underfull \hbox (badness 10000) in paragraph at lines 2305--2307 []\T1/ptm/m/n/10 If [][][]\T1/pcr/m/n/10 is.object[][][](x) []\T1/ptm/m/n/10 is true and it has a [][][]\T1/pcr/m/n/10 class[][][] []\T1/ptm/m/n/10 for which an [37] [38] [39] [40] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2579--2579 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla ss "POSIXlt"[] [41] [42] [43] Underfull \hbox (badness 1107) in paragraph at lines 2783--2785 []\T1/ptm/m/n/10 There are no re-stric-tions on the name given as []\T1/pcr/m/n /10 x[]\T1/ptm/m/n/10 : it can be a non-syntactic name (see [44] [45] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2950--2950 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse1(substitute(what), back tick=FALSE), [46] [47] [48] [49] [50] [51] [52] Underfull \hbox (badness 10000) in paragraph at lines 3413--3416 []\T1/pcr/m/n/10 unCfillPOSIXlt(x) []\T1/ptm/m/n/10 is a fast [][]prim-i-tive[] [][] ver-sion of []\T1/pcr/m/n/10 balancePOSIXlt(x, [53] [54] [55] [56] Overfull \hbox (31.3804pt too wide) in paragraph at lines 3718--3718 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2, lwd = 1, bty="n")[] [57] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3749--3749 []\T1/pcr/m/n/9 plot(range(x0), c(1e-40, 1), log = "xy", xlab = "x", ylab = "" , type = "n",[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3750--3750 [] \T1/pcr/m/n/9 main = "Bessel Functions J_nu(x) near 0\n log - log sc ale") ; axis(2, at=1)[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3757--3757 []\T1/pcr/m/n/9 plot(range(x0), 10^c(-100, 80), log = "xy", xlab = "x", ylab = "", type = "n",[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3758--3758 [] \T1/pcr/m/n/9 main = "Bessel Functions K_nu(x) near 0\n log - log sc ale") ; axis(2, at=1)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3761--3761 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5, sep = ", ")),[] Underfull \vbox (badness 10000) has occurred while \output is active [58] [59] [60] [61] [62] [63] [64] Underfull \hbox (badness 10000) in paragraph at lines 4209--4211 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [65] [66] [67] [68] [69] [70] [71] Underfull \hbox (badness 4927) in paragraph at lines 4714--4718 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an ob-ject Underfull \hbox (badness 2012) in paragraph at lines 4714--4718 \T1/ptm/m/n/10 of class []\T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"[]\T1/ptm/ m/n/10 , []\T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" []\T1/ptm/m/n/10 o r [72] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4798--4798 [] \T1/pcr/m/n/10 Xchk = any(nas %in% c("X11", "jpeg", "png", "tif f")))[] [73] Underfull \hbox (badness 4595) in paragraph at lines 4872--4875 []\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par -i-son[][][] and [74] [75] [76] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5035--5035 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{ ", 1:10, "}:"))[] Underfull \hbox (badness 1199) in paragraph at lines 5064--5070 []\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na med ar-gu- Underfull \hbox (badness 2573) in paragraph at lines 5076--5079 []\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu e and valid [77] [78] [79] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5249--5249 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna mes (default)[] [80] [81] [82] Underfull \hbox (badness 2521) in paragraph at lines 5506--5508 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [83] [84] [85] [86] [87] [88] [89] [90] Underfull \hbox (badness 1270) in paragraph at lines 5998--6006 []\T1/ptm/m/n/10 When a generic func-tion []\T1/pcr/m/n/10 fun []\T1/ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute []\T1/pcr/m/n/10 c("first", [91] [92] [93] [94] [95] [96] [97] [98] Underfull \hbox (badness 1796) in paragraph at lines 6572--6580 []\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i n-tro-duc-tion see [][]$\T1/pcr/m/n/10 https : / / [99] [100] [101] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6769--6769 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile r, math-library:[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 6771--6771 []\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6772--6772 []\T1/pcr/m/n/9 showC(NpNA)# but not always is {shows \TS1/pcr/m/n/9 '\T1/pcr /m/n/9 (R = NaN, I = NA)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 on some platforms}[] [102] [103] Underfull \hbox (badness 1635) in paragraph at lines 6974--6977 []\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class []\T1/pcr/m/n /10 interrupt []\T1/ptm/m/n/10 that in-her-its di-rectly from class Underfull \hbox (badness 3009) in paragraph at lines 6978--6981 []\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols. They can be es-tab-lished us-ing [104] Underfull \hbox (badness 1308) in paragraph at lines 7021--7029 []\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i s []\T1/pcr/m/n/10 interactive[]\T1/ptm/m/n/10 . This should [105] [106] Overfull \hbox (30.78088pt too wide) in paragraph at lines 7185--7185 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e ncoding"))[] [107] Underfull \hbox (badness 4505) in paragraph at lines 7237--7240 []\T1/ptm/m/n/10 character string, par-tially matched to []\T1/pcr/m/n/10 c("de fault", "internal", [108] [109] Underfull \hbox (badness 1997) in paragraph at lines 7374--7379 []\T1/pcr/m/n/10 file[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pipe[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 fifo[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 url[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 gzfile[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 bzfile[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 xzfile[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 unz[]\T1/ptm/m /n/10 , []\T1/pcr/m/n/10 socketConnection[]\T1/ptm/m/n/10 , [110] [111] [112] Underfull \hbox (badness 10000) in paragraph at lines 7622--7624 []\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in g from Underfull \hbox (badness 3302) in paragraph at lines 7664--7671 []\T1/pcr/m/n/10 file []\T1/ptm/m/n/10 can be used with []\T1/pcr/m/n/10 descri ption = "clipboard" []\T1/ptm/m/n/10 in mode []\T1/pcr/m/n/10 "r" []\T1/ptm/m/n /10 only. This Underfull \hbox (badness 6592) in paragraph at lines 7664--7671 \T1/ptm/m/n/10 reads the X11 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http s : / / specifications . freedesktop . Underfull \hbox (badness 1735) in paragraph at lines 7664--7671 []\T1/pcr/m/n/10 "X11_primary" []\T1/ptm/m/n/10 and the sec-ondary se-lec-tion as []\T1/pcr/m/n/10 "X11_secondary"[]\T1/ptm/m/n/10 . On most sys- [113] [114] [115] Underfull \vbox (badness 10000) has occurred while \output is active [116] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7879--7879 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE")) ; close(con)[] [117] [118] [119] [120] Underfull \hbox (badness 10000) in paragraph at lines 8212--8214 []\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th e call to [121] [122] [123] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8370--8370 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect s to https://[] [124] [125] [126] [127] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8604--8604 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng th.out = 24)[] [128] Underfull \hbox (badness 10000) in paragraph at lines 8720--8730 []\T1/pcr/m/n/10 data.frame []\T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing Underfull \hbox (badness 1975) in paragraph at lines 8720--8730 [][][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)[]\T1/ptm/m/n/10 . As that is a generic func-tion, meth-ods can be [129] [130] [131] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8888--8888 [] \T1/pcr/m/n/9 c = seq(as.Date("2004-01-01"), by = "week", l ength.out = 3),[] [132] [133] [134] [135] Underfull \hbox (badness 10000) in paragraph at lines 9216--9228 \T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") []\T1/ptm/m /n/10 may give []\T1/pcr/m/n/10 NA[]\T1/ptm/m/n/10 , and [136] [137] [138] [139] [140] [141] [142] Underfull \hbox (badness 10000) in paragraph at lines 9760--9764 []\T1/pcr/m/n/10 .Defunct []\T1/ptm/m/n/10 is called from de-funct func-tions. Func-tions should be listed in [143] [144] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9851--9851 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: -------- -------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9853--9853 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO !\n"); pi+2})[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9881--9881 [] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "( ", "function"),[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9882--9882 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh owAttributes"),[] [145] [146] Underfull \hbox (badness 5403) in paragraph at lines 10013--10015 []\T1/pcr/m/n/10 ..deparseOpts []\T1/ptm/m/n/10 is the [][][]\T1/pcr/m/n/10 cha racter[][][] []\T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used b y Underfull \hbox (badness 6063) in paragraph at lines 10032--10034 []\T1/ptm/m/n/10 Surround un-eval-u-ated ex-pres-sions, but not [][][]\T1/pcr/m /n/10 formula[][][][]\T1/ptm/m/n/10 s, with [147] [148] [149] Underfull \hbox (badness 1603) in paragraph at lines 10263--10266 []\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t er-mi-nant if [150] [151] [152] [153] [154] [155] [156] Overfull \hbox (12.78088pt too wide) in paragraph at lines 10728--10728 [] \T1/pcr/m/n/10 z <- as.POSIXct(c("2016-12-31 23:59:59", "2017-01-01 00:0 0:01"))[] [157] [158] Underfull \hbox (badness 1917) in paragraph at lines 10892--10897 []\T1/pcr/m/n/10 provideDimnames(x) []\T1/ptm/m/n/10 pro-vides []\T1/pcr/m/n/10 dimnames []\T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has [159] Overfull \hbox (36.7804pt too wide) in paragraph at lines 10947--10947 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE RS)))) # recycling[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10948--10948 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling on both levels[] [160] [161] Underfull \hbox (badness 1168) in paragraph at lines 11050--11055 []\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of []\ T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . Cur-rently this is only used by [162] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11152--11152 []\T1/pcr/m/n/9 ## From R 4.1.0 to 4.1.2, ...names() sometimes did not match n ames(list(...));[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 11154--11154 []\T1/pcr/m/n/9 chk.n2 <- function(...) stopifnot(identical(print(...names()), names(list(...))))[] [163] [164] Underfull \hbox (badness 2828) in paragraph at lines 11273--11278 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19 85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Underfull \hbox (badness 10000) in paragraph at lines 11273--11278 \T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr /m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ Underfull \hbox (badness 10000) in paragraph at lines 11273--11278 \T1/pcr/m/n/10 754-[]2019$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ pcr/m/n/10 https : Overfull \hbox (42.78088pt too wide) in paragraph at lines 11304--11304 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA ttributes"))[] [165] Overfull \hbox (15.18042pt too wide) in paragraph at lines 11378--11378 []\T1/pcr/m/n/9 ## Write an ASCII version of the \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 base\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 function mean() to our temp file, ..[] [166] [167] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11527--11527 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon th.abb[5:9])) [168] [169] [170] Underfull \hbox (badness 6396) in paragraph at lines 11725--11733 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for Underfull \hbox (badness 10000) in paragraph at lines 11734--11736 []\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) []\T1/ptm/m/n/10 is equiv-a-len t to but faster than [171] [172] [173] Underfull \hbox (badness 10000) in paragraph at lines 11951--11954 []\T1/ptm/m/n/10 Do not use []\T1/pcr/m/n/10 dyn.unload []\T1/ptm/m/n/10 on a D LL loaded by [][][]\T1/pcr/m/n/10 library.dynam[][][][]\T1/ptm/m/n/10 : use [174] [175] [176] [177] [178] [179] Underfull \hbox (badness 2744) in paragraph at lines 12398--12400 []\T1/ptm/m/n/10 Changing the cur-rent en-cod-ing from a run-ning R ses-sion ma y lead to con-fu-sion (see [180] Overfull \hbox (20.58041pt too wide) in paragraph at lines 12421--12421 []\T1/pcr/m/n/9 Encoding(x.) # "unknown" (UTF-8 loc.) | "latin1" (8859-1/CP-12 52 loc.) | ....[] [181] [182] [183] Underfull \hbox (badness 5288) in paragraph at lines 12673--12675 []\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val ue of Underfull \hbox (badness 3039) in paragraph at lines 12683--12688 []\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][][]\T1/pcr/m/n/1 0 dev2bitmap[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 bitmap[][][] []\T1/pt m/m/n/10 and [184] Underfull \hbox (badness 10000) in paragraph at lines 12740--12743 []\T1/ptm/m/n/10 The path to HTML []\T1/pcr/m/n/10 tidy[]\T1/ptm/m/n/10 . Used by []\T1/pcr/m/n/10 R CMD check []\T1/ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 12758--12760 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [185] [186] [187] [188] Underfull \hbox (badness 10000) in paragraph at lines 13008--13010 []\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing []\T1/pc r/m/n/10 where []\T1/ptm/m/n/10 as Underfull \hbox (badness 5970) in paragraph at lines 13051--13053 []\T1/pcr/m/n/10 get0(): []\T1/ptm/m/n/10 The object---as from [][][]\T1/pcr/m/ n/10 get[][][](x, *)[]\T1/ptm/m/n/10 --- if []\T1/pcr/m/n/10 exists(x, *) []\T1 /ptm/m/n/10 is true, oth-er-wise [189] [190] [191] [192] [193] [194] [195] [196] [197] [198] [199] [200] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13874--13874 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide a constructor[] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] Underfull \hbox (badness 2253) in paragraph at lines 14602--14604 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see Underfull \hbox (badness 1490) in paragraph at lines 14637--14640 []\T1/ptm/m/n/10 Junction points and sym-bolic links are fol-lowed, so in-for-m a-tion is given about the [211] [212] Underfull \hbox (badness 2573) in paragraph at lines 14770--14772 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as []\T1/pcr /m/n/10 PATH []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 R_LIBS []\T1/ptm/m/n/10 with []\T1/pcr/m/n/10 fsep = [213] [214] Underfull \hbox (badness 10000) in paragraph at lines 14929--14931 []\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See [215] [216] Underfull \hbox (badness 10000) in paragraph at lines 15050--15054 [][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil e.access[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.path[][][][]\T1/ptm/ m/n/10 , [][][]\T1/pcr/m/n/10 file.show[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 list.files[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 unlink[][][][]\T1 /ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 15061--15064 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Overfull \hbox (47.58038pt too wide) in paragraph at lines 15082--15082 [] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B as it exists already[] [217] Overfull \hbox (30.78088pt too wide) in paragraph at lines 15107--15107 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [218] Underfull \hbox (badness 10000) in paragraph at lines 15204--15207 [][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil e.exists[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.path[][][][]\T1/ptm/ m/n/10 , [][][]\T1/pcr/m/n/10 list.files[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/ m/n/10 unlink[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 basename[][][][]\T1/ ptm/m/n/10 , Overfull \hbox (9.78043pt too wide) in paragraph at lines 15214--15214 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu rsive = TRUE)[] [219] Underfull \hbox (badness 10000) in paragraph at lines 15280--15283 []\T1/pcr/m/n/10 packageNotFoundError []\T1/ptm/m/n/10 cre-ates an er-ror con-d i-tion ob-ject of class Overfull \hbox (20.58041pt too wide) in paragraph at lines 15297--15297 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio ns it is found:[] [220] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15326--15326 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE, Underfull \hbox (badness 3965) in paragraph at lines 15358--15362 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [221] [222] [223] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15522--15522 [] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING) Overfull \hbox (0.78088pt too wide) in paragraph at lines 15523--15523 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING)[] [224] [225] [226] [227] Overfull \hbox (63.78036pt too wide) in paragraph at lines 15765--15765 []\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have type symbol (aka name).[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15768--15768 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co mbination with[] [228] Underfull \hbox (badness 1168) in paragraph at lines 15854--15858 []\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real or com-plex vec- Underfull \hbox (badness 2012) in paragraph at lines 15854--15858 \T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger penalty (see [229] Underfull \hbox (badness 6944) in paragraph at lines 15951--15954 [][][]\T1/pcr/m/n/10 formatC[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 paste [][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 as.character[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/pcr/m/n/10 sprintf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 p rint[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 prettyNum[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 toString[][][][]\T1/ptm/m/n/10 , [230] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15976--15976 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1 0,100,1000),[] [231] [232] Underfull \hbox (badness 10000) in paragraph at lines 16114--16116 []\T1/pcr/m/n/10 prettyNum() []\T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (p os-si-bly for-mat-ted) num-bers, also in Overfull \hbox (48.78088pt too wide) in paragraph at lines 16134--16134 [] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = decimal.mark,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16140--16140 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric (x)),[] Underfull \hbox (badness 2790) in paragraph at lines 16147--16150 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] []\T1/pcr/m/n/10 complex[][][] []\T1/ptm/m/n/10 only for [233] Underfull \hbox (badness 1024) in paragraph at lines 16178--16185 []\T1/pcr/m/n/10 "f" []\T1/ptm/m/n/10 gives num-bers in the usual []\T1/pcr/m/n /10 xxx.xxx []\T1/ptm/m/n/10 for-mat; []\T1/pcr/m/n/10 "e" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "E" []\T1/ptm/m/n/10 give [234] Underfull \hbox (badness 10000) in paragraph at lines 16253--16255 []\T1/ptm/m/n/10 This works via []\T1/pcr/m/n/10 prettyNum()[]\T1/ptm/m/n/10 , which calls []\T1/pcr/m/n/10 .format.zeros(*, Underfull \hbox (badness 10000) in paragraph at lines 16275--16280 []\T1/ptm/m/n/10 For num-bers, []\T1/pcr/m/n/10 formatC() []\T1/ptm/m/n/10 call s []\T1/pcr/m/n/10 prettyNum() []\T1/ptm/m/n/10 when needed which it-self calls Underfull \hbox (badness 2426) in paragraph at lines 16281--16283 []\T1/ptm/m/n/10 If you set []\T1/pcr/m/n/10 format []\T1/ptm/m/n/10 it over-ri des the set-ting of []\T1/pcr/m/n/10 mode[]\T1/ptm/m/n/10 , so []\T1/pcr/m/n/10 formatC(123.45, mode = Underfull \hbox (badness 10000) in paragraph at lines 16292--16300 []\T1/pcr/m/n/10 prettyNum []\T1/ptm/m/n/10 is the util-ity func-tion for pret- ti-fy-ing []\T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 x []\T1/ptm/m/n /10 can be com-plex (or [235] [236] Overfull \hbox (4.38043pt too wide) in paragraph at lines 16400--16400 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big .mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 16422--16422 []\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you want see the effect[] Underfull \vbox (badness 10000) has occurred while \output is active [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17256--17256 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil l a DLLInfoList[] [249] [250] Underfull \hbox (badness 2418) in paragraph at lines 17365--17369 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing [ ]\T1/pcr/m/n/10 CRoutine[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 CallRoutine[]\T1/pt m/m/n/10 , Underfull \hbox (badness 6510) in paragraph at lines 17372--17375 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 name []\T1/ptm/m/n/10 con-tains only one s ym-bol name and []\T1/pcr/m/n/10 unlist []\T1/ptm/m/n/10 is []\T1/pcr/m/n/10 TR UE[]\T1/ptm/m/n/10 , then the sin-gle Underfull \hbox (badness 2326) in paragraph at lines 17407--17414 [][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][][]\T1/ptm/m/n/10 , [][][]\T1 /pcr/m/n/10 is.loaded[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .C[][][][]\T 1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .Fortran[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 .External[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .Call[][][][] \T1/ptm/m/n/10 , [251] [252] Underfull \hbox (badness 10000) in paragraph at lines 17513--17517 []\T1/ptm/m/n/10 The spe-cial case []\T1/pcr/m/n/10 bindtextdomain(NULL) []\T1/ ptm/m/n/10 calls C level Underfull \hbox (badness 3302) in paragraph at lines 17513--17517 []\T1/pcr/m/n/10 textdomain(textdomain(NULL)) []\T1/ptm/m/n/10 for the pur-pose of flush-ing (i.e., emp-ty-ing) the [253] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17580--17580 []\T1/pcr/m/n/9 if(is.na(thisLang) || !nzchar(thisLang)) thisLang <- "en" # "f actory" default[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 17583--17583 []\T1/pcr/m/n/9 gettext(enT, domain="R-stats")# "leeres Modell angegeben" (if translation works)[] Underfull \vbox (badness 10000) has occurred while \output is active [254] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17614--17614 []\T1/pcr/m/n/9 ## Here, we reset to the *original* setting before the full ex ample started:[] [255] [256] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17751--17751 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE, Underfull \hbox (badness 1867) in paragraph at lines 17779--17786 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [257] [258] [259] [260] [261] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18097--18097 [] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around "checking hack"[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 18126--18126 []\T1/pcr/m/n/9 name.rex <- "(?[[:upper:]][[:lower:]]+) (?[[:uppe r:]][[:lower:]]+)"[] Underfull \vbox (badness 10000) has occurred while \output is active [262] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18182--18182 [] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F ALSE)[] [263] [264] [265] [266] [267] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18575--18575 []\T1/pcr/m/n/9 (ii <- grouping(x <- c(1, 1, 3:1, 1:4, 3), y <- c(9, 9:1), z < - c(2, 1:9))) [268] Overfull \hbox (4.38043pt too wide) in paragraph at lines 18640--18640 []\T1/pcr/m/n/9 z <- gzcon(url("https://www.stats.ox.ac.uk/pub/datasets/csb/ch 12.dat.gz"))[] [269] [270] [271] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18853--18853 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F ALSE) [272] [273] Underfull \hbox (badness 1360) in paragraph at lines 19017--19022 []\T1/ptm/m/n/10 The most portable name for the ISO 8859-15 en-cod-ing, com-mon ly known as `Latin 9', Underfull \hbox (badness 1953) in paragraph at lines 19017--19022 \T1/ptm/m/n/10 is []\T1/pcr/m/n/10 "iso885915"[]\T1/ptm/m/n/10 : most plat-form s sup-port both []\T1/pcr/m/n/10 "latin-9" []\T1/ptm/m/n/10 and[]\T1/pcr/m/n/10 "latin9" []\T1/ptm/m/n/10 but GNU [274] [275] [276] Underfull \hbox (badness 1163) in paragraph at lines 19233--19235 []\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1 0 https : / / unicode-[]org . github . io / icu / Overfull \hbox (9.78043pt too wide) in paragraph at lines 19241--19241 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s ettings, we can only reset to the default.[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 19271--19271 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE, [277] [278] Overfull \hbox (30.78088pt too wide) in paragraph at lines 19365--19365 [] \T1/pcr/m/n/10 num.eq = FALSE, single.NA = FALSE, attrib.as.se t = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19366--19366 [] \T1/pcr/m/n/10 ignore.bytecode = FALSE, ignore.environment = F ALSE,[] [279] Overfull \hbox (25.98041pt too wide) in paragraph at lines 19419--19419 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------ ----------------[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 19425--19425 []\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is ignored by default[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 19428--19428 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share an environment:[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19434--19434 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi ng "srcref" :[] [280] [281] Overfull \hbox (4.38043pt too wide) in paragraph at lines 19561--19561 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u se ifelse(),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19569--19569 []\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[] [282] [283] [284] Underfull \hbox (badness 10000) in paragraph at lines 19774--19776 []\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][][]\T 1/pcr/m/n/10 stop[][][] []\T1/ptm/m/n/10 and [285] [286] [287] [288] [289] Underfull \hbox (badness 10000) in paragraph at lines 20114--20120 Underfull \hbox (badness 10000) in paragraph at lines 20127--20129 []\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac le . com / cd / E19957-[]01 / 806-[]3568 / ncg _ [290] [291] [292] [293] Underfull \hbox (badness 4699) in paragraph at lines 20371--20374 []\T1/pcr/m/n/10 is.atomic []\T1/ptm/m/n/10 is true for the [][]atomic[][][] ty pes ([]\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "integer"[]\ T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "numeric"[]\T1/ptm/m/n/10 , [294] [295] Overfull \hbox (0.78088pt too wide) in paragraph at lines 20499--20499 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [296] [297] Underfull \hbox (badness 4739) in paragraph at lines 20634--20636 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [298] Overfull \hbox (36.7804pt too wide) in paragraph at lines 20683--20683 []\T1/pcr/m/n/9 isSymmetric(D3) # FALSE (as row and co lumn names differ)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20684--20684 []\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE (as names are not checked)[] [299] [300] Underfull \hbox (badness 2961) in paragraph at lines 20861--20864 []\T1/ptm/m/n/10 LAPACK and LIN-PACK are from [][]$\T1/pcr/m/n/10 https : / / n etlib . org / lapack/$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / [301] [302] [303] [304] [305] [306] [307] Underfull \hbox (badness 1975) in paragraph at lines 21302--21305 []\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to [308] [309] [310] [311] [312] [313] Underfull \hbox (badness 1077) in paragraph at lines 21718--21723 []\T1/ptm/m/n/10 In late 2017 a []\T1/pcr/m/n/10 libcurl []\T1/ptm/m/n/10 in-st al-la-tion was seen di-vided into two li-braries, []\T1/pcr/m/n/10 libcurl []\T 1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 21732--21739 [][][]$\T1/pcr/m/n/10 https : / / curl . se / docs / sslcerts . html$[][] \T1/p tm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / curl . se / docs / [314] Underfull \hbox (badness 1112) in paragraph at lines 21805--21814 []\T1/ptm/m/n/10 At startup, the li-brary search path is ini-tial-ized from the en-vi-ron-ment vari-ables []\T1/pcr/m/n/10 R_LIBS[]\T1/ptm/m/n/10 , [315] Underfull \hbox (badness 2970) in paragraph at lines 21863--21866 []\T1/pcr/m/n/10 LOCALAPPDATA []\T1/ptm/m/n/10 (usu-ally []\T1/pcr/m/n/10 C:\Us ers\username\AppData\Local[]\T1/ptm/m/n/10 ) on Win-dows is a Underfull \hbox (badness 2951) in paragraph at lines 21863--21866 \T1/ptm/m/n/10 hid-den di-rec-tory and may not be viewed by some soft-ware. It may be opened by [316] [317] Underfull \hbox (badness 10000) in paragraph at lines 21976--21980 []\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use Underfull \hbox (badness 1454) in paragraph at lines 21976--21980 [][][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][][]\T1/ptm/m/n/10 : thi s will sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self Underfull \hbox (badness 1221) in paragraph at lines 21981--21988 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 library []\T1/ptm/m/n/10 is called with no []\T1/pcr/m/n/10 package []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 help []\T1/ptm/m /n/10 ar-gu-ment, it lists all avail-able pack- [318] [319] Underfull \hbox (badness 10000) in paragraph at lines 22110--22117 [][][]\T1/pcr/m/n/10 attach[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 detach [][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 search[][][][]\T1/ptm/m/n/10 , [] [][]\T1/pcr/m/n/10 objects[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 autoloa d[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 requireNamespace[][][][]\T1/ptm/ m/n/10 , [320] Underfull \hbox (badness 10000) in paragraph at lines 22231--22235 []\T1/ptm/m/n/10 Do not use [][][]\T1/pcr/m/n/10 dyn.unload[][][] []\T1/ptm/m/n /10 on a DLL loaded by []\T1/pcr/m/n/10 library.dynam[]\T1/ptm/m/n/10 : use [321] Underfull \hbox (badness 5161) in paragraph at lines 22301--22306 []\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di s-tributed un-der the Underfull \hbox (badness 6592) in paragraph at lines 22301--22306 \T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c opy of Underfull \hbox (badness 5133) in paragraph at lines 22301--22306 \T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L GPL-2.1\T1/ptm/m/n/10 ' and can be viewed Underfull \hbox (badness 10000) in paragraph at lines 22301--22306 \T1/ptm/m/n/10 by []\T1/pcr/m/n/10 RShowDoc("LGPL-2.1")[]\T1/ptm/m/n/10 . Ver-s ion 3 of the li-cense can be dis-played by [322] [323] [324] Overfull \hbox (6.78088pt too wide) in paragraph at lines 22469--22469 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 22473--22473 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] [325] Underfull \hbox (badness 3343) in paragraph at lines 22534--22538 [][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil e.access[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 files[][][] []\T1/ptm/ m/n/10 for many more file han-dling func-tions and [326] [327] Overfull \hbox (4.38043pt too wide) in paragraph at lines 22672--22672 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 22683--22683 [] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1, prob = 0.2))),[] [328] [329] Overfull \hbox (9.78043pt too wide) in paragraph at lines 22794--22794 []\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the same names ![] Overfull \hbox (74.58035pt too wide) in paragraph at lines 22797--22797 []\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w / same name in .GlobalEnv[] Underfull \hbox (badness 6380) in paragraph at lines 22844--22852 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- [330] [331] Underfull \hbox (badness 2564) in paragraph at lines 22947--22950 []\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/ ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of Overfull \hbox (4.38043pt too wide) in paragraph at lines 22988--22988 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other Unix-alikes[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 22992--22992 []\T1/pcr/m/n/9 c(m = months(then), wd = weekdays(then)) # in C_TIME locale \T S1/pcr/m/n/9 '\T1/pcr/m/n/9 cT\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 ; typically German [] Overfull \hbox (42.18039pt too wide) in paragraph at lines 22996--22996 []\T1/pcr/m/n/9 c(m = months(then), wd = weekdays(then)) # "standard" (still p latform specific ?)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 23003--23003 []\T1/pcr/m/n/9 ## Not run: Sys.setlocale("LC_COLLATE", "C") # turn off loca le-specific sorting,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 23005--23005 []\T1/pcr/m/n/9 Sys.setenv("LANGUAGE" = "es") # set the language for error/war ning messages[] [332] [333] [334] Underfull \hbox (badness 1400) in paragraph at lines 23179--23183 [][][]\T1/pcr/m/n/10 raw[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logical[] [][] []\T1/ptm/m/n/10 or `number-like' vec-tors (i.e., of types [][][]\T1/pcr/m /n/10 double[][][] []\T1/ptm/m/n/10 (class [335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] Overfull \hbox (52.98038pt too wide) in paragraph at lines 24021--24021 []\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary = r ), complex(real = r , imaginary = NA ),[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 24022--24022 [] \T1/pcr/m/n/9 complex(real = r , imaginary = NaN), complex(real = N aN, imaginary = r ))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 24025--24025 []\T1/pcr/m/n/9 zM ##--> many "NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s" (= 1) and th e four non-NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s (3 different ones, at 7,9,10)[] [347] [348] Overfull \hbox (20.58041pt too wide) in paragraph at lines 24122--24122 []\T1/pcr/m/n/9 match.arg(c("a", ""), c("", NA, "bb", "abc"), several.ok=TRUE ) # |--> "abc"[] Underfull \hbox (badness 1655) in paragraph at lines 24156--24160 []\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion (also known as a `clo-sure'): [349] [350] [351] [352] Underfull \hbox (badness 2277) in paragraph at lines 24407--24410 []\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross\T1/ptm/m/n/10 products, [][] []\T1/pcr/m/n/10 crossprod[][][]() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 tcross prod() []\T1/ptm/m/n/10 are typ-i-cally prefer-able. [353] [354] [355] [356] [357] [358] [359] [360] [361] Underfull \hbox (badness 1484) in paragraph at lines 25007--25015 []\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less the OS's de-fault has been Underfull \hbox (badness 1152) in paragraph at lines 25007--25015 \T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http s : / / docs . microsoft . com / en-[]gb / [362] Overfull \hbox (0.78088pt too wide) in paragraph at lines 25081--25081 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] [363] [364] [365] [366] [367] [368] [369] [370] Underfull \hbox (badness 1448) in paragraph at lines 25633--25641 []\T1/pcr/m/n/10 anyNA(recursive = FALSE) []\T1/ptm/m/n/10 works the same way a s []\T1/pcr/m/n/10 is.na[]\T1/ptm/m/n/10 ; []\T1/pcr/m/n/10 anyNA(recursive = [371] [372] Underfull \hbox (badness 3849) in paragraph at lines 25748--25753 []\T1/pcr/m/n/10 as.name []\T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter- nally to a char-ac-ter vec-tor (so meth-ods for [373] Underfull \hbox (badness 2165) in paragraph at lines 25825--25831 []\T1/ptm/m/n/10 For an [][][]\T1/pcr/m/n/10 environment[][][] env[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 names(env) []\T1/ptm/m/n/10 gives the names of the cor-r e-spond-ing list, Underfull \hbox (badness 1199) in paragraph at lines 25825--25831 \T1/ptm/m/n/10 i.e., []\T1/pcr/m/n/10 names(as.list(env, all.names = TRUE)) []\ T1/ptm/m/n/10 which are also given by [][][]\T1/pcr/m/n/10 ls[][][](env, Underfull \hbox (badness 3148) in paragraph at lines 25825--25831 \T1/pcr/m/n/10 all.names = TRUE, sorted = FALSE)[]\T1/ptm/m/n/10 . If the en-vi -ron-ment is used as a hash ta-ble, [374] [375] Underfull \hbox (badness 2237) in paragraph at lines 25988--25990 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of []\T1/pcr/m/n/1 0 c("bytes", "chars", [376] [377] [378] Underfull \hbox (badness 6188) in paragraph at lines 26215--26218 []\T1/ptm/m/n/10 optional [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 e ven-tu-ally to be passed to []\T1/pcr/m/n/10 print()[]\T1/ptm/m/n/10 , used by [379] [380] [381] Underfull \hbox (badness 1521) in paragraph at lines 26405--26419 \T1/ptm/m/n/10 tion []\T1/pcr/m/n/10 GetFinalPathNameByHandle []\T1/ptm/m/n/10 and in case of an er-ror (such as in-suf-fi-cient per- [382] [383] [384] [385] [386] Underfull \hbox (badness 2197) in paragraph at lines 26719--26723 []\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s tartup mes-sages given by Underfull \hbox (badness 4048) in paragraph at lines 26719--26723 []\T1/pcr/m/n/10 .onAttach[]\T1/ptm/m/n/10 . These mes-sages (and any es-sen-ti al ones from []\T1/pcr/m/n/10 .onLoad[]\T1/ptm/m/n/10 ) should use Underfull \hbox (badness 2846) in paragraph at lines 26733--26737 []\T1/ptm/m/n/10 Uses of []\T1/pcr/m/n/10 library []\T1/ptm/m/n/10 with ar-gu-m ent []\T1/pcr/m/n/10 help []\T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion ab out the pack- Underfull \hbox (badness 1990) in paragraph at lines 26733--26737 \T1/ptm/m/n/10 age should use []\T1/pcr/m/n/10 format []\T1/ptm/m/n/10 on the c om-puted pack-age in-for-ma-tion ob-ject and pass this to Overfull \hbox (12.78088pt too wide) in paragraph at lines 26775--26775 []\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ e.only) [387] Overfull \hbox (0.78088pt too wide) in paragraph at lines 26779--26779 [] \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk gs"))[] [388] Underfull \hbox (badness 10000) in paragraph at lines 26828--26834 []\T1/pcr/m/n/10 loadNamespace []\T1/ptm/m/n/10 does not at-tach the name space it loads to the search path. Underfull \hbox (badness 1168) in paragraph at lines 26828--26834 []\T1/pcr/m/n/10 attachNamespace []\T1/ptm/m/n/10 can be used to at-tach a fram e con-tain-ing the ex-ported val-ues of a Underfull \hbox (badness 10000) in paragraph at lines 26841--26843 []\T1/pcr/m/n/10 isNamespaceLoaded(pkg) []\T1/ptm/m/n/10 is equiv-a-lent to but more ef-fi-cient than []\T1/pcr/m/n/10 pkg %in% [389] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26908--26908 [] \T1/pcr/m/n/9 ## The string "foo" and the symbol \TS1/pcr/m/n/9 '\T1/pcr/m/ n/9 foo\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 can be used interchangably here:[] [390] [391] Underfull \hbox (badness 8189) in paragraph at lines 27103--27109 []\T1/ptm/m/n/10 The de-fault method for []\T1/pcr/m/n/10 is.numeric []\T1/ptm/ m/n/10 re-turns []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode[][][] [392] [393] [394] Underfull \hbox (badness 2591) in paragraph at lines 27329--27337 \T1/ptm/m/n/10 ject as ob-tained by [][][]\T1/pcr/m/n/10 R.version[][][][]\T1/p tm/m/n/10 . For []\T1/pcr/m/n/10 as.numeric_version []\T1/ptm/m/n/10 and [395] [396] [397] [398] [399] Underfull \hbox (badness 1603) in paragraph at lines 27611--27613 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [400] Underfull \hbox (badness 1210) in paragraph at lines 27738--27747 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini- [401] [402] [403] Underfull \hbox (badness 3271) in paragraph at lines 27960--27963 []\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men t vari-able [404] [405] [406] Underfull \hbox (badness 3138) in paragraph at lines 28273--28279 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][][]\T1/pcr/ m/n/10 setRepositories[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 28273--28279 \T1/ptm/m/n/10 e.g. the de-fault `[]\T1/pcr/m/n/10 "https://bioconductor.org"[] \T1/ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 2088) in paragraph at lines 28273--28279 \T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de "[]\T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 1194) in paragraph at lines 28286--28289 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][][]\T1/pcr/m/n/10 create.post[ ][][] []\T1/ptm/m/n/10 (and hence[][][]\T1/pcr/m/n/10 bug.report[][][] []\T1/pt m/m/n/10 and Underfull \hbox (badness 1389) in paragraph at lines 28312--28314 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [407] Underfull \hbox (badness 10000) in paragraph at lines 28339--28345 []\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by Underfull \hbox (badness 3826) in paragraph at lines 28354--28359 []\T1/ptm/m/n/10 Used by [][][]\T1/pcr/m/n/10 install.packages[][][] []\T1/ptm/ m/n/10 (and in-di-rectly Underfull \hbox (badness 1009) in paragraph at lines 28372--28375 []\T1/ptm/m/n/10 default email-ing method used by [][][]\T1/pcr/m/n/10 create.p ost[][][] []\T1/ptm/m/n/10 and hence [][][]\T1/pcr/m/n/10 bug.report[][][] []\T 1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 28388--28391 []\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle d -- see Underfull \hbox (badness 10000) in paragraph at lines 28396--28402 []\T1/pcr/m/n/10 "source" []\T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma-cOS Underfull \hbox (badness 10000) in paragraph at lines 28396--28402 \T1/ptm/m/n/10 build), []\T1/pcr/m/n/10 "mac.binary" []\T1/ptm/m/n/10 and []\T1 /pcr/m/n/10 "both" []\T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS Underfull \hbox (badness 10000) in paragraph at lines 28396--28402 \T1/ptm/m/n/10 builds). ([]\T1/pcr/m/n/10 "mac.binary.el-capitan"[]\T1/ptm/m/n/ 10 , []\T1/pcr/m/n/10 "mac.binary.mavericks"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 5091) in paragraph at lines 28396--28402 []\T1/pcr/m/n/10 "mac.binary.leopard" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "ma c.binary.universal" []\T1/ptm/m/n/10 are no longer [408] [409] [410] [411] [412] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28777--28777 []\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec, 300X faster[] [413] Underfull \hbox (badness 10000) in paragraph at lines 28790--28794 []\T1/ptm/m/n/10 where el-e-ment []\T1/pcr/m/n/10 A[c(arrayindex.x, arrayindex. y)] = FUN(X[arrayindex.x], [414] [415] Underfull \hbox (badness 1210) in paragraph at lines 28937--28940 []\T1/pcr/m/n/10 str2expression(s) []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 str2la ng(s) []\T1/ptm/m/n/10 re-turn spe-cial ver-sions of []\T1/pcr/m/n/10 parse(tex t=s, [416] [417] Overfull \hbox (25.98041pt too wide) in paragraph at lines 29133--29133 []\T1/pcr/m/n/9 tryCatch(parse(text = txt, srcfile = sf), error = function(e) "Syntax error.")[] [418] Underfull \hbox (badness 1478) in paragraph at lines 29163--29168 \T1/ptm/m/n/10 zero-length [][][]\T1/pcr/m/n/10 character[][][](0)[]\T1/ptm/m/n /10 . Note that when []\T1/pcr/m/n/10 collapse []\T1/ptm/m/n/10 is a string, [419] Underfull \hbox (badness 7133) in paragraph at lines 29222--29228 [][][]\T1/pcr/m/n/10 toString[][][] []\T1/ptm/m/n/10 typ-i-cally calls []\T1/pc r/m/n/10 paste(*, collapse=", ")[]\T1/ptm/m/n/10 . String ma-nip-u-la-tion with Overfull \hbox (42.18039pt too wide) in paragraph at lines 29244--29244 []\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as the longest input.[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 29256--29256 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha t you wanted[] Overfull \hbox (17.87582pt too wide) in paragraph at lines 29269--29269 []\T1/pcr/m/n/9 ## zero length arguments recycled as \TS1/cmtt/m/n/9 `\T1/pcr/ m/n/9 ""\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 -- NB: \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 { }\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 <==> character(0) here[] [420] Overfull \hbox (15.18042pt too wide) in paragraph at lines 29272--29272 []\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 recycle0 = TRUE\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 allows standard vectorized behaviour, i.e., zero-length[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 29273--29273 []\T1/pcr/m/n/9 ## recycling resulting in zero-length result character(0):[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 29276--29276 []\T1/pcr/m/n/9 paste("The value is", val[valid], "-- not so good!") # -> ".. value is -- not .."[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 29277--29277 []\T1/pcr/m/n/9 paste("The value is", val[valid], "-- good: empty!", recycle0= TRUE) # -> character(0)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29280--29280 []\T1/pcr/m/n/9 paste("foo", {}, "bar", collapse = "|") # |-- > "foo bar"[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29282--29282 []\T1/pcr/m/n/9 ## If all arguments are empty (and collapse a string), "" r esults always[] [421] [422] [423] Overfull \hbox (25.98041pt too wide) in paragraph at lines 29471--29471 []\T1/pcr/m/n/9 mtcars |> subset(cyl == 4) |> nrow() # same as nrow(subset(mt cars, cyl == 4))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 29489--29489 []\T1/pcr/m/n/9 stop() |> (function(...) {})() # stop() is not used on RHS so is not evaluated[] [424] Underfull \hbox (badness 1360) in paragraph at lines 29544--29548 []\T1/ptm/m/n/10 All other []\T1/pcr/m/n/10 type[]\T1/ptm/m/n/10 s give a warn- ing or an er-ror; us-ing, e.g., []\T1/pcr/m/n/10 type = [425] [426] [427] [428] Underfull \hbox (badness 2277) in paragraph at lines 29856--29861 \T1/ptm/m/n/10 i.e., strictly in-clude the bounds of []\T1/pcr/m/n/10 x[]\T1/pt m/m/n/10 . New from \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0, al-low-ing [429] [430] Underfull \hbox (badness 1701) in paragraph at lines 29972--29976 []\T1/ptm/m/n/10 This func-tion is al-most never used: []\TS1/cmtt/m/n/10 `\T1/ pcr/m/n/10 name\TS1/cmtt/m/n/10 ` []\T1/ptm/m/n/10 or, more care-fully, [][][]\ T1/pcr/m/n/10 get[][][](name, envir = [431] Underfull \hbox (badness 1796) in paragraph at lines 30040--30043 []\T1/ptm/m/n/10 character string (or []\T1/pcr/m/n/10 NULL[]\T1/ptm/m/n/10 ) i n-di-cat-ing [][][]\T1/pcr/m/n/10 NA[][][] []\T1/ptm/m/n/10 val-ues in printed out-put, see [432] [433] [434] [435] Underfull \hbox (badness 10000) in paragraph at lines 30244--30247 []\T1/ptm/m/n/10 Option []\T1/pcr/m/n/10 width []\T1/ptm/m/n/10 con-trols the p rint-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion [436] [437] [438] [439] [440] [441] [442] [443] Underfull \hbox (badness 2961) in paragraph at lines 30790--30793 []\T1/ptm/m/n/10 LAPACK and LIN-PACK are from [][]$\T1/pcr/m/n/10 https : / / n etlib . org / lapack/$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / [444] [445] Overfull \hbox (25.98041pt too wide) in paragraph at lines 30939--30939 [] \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 = rep(c(0,0,1),2))[] [446] [447] [448] [449] Overfull \hbox (15.18042pt too wide) in paragraph at lines 31232--31232 []\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3 \u147b\u203c")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 31243--31243 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\ U147b\U203c"[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 31249--31249 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm l#Literal-constants[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 31255--31255 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow ed (parse errors)[] Underfull \vbox (badness 10000) has occurred while \output is active [450] [451] Underfull \hbox (badness 7415) in paragraph at lines 31352--31358 []\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use []\T1/pcr/m/n/10 R.v ersion$os []\T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use Overfull \hbox (42.18039pt too wide) in paragraph at lines 31376--31376 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu l bottom-right note[] [452] Overfull \hbox (6.78088pt too wide) in paragraph at lines 31422--31422 []\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind = NULL)[] [453] [454] Underfull \hbox (badness 3713) in paragraph at lines 31567--31578 []\T1/pcr/m/n/10 normal.kind []\T1/ptm/m/n/10 can be []\T1/pcr/m/n/10 "Kinderma n-Ramage"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Buggy Kinderman-Ramage" []\T1/ptm /m/n/10 (not [455] Underfull \hbox (badness 1248) in paragraph at lines 31719--31726 \T1/ptm/m/n/10 uni-form pseudo-random num-ber gen-er-a-tor, \T1/ptm/m/it/10 ACM Trans-ac-tions on Mod-el-ing and Com-puter Underfull \hbox (badness 10000) in paragraph at lines 31719--31726 \T1/ptm/m/n/10 Now see [][]$\T1/pcr/m/n/10 http : / / www . math . sci . hirosh ima-[]u . ac . jp / ~m-[]mat / MT / VERSIONS / [456] [457] Underfull \hbox (badness 1533) in paragraph at lines 31837--31840 []\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the [458] [459] Overfull \hbox (42.78088pt too wide) in paragraph at lines 31982--31982 [] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m ax", "min"))[] [460] Underfull \hbox (badness 1038) in paragraph at lines 32000--32011 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no []\T1/pcr/m/n/10 N A[]\T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [461] [462] Overfull \hbox (15.18042pt too wide) in paragraph at lines 32144--32144 []\T1/pcr/m/n/9 rapply(X, function(x) x, how = "replace") -> X.; stopifnot(ide ntical(X, X.))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 32146--32146 []\T1/pcr/m/n/9 rapply(X, deparse, control = "all") # passing extras. argument of deparse()[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 32147--32147 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h ow = "list")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 32148--32148 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h ow = "unlist")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 32149--32149 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", h ow = "unlist")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 32156--32156 []\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h ow = "unlist")[] [463] [464] [465] [466] [467] Overfull \hbox (25.98041pt too wide) in paragraph at lines 32464--32464 []\T1/pcr/m/n/9 ## Bit representation [ sign | exponent | mantissa ] of doubl e prec numbers :[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 32466--32466 []\T1/pcr/m/n/9 bitC <- function(x) noquote(vapply(as.double(x), function(x) { # split one double[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 32476--32476 []\T1/pcr/m/n/9 d2bI <- function(x) vapply(as.double(x), function(x) intToBits (numToInts(x)), raw(64L))[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 32477--32477 []\T1/pcr/m/n/9 d2b <- function(x) vapply(as.double(x), function(x) numToBits(x) , raw(64L))[] [468] Underfull \hbox (badness 4048) in paragraph at lines 32572--32577 []\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor to Underfull \hbox (badness 4582) in paragraph at lines 32572--32577 \T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the mode: Underfull \hbox (badness 1824) in paragraph at lines 32572--32577 \T1/ptm/m/n/10 one of []\T1/pcr/m/n/10 "numeric"[]\T1/ptm/m/n/10 , []\T1/pcr/m/ n/10 "double"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "integer"[]\T1/ptm/m/n/10 , [] \T1/pcr/m/n/10 "int"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/ 10 , [469] [470] [471] [472] [473] [474] [475] [476] Underfull \hbox (badness 2080) in paragraph at lines 33112--33122 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 infoRDS[]\T1/ptm/m/n/10 , an \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 list with el-e-ments []\T1/pcr/m/n/10 version []\T1/ptm/m/n /10 (ver-sion num-ber, cur-rently 2 or 3), [477] Overfull \hbox (4.38043pt too wide) in paragraph at lines 33146--33146 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene d as needed.[] [478] [479] [480] [481] [482] [483] [484] Underfull \hbox (badness 7558) in paragraph at lines 33666--33670 []\T1/pcr/m/n/10 regexpr []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 gregexpr []\T1/p tm/m/n/10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1968) in paragraph at lines 33676--33678 []\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P OSIX stan-dard, and the Underfull \hbox (badness 10000) in paragraph at lines 33687--33689 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / Underfull \hbox (badness 1975) in paragraph at lines 33690--33694 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 pcre2pattern []\T1/ptm/m/n/10 or []\T1/pc r/m/n/10 pcrepattern man []\T1/ptm/m/n/10 page (found as part of [][]$\T1/pcr/m /n/10 https : / / www . [485] [486] Underfull \vbox (badness 10000) has occurred while \output is active [487] [488] [489] [490] Overfull \hbox (4.38043pt too wide) in paragraph at lines 34061--34061 []\T1/pcr/m/n/9 rep(1:4, each = 2, times = 3) # length 24, 3 complete replications[] [491] Underfull \hbox (badness 10000) in paragraph at lines 34132--34136 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [492] [493] [494] Underfull \hbox (badness 2302) in paragraph at lines 34365--34370 []\T1/pcr/m/n/10 signif []\T1/ptm/m/n/10 rounds the val-ues in its first ar-gu- ment to the spec-i-fied num-ber of \T1/ptm/m/it/10 sig-nif-i-cant Underfull \hbox (badness 1824) in paragraph at lines 34365--34370 \T1/ptm/m/n/10 dig-its. Hence, for []\T1/pcr/m/n/10 numeric x[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 signif(x, dig) []\T1/ptm/m/n/10 is the same as []\T1/pcr/m/n/ 10 round(x, dig - [495] [496] Overfull \hbox (12.78088pt too wide) in paragraph at lines 34498--34498 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"))[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 34501--34501 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 34508--34508 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] [497] [498] [499] [500] [501] [502] [503] Overfull \hbox (66.78088pt too wide) in paragraph at lines 34956--34956 [] \T1/pcr/m/n/10 useHash = (n > 1e+07 && !replace && is.null(prob) && size <= n/2))[] [504] [505] [506] [507] [508] [509] Overfull \hbox (12.78088pt too wide) in paragraph at lines 35393--35393 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)[] [510] [511] Underfull \hbox (badness 1158) in paragraph at lines 35497--35502 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 strip.white []\T1/ptm/m/n/10 is of length 1, it ap-plies to all fields; oth-er-wise, if [512] [513] Overfull \hbox (15.18042pt too wide) in paragraph at lines 35683--35683 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data ", sep = "\n") [514] [515] [516] Underfull \hbox (badness 4752) in paragraph at lines 35942--35945 []\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence []\T1/pcr/ m/n/10 1, 2, ..., length(along.with)[]\T1/ptm/m/n/10 . Underfull \hbox (badness 5563) in paragraph at lines 35946--35952 []\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence []\T1/pcr/m/n/10 1, 2 , ..., length(from) []\T1/ptm/m/n/10 (as if ar-gu-ment [517] [518] [519] [520] [521] [522] [523] [524] [525] Underfull \hbox (badness 6094) in paragraph at lines 36532--36536 []\T1/pcr/m/n/10 getAllConnections []\T1/ptm/m/n/10 re-turns a se-quence of in- te-ger con-nec-tion de-scrip-tors for use Underfull \hbox (badness 6559) in paragraph at lines 36532--36536 \T1/ptm/m/n/10 with []\T1/pcr/m/n/10 getConnection[]\T1/ptm/m/n/10 , cor-re-spo nd-ing to the row names of the ta-ble re-turned by [526] [527] Underfull \hbox (badness 3826) in paragraph at lines 36623--36634 []\T1/ptm/m/n/10 In Win-dows, com-mand line in-ter-pre-ta-tion is done by the a p-pli-ca-tion as well as the Underfull \hbox (badness 3492) in paragraph at lines 36623--36634 \T1/ptm/m/n/10 shell. It may de-pend on the com-piler used: Mi-crosoft's rules for the C run-time Underfull \hbox (badness 10000) in paragraph at lines 36623--36634 \T1/ptm/m/n/10 are given at [][]$\T1/pcr/m/n/10 https : / / learn . microsoft . com / en-[]us / cpp / c-[]language / Underfull \hbox (badness 1635) in paragraph at lines 36623--36634 \T1/pcr/m/n/10 parsing-[]c-[]command-[]line-[]arguments ? view = msvc-[]160$[][ ]\T1/ptm/m/n/10 . It may de-pend on the [528] [529] [530] [531] [532] [533] [534] [535] Overfull \hbox (66.78088pt too wide) in paragraph at lines 37177--37177 [] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index .return = FALSE)[] [536] [537] [538] [539] Overfull \hbox (6.78088pt too wide) in paragraph at lines 37429--37429 [] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length = Inf,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 37431--37431 [] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes" , "keepNA"),[] Underfull \hbox (badness 4954) in paragraph at lines 37474--37480 [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 vec-tor, passed as []\T1/ pcr/m/n/10 control []\T1/ptm/m/n/10 to [][][]\T1/pcr/m/n/10 deparse[][][]()[]\T 1/ptm/m/n/10 , see also Underfull \hbox (badness 5050) in paragraph at lines 37474--37480 [][][]\T1/pcr/m/n/10 .deparseOpts[][][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \ T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to [540] [541] Overfull \hbox (20.58041pt too wide) in paragraph at lines 37585--37585 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments should print:)[] [542] [543] [544] [545] [546] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37928--37928 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m /n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37943--37943 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is being added[] [547] [548] [549] Underfull \hbox (badness 10000) in paragraph at lines 38168--38170 [][][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919 799 / functions / [550] [551] [552] Overfull \hbox (12.78088pt too wide) in paragraph at lines 38395--38395 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known") Overfull \hbox (12.78088pt too wide) in paragraph at lines 38396--38396 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile = FALSE)[] [553] [554] [555] [556] [557] Overfull \hbox (63.78036pt too wide) in paragraph at lines 38727--38727 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS E, nowadays often three [558] Underfull \hbox (badness 6110) in paragraph at lines 38823--38833 []\T1/ptm/m/n/10 A func-tion []\T1/pcr/m/n/10 .First []\T1/ptm/m/n/10 (and [][] []\T1/pcr/m/n/10 .Last[][][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-at e `\T1/pcr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or Underfull \hbox (badness 2635) in paragraph at lines 38823--38833 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have been saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want a dif-fer-ent Underfull \hbox (badness 1237) in paragraph at lines 38823--38833 \T1/ptm/m/n/10 set of pack-ages than the de-fault ones when you start, in-sert a call to [][][]\T1/pcr/m/n/10 options[][][] []\T1/ptm/m/n/10 in the Underfull \hbox (badness 1231) in paragraph at lines 38823--38833 \T1/pcr/m/n/10 = character()) []\T1/ptm/m/n/10 will at-tach no ex-tra pack-ages on startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (or Underfull \hbox (badness 1112) in paragraph at lines 38823--38833 \T1/ptm/m/n/10 set []\T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL []\T1/ptm/m/n/10 as an en-vi-ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/10 ). Us-ing [559] Underfull \hbox (badness 10000) in paragraph at lines 38879--38885 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 38879--38885 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1496) in paragraph at lines 38879--38885 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be Underfull \hbox (badness 1460) in paragraph at lines 38894--38901 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 38894--38901 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 38894--38901 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment [560] Overfull \hbox (4.38043pt too wide) in paragraph at lines 38956--38956 []\T1/pcr/m/n/9 # Variable expansion in double quotes, string literals with ba ckslashes in[] [561] [562] [563] Underfull \hbox (badness 1484) in paragraph at lines 39129--39133 []\T1/ptm/m/n/10 alternative to []\T1/pcr/m/n/10 exprs []\T1/ptm/m/n/10 or []\T 1/pcr/m/n/10 ...[]\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an Overfull \hbox (60.78088pt too wide) in paragraph at lines 39194--39194 [] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e xprs = exprs))) [564] Overfull \hbox (9.78043pt too wide) in paragraph at lines 39220--39220 []\T1/pcr/m/n/9 stopifnot(all.equal(pi, 3.141593), 2 < 2, (1:10 < 12), "a" < "b") |> try()[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 39236--39236 []\T1/pcr/m/n/9 stopifnot(all.equal(rep(list(pi),4), list(3.1, 3.14, 3.141, 3. 1415))) |> try()[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 39244--39244 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 {Yes, learn how to use do.c all(substitute, ...) in a powerful manner !!}[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 39246--39246 []\T1/pcr/m/n/9 bdy <- do.call(substitute, list(bdy, list(stopifnot = quote(warnifnot))))[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 39247--39247 []\T1/pcr/m/n/9 bdy[[N-1]] <- do.call(substitute, list(bdy[[N-1]], list(stop = quote(warning))))[] [565] Underfull \hbox (badness 1436) in paragraph at lines 39307--39311 []\T1/ptm/m/n/10 integer de-ter-min-ing the []\T1/pcr/m/n/10 format()[]\T1/ptm/ m/n/10 ing of sec-onds when needed. Note [566] [567] [568] [569] [570] Overfull \hbox (15.18042pt too wide) in paragraph at lines 39700--39700 []\T1/pcr/m/n/9 z3 # prints without fractional seconds by default, digits.sec = NULL ("= 0")[] [571] Overfull \hbox (9.78043pt too wide) in paragraph at lines 39728--39728 []\T1/pcr/m/n/9 format(s1 <- seq.Date(as.Date(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 19 78-01-01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ), by = \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 day \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , len = 7), "%a")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 39729--39729 []\T1/pcr/m/n/9 format(s2 <- seq.Date(as.Date(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 20 00-01-01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ), by = \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 mon th\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , len = 12), "%b")[] [572] [573] Overfull \hbox (0.78088pt too wide) in paragraph at lines 39841--39841 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [574] [575] [576] Overfull \hbox (6.78088pt too wide) in paragraph at lines 40104--40104 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] [577] Overfull \hbox (4.38043pt too wide) in paragraph at lines 40148--40148 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [578] [579] [580] [581] [582] [583] [584] Overfull \hbox (52.98038pt too wide) in paragraph at lines 40595--40595 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e verything gets added.[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 40598--40598 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also missing, ....[] [585] Underfull \hbox (badness 10000) in paragraph at lines 40649--40656 []\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][][]\T1/pcr/m/n/ 10 signif[][][]() []\T1/ptm/m/n/10 (for Underfull \hbox (badness 10000) in paragraph at lines 40649--40656 []\T1/pcr/m/n/10 summary.default[]\T1/ptm/m/n/10 ) or [][][]\T1/pcr/m/n/10 form at[][][]() []\T1/ptm/m/n/10 (for []\T1/pcr/m/n/10 summary.data.frame[]\T1/ptm/m /n/10 ). [586] Overfull \hbox (4.38043pt too wide) in paragraph at lines 40702--40702 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision [587] [588] [589] [590] Overfull \hbox (31.3804pt too wide) in paragraph at lines 41016--41016 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw ise: last"),"\n")[] [591] [592] [593] [594] Overfull \hbox (20.58041pt too wide) in paragraph at lines 41221--41221 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, macOS, FreeBSD:[] Underfull \hbox (badness 2293) in paragraph at lines 41251--41257 []\T1/ptm/m/n/10 This ex-pands tilde (see [][]tilde ex-pan-sion[][][]) and wild -cards in file paths. For pre-cise de- Underfull \hbox (badness 1237) in paragraph at lines 41251--41257 \T1/ptm/m/n/10 tails of wild-cards ex-pan-sion, see your sys-tem's doc-u-men-ta -tion on the []\T1/pcr/m/n/10 glob []\T1/ptm/m/n/10 sys-tem call. Underfull \hbox (badness 4792) in paragraph at lines 41270--41275 []\T1/ptm/m/n/10 If a file-name starts with []\T1/pcr/m/n/10 . []\T1/ptm/m/n/10 this may need to be matched ex-plic-itly: for ex-am-ple Underfull \hbox (badness 1107) in paragraph at lines 41270--41275 []\T1/pcr/m/n/10 Sys.glob("*.RData") []\T1/ptm/m/n/10 may or may not match `\T1 /pcr/m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match [595] [596] [597] [598] Underfull \hbox (badness 10000) in paragraph at lines 41558--41562 []\T1/pcr/m/n/10 sys.status() []\T1/ptm/m/n/10 re-turns a list with com-po-nent s []\T1/pcr/m/n/10 sys.calls[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sys.parents []\ T1/ptm/m/n/10 and Underfull \hbox (badness 1584) in paragraph at lines 41573--41576 []\T1/pcr/m/n/10 sys.call []\T1/ptm/m/n/10 re-turns a call, []\T1/pcr/m/n/10 sy s.function []\T1/ptm/m/n/10 a func-tion def-i-ni-tion, and []\T1/pcr/m/n/10 sys .frame []\T1/ptm/m/n/10 and [599] [600] [601] Overfull \hbox (25.98041pt too wide) in paragraph at lines 41711--41711 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths ), keepNA=TRUE))[] [602] Overfull \hbox (19.22812pt too wide) in paragraph at lines 41792--41792 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/cmtt /m/n/9 `\T1/pcr/m/n/9 A+C\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 could also be used [603] [604] Underfull \hbox (badness 1082) in paragraph at lines 41937--41940 []\T1/ptm/m/n/10 logical. If []\T1/pcr/m/n/10 TRUE[]\T1/ptm/m/n/10 , func-tions keep their source in-clud-ing com-ments, see Underfull \hbox (badness 10000) in paragraph at lines 41964--41966 [][][]\T1/pcr/m/n/10 source[][][][]\T1/ptm/m/n/10 , and [][][]\T1/pcr/m/n/10 lo adNamespace[][][] []\T1/ptm/m/n/10 which is called from [][][]\T1/pcr/m/n/10 li brary[][][](.) []\T1/ptm/m/n/10 and uses [605] [606] [607] Underfull \hbox (badness 1038) in paragraph at lines 42130--42133 []\T1/ptm/m/n/10 a log-i-cal (not []\T1/pcr/m/n/10 NA[]\T1/ptm/m/n/10 ) in-di-c at-ing whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or [608] [609] [610] [611] [612] Underfull \hbox (badness 1442) in paragraph at lines 42495--42499 \T1/ptm/m/n/10 con-sider it to be piped or redi-rected: []\T1/pcr/m/n/10 stdout = TRUE []\T1/ptm/m/n/10 uses a pipe whereas []\T1/pcr/m/n/10 stdout = [613] [614] [615] [616] Underfull \hbox (badness 4096) in paragraph at lines 42749--42752 []\T1/ptm/m/n/10 Use [][][]\T1/pcr/m/n/10 ftable[][][] []\T1/ptm/m/n/10 for pri nt-ing (and more) of mul-ti-di-men-sional ta-bles. [][][]\T1/pcr/m/n/10 margin. table[][][][]\T1/ptm/m/n/10 , [617] Underfull \hbox (badness 7888) in paragraph at lines 42863--42867 []\T1/ptm/m/n/10 On 64-bit plat-forms []\T1/pcr/m/n/10 bin []\T1/ptm/m/n/10 can have $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., []\T1/pcr/ m/n/10 length(bin) > [618] [619] [620] Overfull \hbox (63.78036pt too wide) in paragraph at lines 43025--43025 [] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1" , "2"), c("A", "B")))),[] Overfull \hbox (30.0281pt too wide) in paragraph at lines 43027--43027 [] \T1/pcr/m/n/9 array(list(\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 2\TS1/cm tt/m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), names = nq),[] Overfull \hbox (55.67578pt too wide) in paragraph at lines 43029--43029 [] \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 4\TS1/cmtt/m/n/9 ` \T1/pcr/m /n/9 = NULL, \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 5\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 = NULL), dim=4, dimnames=list(as.character(2:5)))))[] Underfull \hbox (badness 10000) in paragraph at lines 43042--43044 []\T1/pcr/m/n/10 removeTaskCallback []\T1/ptm/m/n/10 un-registers a func-tion t hat was reg-is-tered ear-lier via [621] Underfull \hbox (badness 10000) in paragraph at lines 43122--43125 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . [622] [623] Underfull \hbox (badness 3872) in paragraph at lines 43240--43243 []\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call -backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer . [624] Underfull \hbox (badness 5475) in paragraph at lines 43306--43310 [][][]\T1/pcr/m/n/10 addTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 removeTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 taskCallback Manager[][][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / [625] [626] [627] [628] [629] [630] Underfull \hbox (badness 1655) in paragraph at lines 43729--43736 \T1/ptm/m/n/10 may also be known as `[]\T1/pcr/m/n/10 GB[]\T1/ptm/m/n/10 ', `[] \T1/pcr/m/n/10 GB-Eire[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 Europe/Belfast[]\T1 /ptm/m/n/10 ', `[]\T1/pcr/m/n/10 Europe/Guernsey[]\T1/ptm/m/n/10 ', Underfull \hbox (badness 2253) in paragraph at lines 43737--43742 []\T1/pcr/m/n/10 OlsonNames []\T1/ptm/m/n/10 re-turns a char-ac-ter vec-tor, se e the ex-am-ples for typ-i-cal cases. It may Underfull \hbox (badness 1655) in paragraph at lines 43737--43742 \T1/ptm/m/n/10 have an at-tribute []\T1/pcr/m/n/10 "Version"[]\T1/ptm/m/n/10 , some-thing like `[]\T1/pcr/m/n/10 "2023a"[]\T1/ptm/m/n/10 '. (It does on sys-te ms us-ing [631] Underfull \hbox (badness 4467) in paragraph at lines 43787--43796 []\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 OlsonNames []\T1/ptm/m/n/10 re- turns the time-zone names known to the cur-rently se- Underfull \hbox (badness 3954) in paragraph at lines 43787--43796 \T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t he file sys-tem varies, [632] Underfull \hbox (badness 1337) in paragraph at lines 43890--43898 \T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 / usr/local/etc\T1/ptm/m/n/10 ' or Underfull \hbox (badness 10000) in paragraph at lines 43899--43902 []\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym -link tar-get name of [633] Underfull \hbox (badness 3460) in paragraph at lines 43955--43958 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / data . iana . org / Underfull \hbox (badness 4429) in paragraph at lines 43959--43961 [][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol- Overfull \hbox (31.3804pt too wide) in paragraph at lines 43968--43968 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET", "Eire", ..., but[] [634] [635] [636] [637] [638] Overfull \hbox (15.18042pt too wide) in paragraph at lines 44311--44311 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15 g)\n", ncp))),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 44313--44313 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp root finding:[] [639] [640] Overfull \hbox (84.78088pt too wide) in paragraph at lines 44413--44413 [] \T1/pcr/m/n/10 getOption("deparse .max.lines", -1L)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 44415--44415 [] \T1/pcr/m/n/10 getOption("deparse .max.lines", -1L)))[] [641] [642] [643] Underfull \hbox (badness 6542) in paragraph at lines 44689--44691 []\T1/pcr/m/n/10 cospi(x)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sinpi(x)[]\T1/ptm/ m/n/10 , and []\T1/pcr/m/n/10 tanpi(x)[]\T1/ptm/m/n/10 , com-pute []\T1/pcr/m/n /10 cos(pi*x)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sin(pi*x)[]\T1/ptm/m/n/10 , an d [644] [645] Overfull \hbox (30.78088pt too wide) in paragraph at lines 44808--44808 []\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[ \t\r\n]") [646] Underfull \hbox (badness 1708) in paragraph at lines 44876--44884 []\T1/pcr/m/n/10 try []\T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any er-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 3713) in paragraph at lines 44876--44884 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ][]\T1/pcr/m/n/10 stderr[][][] []\T1/ptm/m/n/10 con-nec-tion un-less [647] Underfull \hbox (badness 4859) in paragraph at lines 44916--44921 [][][]\T1/pcr/m/n/10 options[][][] []\T1/ptm/m/n/10 for set-ting er-ror han-dle rs and sup-press-ing the print-ing of er-ror mes-sages; [648] Underfull \hbox (badness 3895) in paragraph at lines 44978--44990 []\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the struc-ture []\T1/pcr/m/n/10 TypeTable []\T1/ptm/m/n/10 in Underfull \hbox (badness 1303) in paragraph at lines 44978--44990 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue s are the vec-tor types []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/ m/n/10 "integer"[]\T1/ptm/m/n/10 , [649] [650] [651] [652] [653] Overfull \hbox (9.78043pt too wide) in paragraph at lines 45326--45326 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp ression(1+x))[] [654] [655] Underfull \hbox (badness 1137) in paragraph at lines 45420--45427 []\T1/ptm/m/n/10 When a func-tion call-ing []\T1/pcr/m/n/10 UseMethod("fun") [] \T1/ptm/m/n/10 is ap-plied to an ob-ject with class vec-tor [656] [657] [658] [659] [660] Overfull \hbox (4.38043pt too wide) in paragraph at lines 45798--45798 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local es and fonts[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 45807--45807 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little- endian platforms[] [661] Underfull \hbox (badness 2057) in paragraph at lines 45873--45879 [][][]\T1/pcr/m/n/10 file[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.acc ess[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.append[][][][]\T1/ptm/m/n /10 , [][][]\T1/pcr/m/n/10 file.copy[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 file.create[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.exists[][][][] \T1/ptm/m/n/10 , Underfull \hbox (badness 3861) in paragraph at lines 45882--45887 [][][]\T1/pcr/m/n/10 dir.create[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 di r.exists[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 normalizePath[][][][]\T1/ ptm/m/n/10 , [][][]\T1/pcr/m/n/10 path.expand[][][][]\T1/ptm/m/n/10 , [][][]\T1 /pcr/m/n/10 pipe[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Sys.glob[][][][]\ T1/ptm/m/n/10 , [662] Overfull \hbox (36.7804pt too wide) in paragraph at lines 45975--45975 []\T1/pcr/m/n/9 try( substr(x, 1,1) ) # gives \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 in valid multibyte string\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 error in a UTF-8 locale[] [663] Underfull \hbox (badness 1803) in paragraph at lines 46038--46041 []\T1/ptm/m/n/10 The atomic modes are []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "integer"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "numeric" []\ T1/ptm/m/n/10 (syn-onym []\T1/pcr/m/n/10 "double"[]\T1/ptm/m/n/10 ), Underfull \hbox (badness 3471) in paragraph at lines 46042--46048 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 mode = "any"[]\T1/ptm/m/n/10 , []\T1/pcr/m /n/10 is.vector []\T1/ptm/m/n/10 may re-turn []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/ n/10 for the atomic modes, [][][]\T1/pcr/m/n/10 list[][][] []\T1/ptm/m/n/10 and [664] [665] [666] [667] Underfull \hbox (badness 1014) in paragraph at lines 46271--46274 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the warn-ing should be out-put im-me -di-ately, even if [668] Overfull \hbox (36.78088pt too wide) in paragraph at lines 46380--46380 [] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes sages:\n"),[] [669] Overfull \hbox (4.38043pt too wide) in paragraph at lines 46455--46455 []\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n /9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 46463--46463 []\T1/pcr/m/n/9 x <- 1:36; for(n in 1:13) for(m in 1:12) A <- matrix(x, n,m) # There were 105 warnings ...[] [670] Underfull \hbox (badness 1783) in paragraph at lines 46528--46530 []\T1/pcr/m/n/10 weekdays []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 months []\T1/pt m/m/n/10 re-turn a char-ac-ter vec-tor of names in the lo-cale in use, i.e., [671] Overfull \hbox (25.98041pt too wide) in paragraph at lines 46558--46558 []\T1/pcr/m/n/9 ## Show how easily you get month, day, year, day (of {month, w eek, yr}), ... :[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 46570--46570 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Even simpler: Date -> Matrix - dropping time info {sec,min,hour, isdst}[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 46573--46573 []\T1/pcr/m/n/9 d2mat(seq(as.Date("2000-02-02"), by=1, length.out=30)) # has R 1.0.0\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s release date[] [672] Underfull \hbox (badness 10000) in paragraph at lines 46635--46640 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 arr.ind == TRUE []\T1/ptm/m/n/10 and []\T1 /pcr/m/n/10 x []\T1/ptm/m/n/10 is an [][][]\T1/pcr/m/n/10 array[][][] []\T1/ptm /m/n/10 (has a [][][]\T1/pcr/m/n/10 dim[][][] []\T1/ptm/m/n/10 at-tribute), the re-sult is Underfull \hbox (badness 2564) in paragraph at lines 46635--46640 []\T1/pcr/m/n/10 arrayInd(which(x), dim(x), dimnames(x))[]\T1/ptm/m/n/10 , name ly a ma-trix whose rows each [673] Underfull \hbox (badness 2818) in paragraph at lines 46731--46737 []\T1/ptm/m/n/10 For a [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 vec- tor []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 with both []\T1/pcr/m/n/10 FALSE []\T1/ ptm/m/n/10 and []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 val-ues, []\T1/pcr/m/n/10 which.min(x) []\T1/ptm/m/n/10 and [674] Overfull \hbox (15.18042pt too wide) in paragraph at lines 46766--46766 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is at least one:[] [675] [676] [677] [678] [679] [680] Underfull \hbox (badness 2846) in paragraph at lines 47227--47231 []\T1/pcr/m/n/10 .packages() []\T1/ptm/m/n/10 re-turns the names of the cur-ren tly at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [681] Overfull \hbox (4.38043pt too wide) in paragraph at lines 47267--47267 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 47288--47292 []\T1/pcr/m/n/10 .standard_regexps []\T1/ptm/m/n/10 re-turns a list of `stan-da rd' reg-exps, in-clud-ing el-e-ments named [682]) (./compiler-pkg.tex Chapter 2. [683] Underfull \hbox (badness 2884) in paragraph at lines 106--120 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 options []\T1/ptm/m/n/10 ar-gu-ment can b e used to con-trol com-piler op-er-a-tion. There are cur- Underfull \hbox (badness 10000) in paragraph at lines 106--120 \T1/ptm/m/n/10 rently four op-tions: []\T1/pcr/m/n/10 optimize[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 suppressAll[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 suppressUndef ined[]\T1/ptm/m/n/10 , and [684] [685] [686]) (./datasets-pkg.tex Chapter 3. [687] [688] [689] [690] [691] Overfull \hbox (15.18042pt too wide) in paragraph at lines 301--301 [] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang e", cex = 1.2,[] [692] Overfull \hbox (4.38043pt too wide) in paragraph at lines 379--379 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi ven = FALSE)[] [693] [694] [695] [696] Overfull \hbox (4.38043pt too wide) in paragraph at lines 617--617 [] \T1/pcr/m/n/9 start = c(lrc = log(.35)), algorithm = "plinear", t race = TRUE)[] [697] Underfull \hbox (badness 4779) in paragraph at lines 704--707 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [698] [699] Underfull \hbox (badness 4779) in paragraph at lines 837--840 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [700] [701] [702] Underfull \hbox (badness 1097) in paragraph at lines 1037--1041 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [703] Underfull \hbox (badness 4779) in paragraph at lines 1152--1155 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [704] [705] [706] [707] [708] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1464--1464 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption time (sec)")[] [709] [710] Underfull \hbox (badness 10000) in paragraph at lines 1549--1552 []\T1/ptm/m/n/10 Finally, []\T1/pcr/m/n/10 freeny []\T1/ptm/m/n/10 is a data fr ame with vari-ables []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lag.q uarterly.revenue[]\T1/ptm/m/n/10 , Underfull \hbox (badness 2903) in paragraph at lines 1549--1552 []\T1/pcr/m/n/10 price.index[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 income.level[]\ T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 market.potential []\T1/ptm/m/n/10 ob-taine d from the above [711] [712] [713] Underfull \hbox (badness 4779) in paragraph at lines 1738--1741 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [714] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1832--1832 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil y = binomial())[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1840--1840 [] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum), data = infert)[] [715] [716] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1956--1956 [] \T1/pcr/m/n/9 sub(" W.",".Width", dn i3[[2]])))),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1957--1957 [] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d ni3[[3]]))))[] [717] [718] [719] [720] Underfull \hbox (badness 4779) in paragraph at lines 2160--2163 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [721] [722] [723] [724] [725] [726] [727] [728] Underfull \hbox (badness 4779) in paragraph at lines 2725--2728 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [729] [730] [731] [732] [733] [734] [735] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3154--3154 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 1.2, pch = ".")[] [736] [737] [738] [739] [740] [741] Overfull \hbox (47.58038pt too wide) in paragraph at lines 3505--3505 []\T1/pcr/m/n/9 ## Alaska and Hawaii are placed just off the West Coast (for c ompact map drawing):[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3507--3507 []\T1/pcr/m/n/9 ## state.center2 := version of state.center with "correct" coo rdinates for AK & HI:[] Overfull \hbox (85.38034pt too wide) in paragraph at lines 3508--3508 []\T1/pcr/m/n/9 ## From https://pubs.usgs.gov/gip/Elevations-Distances/elvadis t.html#Geographic%20Centers[] [742] [743] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3639--3639 [] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t he monthly one:[] [744] [745] Underfull \hbox (badness 4779) in paragraph at lines 3787--3790 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [746] [747] [748] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3996--3996 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] [749] Underfull \hbox (badness 10000) in paragraph at lines 4034--4036 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/pcr/m/n/10 h ttps : / / web . archive . org / web / Underfull \hbox (badness 10000) in paragraph at lines 4034--4036 \T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma n / sitephotos / [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762]) (./grDevices-pkg.tex Chapter 4. [763] [764] [765] [766] Underfull \hbox (badness 4752) in paragraph at lines 298--303 []\T1/ptm/m/n/10 Apart from that, [][][]\T1/pcr/m/n/10 axisTicks[][][]() []\T1/ ptm/m/n/10 just calls the C func-tion []\T1/pcr/m/n/10 CreateAtVector() []\T1/p tm/m/n/10 in [767] [768] [769] [770] Overfull \hbox (6.78088pt too wide) in paragraph at lines 519--519 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d .pdf",[] [771] [772] [773] [774] [775] [776] [777] [778] [779] [780] Underfull \hbox (badness 5175) in paragraph at lines 1193--1195 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [781] [782] [783] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1364--1364 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", scale.in = 255))[] [784] [785] [786] Underfull \hbox (badness 3302) in paragraph at lines 1625--1629 []\T1/ptm/m/n/10 character: Does the de-vice sup-port pat-tern fills? One or mo re of Underfull \hbox (badness 10000) in paragraph at lines 1625--1629 []\T1/pcr/m/n/10 c("LinearGradient", "RadialGradient", "TilingPattern") [787] [788] [789] [790] [791] Underfull \hbox (badness 1565) in paragraph at lines 1916--1921 []\T1/ptm/m/n/10 The de-fault for []\T1/pcr/m/n/10 dev.print []\T1/ptm/m/n/10 i s to pro-duce and print a postscript copy. This will not Underfull \hbox (badness 1354) in paragraph at lines 1916--1921 \T1/ptm/m/n/10 sys-tem: see [][][]\T1/pcr/m/n/10 postscript[][][] []\T1/ptm/m/n /10 for how to set this up. Win-dows users may pre-fer to use [792] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1999--1999 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] [793] Underfull \hbox (badness 1184) in paragraph at lines 2040--2050 []\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of []\T1/pcr /m/n/10 ghostscript[]\T1/ptm/m/n/10 , but are likely to in- Underfull \hbox (badness 2057) in paragraph at lines 2040--2050 []\T1/pcr/m/n/10 "tiffg4"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiffgray"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "tifflzw"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiffp ack"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiff12nc"[]\T1/ptm/m/n/10 , []\T1/pcr/ m/n/10 "tiff24nc"[]\T1/ptm/m/n/10 , [794] Underfull \hbox (badness 10000) in paragraph at lines 2152--2154 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [795] [796] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2288--2288 []\T1/pcr/m/n/10 embedGlyphs(file, glyphInfo, outfile = file, options = charac ter())[] [797] Underfull \hbox (badness 6758) in paragraph at lines 2338--2341 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [798] [799] Underfull \hbox (badness 2326) in paragraph at lines 2456--2466 []\T1/ptm/m/n/10 are given, then it uses those in a call to []\T1/pcr/m/n/10 se tGraphicsEventHandlers []\T1/ptm/m/n/10 to re-place Underfull \hbox (badness 2318) in paragraph at lines 2456--2466 \T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co m-pat-i-bil-ity with pre-2.12.0 Underfull \hbox (badness 2460) in paragraph at lines 2456--2466 \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e vent han-dlers is to set them us-ing Underfull \hbox (badness 1221) in paragraph at lines 2456--2466 []\T1/pcr/m/n/10 setGraphicsEventHandlers []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 setGraphicsEventEnv []\T1/ptm/m/n/10 on one or more graph-ics [800] [801] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2559--2559 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r" , yaxs = "r") {[] Underfull \vbox (badness 10000) has occurred while \output is active [802] [803] [804] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2815--2815 []\T1/pcr/m/n/10 gray.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re v = FALSE) Overfull \hbox (30.78088pt too wide) in paragraph at lines 2816--2816 []\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re v = FALSE)[] [805] [806] [807] [808] [809] Underfull \hbox (badness 10000) in paragraph at lines 3089--3090 [810] [811] [812] [813] [814] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3422--3422 []\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized = FALSE)[] [815] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3506--3506 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", scale.in = 255))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3507--3507 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale. out = NULL))[] [816] [817] [818] Underfull \hbox (badness 10000) in paragraph at lines 3665--3671 []\T1/pcr/m/n/10 nclass.FD []\T1/ptm/m/n/10 uses the Freedman-Diaconis choice b ased on the inter-quartile range [819] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3740--3740 []\T1/pcr/m/n/10 palette.colors(n = NULL, palette = "Okabe-Ito", alpha, recycl e = FALSE)[] [820] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3824--3824 []\T1/pcr/m/n/9 (palette(gray(seq(0,.9,length.out = 25)))) # gray scales; prin t old palette[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3844--3844 []\T1/pcr/m/n/9 ## Demonstrate the colors 1:8 in different palettes using a cu stom matplot()[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3851--3851 [] \T1/pcr/m/n/9 matplot(x, type = "l", lwd = 4, lty = 1, col = 1:8, ylab = "", main=main)[] [821] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3907--3907 []\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE, fixup = TRUE) [822] Underfull \hbox (badness 8170) in paragraph at lines 3936--3939 []\T1/ptm/m/n/10 the type of palettes to list: []\T1/pcr/m/n/10 "qualitative"[] \T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sequential"[]\T1/ptm/m/n/10 , [823] Underfull \hbox (badness 2189) in paragraph at lines 3997--4002 []\T1/ptm/m/n/10 For ex-am-ple, []\T1/pcr/m/n/10 "Dark 3" []\T1/ptm/m/n/10 work s well for shad-ing points or lines in up to five groups, Underfull \hbox (badness 10000) in paragraph at lines 4035--4039 \T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space & oldid = 883465135$[][]\T1/ptm/m/n/10 . [824] Underfull \vbox (badness 10000) has occurred while \output is active [825] Underfull \hbox (badness 5260) in paragraph at lines 4165--4168 []\T1/ptm/m/n/10 For use with []\T1/pcr/m/n/10 onefile = FALSE []\T1/ptm/m/n/10 give a C in-te-ger for-mat such as [826] [827] [828] [829] [830] Underfull \hbox (badness 5939) in paragraph at lines 4504--4509 []\T1/ptm/m/n/10 arguments []\T1/pcr/m/n/10 width[]\T1/ptm/m/n/10 , []\T1/pcr/m /n/10 height[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 onefile[]\T1/ptm/m/n/10 , []\T1 /pcr/m/n/10 family[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 title[]\T1/ptm/m/n/10 , [ ]\T1/pcr/m/n/10 fonts[]\T1/ptm/m/n/10 , [831] [832] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.symbol}) has been already used, duplicate ignored \relax l.4681 \aliasA{symbol}{plotmath}{symbol} [833] [834] [835] [836] [837] [838] Overfull \hbox (60.78088pt too wide) in paragraph at lines 5025--5025 [] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz w+p", "zip+p"),[] [839] [840] Underfull \hbox (badness 1348) in paragraph at lines 5236--5239 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, [][]$\T1/pcr/m/n/10 https : / / ww w . iso . org / standard / 34342 . html$[][]\T1/ptm/m/n/10 . See also [841] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5263--5263 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, height = 768)[] Underfull \hbox (badness 7522) in paragraph at lines 5304--5310 []\T1/ptm/m/n/10 For use with []\T1/pcr/m/n/10 onefile = FALSE []\T1/ptm/m/n/10 give a []\T1/pcr/m/n/10 printf []\T1/ptm/m/n/10 for-mat such as [842] Underfull \hbox (badness 1112) in paragraph at lines 5337--5341 []\T1/ptm/m/n/10 as `\T1/pcr/m/n/10 "CP1250.enc"\T1/ptm/m/n/10 ' (Cen-tral Eu-r o-pean), []\T1/pcr/m/n/10 "CP1251.enc" [843] [844] Underfull \hbox (badness 1755) in paragraph at lines 5481--5483 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [845] [846] Underfull \hbox (badness 7344) in paragraph at lines 5664--5666 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso Underfull \hbox (badness 7397) in paragraph at lines 5675--5679 [][][]\T1/pcr/m/n/10 postscriptFonts[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 Devices[][][][]\T1/ptm/m/n/10 , and [][][]\T1/pcr/m/n/10 check.options[][][] []\T1/ptm/m/n/10 which is called from both [847] [848] Underfull \hbox (badness 1552) in paragraph at lines 5802--5811 []\T1/pcr/m/n/10 "AvantGarde"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Bookman"[]\T1 /ptm/m/n/10 , []\T1/pcr/m/n/10 "Courier"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "He lvetica"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Helvetica-Narrow"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5802--5811 []\T1/pcr/m/n/10 "NewCenturySchoolbook"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Pal atino" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "Times"[]\T1/ptm/m/n/10 ; []\T1/pc r/m/n/10 "URWGothic"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5802--5811 []\T1/pcr/m/n/10 "URWBookman"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "NimbusMon"[]\ T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "NimbusSan" []\T1/ptm/m/n/10 (syn-onym []\T1/p cr/m/n/10 "URWHelvetica"[]\T1/ptm/m/n/10 ), Underfull \hbox (badness 2221) in paragraph at lines 5812--5814 []\T1/ptm/m/n/10 There are also map-pings for []\T1/pcr/m/n/10 "ComputerModern" []\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ComputerModernItalic" []\T1/ptm/m/n/10 and Underfull \hbox (badness 4686) in paragraph at lines 5844--5850 []\T1/pcr/m/n/10 "Japan1"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Japan1HeiMin"[]\T 1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Japan1GothicBBB"[]\T1/ptm/m/n/10 , and []\T1/p cr/m/n/10 "Japan1Ryumin" []\T1/ptm/m/n/10 for [849] Underfull \hbox (badness 5388) in paragraph at lines 5870--5872 []\T1/pcr/m/n/10 BousungEG-Light-GB []\T1/ptm/m/n/10 can be found at [][]$\T1/p cr/m/n/10 https : / / ftp . gnu . org / pub / non-[]gnu / [850] [851] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5974--5974 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r eg-tests-1c.R[] [852] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6086--6086 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100 , ...)[] [853] [854] Underfull \hbox (badness 10000) in paragraph at lines 6173--6175 []\T1/ptm/m/n/10 Calling []\T1/pcr/m/n/10 quartz() []\T1/ptm/m/n/10 sets [][][] \T1/pcr/m/n/10 .Device[][][] []\T1/ptm/m/n/10 to []\T1/pcr/m/n/10 "quartz" []\T 1/ptm/m/n/10 for on-screen de-vices and to [855] [856] [857] [858] [859] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6540--6540 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15, sep = "."))[] Underfull \hbox (badness 10000) in paragraph at lines 6554--6557 []\T1/pcr/m/n/10 rgb2hsv []\T1/ptm/m/n/10 trans-forms col-ors from RGB space (r ed/green/blue) into HSV space [860] [861] [862] [863] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6774--6774 []\T1/pcr/m/n/9 p <- persp(x, y, fxy <- outer(x,y), phi = 20, theta = 15, r = 3, ltheta = -75,[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6785--6785 []\T1/pcr/m/n/9 ## now some "horizontal rays" (going from center to very left or very right):[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 6787--6787 [] \T1/pcr/m/n/9 lines(trans3d(x=seq(x1, x2, by=0.5), y= -0.7, z = z, pmat = p, continuous = CNT),[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6789--6789 []\T1/pcr/m/n/9 doHor(-10, 0, z = -0.5, col = 2) # x in [-10, 0] -- to the v ery left : fine[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 6790--6790 []\T1/pcr/m/n/9 doHor(-.5, 2, z = -0.52,col = 4) # x in [-0.5, 2] only {to th e right} --> all fine[] Overfull \hbox (117.7803pt too wide) in paragraph at lines 6791--6791 []\T1/pcr/m/n/9 ## but now, x in [-0.5, 20] -- "too far" ==> "wrap around" pro blem (without \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 continuous=TRUE\TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 ):[] [864] [865] Overfull \hbox (0.78088pt too wide) in paragraph at lines 6923--6923 []\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp inch, Overfull \hbox (0.78088pt too wide) in paragraph at lines 6930--6930 []\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize = 12,[] [866] [867] [868] [869] Underfull \hbox (badness 10000) in paragraph at lines 7196--7201 []\T1/ptm/m/n/10 arguments []\T1/pcr/m/n/10 width[]\T1/ptm/m/n/10 , []\T1/pcr/m /n/10 height[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pointsize[]\T1/ptm/m/n/10 , []\ T1/pcr/m/n/10 record[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 rescale[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1803) in paragraph at lines 7196--7201 []\T1/pcr/m/n/10 xpinch[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 ypinch[]\T1/ptm/m/n/ 10 , []\T1/pcr/m/n/10 bg[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 canvas[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 gamma[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 xpos[]\T1/ptm/m /n/10 , []\T1/pcr/m/n/10 ypos[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 buffered[]\T1/ ptm/m/n/10 , Underfull \hbox (badness 2941) in paragraph at lines 7196--7201 []\T1/pcr/m/n/10 restoreConsole[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 clickToConfi rm[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 title[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 fillOddEven []\T1/ptm/m/n/10 and [870] [871] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7302--7302 []\T1/pcr/m/n/9 windows() # make sure we have the right device type (availabl e on Windows only)[] Underfull \hbox (badness 3590) in paragraph at lines 7341--7344 []\T1/ptm/m/n/10 The \T1/phv/m/n/10 R \T1/ptm/m/n/10 func-tion is a wrap-per fo r two de-vices, one based on Xlib ([][]$\T1/pcr/m/n/10 https : / / Underfull \hbox (badness 2393) in paragraph at lines 7341--7344 \T1/pcr/m/n/10 en . wikipedia . org / wiki / Xlib$[][]\T1/ptm/m/n/10 ) and one us-ing cairo-graph-ics ([][]$\T1/pcr/m/n/10 https : / / www . Overfull \hbox (12.78088pt too wide) in paragraph at lines 7352--7352 [] \T1/pcr/m/n/10 fonts, family, xpos, ypos, title, type, antialias, symbol family)[] [872] Underfull \hbox (badness 1189) in paragraph at lines 7417--7419 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [873] [874] Underfull \hbox (badness 10000) in paragraph at lines 7522--7524 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" []\T1/ptm/m/n/10 for CJ K lan-guages and Underfull \hbox (badness 10000) in paragraph at lines 7568--7575 []\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of [] \T1/pcr/m/n/10 quote(pi) []\T1/ptm/m/n/10 and Underfull \hbox (badness 2469) in paragraph at lines 7568--7575 []\T1/pcr/m/n/10 expression(10^degree)[]\T1/ptm/m/n/10 ) have been seen on Linu x sys-tems which have the Wine [875] Underfull \hbox (badness 5607) in paragraph at lines 7652--7656 []\T1/pcr/m/n/10 type = "Xlib" []\T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-d o-Color', `GrayScale', []\T1/pcr/m/n/10 StaticGray []\T1/ptm/m/n/10 and [876] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7704--7704 [] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height = 6, xpos = 0,[] [877] [878] Underfull \hbox (badness 5637) in paragraph at lines 7836--7842 []\T1/pcr/m/n/10 "Courier"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Helvetica" []\T1 /ptm/m/n/10 (the de-fault), []\T1/pcr/m/n/10 "Helvetica-Narrow"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1721) in paragraph at lines 7869--7872 []\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt p : / / www . schmidt-[]web-[]berlin . de / [879] [880] Overfull \hbox (63.78036pt too wide) in paragraph at lines 8004--8004 []\T1/pcr/m/n/9 op <- options(warn = 2)# ==> warnings would be errors, we supp ress the one "we know":[] [881] Underfull \hbox (badness 1231) in paragraph at lines 8043--8045 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., []\T1/pcr/m/n/10 number[i] []\T1/ptm/m/n/10 is the mul-ti-plic-ity of [882] [883] [884]) (./graphics-pkg.tex Chapter 5. Underfull \hbox (badness 4647) in paragraph at lines 16--18 []\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag es, use []\T1/pcr/m/n/10 library(help = [885] [886] [887] [888] [889] [890] [891] Overfull \hbox (6.05087pt too wide) in paragraph at lines 450--450 [] \T1/pcr/m/n/10 gap.axis <- if(perpendicular(side, las)) 0.25 else 1[] Underfull \hbox (badness 4048) in paragraph at lines 482--488 []\T1/ptm/m/n/10 When []\T1/pcr/m/n/10 at = NULL[]\T1/ptm/m/n/10 , pretty tick mark lo-ca-tions are com-puted in-ter-nally (the same way [892] [893] Overfull \hbox (47.58038pt too wide) in paragraph at lines 580--580 []\T1/pcr/m/n/9 ## now shrink the window (in x- and y-direction) and observe t he axis labels drawn[] [894] Overfull \hbox (15.18042pt too wide) in paragraph at lines 692--692 []\T1/pcr/m/n/9 axis.Date(3, at = as.integer(as.Date("2023-04-01")), col.axis = "darkgreen")[] [895] Overfull \hbox (15.18042pt too wide) in paragraph at lines 707--707 []\T1/pcr/m/n/9 axis.POSIXct(3, at = as.POSIXct("2022-10-01 00:01:30"), col.ax is = "orange")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 712--712 []\T1/pcr/m/n/9 axis.POSIXct(3, at = as.numeric(as.POSIXct("2022-10-01 00:00:3 0")) + 0.25,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 713--713 [] \T1/pcr/m/n/9 col.axis = "forestgreen", col = "darkgreen", m gp = c(3,2,0))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 719--719 []\T1/pcr/m/n/9 plot(data.frame(HST, y = 1), xaxt = "n", xlab = "Hawaii Standa rd Time (HST)")[] Underfull \hbox (badness 10000) in paragraph at lines 746--750 []\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][][]\T1/pcr /m/n/10 par[][][]("xaxp") []\T1/ptm/m/n/10 or Underfull \hbox (badness 3250) in paragraph at lines 746--750 [][][]\T1/pcr/m/n/10 par[][][]("yaxp") []\T1/ptm/m/n/10 de-pend-ing on the []\T 1/pcr/m/n/10 side []\T1/ptm/m/n/10 ar-gu-ment ([]\T1/pcr/m/n/10 par("xaxp") []\ T1/ptm/m/n/10 if [896] [897] Overfull \hbox (4.38043pt too wide) in paragraph at lines 833--833 [] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n intLog = 5))[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 870--870 [] \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend = NULL, ...)[] [898] [899] Underfull \hbox (badness 10000) in paragraph at lines 1017--1021 [][][]\T1/pcr/m/n/10 plot[][][](..., type = "h")[]\T1/ptm/m/n/10 , [][][]\T1/pc r/m/n/10 dotchart[][][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 hist[][][] []\T1 /ptm/m/n/10 for bars of a \T1/ptm/m/it/10 con-tin-u-ous \T1/ptm/m/n/10 vari-abl e. [900] Overfull \hbox (133.98029pt too wide) in paragraph at lines 1034--1034 [] \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = " # {passengers}", legend.text = TRUE)[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1036--1036 []\T1/pcr/m/n/9 (xt <- xtabs(Freq ~ Survived + Class + Sex, d.Titanic, subset = Age=="Adult"))[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 1038--1038 []\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur vived, *)", color=TRUE)[] Underfull \vbox (badness 10000) has occurred while \output is active [901] [902] [903] [904] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1322--1322 []\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches .. outside hinges"):[] [905] [906] [907] Underfull \hbox (badness 2503) in paragraph at lines 1484--1493 \T1/ptm/m/n/10 when []\T1/pcr/m/n/10 horizontal []\T1/ptm/m/n/10 is false, and []\T1/pcr/m/n/10 xlim []\T1/ptm/m/n/10 hor-i-zon-tally. []\T1/pcr/m/n/10 xaxt[] \T1/ptm/m/n/10 , []\T1/pcr/m/n/10 yaxt[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3375) in paragraph at lines 1519--1521 []\T1/ptm/m/n/10 whisker line type (de-fault: []\T1/pcr/m/n/10 "dashed"[]\T1/pt m/m/n/10 ), [908] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1593--1593 []\T1/pcr/m/n/9 boxplot(z, col.axis = "skyblue3", main = "boxplot(*, col.axi s=..,main=..)")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1594--1594 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main = "plot(*, col.axi s=..,main=..)")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1600--1600 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill = "grey40",[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1601--1601 [] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl ty = 1, outpch = NA)[] [909] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1634--1634 [] \T1/pcr/m/n/10 yaxlabels = NULL, xlim = NULL, ylim = c(0, 1), weights = NU LL, ...)[] [910] [911] [912] [913] Underfull \hbox (badness 10000) in paragraph at lines 1907--1913 [][][]\T1/pcr/m/n/10 contourLines[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 filled.contour[][][] []\T1/ptm/m/n/10 for color-filled con-tours, [][][]\T1/pcr /m/n/10 contourplot[][][] []\T1/ptm/m/n/10 (and [914] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1927--1927 []\T1/pcr/m/n/9 contour(x, x, z, ylim = c(-6, 6), nlevels = 20, lty = 2, metho d = "simple",[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 1939--1939 []\T1/pcr/m/n/9 contour(z, levels=levs[-c(1,length(levs))], col = 1:5, lwd = 1 :3 *1.5, lty = 1:3)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1955--1955 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1964--1964 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [915] [916] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2049--2049 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [917] [918] Overfull \hbox (31.3804pt too wide) in paragraph at lines 2178--2178 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.values = given .depth, rows = 1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2183--2183 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c( TRUE, FALSE))[] [919] [920] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2357--2357 []\T1/pcr/m/n/10 dotchart(x, labels = NULL, groups = NULL, gdata = NULL, offse t = 1/8, Overfull \hbox (54.78088pt too wide) in paragraph at lines 2358--2358 [] \T1/pcr/m/n/10 ann = par("ann"), xaxt = par("xaxt"), frame.plot = T RUE, log = "",[] [921] Underfull \hbox (badness 1430) in paragraph at lines 2388--2390 []\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use []\T1/pcr/m/n/10 "n" []\T1/ptm/m/n/10 to sup-press and see also [922] Overfull \hbox (78.78088pt too wide) in paragraph at lines 2469--2469 [] \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO rRd", rev = TRUE),[] Underfull \hbox (badness 1009) in paragraph at lines 2481--2488 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [923] Underfull \hbox (badness 7273) in paragraph at lines 2563--2567 [][][]\T1/pcr/m/n/10 contour[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 image [][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 hcl.colors[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gray.colors[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 palette[][][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 contourplot[][][] []\T1/p tm/m/n/10 and [924] [925] [926] [927] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2811--2811 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [928] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2848--2848 [] \T1/pcr/m/n/10 density = NULL, angle = 45, col = "lightgray", border = NULL,[] [929] [930] Underfull \hbox (badness 1226) in paragraph at lines 2975--2979 \T1/pcr/m/n/10 1)[]\T1/ptm/m/n/10 , they are the rel-a-tive fre-quen-cies []\T1 /pcr/m/n/10 counts/n []\T1/ptm/m/n/10 and in gen-eral sat-isfy [931] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3028--3028 []\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3032--3032 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a suggestion only"[] [932] Underfull \hbox (badness 10000) in paragraph at lines 3094--3097 [][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][][]\T1 /pcr/m/n/10 hist.default[][][] []\T1/ptm/m/n/10 such as Overfull \hbox (15.18042pt too wide) in paragraph at lines 3145--3145 []\T1/pcr/m/n/9 ## The default fuzz in hist.default() "kills" this, with a "w rong" message:[] [933] [934] [935] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3309--3309 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL SE, pch = 19, ...)[] Overfull \hbox (79.98035pt too wide) in paragraph at lines 3314--3314 [] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel) , n = 1, plot = plot, ...)[] [936] [937] Underfull \hbox (badness 10000) in paragraph at lines 3456--3461 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 useRaster []\T1/ptm/m/n/10 is not spec-i-f ied, raster im-ages are used when the Underfull \hbox (badness 10000) in paragraph at lines 3456--3461 [][][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") []\T1/ptm/m/n/10 is true, the grid is reg-u-lar and ei-ther Underfull \hbox (badness 10000) in paragraph at lines 3456--3461 [][][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage []\T1/pt m/m/n/10 is []\T1/pcr/m/n/10 "yes" []\T1/ptm/m/n/10 or it is Overfull \hbox (31.3804pt too wide) in paragraph at lines 3491--3491 []\T1/pcr/m/n/9 # Visualize as matrix. Need to transpose matrix and then flip it horizontally:[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 3493--3493 []\T1/pcr/m/n/9 imageM <- function(m, grid = max(dim(m)) <= 25, asp = (nrow(m) -1)/(ncol(m)-1), ...) {[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3496--3496 [] \T1/pcr/m/n/9 axis(side, at=at, labels=as.character(j+1L), col="gray ", col.axis=1, ...)[] [938] [939] [940] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3653--3653 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 0, horiz = TRUE)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3672--3672 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3676--3676 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [941] [942] [943] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3861--3861 [] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c ex = 0.8, adj = 0)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3862--3862 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3866--3866 [] \T1/pcr/m/n/9 cex = 1+(-1:2)/8, trace = TRUE)# trace: show computed l engths & coords[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3876--3876 [] \T1/pcr/m/n/9 title("legend(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 top\TS1/pcr/m/n/ 9 '\T1/pcr/m/n/9 , lty = c(2, -1, 1), pch = c(NA, 3, 4), merge = TRUE)",[] [944] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3907--3907 [] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj = c(0, 0.3))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3933--3933 []\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Filled\TS1/pcr/m/n/9 ' \T1/pc r/m/n/9 boxes -- see also example(barplot) which may call legend(*, fill=)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3935--3935 []\T1/pcr/m/n/9 legend("topright", rownames(VADeaths), fill = gray.colors(nrow (VADeaths)))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3946--3946 []\T1/pcr/m/n/9 legend("bottomright", paste("sin(", 1:7, "pi * x)"), col = 1:7 , lty = 1:7,[] Underfull \vbox (badness 10000) has occurred while \output is active [945] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3961--3961 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c ol = "blue")[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3969--3969 []\T1/pcr/m/n/9 legend("topleft", "(x,y)", pch=1, title= "topleft, inset = .05", inset = .05)[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3971--3971 []\T1/pcr/m/n/9 legend("topright", "(x,y)", pch=1, title= "topright, inset = .02",inset = .02)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3979--3979 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3989--3989 []\T1/pcr/m/n/9 legend("bottomleft", c("This legend", "has", "optimally sized" , "columns."),[] [946] Underfull \hbox (badness 10000) in paragraph at lines 4051--4055 [][][]\T1/pcr/m/n/10 lines.formula[][][] []\T1/ptm/m/n/10 for the for-mula meth od; [][][]\T1/pcr/m/n/10 points[][][][]\T1/ptm/m/n/10 , par-tic-u-larly for []\ T1/pcr/m/n/10 type %in% [947] [948] Overfull \hbox (6.78088pt too wide) in paragraph at lines 4163--4163 [] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb ose"))[] [949] [950] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4317--4317 []\T1/pcr/m/n/9 nd <- length(dv <- seq(as.Date("1959-02-21"), by = "weeks", le ngth.out = 100))[] [951] Underfull \hbox (badness 3930) in paragraph at lines 4396--4398 []\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a mul-ti-ple of [952] [953] [954] [955] [956] Underfull \hbox (badness 1286) in paragraph at lines 4707--4710 []\T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify []\T1/pcr/m/n /10 oma []\T1/ptm/m/n/10 when chang-ing Underfull \hbox (badness 3229) in paragraph at lines 4715--4720 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used, see [957] [958] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4811--4811 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel = panel.cor,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4816--4816 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] [959] Underfull \hbox (badness 1264) in paragraph at lines 5007--5020 \T1/ptm/m/n/10 func-tions such as [][][]\T1/pcr/m/n/10 plot.default[][][][]\T1/ ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.window[][][][]\T1/ptm/m/n/10 , [][][]\T1 /pcr/m/n/10 points[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lines[][][][]\T 1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 abline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc r/m/n/10 axis[][][][]\T1/ptm/m/n/10 , [960] [961] [962] [963] Underfull \hbox (badness 10000) in paragraph at lines 5273--5276 [964 ] Underfull \hbox (badness 10000) in paragraph at lines 5334--5336 [965 ] [966] [967] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5580--5580 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, physicians = 9,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5581--5581 [] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t eachers = 4,[] Underfull \vbox (badness 10000) has occurred while \output is active [968] [969] [970] [971] [972] [973] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5945--5945 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p yramid" = 5),[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 5946--5946 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] [974] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot}) ha s been already used, duplicate ignored \relax l.6005 \aliasA{plot}{plot.default}{plot} [975] [976] [977] [978] [979] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6337--6337 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6343--6343 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [980] [981] Overfull \hbox (66.78088pt too wide) in paragraph at lines 6467--6467 [] \T1/pcr/m/n/10 main = paste("Histogram of", paste(x$xname, co llapse = "\n")),[] [982] [983] [984] [985] Underfull \hbox (badness 10000) in paragraph at lines 6772--6774 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [986] [987] Underfull \hbox (badness 1028) in paragraph at lines 6866--6868 []\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th is works as a mul-ti-ple of Overfull \hbox (31.57222pt too wide) in paragraph at lines 6909--6910 [][] [988 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7003--7003 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [989] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7034--7034 [] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab = "", main = main)[] Underfull \vbox (badness 10000) has occurred while \output is active [990] [991] Underfull \hbox (badness 10000) in paragraph at lines 7156--7158 []\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev in Buhr Overfull \hbox (15.18042pt too wide) in paragraph at lines 7183--7183 [] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b order = "red")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7189--7189 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [992] Underfull \hbox (badness 2600) in paragraph at lines 7246--7248 []\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther []\T 1/pcr/m/n/10 "winding" []\T1/ptm/m/n/10 or [993] [994] [995] [996] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7478--7478 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7 , end = 0.1))[] [997] [998] [999] [1000] [1001] [1002] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7865--7865 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp ace = "Lab")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7869--7869 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [1003] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7881--7881 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 7908--7908 [] \T1/pcr/m/n/10 xlim = NULL, ylim = c(0, 1), axes = TRUE, weights = NULL, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 7917--7917 [] \T1/pcr/m/n/10 subset = NULL, weights = NULL, drop.unused.levels = FALSE)[] [1004] [1005] [1006] [1007] [1008] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8234--8234 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8237--8237 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] [1009] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8241--8241 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [1010] [1011] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8412--8412 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...) Overfull \hbox (36.78088pt too wide) in paragraph at lines 8413--8413 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [1012] [1013] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8517--8517 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] [1014] Underfull \hbox (badness 1112) in paragraph at lines 8576--8580 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 number[i] == 1[]\T1/ptm/m/n/10 , a (sligh tly en-larged) usual plot-ting sym-bol ([]\T1/pcr/m/n/10 pch[]\T1/ptm/m/n/10 ) is drawn. For [1015] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8636--8636 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035 , seg.lwd = .8)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8651--8651 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [1016] [1017] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8788--8788 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [1018] [1019] [1020] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8973--8973 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est facile: Règles, Liberté, Egalité, Fraternité...")[] Underfull \hbox (badness 1215) in paragraph at lines 9001--9003 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color []\T1/pcr/m /n/10 par(c("font.sub", Underfull \hbox (badness 1584) in paragraph at lines 9035--9041 []\T1/ptm/m/n/10 The po-si-tions of []\T1/pcr/m/n/10 xlab[]\T1/ptm/m/n/10 , []\ T1/pcr/m/n/10 ylab []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 sub []\T1/ptm/m/n/10 a re []\T1/pcr/m/n/10 line []\T1/ptm/m/n/10 (de-fault for []\T1/pcr/m/n/10 xlab [ ]\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 ylab []\T1/ptm/m/n/10 be-ing [1021] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.units}) h as been already used, duplicate ignored \relax l.9083 \HeaderA{units}{Graphical Units}{units} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.units.1}) has been already used, duplicate ignored \relax l.9083 \HeaderA{units}{Graphical Units}{units} [1022] Underfull \hbox (badness 1205) in paragraph at lines 9148--9150 []\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th e poly-gon. See [1023] [1024] Overfull \hbox (25.98041pt too wide) in paragraph at lines 9267--9267 []\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code = 2, length = 0.1)[] [1025]) (./grid-pkg.tex [1026] Chapter 6. [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] Underfull \hbox (badness 4859) in paragraph at lines 634--637 []\T1/ptm/m/n/10 Modification of the view-port (should all be valid ar-gu-ments to the [1037] [1038] [1039] [1040] [1041] [1042] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1028--1028 [] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un it(1, "inches")))[] [1043] [1044] [1045] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1239--1239 [] \T1/pcr/m/n/9 vpList(vpStack(viewport(x=0.1, y=0.1, width=0.5 , height=0.5,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1240--1240 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1241--1241 [] \T1/pcr/m/n/9 viewport(x=0.1, y=0.1, width=0.5 , height=0.5,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1242--1242 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1243--1243 [] \T1/pcr/m/n/9 viewport(x=0.1, y=0.1, width=0.5 , height=0.5,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1244--1244 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] [1046] [1047] [1048] [1049] Underfull \hbox (badness 3219) in paragraph at lines 1503--1506 []\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject de-scrib-ing a cir-cle), but only [1050] [1051] [1052] [1053] [1054] [1055] [1056] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1891--1891 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [1057] [1058] [1059] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2105--2105 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla ck"), name="r1")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2106--2106 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey" ), name="r2")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2107--2107 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [1060] Underfull \hbox (badness 2961) in paragraph at lines 2142--2147 []\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio ns []\T1/pcr/m/n/10 preDrawDetails[]\T1/ptm/m/n/10 , [1061] Underfull \hbox (badness 4479) in paragraph at lines 2230--2233 []\T1/ptm/m/n/10 Both func-tions call []\T1/pcr/m/n/10 editDetails []\T1/ptm/m/ n/10 to al-low a grob to per-form cus-tom ac-tions and [1062] [1063] [1064] Underfull \hbox (badness 2894) in paragraph at lines 2437--2444 []\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de -scrib-ing a frame), but only [1065] [1066] [1067] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2593--2593 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] [1068] Underfull \hbox (badness 1014) in paragraph at lines 2679--2684 []\T1/ptm/m/n/10 The jus-ti-fi-ca-tion of the glyphs rel-a-tive to the ([]\T1/p cr/m/n/10 x[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 ) lo-ca-tion. Can be [1069] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2725--2725 []\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs = FALSE,[] [1070] [1071] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2887--2887 [] \T1/pcr/m/n/9 children=gList(grob(name="child", vp ="vp1::vp2")),[] [1072] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2919--2919 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [1073] [1074] Underfull \hbox (badness 10000) in paragraph at lines 3102--3104 []\T1/ptm/m/n/10 A func-tion that re-turns an affine trans-for-ma-tion ma-trix; see [1075] Underfull \hbox (badness 1077) in paragraph at lines 3119--3138 []\T1/ptm/m/n/10 Another pos-si-ble use of []\T1/pcr/m/n/10 grid.group() []\T1/ ptm/m/n/10 is to spec-ify both []\T1/pcr/m/n/10 src []\T1/ptm/m/n/10 and []\T1/ pcr/m/n/10 dst []\T1/ptm/m/n/10 and com-bine Underfull \hbox (badness 1622) in paragraph at lines 3119--3138 []\T1/ptm/m/n/10 is only drawn where it is NOT over-lapped by []\T1/pcr/m/n/10 src[]\T1/ptm/m/n/10 . The fol-low-ing (ex-tended) Porter- Underfull \hbox (badness 2057) in paragraph at lines 3119--3138 []\T1/pcr/m/n/10 "multiply"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "screen"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "overlay"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "darke n"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lighten"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n /10 "color.dodge"[]\T1/ptm/m/n/10 , [1076] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3191--3191 [] \T1/pcr/m/n/9 mask <- as.mask(rectGrob(gp=gpar(col=NA, fill="grey50")), ty pe="luminance")[] [1077] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3307--3307 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [1078] [1079] [1080] [1081] [1082] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3622--3622 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [1083] [1084] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3718--3718 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, width=0.25, height=0.25, just= c("left", "bottom")))[] Underfull \hbox (badness 2799) in paragraph at lines 3755--3761 []\T1/ptm/m/n/10 There are two hooks called []\T1/pcr/m/n/10 "before.grid.newpa ge" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "grid.newpage" []\T1/ptm/m/n/10 (see [1085] [1086] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3847--3847 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3854--3854 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [1087] [1088] [1089] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4055--4055 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] [1090] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4070--4070 [] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other anti-clockwise")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4091--4091 []\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s ame path, thus[] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] Underfull \hbox (badness 1067) in paragraph at lines 4840--4843 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1103] [1104] [1105] [1106] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5056--5056 [] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un it(1, "inches")))[] [1107] [1108] Underfull \hbox (badness 7256) in paragraph at lines 5191--5193 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1109] Overfull \hbox (69.18036pt too wide) in paragraph at lines 5258--5258 []\T1/pcr/m/n/9 grid.text(quote(frac(e^{-x^2/2}, sqrt(2*pi))), x=x, y=y, rot=s tats::runif(20, -45,45),[] [1110] [1111] [1112] [1113] [1114] [1115] Underfull \hbox (badness 2726) in paragraph at lines 5645--5649 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 gridCoords []\T1/ptm/m/n/10 a nu-meric ve c-tor. For []\T1/pcr/m/n/10 gridGrobCoords []\T1/ptm/m/n/10 a list Underfull \hbox (badness 1231) in paragraph at lines 5645--5649 \T1/ptm/m/n/10 of []\T1/pcr/m/n/10 "GridCoords" []\T1/ptm/m/n/10 ob-jects. For []\T1/pcr/m/n/10 gridGTreeCoords []\T1/ptm/m/n/10 a list of ei-ther [1116] Underfull \hbox (badness 2080) in paragraph at lines 5727--5732 []\T1/ptm/m/n/10 Either a []\T1/pcr/m/n/10 "GridGrobCoords" []\T1/ptm/m/n/10 ob -ject (a list of lists with com-po-nents []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 an d []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 ) or a [1117] [1118] [1119] Underfull \hbox (badness 10000) in paragraph at lines 5907--5909 []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 grid.legend()[]\T1/ptm/m/n/10 : all the a r-gu-ments above are passed to [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7002--7002 []\T1/pcr/m/n/9 unitType(min(unit(1, "in"), unit(1, "npc") + unit(1, "mm")), r ecurse=TRUE)[] [1137] [1138] Overfull \hbox (54.78088pt too wide) in paragraph at lines 7122--7122 []\T1/pcr/m/n/10 viewportTransform(group, shear=groupShear(), flip=groupFlip() , device=TRUE) [1139] Underfull \hbox (badness 1867) in paragraph at lines 7224--7226 []\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for use in []\T1/pcr/m/n/10 downViewport []\T1/ptm/m/n/10 or [1140] Underfull \hbox (badness 10000) in paragraph at lines 7261--7267 [][][]\T1/pcr/m/n/10 viewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 push Viewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 popViewport[][][][]\T1/pt m/m/n/10 , [][][]\T1/pcr/m/n/10 downViewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 seekViewport[][][][]\T1/ptm/m/n/10 , [1141] [1142] [1143] Underfull \vbox (badness 10000) has occurred while \output is active [1144] [1145] [1146] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7597--7597 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp ar(col="red"))))[] [1147]) (./methods-pkg.tex [1148] Chapter 7. [1149] [1150] Underfull \hbox (badness 1688) in paragraph at lines 166--171 []\T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how co-erce meth-ods work. Use [1151] [1152] [1153] Underfull \hbox (badness 1348) in paragraph at lines 392--395 [][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] []\T1/ptm/m/n/10 for other in- for-ma-tion about group generic func-tions; [][]Meth- [1154] [1155] Overfull \hbox (15.18042pt too wide) in paragraph at lines 558--558 []\T1/pcr/m/n/9 ## vector. The next method will always be the default, usuall y a primitive.[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w ith no arguments[] [1156] Overfull \hbox (4.38043pt too wide) in paragraph at lines 619--619 []\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho ut arguments[] Underfull \vbox (badness 10000) has occurred while \output is active [1157] Overfull \hbox (25.98041pt too wide) in paragraph at lines 637--637 []\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th e default method[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 640--640 []\T1/pcr/m/n/9 ## call f() with 1 argument: the default "B0" is not passed b y callNextMethod[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 657--657 []\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the "B0" method[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 672--672 []\T1/pcr/m/n/9 ## Although the argument here is numeric, it\TS1/pcr/m/n/9 '\T 1/pcr/m/n/9 s still the "B0" method that\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s called[ ] Underfull \vbox (badness 10000) has occurred while \output is active [1158] [1159] [1160] [1161] [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1794--1794 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N umber" method[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1796--1796 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE)) ) # the default[] [1173] [1174] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to []\T1/pcr/m/n/10 insertSource []\T1/ptm/m/n/ 10 can be an ob-ject of class [1175] [1176] [1177] Underfull \hbox (badness 1478) in paragraph at lines 2213--2218 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use []\T1/pcr/m/n/10 where = [1178] [1179] Underfull \hbox (badness 10000) in paragraph at lines 2327--2331 []\T1/ptm/m/n/10 To see the ac-tual ta-ble (an [][][]\T1/pcr/m/n/10 environment [][][][]\T1/ptm/m/n/10 ) used for meth-ods dis-patch, call [1180] [1181] [1182] Underfull \hbox (badness 3792) in paragraph at lines 2573--2576 []\T1/ptm/m/n/10 As you might ex-pect [][][]\T1/pcr/m/n/10 setGeneric[][][] []\ T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 setGroupGeneric[][][] []\T1/ptm/m/n/10 c re-ate ob-jects of class Underfull \hbox (badness 1194) in paragraph at lines 2604--2608 []\T1/ptm/m/n/10 Object of class []\T1/pcr/m/n/10 "optionalMethod" []\T1/ptm/m/ n/10 (a union of classes []\T1/pcr/m/n/10 "function" []\T1/ptm/m/n/10 and [1183] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2660--2660 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin g(where))[] [1184] [1185] [1186] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2879--2879 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers ions visible:[] [1187] [1188] [1189] [1190] [1191] [1192] [1193] Underfull \hbox (badness 10000) in paragraph at lines 3402--3407 []\T1/ptm/m/n/10 Function []\T1/pcr/m/n/10 implicitGeneric() []\T1/ptm/m/n/10 r e-turns the im-plicit generic ver-sion, Underfull \hbox (badness 6268) in paragraph at lines 3402--3407 []\T1/pcr/m/n/10 setGenericImplicit() []\T1/ptm/m/n/10 turns a generic im-plici t, []\T1/pcr/m/n/10 prohibitGeneric() []\T1/ptm/m/n/10 pre-vents [1194] [1195] Underfull \hbox (badness 10000) in paragraph at lines 3530--3534 []\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][][]\T1/pcr/m/n/10 getClass[][][] []\T1/ptm/m/n/10 and the de-scrip-tion of class [1196] Overfull \hbox (14.78088pt too wide) in paragraph at lines 3641--3650 [] [1197] [1198] Underfull \hbox (badness 10000) in paragraph at lines 3761--3762 [] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longit ude = Underfull \hbox (badness 10000) in paragraph at lines 3808--3809 []\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) { [1199] Underfull \hbox (badness 10000) in paragraph at lines 3845--3846 []\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , Underfull \hbox (badness 6157) in paragraph at lines 3907--3911 []\T1/ptm/m/n/10 A call to [][][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) [] \T1/ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to [1200] [1201] [1202] [1203] [1204] [1205] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4312--4312 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char acter(), Overfull \hbox (0.78088pt too wide) in paragraph at lines 4313--4313 [] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac cess,[] [1206] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4370--4370 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w here) [1207] [1208] [1209] Underfull \hbox (badness 2126) in paragraph at lines 4578--4586 []\T1/ptm/m/n/10 For ad-di-tional in-for-ma-tion see doc-u-men-ta-tion for the im-por-tant steps: ([][][]\T1/pcr/m/n/10 setMethod[][][]()[]\T1/ptm/m/n/10 , [1210] [1211] [1212] Underfull \hbox (badness 10000) in paragraph at lines 4815--4824 []\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha t eval-u-ates a call to [1213] [1214] [1215] [1216] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5203--5203 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate inheritance[] [1217] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5231--5231 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli er fails here)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5245--5245 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho d for classB[] Underfull \vbox (badness 10000) has occurred while \output is active [1218] [1219] Underfull \hbox (badness 10000) in paragraph at lines 5363--5364 []\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1220] [1221] Underfull \hbox (badness 3803) in paragraph at lines 5520--5522 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1222] [1223] [1224] Underfull \hbox (badness 1087) in paragraph at lines 5752--5757 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1225] [1226] [1227] [1228] [1229] [1230] Underfull \hbox (badness 10000) in paragraph at lines 6218--6234 []\T1/ptm/m/n/10 The de-fault method for []\T1/pcr/m/n/10 $initialize() []\T1/p tm/m/n/10 is equiv-a-lent to in-vok-ing the method [1231] [1232] Underfull \hbox (badness 1248) in paragraph at lines 6351--6355 []\T1/ptm/m/n/10 Typically, a spe-cial-ized []\T1/pcr/m/n/10 $initialize() []\T 1/ptm/m/n/10 method car-ries out its own com-pu-ta-tions, Underfull \hbox (badness 1960) in paragraph at lines 6351--6355 \T1/ptm/m/n/10 then in-vokes []\T1/pcr/m/n/10 $initFields() []\T1/ptm/m/n/10 to per-form stan-dard ini-tial-iza-tion, as shown in the [1233] Underfull \hbox (badness 4647) in paragraph at lines 6506--6508 []\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func- tion re-turned by [1234] [1235] Underfull \hbox (badness 2875) in paragraph at lines 6655--6664 []\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen se as any S4 class (see Underfull \hbox (badness 1436) in paragraph at lines 6655--6664 [][][]\T1/pcr/m/n/10 setValidity[][][][]\T1/ptm/m/n/10 ). Such meth-ods are of- ten a good idea; they will be called by call-ing [1236] Underfull \vbox (badness 10000) has occurred while \output is active [1237] [1238] [1239] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6981 \aliasA{S4}{S3Part}{S4} [1240] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7017--7017 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement version of as().[] [1241] [1242] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7208--7208 []\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data = datasets::iris)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7212--7212 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con tains = "mlm")[] [1243] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Complex}) has been already used, duplicate ignored \relax l.7237 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Logic}) h as been already used, duplicate ignored \relax l.7239 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) ha s been already used, duplicate ignored \relax l.7240 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7242 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignored \relax l.7243 \aliasA{Summary}{S4groupGeneric}{Summary} Underfull \hbox (badness 2050) in paragraph at lines 7304--7308 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1244] Underfull \hbox (badness 6708) in paragraph at lines 7317--7329 []\T1/pcr/m/n/10 "abs"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sign"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "sqrt"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ceiling"[]\T1/p tm/m/n/10 , []\T1/pcr/m/n/10 "floor"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "trunc" []\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cummax"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 2012) in paragraph at lines 7317--7329 []\T1/pcr/m/n/10 "acosh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "asin"[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 "asinh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "atan"[]\T1/p tm/m/n/10 , []\T1/pcr/m/n/10 "atanh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "exp"[] \T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "expm1"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "c os"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3209) in paragraph at lines 7317--7329 []\T1/pcr/m/n/10 "cosh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cospi"[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 "sin"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sinh"[]\T1/ptm /m/n/10 , []\T1/pcr/m/n/10 "sinpi"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tan"[]\T 1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tanh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tanp i"[]\T1/ptm/m/n/10 , [1245] [1246] Underfull \hbox (badness 1694) in paragraph at lines 7480--7482 []\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t ion ob-ject (see Underfull \hbox (badness 10000) in paragraph at lines 7504--7507 []\T1/ptm/m/n/10 The typ-i-cal user level func-tion is []\T1/pcr/m/n/10 selectS uperClasses() []\T1/ptm/m/n/10 which calls [1247] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7525--7525 []\T1/pcr/m/n/9 selectSuperClasses("C", dropVirtual=TRUE, directOnly=FALSE)# d itto w/o "Root"[] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8630--8630 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact er(), [1261] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8705--8705 [] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class Def =,[] [1262] [1263] [1264] [1265] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8967--8967 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col umn matrices[] [1266] [1267] [1268] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9175--9175 [] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns), "setCount")[] [1269] [1270] [1271] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9437--9437 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo rmal arguments[] [1272] [1273] [1274] [1275] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9745--9745 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre es of freedom[] [1276] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9855--9855 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9866--9866 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] Underfull \hbox (badness 10000) in paragraph at lines 10564--10566 []\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., []\T1/pcr/m/n/10 "functi on" []\T1/ptm/m/n/10 for class Underfull \hbox (badness 1852) in paragraph at lines 10572--10576 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., Underfull \hbox (badness 1681) in paragraph at lines 10572--10576 []\T1/pcr/m/n/10 "functionWithTrace" []\T1/ptm/m/n/10 ex-tends []\T1/pcr/m/n/10 "function"[]\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends [1287] [1288] [1289]) (./parallel-pkg.tex [1290] Chapter 8. Underfull \hbox (badness 2418) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `[]\T1/p cr/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"[]\T1/ptm/m/n/10 ' [][] RNG[][][]: see [1291] Underfull \hbox (badness 4242) in paragraph at lines 97--99 []\T1/ptm/m/n/10 a vec-tor for []\T1/pcr/m/n/10 clusterApply []\T1/ptm/m/n/10 a nd []\T1/pcr/m/n/10 clusterApplyLB[]\T1/ptm/m/n/10 , a ma-trix for [1292] [1293] Underfull \hbox (badness 1024) in paragraph at lines 214--217 []\T1/ptm/m/n/10 Two ex-cep-tions: []\T1/pcr/m/n/10 parLapply []\T1/ptm/m/n/10 has ar-gu-ment []\T1/pcr/m/n/10 X []\T1/ptm/m/n/10 not []\T1/pcr/m/n/10 x []\T1 /ptm/m/n/10 for con-sis-tency with [][][]\T1/pcr/m/n/10 lapply[][][][]\T1/ptm/m /n/10 , and [1294] Underfull \hbox (badness 1320) in paragraph at lines 301--304 []\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD, So-laris and Win-dows. [1295] [1296] Underfull \hbox (badness 10000) in paragraph at lines 437--439 []\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for []\T1/pcr/m/ n/10 Rscript []\T1/ptm/m/n/10 such as [1297] [1298] [1299] [1300] [1301] Underfull \hbox (badness 1917) in paragraph at lines 771--780 []\T1/pcr/m/n/10 mcfork []\T1/ptm/m/n/10 re-turns an ob-ject of the class []\T1 /pcr/m/n/10 "childProcess" []\T1/ptm/m/n/10 to the mas-ter and of class Underfull \hbox (badness 1178) in paragraph at lines 771--780 []\T1/pcr/m/n/10 "masterProcess" []\T1/ptm/m/n/10 to the child: both the classe s in-herit from class []\T1/pcr/m/n/10 "process"[]\T1/ptm/m/n/10 . If [1302] Overfull \hbox (60.78088pt too wide) in paragraph at lines 864--864 [] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini ty.list = NULL)[] [1303] [1304] [1305] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1055--1055 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit y.list = affL)[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 1059--1059 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch eduled to suitable CPUs[] [1306] [1307] Underfull \hbox (badness 5388) in paragraph at lines 1174--1179 []\T1/pcr/m/n/10 mcparallel []\T1/ptm/m/n/10 re-turns an ob-ject of the class [ ]\T1/pcr/m/n/10 "parallelJob" []\T1/ptm/m/n/10 which in-her-its from Underfull \hbox (badness 10000) in paragraph at lines 1198--1206 []\T1/ptm/m/n/10 The be-haviour with []\T1/pcr/m/n/10 mc.set.seed = TRUE []\T1/ ptm/m/n/10 is dif-fer-ent only if [1308] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1235--1235 []\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[] [1309] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1351--1351 [] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif (N, 1, 28)))[] [1310] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1365--1365 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format = "%Y-%m-%d")))[] Underfull \hbox (badness 1577) in paragraph at lines 1394--1397 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by []\T1/pcr/m/n/10 .Random.seed []\T1/ptm/m/n/10 when the [1311] Underfull \hbox (badness 3375) in paragraph at lines 1441--1443 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 nextRNGStream []\T1/ptm/m/n/10 and []\T1/ pcr/m/n/10 nextRNGSubStream[]\T1/ptm/m/n/10 , a value which can be as-signed to [1312] [1313]) (./splines-pkg.tex [1314] Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1315] [1316] [1317] [1318] [1319] [1320] [1321] [1322] Overfull \hbox (4.38043pt too wide) in paragraph at lines 499--499 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl ine = TRUE))[] [1323] Underfull \hbox (badness 1043) in paragraph at lines 600--602 []\T1/ptm/m/n/10 An in-te-ger be-tween 0 and []\T1/pcr/m/n/10 splineOrder(objec t) - 1 []\T1/ptm/m/n/10 spec-i-fy-ing the [1324] [1325] Overfull \hbox (25.98041pt too wide) in paragraph at lines 715--715 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, sparse = TRUE)))[] [1326] [1327] [1328]) (./stats-pkg.tex Chapter 10. [1329] Underfull \hbox (badness 1077) in paragraph at lines 71--74 []\T1/pcr/m/n/10 .MFclass() []\T1/ptm/m/n/10 re-turns a char-ac-ter string, one of []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ordered"[]\T 1/ptm/m/n/10 , []\T1/pcr/m/n/10 "factor"[]\T1/ptm/m/n/10 , Overfull \hbox (69.18036pt too wide) in paragraph at lines 91--91 []\T1/pcr/m/n/9 (xl <- .getXlevels(terms(mf), mf)) # a list with one entry " $ Species" with 3 levels:[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 94--94 [] \T1/pcr/m/n/9 identical(.getXlevels(terms(mc), mc), xl[0]) # a empty named list, as no factors[] [1330] [1331] [1332] [1333] [1334] Overfull \hbox (20.58041pt too wide) in paragraph at lines 445--445 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea rson Chi-square[] [1335] Overfull \hbox (6.78088pt too wide) in paragraph at lines 468--468 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = FALSE) [1336] [1337] [1338] [1339] [1340] [1341] Underfull \hbox (badness 1024) in paragraph at lines 901--903 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from []\T1/pcr/m/n/10 l m []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 aov[]\T1/ptm/m/n/10 , or a for-mula for [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1640--1640 [] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm = TRUE)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1643--1643 [] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm = TRUE)[] [1354] [1355] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1790--1790 [] \T1/pcr/m/n/9 approx(xn, yn, xout=xout, method=M, rule=R, n a.rm=na.)$y),[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1802--1802 []\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$y) # warning, can be avoided by specifying \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ties=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[ ] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2820--2820 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F ALSE) [1371] [1372] [1373] [1374] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3068--3068 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co l = "green")[] [1375] [1376] [1377] Underfull \hbox (badness 10000) in paragraph at lines 3279--3281 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Bartlett test of homo geneity of [1378] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3328--3328 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3329--3329 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1379] [1380] [1381] [1382] Package amsmath Warning: Foreign command \atopwithdelims; (amsmath) \frac or \genfrac should be used instead (amsmath) on input line 3658. [1383] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3724--3724 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = " log density",[] [1384] [1385] [1386] [1387] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4003--4003 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0) [1388] [1389] [1390] [1391] [1392] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4292--4292 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4293--4293 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1393] [1394] [1395] [1396] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4534--4534 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1397] [1398] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4709--4709 [] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df = df, ncp = L)),[] [1399] [1400] Underfull \hbox (badness 3989) in paragraph at lines 4803--4810 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1401] [1402] [1403] [1404] [1405] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5192--5192 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1)) , ci = c(-1,-1))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5194--5194 []\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci = c(-0.9,0.1))[] [1406] [1407] [1408] [1409] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5416--5416 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works with these :[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5434--5434 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter")) [1410] [1411] [1412] Underfull \hbox (badness 1436) in paragraph at lines 5644--5649 []\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i ng co-vari-ances Underfull \hbox (badness 1377) in paragraph at lines 5644--5649 \T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi -a-tion of) Underfull \hbox (badness 1448) in paragraph at lines 5644--5649 \T1/ptm/m/n/10 one of the strings []\T1/pcr/m/n/10 "everything"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "all.obs"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "complete.obs" []\T1/ptm/m/n/10 , [1413] [1414] Underfull \vbox (badness 10000) has occurred while \output is active [1415] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5847--5847 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1416] [1417] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6014--6014 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE, [1418] [1419] [1420] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6199--6199 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL) [1421] [1422] Overfull \hbox (84.78088pt too wide) in paragraph at lines 6307--6307 []\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en v = parent.frame())[] [1423] [1424] [1425] [1426] Underfull \hbox (badness 5954) in paragraph at lines 6570--6572 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1427] Underfull \hbox (badness 2503) in paragraph at lines 6652--6655 []\T1/ptm/m/n/10 Objects of class []\T1/pcr/m/n/10 "hclust" []\T1/ptm/m/n/10 ca n be con-verted to class []\T1/pcr/m/n/10 "dendrogram" []\T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 5563) in paragraph at lines 6656--6658 []\T1/pcr/m/n/10 rev.dendrogram []\T1/ptm/m/n/10 sim-ply re-turns the den-dro-g ram []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 with re-versed nodes, see also Underfull \hbox (badness 1655) in paragraph at lines 6659--6664 \T1/ptm/m/n/10 has []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 y [ ]\T1/ptm/m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be- fore \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.1.2, [1428] Underfull \hbox (badness 7238) in paragraph at lines 6695--6698 [][][]\T1/pcr/m/n/10 dendrapply[][][] []\T1/ptm/m/n/10 for ap-ply-ing a func-ti on to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][][]\T1/pcr/m/n/10 order.dend rogram[][][] []\T1/ptm/m/n/10 and Overfull \hbox (4.38043pt too wide) in paragraph at lines 6707--6707 []\T1/pcr/m/n/9 str(dend1, max.level = 2, last.str = "\TS1/pcr/m/n/9 '\T1/pcr /m/n/9 ") # only the first two sub-levels[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6730--6730 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, type = "tr")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6745--6745 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] [1429] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6760--6760 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h oriz = TRUE)[] [1430] [1431] [1432] Underfull \vbox (badness 10000) has occurred while \output is active [1433] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7028--7028 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] [1434] [1435] Underfull \vbox (badness 10000) has occurred while \output is active [1436] [1437] [1438] [1439] Underfull \hbox (badness 10000) in paragraph at lines 7428--7432 []\T1/pcr/m/n/10 "maximum"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "manhattan"[]\T1/ ptm/m/n/10 , []\T1/pcr/m/n/10 "canberra"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "bi nary" []\T1/ptm/m/n/10 or [1440] Underfull \hbox (badness 6493) in paragraph at lines 7531--7534 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][][] \T1/pcr/m/n/10 dist[][][]()[]\T1/ptm/m/n/10 , the [1441] [1442] Underfull \hbox (badness 10000) in paragraph at lines 7668--7671 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht tps : / / CRAN . R-[]project . org / view = [1443] [1444] [1445] [1446] [1447] [1448] Underfull \hbox (badness 10000) in paragraph at lines 8080--8085 []\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences [] \T1/pcr/m/n/10 x[t][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 x[t-1][]\T1/ptm/m/n/10 , ..., [1449] [1450] [1451] [1452] [1453] [1454] Underfull \hbox (badness 1210) in paragraph at lines 8435--8437 []\T1/ptm/m/n/10 Components of []\T1/pcr/m/n/10 control []\T1/ptm/m/n/10 can al so be sup-plied as named ar-gu-ments to [1455] [1456] [1457] [1458] [1459] [1460] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8901--8901 []\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q uasipoisson())[] [1461] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8946--8946 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link = "log")) # fails[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 8949--8949 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit "), start = c(0,1))[] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9529--9529 [] \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4 0k", "> 40k"),[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 9530--9530 [] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod erateS", "VeryS")))[] [1470] [1471] [1472] Underfull \hbox (badness 7291) in paragraph at lines 9709--9711 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Fligner-Killeen test of homogeneity of [1473] [1474] [1475] [1476] [1477] [1478] [1479] Underfull \hbox (badness 6944) in paragraph at lines 10201--10207 [][][]\T1/pcr/m/n/10 ftable.formula[][][] []\T1/ptm/m/n/10 for the for-mula in- ter-face (which al-lows a []\T1/pcr/m/n/10 data = . []\T1/ptm/m/n/10 ar-gu-ment ); [1480] [1481] [1482] Underfull \hbox (badness 3758) in paragraph at lines 10415--10418 []\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or [1483] [1484] [1485] [1486] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10659--10659 [] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL , ...)[] Underfull \hbox (badness 4518) in paragraph at lines 10685--10690 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1487] Underfull \hbox (badness 4132) in paragraph at lines 10724--10728 []\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth od Underfull \hbox (badness 1112) in paragraph at lines 10778--10784 []\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form []\T1/pcr/m/n/10 first:second []\T1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak- [1488] Underfull \hbox (badness 10000) in paragraph at lines 10829--10832 []\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][][]\T1/pcr/m/n/10 coeffic ients[][][][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 effects[]\T1/ptm/m/n/10 , []\T1/ pcr/m/n/10 fitted.values []\T1/ptm/m/n/10 and [1489] [1490] [1491] Underfull \hbox (badness 2142) in paragraph at lines 11046--11049 []\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1 0 dev \OMS/cmsy/m/n/10 ^^@ [1492] Underfull \hbox (badness 1708) in paragraph at lines 11127--11131 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1493] Underfull \hbox (badness 10000) in paragraph at lines 11169--11175 [][][]\T1/pcr/m/n/10 glm[][][] []\T1/ptm/m/n/10 for com-put-ing []\T1/pcr/m/n/1 0 glm.obj[]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 anova.glm[][][][]\T1/ptm/m/n/1 0 ; the cor-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions, Underfull \hbox (badness 1418) in paragraph at lines 11207--11212 []\T1/pcr/m/n/10 "average" []\T1/ptm/m/n/10 (= UP-GMA), []\T1/pcr/m/n/10 "mcqui tty" []\T1/ptm/m/n/10 (= WPGMA), []\T1/pcr/m/n/10 "median" []\T1/ptm/m/n/10 (= [1494] [1495] Underfull \hbox (badness 2635) in paragraph at lines 11340--11343 \T1/ptm/m/n/10 There are [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/n/10 , [][ ][]\T1/pcr/m/n/10 plot[][][] []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 identify []\ T1/ptm/m/n/10 (see [][][]\T1/pcr/m/n/10 identify.hclust[][][][]\T1/ptm/m/n/10 ) meth-ods and the [1496] [1497] [1498] Underfull \hbox (badness 1694) in paragraph at lines 11523--11526 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1499] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11621--11621 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col SideColors = cc,[] [1500] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11654--11654 [] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 0.1),[] Underfull \hbox (badness 10000) in paragraph at lines 11667--11671 []\T1/ptm/m/n/10 Character string to se-lect an []\T1/pcr/m/n/10 "additive" []\ T1/ptm/m/n/10 (the de-fault) or [1501] [1502] [1503] [1504] [1505] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11989--11989 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] [1506] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.12004 \aliasA{hat}{influence.measures}{hat} Overfull \hbox (0.78088pt too wide) in paragraph at lines 12064--12064 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] [1507] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12076--12076 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] Underfull \hbox (badness 1062) in paragraph at lines 12129--12134 []\T1/ptm/m/n/10 The op-tional []\T1/pcr/m/n/10 infl[]\T1/ptm/m/n/10 , []\T1/pc r/m/n/10 res []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 sd []\T1/ptm/m/n/10 ar-gu-me nts are there to en-cour-age the use of these di- Underfull \hbox (badness 1052) in paragraph at lines 12146--12148 []\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 hat() []\T1/ptm/m/n/10 ex-ists mainly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1508] [1509] [1510] [1511] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12401--12401 [] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = TRUE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12402--12402 [] \T1/pcr/m/n/10 trace.label = deparse1(substitute(trace.fact or)),[] [1512] [1513] [1514] [1515] [1516] [1517] Underfull \hbox (badness 10000) in paragraph at lines 12749--12751 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][][]\T1/pcr/m/n/10 solve.de fault[][][] []\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 SSinit = Underfull \hbox (badness 4739) in paragraph at lines 12772--12774 []\T1/ptm/m/n/10 the es-ti-mate at time $\OML/cmm/m/it/10 t \OMS/cmsy/m/n/10 ^^ @ \OT1/cmr/m/n/10 1$ \T1/ptm/m/n/10 of the state un-cer-tainty ma-trix $\OML/cm m/m/it/10 Q$ \T1/ptm/m/n/10 (not up-dated by [1518] [1519] [1520] [1521] [1522] Underfull \hbox (badness 3417) in paragraph at lines 13079--13081 []\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class []\T1/pcr/ m/n/10 "kmeans"[]\T1/ptm/m/n/10 , typ-i-cally the re-sult []\T1/pcr/m/n/10 ob [ ]\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 ob <- Underfull \hbox (badness 2894) in paragraph at lines 13085--13089 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method Underfull \hbox (badness 1038) in paragraph at lines 13085--13089 \T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 "Hartigan-Wong"[]\T1/ptm/m/n/10 ): if pos-i-ti ve (or true), trac-ing in-for-ma-tion on the [1523] [1524] [1525] [1526] [1527] [1528] Underfull \hbox (badness 1496) in paragraph at lines 13508--13514 []\T1/ptm/m/n/10 Gunar Schröer and Di-et-rich Tren-kler (1995). Ex-act and Ran- dom-iza-tion Dis-tri-bu-tions of [1529] [1530] [1531] [1532] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13757--13757 []\T1/pcr/m/n/9 lag.plot(sqrt(sunspots), set.lags = c(1:4, 9:12), pch = ".", c ol = "gold")[] [1533] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13858--13858 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep t", "slope"))[] [1534] Underfull \hbox (badness 4518) in paragraph at lines 13906--13911 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1535] [1536] [1537] Underfull \hbox (badness 10000) in paragraph at lines 14107--14111 []\T1/ptm/m/n/10 More []\T1/pcr/m/n/10 lm() []\T1/ptm/m/n/10 ex-am-ples are ava il-able e.g., in [][][]\T1/pcr/m/n/10 anscombe[][][][]\T1/ptm/m/n/10 , [][][]\T 1/pcr/m/n/10 attitude[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 freeny[][][] []\T1/ptm/m/n/10 , [1538] [1539] [1540] [1541] [1542] Underfull \hbox (badness 1163) in paragraph at lines 14446--14454 \T1/ptm/m/n/10 els, [][][]\T1/pcr/m/n/10 influence[][][] []\T1/ptm/m/n/10 (etc on that page) for re-gres-sion di-ag-nos-tics, [][][]\T1/pcr/m/n/10 weighted.re siduals[][][][]\T1/ptm/m/n/10 , [1543] [1544] Underfull \hbox (badness 4518) in paragraph at lines 14566--14571 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1545] [1546] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14754--14754 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14755--14755 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1547] [1548] [1549] [1550] [1551] Overfull \hbox (6.78088pt too wide) in paragraph at lines 15098--15098 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 15099--15099 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1552] [1553] Overfull \hbox (18.78088pt too wide) in paragraph at lines 15192--15192 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra nge(x))) [1554] [1555] [1556] [1557] [1558] [1559] Underfull \hbox (badness 2726) in paragraph at lines 15601--15604 []\T1/ptm/m/n/10 character; one of []\T1/pcr/m/n/10 "logit"[]\T1/ptm/m/n/10 , [ ]\T1/pcr/m/n/10 "probit"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cauchit"[]\T1/ptm/ m/n/10 , []\T1/pcr/m/n/10 "cloglog"[]\T1/ptm/m/n/10 , [1560] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15695--15695 []\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i n R <= 3.5.0[] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] Overfull \hbox (31.3804pt too wide) in paragraph at lines 16324--16324 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc gp, data = esoph) [1571] [1572] Underfull \hbox (badness 1490) in paragraph at lines 16471--16476 \T1/ptm/m/n/10 those spec-i-fied in []\T1/pcr/m/n/10 ... []\T1/ptm/m/n/10 which are re-cy-cled to the num-ber of data frame rows. Un-like [1573] Underfull \hbox (badness 1648) in paragraph at lines 16539--16541 []\T1/ptm/m/n/10 a data frame cre-ated with [][][]\T1/pcr/m/n/10 model.frame[][ ][][]\T1/ptm/m/n/10 . If an-other sort of ob-ject, [1574] Overfull \hbox (36.7804pt too wide) in paragraph at lines 16624--16624 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts.arg = list(a = "contr.sum" , b = contr.poly))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16625--16625 []\T1/pcr/m/n/9 m.orth <- model.matrix(~a+b, dd, contrasts.arg = list(a = "con tr.helmert"))[] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17182--17182 []\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3)) # does not affect objects with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[] [1584] [1585] [1586] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17414--17414 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, s, prob = 0.4)),[] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] Underfull \vbox (badness 10000) has occurred while \output is active [1597] Overfull \hbox (42.18039pt too wide) in paragraph at lines 18136--18136 []\T1/pcr/m/n/9 ## adjusting the convergence test by adding \TS1/pcr/m/n/9 '\T 1/pcr/m/n/9 scaleOffset\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 to its denominator RSS:[] Underfull \vbox (badness 10000) has occurred while \output is active [1598] Overfull \hbox (74.58035pt too wide) in paragraph at lines 18154--18154 []\T1/pcr/m/n/9 ## Here, requiring close convergence, must use more accurate n umerical differentiation,[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 18155--18155 []\T1/pcr/m/n/9 ## as this typically gives Error: "step factor .. reduced belo w \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 minFactor\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 .."[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 18159--18159 []\T1/pcr/m/n/9 ## central differencing works here typically (PR#18165: not co nverging on *some*):[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18160--18160 []\T1/pcr/m/n/9 ctr2 <- nls.control(nDcentral=TRUE, tol = 8e-8, # <- even smal ler than above[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 18163--18163 [] \T1/pcr/m/n/9 (grepl("^aarch64.*linux", R.version$platform) && grepl ("^NixOS", osVersion)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18195--18195 [] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21 ), th = b[1]))[] [1599] [1600] [1601] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18371--18371 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi ty), DNase.2)[] [1602] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18418--18418 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18465--18465 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1603] [1604] [1605] [1606] Overfull \hbox (102.78088pt too wide) in paragraph at lines 18678--18678 [] \T1/pcr/m/n/10 eps = .Machine$double.eps ^ (1/if(central) 3 els e 2), central = FALSE)[] [1607] [1608] [1609] [1610] [1611] Underfull \hbox (badness 1248) in paragraph at lines 18993--18996 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 1661) in paragraph at lines 19006--19010 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 1478) in paragraph at lines 19014--19018 \T1/ptm/m/n/10 if []\T1/pcr/m/n/10 control$trace []\T1/ptm/m/n/10 is pos-i-tive . De-faults to ev-ery 10 it-er-a-tions for []\T1/pcr/m/n/10 "BFGS" []\T1/ptm/m/ n/10 and [1612] Underfull \hbox (badness 2042) in paragraph at lines 19072--19074 []\T1/ptm/m/n/10 indicates an er-ror from the []\T1/pcr/m/n/10 "L-BFGS-B" []\T1 /ptm/m/n/10 method; see com-po-nent [1613] Overfull \hbox (15.18042pt too wide) in paragraph at lines 19178--19178 [] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no t* at boundary[] [1614] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19221--19221 [] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", axes = FALSE)[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 19239--19239 []\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 19242--19242 []\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 19262--19262 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max (interval), [1615] Overfull \hbox (36.78088pt too wide) in paragraph at lines 19265--19265 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max (interval),[] Underfull \hbox (badness 2564) in paragraph at lines 19300--19311 []\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 f []\T1/ptm/m/n/10 is never eva l-u-ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m /n/10 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/ 10 tol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 , Underfull \hbox (badness 1082) in paragraph at lines 19300--19311 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately []\T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) []\T1/ptm/m/n/10 and $\OML /cmm/m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa [1616] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19363--19363 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1617] [1618] [1619] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19590--19590 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 1, lty = 1:6,[] [1620] [1621] Underfull \hbox (badness 1337) in paragraph at lines 19701--19704 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1622] [1623] [1624] [1625] [1626] Overfull \hbox (0.78088pt too wide) in paragraph at lines 20020--20020 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1627] [1628] Overfull \hbox (24.78088pt too wide) in paragraph at lines 20108--20108 [] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist vs Leverage* " * h[ii] / (1 - h[ii]))),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 20110--20110 [] \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else points,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20112--20112 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1629] Underfull \hbox (badness 10000) in paragraph at lines 20172--20178 \T1/pcr/m/n/10 "bottomleft", legend = "Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s di stance", lty = cook.lty, Underfull \hbox (badness 10000) in paragraph at lines 20172--20178 \T1/pcr/m/n/10 col = cook.col, text.col = cook.col, bty = "n", x.intersp Underfull \hbox (badness 10000) in paragraph at lines 20180--20186 []\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment []\T 1/pcr/m/n/10 iter []\T1/ptm/m/n/10 in Underfull \hbox (badness 10000) in paragraph at lines 20191--20194 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 1 or 2, to be used in []\T1/pcr/m /n/10 ylim <- [1630] [1631] [1632] [1633] [1634] Overfull \hbox (0.78088pt too wide) in paragraph at lines 20500--20500 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] Underfull \hbox (badness 1194) in paragraph at lines 20510--20513 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1635] Underfull \hbox (badness 1107) in paragraph at lines 20568--20570 []\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate [] \T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . De-faults to [1636] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20623--20623 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange ") # all colors[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 20630--20630 []\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 1, y.intersp = 1)[] [1637] [1638] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20724--20724 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1639] [1640] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20853--20853 [] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no cancellation[] [1641] Underfull \hbox (badness 7740) in paragraph at lines 20916--20918 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Exact Poisson test" [ ]\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 "Comparison of Overfull \hbox (6.78088pt too wide) in paragraph at lines 20964--20964 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) [1642] Underfull \hbox (badness 10000) in paragraph at lines 21020--21022 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 poly(*, simple=TRUE)[]\T1/ptm/m/n/10 , [] \T1/pcr/m/n/10 polym(*, coefs=)[]\T1/ptm/m/n/10 , and [1643] Overfull \hbox (4.38043pt too wide) in paragraph at lines 21057--21057 [] \T1/pcr/m/n/9 zm <- zapsmall(polym ( 1:4, c(1, 4:6), degree = 3)) # or just poly():[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 21062--21062 []\T1/pcr/m/n/9 ## poly(, df) --- used to fail till July 14 (vive la F rance!), 2017:[] [1644] [1645] [1646] [1647] [1648] [1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656] Overfull \hbox (58.38037pt too wide) in paragraph at lines 21917--21917 [] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tolerance = 1e-15)) # e xactly equal typically[] [1657] Underfull \hbox (badness 6859) in paragraph at lines 21984--21991 [][][]\T1/pcr/m/n/10 predict.glm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 p redict.lm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.loess[][][][]\T1 /ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.nls[][][][]\T1/ptm/m/n/10 , [][][]\T 1/pcr/m/n/10 predict.poly[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 21995--22001 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][][]\T1/pcr/m/n/10 predict.ar[ ][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.Arima[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/pcr/m/n/10 predict.arima0[][][][]\T1/ptm/m/n/10 , [1658] [1659] [1660] [1661] [1662] Overfull \hbox (54.78088pt too wide) in paragraph at lines 22283--22283 [] \T1/pcr/m/n/10 rankdeficient = c("warnif", "simple", "non-estim", "N A", "NAwarn"),[] Underfull \hbox (badness 10000) in paragraph at lines 22309--22312 []\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string spec-i-fy-ing what should hap-pen in the Underfull \hbox (badness 10000) in paragraph at lines 22309--22312 \T1/ptm/m/n/10 case of a rank de-fi-cient model, i.e., when []\T1/pcr/m/n/10 ob ject$rank < [1663] Underfull \hbox (badness 5832) in paragraph at lines 22314--22319 \T1/ptm/m/n/10 cases, i.e., vec-tors not in the same pre-dic-tor sub-space as t he Underfull \hbox (badness 8151) in paragraph at lines 22314--22319 \T1/ptm/m/n/10 orig-i-nal data (with tol-er-ance []\T1/pcr/m/n/10 tol[]\T1/ptm/ m/n/10 ). In that case, the non- Underfull \hbox (badness 1184) in paragraph at lines 22314--22319 \T1/ptm/m/n/10 estimable in-dices are also re-turned as at-tribute []\T1/pcr/m/ n/10 "non-estim" []\T1/ptm/m/n/10 (see [1664] [1665] [1666] [1667] [1668] [1669] [1670] Overfull \hbox (48.78088pt too wide) in paragraph at lines 22782--22782 [] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign = TRUE, ...)[] [1671] [1672] [1673] [1674] Overfull \hbox (0.78088pt too wide) in paragraph at lines 23066--23066 [] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x )) &&[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 23067--23067 [] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr(" , "p-v"),[] [1675] [1676] [1677] [1678] [1679] Underfull \hbox (badness 1337) in paragraph at lines 23393--23399 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1680] [1681] [1682] [1683] [1684] Overfull \hbox (15.18042pt too wide) in paragraph at lines 23705--23705 []\T1/pcr/m/n/9 with(d, qqplot(Female, Male, pch = 19, xlim = c(-31, 31), ylim = c(-31, 31),[] [1685] [1686] [1687] [1688] Underfull \hbox (badness 10000) in paragraph at lines 24017--24019 []\T1/ptm/m/n/10 Wicklin, R. (2017) Sam-ple quan-tiles: A com-par-i-son of 9 de f-i-ni-tions; Underfull \hbox (badness 10000) in paragraph at lines 24017--24019 \T1/ptm/m/n/10 SAS Blog. [][]$\T1/pcr/m/n/10 https : / / blogs . sas . com / co ntent / iml / 2017 / 05 / 24 / [1689] Underfull \hbox (badness 10000) in paragraph at lines 24024--24025 []\T1/ptm/m/n/10 Wikipedia: [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . or g / wiki / Quantile # Estimating _ [1690] Overfull \hbox (48.78088pt too wide) in paragraph at lines 24135--24135 [] \T1/pcr/m/n/10 method = c("non.compact", "row.compact", "col.compact" , "compact"),[] [1691] Underfull \hbox (badness 1028) in paragraph at lines 24193--24196 []\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for []\T 1/pcr/m/n/10 write() []\T1/ptm/m/n/10 and [1692] [1693] Underfull \hbox (badness 10000) in paragraph at lines 24308--24311 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1694] Underfull \hbox (badness 7099) in paragraph at lines 24363--24365 []\T1/ptm/m/n/10 This, as [][][]\T1/pcr/m/n/10 reorder[][][]()[]\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [][][]\T1/pcr/m/n/10 factor[][][](x, l evels = [1695] Underfull \hbox (badness 7099) in paragraph at lines 24427--24429 []\T1/ptm/m/n/10 This, as [][][]\T1/pcr/m/n/10 relevel[][][]()[]\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [][][]\T1/pcr/m/n/10 factor[][][](x, l evels = Overfull \hbox (31.3804pt too wide) in paragraph at lines 24462--24462 []\T1/pcr/m/n/9 bymedianR <- with(InsectSprays, reorder(spray, count, median, decreasing=TRUE))[] [1696] [1697] Overfull \hbox (9.78043pt too wide) in paragraph at lines 24538--24538 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")[] [1698] [1699] Overfull \hbox (0.78088pt too wide) in paragraph at lines 24655--24655 []\T1/pcr/m/n/10 # varying = ___, # list / matrix / vector (use with care)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 24656--24656 []\T1/pcr/m/n/10 # v.names = ___, # vector of variable names in long format[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 24657--24657 []\T1/pcr/m/n/10 # timevar, times, # name / values of constructed time variable[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 24658--24658 []\T1/pcr/m/n/10 # idvar, ids) # name / values of constructed id v ariable[] [1700] [1701] Underfull \hbox (badness 10000) in paragraph at lines 24818--24823 [][][]\T1/pcr/m/n/10 stack[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 aperm[] [][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 relist[][][] []\T1/ptm/m/n/10 for r e-shap-ing the re-sult of [][][]\T1/pcr/m/n/10 unlist[][][][]\T1/ptm/m/n/10 . [ ][][]\T1/pcr/m/n/10 xtabs[][][] []\T1/ptm/m/n/10 and Underfull \hbox (badness 2495) in paragraph at lines 24818--24823 [][][]\T1/pcr/m/n/10 as.data.frame.table[][][] []\T1/ptm/m/n/10 for cre-at-ing con-tin-gency ta-bles and con-vert-ing them back to Overfull \hbox (15.18042pt too wide) in paragraph at lines 24829--24829 []\T1/pcr/m/n/9 ## long to wide (direction = "wide") requires idvar and timeva r at a minimum[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 24830--24830 []\T1/pcr/m/n/9 reshape(Indometh, direction = "wide", idvar = "Subject", timev ar = "time")[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 24849--24849 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide ", v.names = "x")[] [1702] [1703] Overfull \hbox (60.78088pt too wide) in paragraph at lines 24953--24953 [] \T1/pcr/m/n/10 na.action = c("+Big_alternate", "-Big_alternate", "na. omit", "fail"),[] Underfull \hbox (badness 1033) in paragraph at lines 24996--25002 \T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/ m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where [1704] Underfull \hbox (badness 10000) in paragraph at lines 25017--25020 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult []\T1/pcr/m/n/10 y = r unmed(x, k) []\T1/ptm/m/n/10 sim-ply has []\T1/pcr/m/n/10 y[j] = [1705] Overfull \hbox (9.78043pt too wide) in paragraph at lines 25099--25099 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi ans Example")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 25128--25128 []\T1/pcr/m/n/9 ## An example with initial NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s - used to fail badly (notably for "Turlach"):[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 25140--25140 []\T1/pcr/m/n/9 matplot(y = cbind(x15, rT15), type = "b", ylim = c(1,9), pch=1 :5, xlab = NA,[] [1706] [1707] [1708] [1709] [1710] [1711] Underfull \vbox (badness 10000) has occurred while \output is active [1712] [1713] Underfull \hbox (badness 6268) in paragraph at lines 25599--25604 [][][]\T1/pcr/m/n/10 SSasympOrig[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 S Sbiexp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSfol[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSfpl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSgo mpertz[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSlogis[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 SSmicmen[][][][]\T1/ptm/m/n/10 , [1714] [1715] [1716] Underfull \hbox (badness 1867) in paragraph at lines 25809--25811 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 25825--25829 []\T1/ptm/m/n/10 where []\T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallba ck = use.fallback) []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 PP Underfull \hbox (badness 10000) in paragraph at lines 25825--25829 \T1/pcr/m/n/10 <- sum(!is.na([][]coef[][][](object))) []\T1/ptm/m/n/10 -- where in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was [1717] Overfull \hbox (20.58041pt too wide) in paragraph at lines 25867--25867 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr om summary(lm1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 25874--25874 []\T1/pcr/m/n/9 stopifnot(all.equal(sigma(fm.DN1), summary(fm.DN1)$sigma, tole rance=1e-15))[] [1718] [1719] [1720] Underfull \hbox (badness 2495) in paragraph at lines 26057--26066 []\T1/ptm/m/n/10 For an in-verse gaus-sian GLM the model as-sumed is $\OML/cmm/ m/it/10 IG\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^V[]; ^^Uw[]\OT1/cmr/m/n/10 )$ \T1 /ptm/m/n/10 (see [][]$\T1/pcr/m/n/10 https : / / en . [1721] [1722] Underfull \hbox (badness 2197) in paragraph at lines 26199--26202 []\T1/pcr/m/n/10 psmirnov []\T1/ptm/m/n/10 gives the dis-tri-bu-tion func-tion, []\T1/pcr/m/n/10 qsmirnov []\T1/ptm/m/n/10 gives the quan-tile func-tion, and Overfull \hbox (24.78088pt too wide) in paragraph at lines 26219--26219 [] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)[] Underfull \hbox (badness 1412) in paragraph at lines 26226--26228 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1723] Overfull \hbox (25.98041pt too wide) in paragraph at lines 26313--26313 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS S"), smooth(x)))[] [1724] Overfull \hbox (84.78088pt too wide) in paragraph at lines 26338--26338 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda = NULL, cv = FALSE, Overfull \hbox (66.78088pt too wide) in paragraph at lines 26341--26341 [] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee p.stuff = FALSE)[] [1725] [1726] [1727] Overfull \hbox (6.78088pt too wide) in paragraph at lines 26576--26576 [] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / t ol) ))[] Underfull \hbox (badness 2547) in paragraph at lines 26580--26586 []\T1/ptm/m/n/10 The de-fault []\T1/pcr/m/n/10 all.knots = FALSE []\T1/ptm/m/n/ 10 and []\T1/pcr/m/n/10 nknots = .nknots.smspl[]\T1/ptm/m/n/10 , en-tails us-in g only [1728] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26627--26627 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi ng splines")[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 26648--26648 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # = = unique(cars$speed)[] Underfull \vbox (badness 10000) has occurred while \output is active [1729] [1730] [1731] Overfull \hbox (0.78088pt too wide) in paragraph at lines 26840--26840 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail, [1732] [1733] [1734] [1735] [1736] [1737] Overfull \hbox (36.78088pt too wide) in paragraph at lines 27220--27220 [] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC" , "hyman"),[] [1738] [1739] Overfull \hbox (69.18036pt too wide) in paragraph at lines 27401--27401 []\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi * x) + rnorm(30)/10, 3)[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 27407--27407 []\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean)) for when x has ties")[] Underfull \vbox (badness 10000) has occurred while \output is active [1740] Overfull \hbox (31.3804pt too wide) in paragraph at lines 27416--27416 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c ol = 3, n = 1001)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 27417--27417 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c ol = 4, n = 1001)[] [1741] Underfull \hbox (badness 2922) in paragraph at lines 27486--27491 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (9.78043pt too wide) in paragraph at lines 27523--27523 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim = c(-.3, 5),[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 27526--27526 [] \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^ {-e^{phi[3]}*~x}}))[] [1742] Overfull \hbox (20.58041pt too wide) in paragraph at lines 27535--27535 [] \T1/pcr/m/n/9 c(0 , 1 ), 1, length = 0.08, angle = 25); text(0. 5, 1, quote(1))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27536--27536 [] \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3 # (Asym + R0)/2[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 27540--27540 [] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi [1]+phi[2],2), phi[1]),[] Underfull \hbox (badness 3240) in paragraph at lines 27594--27597 [][][]\T1/pcr/m/n/10 nls[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 selfStart [][][][]\T1/ptm/m/n/10 ; []\T1/pcr/m/n/10 example(SSasympOff) []\T1/ptm/m/n/10 gives graph show-ing the []\T1/pcr/m/n/10 SSasympOff [1743] Overfull \hbox (36.7804pt too wide) in paragraph at lines 27615--27615 [] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log( 0.4), c0 = 3/4)) )[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27618--27618 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim = c(-1, 8),[] [1744] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27701--27701 [] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log (log(2)))) )[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27705--27705 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim = c(-1/4, 5),[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 27715--27715 [] \T1/pcr/m/n/9 axis(2, at = 5*c(1/2,1), labels= expression(frac(phi[1],2), phi[1]), pos=0, las=1)[] [1745] Overfull \hbox (106.98032pt too wide) in paragraph at lines 27720--27720 [] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] Underfull \hbox (badness 2922) in paragraph at lines 27756--27762 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 27778--27778 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat a = Indo.1),[] [1746] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27794--27794 [] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 1.5 * exp(-x)"),[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 27808--27808 []\T1/pcr/m/n/9 ## Fails by default (scaleOffset=0) on most platforms {also af ter increasing maxiter !}[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27810--27810 [] \T1/pcr/m/n/9 nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d atN, trace=TRUE)[] Overfull \hbox (128.58029pt too wide) in paragraph at lines 27813--27813 []\T1/pcr/m/n/9 fmX1 <- nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d atN, control = list(scaleOffset=1))[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 27815--27815 [] \T1/pcr/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol=1 e-11, nDcentral=TRUE), trace=TRUE)[] [1747] [1748] Overfull \hbox (30.78088pt too wide) in paragraph at lines 27927--27927 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK a)*input)) [1749] Underfull \hbox (badness 2922) in paragraph at lines 27989--27994 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1750] Overfull \hbox (69.18036pt too wide) in paragraph at lines 28027--28027 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm id", phi[4] == "scal")))[] Underfull \hbox (badness 2922) in paragraph at lines 28076--28081 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1751] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28107--28107 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = " red", lwd=2)[] Underfull \hbox (badness 2922) in paragraph at lines 28141--28146 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1752] Overfull \hbox (25.98041pt too wide) in paragraph at lines 28166--28166 []\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number of iter...: 0" :[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 28170--28170 []\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR UE), trace = TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28190--28190 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] == "scal")))[] [1753] Overfull \hbox (20.58041pt too wide) in paragraph at lines 28200--28200 [] \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0, 2.5,3.5), # NB. SSlogis(x = xmid = 2) = 2.5[] Underfull \hbox (badness 2922) in paragraph at lines 28235--28240 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 28257--28257 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt), digits = 3)[] [1754] Overfull \hbox (15.18042pt too wide) in paragraph at lines 28275--28275 [] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS micmen model")[] [1755] Underfull \hbox (badness 6493) in paragraph at lines 28327--28332 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 x[]\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 28355--28355 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28358--28358 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 28361--28361 []\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul l() fit to Chick.6")[] Overfull \hbox (69.18036pt too wide) in paragraph at lines 28364--28364 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f m1)[["Drop"]]), lty = 3)[] [1756] [1757] [1758] [1759] [1760] [1761] [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] Underfull \hbox (badness 3396) in paragraph at lines 29248--29250 []\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.glm"[]\T1/ptm/m/ n/10 , usu-ally, a re-sult of a call to [1770] [1771] [1772] Underfull \hbox (badness 2237) in paragraph at lines 29427--29429 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /pcr/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1773] [1774] Underfull \hbox (badness 2591) in paragraph at lines 29591--29593 []\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.nls"[]\T1/ptm/m/ n/10 , usu-ally the re-sult of a call to [1775] Underfull \hbox (badness 2237) in paragraph at lines 29637--29640 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /pcr/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1776] Overfull \hbox (48.78088pt too wide) in paragraph at lines 29710--29710 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t race = FALSE) [1777] [1778] Underfull \hbox (badness 3407) in paragraph at lines 29819--29823 []\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m ented\T1/ptm/m/n/10 , see []\T1/pcr/m/n/10 corr []\T1/ptm/m/n/10 be-low) [1779] Overfull \hbox (47.58038pt too wide) in paragraph at lines 29889--29889 []\T1/pcr/m/n/9 symnum(ii, cutpoints = 2*(0:4), symbols = c(".", "-", "+", "$ "), show.max = TRUE)[] [1780] Underfull \hbox (badness 1337) in paragraph at lines 29952--29956 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1781] [1782] [1783] [1784] Overfull \hbox (9.78043pt too wide) in paragraph at lines 30219--30219 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, main = t.tit,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30262--30262 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] [1785] Underfull \hbox (badness 1616) in paragraph at lines 30288--30291 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1786] Overfull \hbox (20.58041pt too wide) in paragraph at lines 30367--30367 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1787] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30445--30445 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1788] [1789] Underfull \hbox (badness 2205) in paragraph at lines 30540--30545 []\T1/ptm/m/n/10 If a []\T1/pcr/m/n/10 specials []\T1/ptm/m/n/10 ar-gu-ment was given to [][][]\T1/pcr/m/n/10 terms.formula[][][] []\T1/ptm/m/n/10 there is a [1790] [1791] Overfull \hbox (12.78088pt too wide) in paragraph at lines 30681--30681 []\T1/pcr/m/n/10 toeplitz2(x, nrow = length(x) +1 - ncol, ncol = length(x) +1 - nrow)[] Underfull \hbox (badness 2913) in paragraph at lines 30687--30691 []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 toeplitz(x, *)[]\T1/ptm/m/n/10 : the firs t col-umn of the Toeplitz ma-trix; for [1792] Overfull \hbox (36.7804pt too wide) in paragraph at lines 30724--30724 []\T1/pcr/m/n/9 # Matrix of character (could also have logical, raw, complex . .) {also warning}:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 30737--30737 [] \T1/pcr/m/n/9 colnames(W) <- paste0(",", if(n <= 9) 1:n else c(1:9, lette rs[seq_len(n-9)]))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 30748--30748 []\T1/pcr/m/n/9 y.hat <- W. %*% y # y.hat := smoothed(y) ("mass preserving" -> longer than y)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 30750--30750 []\T1/pcr/m/n/9 plot(x,y, type="b", xlim=c(1,m)); curve(f(x), 1,n, col="gray", lty=2, add=TRUE)[] [1793] Overfull \hbox (30.78088pt too wide) in paragraph at lines 30780--30780 [] \T1/pcr/m/n/10 class = if(nseries > 1) c("mts", "ts", "matrix", "array") else "ts",[] [1794] Underfull \hbox (badness 1655) in paragraph at lines 30858--30861 []\T1/pcr/m/n/10 is.mts(x) []\T1/ptm/m/n/10 tests if an ob-ject []\T1/pcr/m/n/1 0 x []\T1/ptm/m/n/10 is a mul-ti-vari-ate time se-ries, i.e., ful-fills []\T1/p cr/m/n/10 is.ts(x)[]\T1/ptm/m/n/10 , [1795] [1796] [1797] [1798] [1799] Overfull \hbox (12.78088pt too wide) in paragraph at lines 31222--31222 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE) Overfull \hbox (12.78088pt too wide) in paragraph at lines 31223--31223 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1800] [1801] [1802] [1803] [1804] Overfull \hbox (30.78088pt too wide) in paragraph at lines 31523--31523 [] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con v = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 31524--31524 [] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace = 0)[] [1805] [1806] Overfull \hbox (31.3804pt too wide) in paragraph at lines 31653--31653 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 31662--31662 []\T1/pcr/m/n/9 ## where as \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 simply first enlarges the search interval:[] Underfull \vbox (badness 10000) has occurred while \output is active [1807] [1808] [1809] Underfull \hbox (badness 1337) in paragraph at lines 31879--31883 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1810] [1811] [1812] [1813] [1814] [1815] [1816] [1817] Underfull \hbox (badness 1337) in paragraph at lines 32408--32412 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1818] [1819] [1820] Overfull \hbox (117.7803pt too wide) in paragraph at lines 32616--32616 []\T1/pcr/m/n/9 wilcox.test( 4:2, 3:1, paired=TRUE) # Warning: canno t compute exact p-value with ties[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 32618--32618 []\T1/pcr/m/n/9 wilcox.test((4:2)/10, (3:1)/10, paired=TRUE, digits.rank = 9) # same ties as (4:2, 3:1)[] [1821] [1822] [1823] Overfull \hbox (138.78088pt too wide) in paragraph at lines 32777--32777 [] \T1/pcr/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps = getOption("ts.eps"), ...)[] [1824] Overfull \hbox (0.78088pt too wide) in paragraph at lines 32862--32862 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, [1825] [1826] Overfull \hbox (47.58038pt too wide) in paragraph at lines 32995--32995 []\T1/pcr/m/n/9 ## The Female:Rejected combination has NA \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 Freq\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 (and NA prints \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 invisibly\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 as "")[] [1827]) (./stats4-pkg.tex [1828] Chapter 11. [1829] [1830] [1831] Overfull \hbox (15.18042pt too wide) in paragraph at lines 224--224 [] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf)) , log = TRUE))[] Underfull \vbox (badness 10000) has occurred while \output is active [1832] Overfull \hbox (9.78043pt too wide) in paragraph at lines 278--278 []\T1/pcr/m/n/9 ## Boundary case: This works, but fails if limits are set clos er to 0 and 1[] [1833] [1834] [1835] [1836] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdas h.methods}) has been already used, duplicate ignored \relax l.503 ...Package \pkg{stats4}}{show.Rdash.methods} [1837] [1838] [1839]) (./tcltk-pkg.tex [1840] Chapter 12. [1841] [1842] [1843] [1844] [1845] Overfull \hbox (36.7804pt too wide) in paragraph at lines 360--360 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all.names = TRUE) # .Tcl.args put a ca llback ref in here[] [1846] [1847] Underfull \vbox (badness 10000) has occurred while \output is active [1848] Underfull \hbox (badness 1292) in paragraph at lines 671--678 []\T1/pcr/m/n/10 tcl []\T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-i ng any Tk or Tcl com-mand by sim-ply run-ning Underfull \vbox (badness 1603) has occurred while \output is active [1849] [1850] [1851] [1852] [1853] Underfull \vbox (badness 10000) has occurred while \output is active [1854] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1084--1084 []\T1/pcr/m/n/9 eval.txt <- function() eval(str2lang(tclvalue(tkget(txt.w, "0. 0", "end"))))[] [1855] [1856] [1857] [1858] [1859] Underfull \hbox (badness 1189) in paragraph at lines 1412--1415 [][][]\T1/pcr/m/n/10 select.list[][][] []\T1/ptm/m/n/10 (a text ver-sion ex-cep t on Win-dows and the ma-cOS GUI), [][][]\T1/pcr/m/n/10 menu[][][] []\T1/ptm/m/ n/10 (whose [1860]) (./tools-pkg.tex Chapter 13. [1861] Overfull \hbox (9.78043pt too wide) in paragraph at lines 69--69 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for new methods.[] [1862] Underfull \hbox (badness 1253) in paragraph at lines 167--170 []\T1/pcr/m/n/10 assertWarning() []\T1/ptm/m/n/10 as-serts that a warn-ing will be sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1863] Overfull \hbox (4.38043pt too wide) in paragraph at lines 218--218 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch ing warning)[] [1864] Underfull \hbox (badness 5147) in paragraph at lines 288--301 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 Underfull \hbox (badness 4792) in paragraph at lines 288--301 \T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][][]\T1/pcr/m/n /10 bibentry[][][] []\T1/ptm/m/n/10 as well as sev-eral other rou- Underfull \hbox (badness 2237) in paragraph at lines 288--301 \T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named []\T1/pcr/m/n /10 formatArticle[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 formatBook[]\T1/ptm/m/n/10 , [1865] Overfull \hbox (42.78088pt too wide) in paragraph at lines 373--373 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta ngle = TRUE, Underfull \hbox (badness 2460) in paragraph at lines 392--394 []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gin e to use. Over-rides any [1866] [1867] Underfull \hbox (badness 1142) in paragraph at lines 464--468 \T1/ptm/m/n/10 If given, vi-gnette source files are by de-fault looked for in s ub-di-rec-tory [1868] [1869] [1870] [1871] [1872] [1873] [1874] Overfull \hbox (0.78088pt too wide) in paragraph at lines 921--921 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", " xz"),[] [1875] Overfull \hbox (31.3804pt too wide) in paragraph at lines 976--976 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co mpress == "none")[] [1876] [1877] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1145--1145 [] \T1/pcr/m/n/10 outputs = FALSE, sources = FALS E, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1146--1146 []\T1/pcr/m/n/10 check_packages_in_dir_details(dir, logs = NULL, drop_ok = TRU E, ...)[] [1878] Underfull \hbox (badness 1014) in paragraph at lines 1188--1190 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1194--1196 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous [1879] Underfull \hbox (badness 10000) in paragraph at lines 1231--1234 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us- Underfull \hbox (badness 10000) in paragraph at lines 1231--1234 \T1/ptm/m/n/10 ing []\T1/pcr/m/n/10 summarize_check_packages_in_dir_results []\ T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 1239--1242 []\T1/pcr/m/n/10 check_packages_in_dir []\T1/ptm/m/n/10 re-turns an ob-ject in- her-it-ing from class [1880] [1881] Underfull \hbox (badness 10000) in paragraph at lines 1386--1389 []\T1/pcr/m/n/10 codocClasses []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 codocData [ ]\T1/ptm/m/n/10 re-turn ob-jects of class []\T1/pcr/m/n/10 "codocClasses" []\T1 /ptm/m/n/10 and [1882] [1883] Underfull \hbox (badness 4647) in paragraph at lines 1557--1562 []\T1/pcr/m/n/10 CRAN_package_db() []\T1/ptm/m/n/10 re-turns a data frame with char-ac-ter columns con-tain-ing most Underfull \hbox (badness 7869) in paragraph at lines 1557--1562 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' meta-data for the cu r-rent pack-ages in the CRAN pack-age repos-i- Underfull \hbox (badness 1681) in paragraph at lines 1557--1562 \T1/ptm/m/n/10 tory, in-clud-ing in par-tic-u-lar the De-scrip-tion and Main-ta iner in-for-ma-tion not pro-vided by [1884] Underfull \hbox (badness 2762) in paragraph at lines 1606--1609 []\T1/ptm/m/n/10 Internal func-tions []\T1/pcr/m/n/10 CRAN_aliases_db[]\T1/ptm/ m/n/10 , []\T1/pcr/m/n/10 CRAN_archive_db[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 CR AN_current_db []\T1/ptm/m/n/10 and [1885] [1886] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1718--1718 [] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En hances"))[] Underfull \hbox (badness 7981) in paragraph at lines 1725--1733 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 1725--1733 []\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", Underfull \hbox (badness 1558) in paragraph at lines 1725--1733 \T1/pcr/m/n/10 "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string []\T1/pcr/m/n/1 0 "all" []\T1/ptm/m/n/10 is short-hand for that vec-tor, [1887] [1888] [1889] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.GSC}) has been already used, duplicate ignored \relax l.1937 \aliasA{GSC}{find\_gs\_cmd}{GSC} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSC MD}) has been already used, duplicate ignored \relax l.1938 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1890] [1891] [1892] [1893] Underfull \hbox (badness 1142) in paragraph at lines 2207--2213 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 loadPkgRdMacros []\T1/ptm/m/n/10 func-tio n first looks for an []\T1/pcr/m/n/10 "RdMacros" []\T1/ptm/m/n/10 en-try in the pack-age [1894] Underfull \hbox (badness 2359) in paragraph at lines 2271--2278 []\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user and site spe-cific com-pi-la- Underfull \hbox (badness 1102) in paragraph at lines 2271--2278 \T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1 0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com- Underfull \hbox (badness 4168) in paragraph at lines 2271--2278 \T1/ptm/m/n/10 pi-la-tions in sub-di-rec-to-ries of `\T1/pcr/m/n/10 src\T1/ptm/ m/n/10 '), e.g., by adding con-fig-ure code call-ing \T1/phv/m/n/10 R \T1/ptm/m /n/10 with [1895] Underfull \hbox (badness 1342) in paragraph at lines 2323--2329 \T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in Underfull \hbox (badness 10000) in paragraph at lines 2348--2355 []\T1/pcr/m/n/10 matchConcordance []\T1/ptm/m/n/10 con-verts from out-put lo-ca -tions to source lo-ca-tions. 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[1897] [1898] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2537--2537 []\T1/pcr/m/n/10 package_dependencies(packages = NULL, db = NULL, which = "str ong", Underfull \hbox (badness 7981) in paragraph at lines 2552--2560 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 2552--2560 []\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", Underfull \hbox (badness 1558) in paragraph at lines 2552--2560 \T1/pcr/m/n/10 "Enhances")[]\T1/ptm/m/n/10 . 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Rd"),[] [1904] Underfull \hbox (badness 2486) in paragraph at lines 2950--2958 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion 3.2.0, User-d efined macros may be given in a sep-a-rate file us-ing [1905] [1906] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3162--3162 []\T1/pcr/m/n/10 checkDocFiles (package, dir, lib.loc = NULL, chkInternal = FALSE) [1907] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3166--3166 []\T1/pcr/m/n/10 checkRdContents (package, dir, lib.loc = NULL, chkInternal = FALSE)[] [1908] [1909] [1910] Underfull \hbox (badness 1072) in paragraph at lines 3358--3360 []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec- tor of links, as re-turned by [1911] [1912] [1913] [1914] [1915] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3706--3706 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro s", "system.Rd"))[] Underfull \hbox (badness 5417) in paragraph at lines 3744--3754 []\T1/ptm/m/n/10 By de-fault, the tags \T1/pcr/m/n/10 \S3method\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \S4method\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \command\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \docType\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \email\T1/ptm/m/n/10 , [1916] [1917] [1918] Underfull \hbox (badness 4108) in paragraph at lines 3960--3967 []\T1/ptm/m/n/10 This func-tion starts the in-ter-nal HTTP server, which runs o n the loop-back in-ter-face [1919] [1920] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4060--4060 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 4063--4063 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 4080--4082 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1921] Underfull \hbox (badness 2932) in paragraph at lines 4097--4103 []\T1/pcr/m/n/10 testInstalledBasic []\T1/ptm/m/n/10 runs the ba-sic tests, if in-stalled. This should be run with [1922] Underfull \hbox (badness 7832) in paragraph at lines 4219--4222 []\T1/ptm/m/n/10 Where sup-ported ([]\T1/pcr/m/n/10 texi2dvi []\T1/ptm/m/n/10 5 .0 and later; []\T1/pcr/m/n/10 texify.exe []\T1/ptm/m/n/10 from MiK-TeX), op-ti on [1923] [1924] [1925] [1926] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4454--4454 [] \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry run),[] [1927] [1928] Overfull \hbox (96.78088pt too wide) in paragraph at lines 4616--4616 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, mergeOpts = "", copyright, bugs) Underfull \hbox (badness 3118) in paragraph at lines 4627--4631 []\T1/ptm/m/n/10 a string, by de-fault empty, of op-tions to []\T1/pcr/m/n/10 m sgmerge []\T1/ptm/m/n/10 in ad-di-tion to Underfull \hbox (badness 10000) in paragraph at lines 4631--4634 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `[]\T1/pcr/m/n/10 Copyrig ht[]\T1/ptm/m/n/10 ' and [1929] Underfull \hbox (badness 6859) in paragraph at lines 4647--4652 []\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory []\T1/pcr/m/n/10 po []\T1/ ptm/m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\ T1/ptm/m/n/10 ' are up-dated from Underfull \hbox (badness 1184) in paragraph at lines 4655--4661 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po /\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T he Underfull \hbox (badness 2941) in paragraph at lines 4655--4661 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t he pack-age are ex-am-ined to cre-ate a file [1930] [1931] [1932] Underfull \hbox (badness 10000) in paragraph at lines 4889--4891 []\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 vignetteEngine[][][][]\T1/ptm/m/n/10 , such as []\T1/pcr/m/n/10 "utils::Sweave" []\T1/ptm/m/n/10 or [1933] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4918--4918 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4919--4919 [] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr ess = "xz",[] Underfull \hbox (badness 3240) in paragraph at lines 4932--4935 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T 1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ', Underfull \hbox (badness 1742) in paragraph at lines 4936--4946 []\T1/pcr/m/n/10 "Package"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Version"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "Priority"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Depe nds"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Imports"[]\T1/ptm/m/n/10 , [1934] Underfull \hbox (badness 1127) in paragraph at lines 4974--4980 []\T1/pcr/m/n/10 write_PACKAGES []\T1/ptm/m/n/10 scans the named di-rec-tory fo r R pack-ages, ex-tracts in-for-ma-tion from Underfull \hbox (badness 1635) in paragraph at lines 4974--4980 \T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file , and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1 0 ', Underfull \hbox (badness 1571) in paragraph at lines 5002--5006 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by Underfull \hbox (badness 2772) in paragraph at lines 5028--5033 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 PACKAGES.gz\T1/ptm/m/n/10 ' files. See [][][ ]\T1/pcr/m/n/10 update_PACKAGES[][][] []\T1/ptm/m/n/10 for ef-fi-ciently up-dat -ing ex-ist-ing [1935] [1936] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5170--5170 []\T1/pcr/m/n/9 xgettext(tmpPkg, asCall=TRUE )[[1]] # default; shows \TS1/pcr /m/n/9 ' \T1/pcr/m/n/9 sqrt(as.complex(x)) \TS1/pcr/m/n/9 '[] [1937]) (./utils-pkg.tex [1938] Chapter 14. Underfull \hbox (badness 1072) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[] \T1/pcr/m/n/10 insertions[]\T1/ptm/m/n/10 ', [1939] [1940] [1941] [1942] Overfull \hbox (4.38043pt too wide) in paragraph at lines 261--261 []\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with these names[] [1943] [1944] Underfull \hbox (badness 10000) in paragraph at lines 381--386 \T1/ptm/m/n/10 are []\T1/pcr/m/n/10 c("vertical", "horizontal", "cascade", "min imize", Underfull \hbox (badness 10000) in paragraph at lines 387--389 []\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 list[][][] []\T1/ptm/m/n/10 of win-dow han-dles, by de-fault pro-duced by [1945] Overfull \hbox (9.78043pt too wide) in paragraph at lines 453--453 []\T1/pcr/m/n/9 # This default is useful only in SDI mode: it will tile any F irefox window[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 455--455 []\T1/pcr/m/n/9 .arrangeWindowsDefaults <- list(c("R", "all"), pattern = c("", "Firefox"))[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 472--472 [] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No ", "Cancel"))),[] [1946] [1947] [1948] Overfull \hbox (0.78088pt too wide) in paragraph at lines 686--686 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc es"), Overfull \hbox (6.78088pt too wide) in paragraph at lines 692--692 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 693--693 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 694--694 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 695--695 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] [1949] Underfull \hbox (badness 10000) in paragraph at lines 729--735 []\T1/ptm/m/n/10 Functions []\T1/pcr/m/n/10 aspell_package_Rd_files[]\T1/ptm/m/ n/10 , []\T1/pcr/m/n/10 aspell_package_vignettes[]\T1/ptm/m/n/10 , Underfull \hbox (badness 4416) in paragraph at lines 729--735 []\T1/pcr/m/n/10 aspell_package_R_files []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 a spell_package_C_files []\T1/ptm/m/n/10 per-form spell check- [1950] [1951] [1952] [1953] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1053--1053 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL, [1954] Underfull \hbox (badness 7649) in paragraph at lines 1127--1133 [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 in-di-cat-ing if Bib-TeX co de should be given ad-di-tion-ally; Underfull \hbox (badness 5533) in paragraph at lines 1127--1133 \T1/ptm/m/n/10 cur-rently ap-plies only to []\T1/pcr/m/n/10 style = "citation"[ ]\T1/ptm/m/n/10 . The de-fault for Underfull \hbox (badness 4739) in paragraph at lines 1127--1133 \T1/ptm/m/n/10 the []\T1/pcr/m/n/10 print() []\T1/ptm/m/n/10 method de-pends on the num-ber of (bib) en-tries and Underfull \hbox (badness 1817) in paragraph at lines 1127--1133 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 1136--1138 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1955] [1956] Underfull \hbox (badness 10000) in paragraph at lines 1255--1258 []\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Digital _ Object _ [1957] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1338--1338 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] Underfull \vbox (badness 10000) has occurred while \output is active [1958] [1959] [1960] [1961] [1962] [1963] Underfull \hbox (badness 1859) in paragraph at lines 1747--1756 []\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b e quite large the com- Underfull \hbox (badness 2042) in paragraph at lines 1747--1756 \T1/ptm/m/n/10 mand []\T1/pcr/m/n/10 data.frame(x, y, z, monday, tuesday) []\T1 /ptm/m/n/10 never re-turns. Do not re-port that [1964] [1965] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1852--1852 [] \T1/pcr/m/n/9 data = infert, family = b inomial())))[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 1887--1887 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b efore$timestamp,[] [1966] [1967] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2033--2033 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp" ), md5sum=TRUE)[] [1968] Underfull \hbox (badness 2277) in paragraph at lines 2102--2107 []\T1/pcr/m/n/10 charClass []\T1/ptm/m/n/10 was added in \T1/phv/m/n/10 R \T1/p tm/m/n/10 4.1.0. A less di-rect way to ex-am-ine char-ac-ter classes [1969] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2134--2134 []\T1/pcr/m/n/9 cl <- c("alnum", "alpha", "blank", "digit", "graph", "punct", "upper", "xdigit")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2136--2136 []\T1/pcr/m/n/9 X <- as.data.frame(X); row.names(X) <- sQuote(intToUtf8(x, mul tiple = TRUE))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2144--2144 []\T1/pcr/m/n/9 ## How many printable characters are there? (Around 280,000 in Unicode 13.)[] [1970] [1971] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2292--2292 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind = NULL, [1972] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2344--2344 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind = NULL, [1973] Underfull \hbox (badness 1117) in paragraph at lines 2459--2466 []\T1/ptm/m/n/10 If the ob-ject re-turned by []\T1/pcr/m/n/10 citation() []\T1/ ptm/m/n/10 con-tains only one ref-er-ence, the as-so-ci-ated print Underfull \hbox (badness 1400) in paragraph at lines 2459--2466 \T1/ptm/m/n/10 method shows both a text ver-sion and a Bib-TeX en-try for it. I f a pack-age has more [1974] [1975] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2542--2542 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after = NULL,[] [1976] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2662--2662 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1977] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2702--2702 []\T1/pcr/m/n/10 citEntry(entry, textVersion = NULL, header = NULL, footer = N ULL, ...) Underfull \hbox (badness 1082) in paragraph at lines 2731--2735 [][][]\T1/pcr/m/n/10 citation[][][] []\T1/ptm/m/n/10 for more in-for-ma-tion ab out cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file s; [1978] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard }) has been already used, duplicate ignored \relax l.2736 ... the Clipboard in MS Windows}{clipboard} Underfull \hbox (badness 1163) in paragraph at lines 2767--2769 []\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats: see e.g. [][]$\T1/pcr/m/n/10 https : / / docs . [1979] [1980] Underfull \hbox (badness 10000) in paragraph at lines 2860--2862 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [1981] [1982] [1983] Underfull \hbox (badness 10000) in paragraph at lines 3078--3080 []\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see [1984] [1985] [1986] [1987] Underfull \hbox (badness 1762) in paragraph at lines 3371--3374 []\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re c-tory of the cur-rent work-ing di-rec-tory, set []\T1/pcr/m/n/10 package = [1988] Overfull \hbox (63.78036pt too wide) in paragraph at lines 3463--3463 []\T1/pcr/m/n/9 try(data(package = "rpart"), silent = TRUE) # list the data se ts in the rpart package[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3464--3464 []\T1/pcr/m/n/9 data(USArrests, "VADeaths") # load the data sets \TS1/pcr/m /n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] [1989] Underfull \hbox (badness 2452) in paragraph at lines 3538--3541 []\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class []\ T1/pcr/m/n/10 R_dataentry[]\T1/ptm/m/n/10 . Re-sources [1990] [1991] [1992] [1993] [1994] [1995] Overfull \hbox (74.58035pt too wide) in paragraph at lines 3967--3967 [] \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf orm$r_arch, "stats.dll"))[] [1996] Underfull \hbox (badness 4779) in paragraph at lines 4046--4051 []\T1/ptm/m/n/10 Support for method []\T1/pcr/m/n/10 "libcurl" []\T1/ptm/m/n/10 was op-tional on Win-dows prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0: use [1997] Underfull \hbox (badness 1072) in paragraph at lines 4109--4113 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the []\T1/pcr/m/n/10 quiet []\T1/ptm/m/n/10 ar-gu-ment and the [1998] Underfull \hbox (badness 7238) in paragraph at lines 4165--4170 []\T1/ptm/m/n/10 For the []\T1/pcr/m/n/10 "libcurl" []\T1/ptm/m/n/10 and []\T1/ pcr/m/n/10 "curl" []\T1/ptm/m/n/10 meth-ods, prox-ies can be set \T1/ptm/m/it/1 0 via \T1/ptm/m/n/10 the en-vi-ron- Underfull \hbox (badness 1337) in paragraph at lines 4165--4170 \T1/ptm/m/n/10 ment vari-ables []\T1/pcr/m/n/10 http_proxy []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 ftp_proxy[]\T1/ptm/m/n/10 . See [][]$\T1/pcr/m/n/10 https : / / curl . se / libcurl / c / Underfull \hbox (badness 1184) in paragraph at lines 4180--4196 \T1/ptm/m/n/10 string con-tain-ing `[]\T1/pcr/m/n/10 "Schannel"[]\T1/ptm/m/n/10 '. If it does not, for ver-i-fi-ca-tion to be on the en-vi-ron- [1999] [2000] Underfull \hbox (badness 4660) in paragraph at lines 4306--4309 \T1/ptm/m/n/10 able at the repos-i-to-ries, or []\T1/pcr/m/n/10 NULL []\T1/ptm/ m/n/10 which makes an in-ter-nal call to Underfull \hbox (badness 10000) in paragraph at lines 4330--4332 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][][]\T1/pcr/m/n/10 do wnload.file[][][] []\T1/ptm/m/n/10 and [2001] [2002] [2003] Underfull \hbox (badness 1565) in paragraph at lines 4517--4521 []\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of [2004] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4600--4600 [] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F ALSE,[] [2005] Underfull \hbox (badness 1910) in paragraph at lines 4634--4641 \T1/ptm/m/n/10 is saved, then ini-tial-ized to a spec-i-fied state, the ex-am-p le is run and Underfull \hbox (badness 1655) in paragraph at lines 4634--4641 \T1/ptm/m/n/10 the (saved) state is re-stored. []\T1/pcr/m/n/10 setRNG = TRUE [ ]\T1/ptm/m/n/10 sets the same state as Underfull \hbox (badness 2846) in paragraph at lines 4634--4641 []\T1/pcr/m/n/10 R CMD [][]check[][][] []\T1/ptm/m/n/10 does for run-ning a pac k-age's ex-am-ples. This is cur- Underfull \hbox (badness 3460) in paragraph at lines 4634--4641 \T1/ptm/m/n/10 rently equiv-a-lent to []\T1/pcr/m/n/10 setRNG = {RNGkind("defau lt", "default", Underfull \hbox (badness 1931) in paragraph at lines 4641--4648 []\T1/ptm/m/n/10 logical (or []\T1/pcr/m/n/10 "default"[]\T1/ptm/m/n/10 ) in-di -cat-ing if [][][]\T1/pcr/m/n/10 devAskNewPage[][][](ask = TRUE) [2006] [2007] [2008] Underfull \hbox (badness 5939) in paragraph at lines 4887--4889 []\T1/ptm/m/n/10 An en-try in []\T1/pcr/m/n/10 getOption("repos") []\T1/ptm/m/n /10 named `[]\T1/pcr/m/n/10 CRAN[]\T1/ptm/m/n/10 ' which is not the de-fault [2009] [2010] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5030--5030 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [2011] [2012] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.5101 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format.1} ) has been already used, duplicate ignored \relax l.5101 ...mat Unordered and Ordered Lists}{format} [2013] [2014] [2015] [2016] [2017] [2018] [2019] [2020] Underfull \hbox (badness 1622) in paragraph at lines 5624--5628 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [2021] [2022] [2023] [2024] [2025] Underfull \hbox (badness 1448) in paragraph at lines 6003--6008 []\T1/ptm/m/n/10 External pointer ob-jects are com-pared as ref-er-ence ob-ject s, cor-re-spond-ing to call-ing [2026] [2027] Overfull \hbox (96.78088pt too wide) in paragraph at lines 6153--6153 []\T1/pcr/m/n/10 ## NB: The methods for \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 data.f rame\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 and \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 array\ TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 are identical to the \TS1/pcr/m/n/10 '\T1/pcr/ m/n/10 matrix\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 one[] [2028] Overfull \hbox (66.78088pt too wide) in paragraph at lines 6165--6165 []\T1/pcr/m/n/10 tail(x, n = 6L, keepnums = TRUE, addrownums, ...) # exported as tail.matrix()[] [2029] [2030] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6299--6299 [] \T1/pcr/m/n/9 ## BUT if I use "useAttrib(.)", this is *not* ok, when n i s of length 2:[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 6300--6300 [] \T1/pcr/m/n/9 ## --- because [i,j]-indexing of data frames *also* drops "other" attributes ..[] [2031] [2032] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6510--6510 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h elp(dgamma):[] [2033] Underfull \hbox (badness 10000) in paragraph at lines 6594--6596 []\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 https : / / www . r-[] project . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also [2034] Underfull \hbox (badness 1502) in paragraph at lines 6643--6648 []\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words '. `Key- Underfull \hbox (badness 2103) in paragraph at lines 6643--6648 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2035] [2036] [2037] Underfull \hbox (badness 10000) in paragraph at lines 6816--6825 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, Underfull \hbox (badness 10000) in paragraph at lines 6816--6825 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10 ', which can be re-made by [2038] Underfull \hbox (badness 2150) in paragraph at lines 6880--6883 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See Underfull \hbox (badness 5175) in paragraph at lines 6896--6899 []\T1/pcr/m/n/10 hsearch_db() []\T1/ptm/m/n/10 builds and caches the help searc h database for sub-se-quent use by [2039] [2040] Underfull \hbox (badness 3118) in paragraph at lines 7019--7021 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for [2041] [2042] Underfull \hbox (badness 5091) in paragraph at lines 7194--7196 []\T1/ptm/m/n/10 download method, see [][][]\T1/pcr/m/n/10 download.file[][][][ ]\T1/ptm/m/n/10 . Un-used if a non-[]\T1/pcr/m/n/10 NULL Underfull \hbox (badness 10000) in paragraph at lines 7224--7231 []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 means to use []\T1/pcr/m/n/10 c("Depends ", "Imports", "LinkingTo", Underfull \hbox (badness 10000) in paragraph at lines 7224--7231 \T1/pcr/m/n/10 "Suggests") []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pkgs []\T1/ptm /m/n/10 and []\T1/pcr/m/n/10 c("Depends", "Imports", Underfull \hbox (badness 1270) in paragraph at lines 7224--7231 \T1/pcr/m/n/10 "LinkingTo") []\T1/ptm/m/n/10 for added de-pen-den-cies: this in -stalls all the pack-ages [2043] Underfull \hbox (badness 1270) in paragraph at lines 7239--7249 \T1/ptm/m/n/10 for the `[]\T1/pcr/m/n/10 --configure-args[]\T1/ptm/m/n/10 ' fla g in the call to []\T1/pcr/m/n/10 R CMD INSTALL[]\T1/ptm/m/n/10 . If Underfull \hbox (badness 4441) in paragraph at lines 7282--7285 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed to Underfull \hbox (badness 2837) in paragraph at lines 7282--7285 []\T1/pcr/m/n/10 R CMD INSTALL []\T1/ptm/m/n/10 for a source pack-age in-stall. E.g., []\T1/pcr/m/n/10 c("--html", Underfull \hbox (badness 1424) in paragraph at lines 7290--7293 []\T1/ptm/m/n/10 logical: if true, re-duce the amount of out-put. This is \T1/p tm/m/it/10 not \T1/ptm/m/n/10 passed to [2044] Underfull \hbox (badness 2376) in paragraph at lines 7361--7368 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is []\T1/pcr/m/n /10 "both" []\T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 7361--7368 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 7361--7368 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1087) in paragraph at lines 7369--7372 []\T1/ptm/m/n/10 Using pack-ages with []\T1/pcr/m/n/10 type = "source" []\T1/pt m/m/n/10 al-ways works pro-vided the pack-age con-tains no [2045] Underfull \hbox (badness 1314) in paragraph at lines 7449--7456 []\T1/pcr/m/n/10 install.packages []\T1/ptm/m/n/10 needs to be able to com-pute all the de-pen-den-cies of []\T1/pcr/m/n/10 pkgs []\T1/ptm/m/n/10 from [2046] Underfull \hbox (badness 10000) in paragraph at lines 7532--7537 [][][]\T1/pcr/m/n/10 update.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 download.pac kages[][][][]\T1/ptm/m/n/10 , Overfull \hbox (25.98041pt too wide) in paragraph at lines 7555--7555 [] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc lude/udunits2"))[] [2047] Underfull \hbox (badness 5133) in paragraph at lines 7591--7595 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each pack-age's Underfull \hbox (badness 1983) in paragraph at lines 7605--7608 []\T1/pcr/m/n/10 installed.packages []\T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along [2048] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7652--7652 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields = "License")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7657--7657 []\T1/pcr/m/n/9 ## Keep packages that come with R (priority="high") and all ot hers separate![] [2049] [2050] Underfull \hbox (badness 4132) in paragraph at lines 7783--7785 []\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion of []\T1/pcr/m/n/10 libtool []\T1/ptm/m/n/10 in-stalled at [2051] [2052] [2053] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7950--7950 []\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h ave defined?[] [2054] [2055] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8093--8093 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE) [2056] Underfull \hbox (badness 10000) in paragraph at lines 8133--8135 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [2057] Underfull \hbox (badness 10000) in paragraph at lines 8240--8242 []\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if Underfull \hbox (badness 10000) in paragraph at lines 8252--8254 []\T1/ptm/m/n/10 typically the re-sult of []\T1/pcr/m/n/10 methods(..)[]\T1/ptm /m/n/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of S3 class [2058] [2059] [2060] [2061] Underfull \hbox (badness 1859) in paragraph at lines 8482--8485 []\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br owser (by Underfull \hbox (badness 1052) in paragraph at lines 8501--8511 \T1/ptm/m/n/10 ac-cord-ing to ver-sion us-ing \T1/pcr/m/n/10 section \T1/ptm/m/ n/10 el-e-ments with names start-ing with a suit-able pre-fix [2062] Underfull \hbox (badness 1655) in paragraph at lines 8576--8579 []\T1/ptm/m/n/10 A data frame in-her-it-ing from class []\T1/pcr/m/n/10 "news_d b"[]\T1/ptm/m/n/10 , with [][][]\T1/pcr/m/n/10 attributes[][][] "package" []\T1 /ptm/m/n/10 (and Overfull \hbox (25.98041pt too wide) in paragraph at lines 8587--8587 []\T1/pcr/m/n/9 db4 <- news(Version == "4.0.0" & grepl("^BUG", Category) & gre pl("PR#", Text),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8595--8595 []\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[] [2063] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8603--8603 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st andardize a bit more[] [2064] Underfull \hbox (badness 1917) in paragraph at lines 8690--8692 []\T1/pcr/m/n/10 "B"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "KiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "MiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "GiB"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "TiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "PiB"[]\T1/ptm/m/ n/10 , [2065] [2066] [2067] [2068] Overfull \hbox (66.78088pt too wide) in paragraph at lines 8964--8964 [] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica tion", "Built"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8965--8965 [] \T1/pcr/m/n/10 tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%D", "%m/ %d/%y"),[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 8966--8966 [] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f ields=date.fields))[] [2069] Underfull \hbox (badness 10000) in paragraph at lines 8994--8996 []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 asDateBuilt()[]\T1/ptm/m/n/10 , a [][][]\ T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string as from Underfull \hbox (badness 10000) in paragraph at lines 9008--9010 []\T1/pcr/m/n/10 packageVersion() []\T1/ptm/m/n/10 is a con-ve-nience short-cut , al-low-ing things like []\T1/pcr/m/n/10 if Underfull \hbox (badness 1259) in paragraph at lines 9016--9021 []\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2070] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9060--9060 [] \T1/pcr/m/n/9 identical(pu, packageDate("stats"))) # as "utils" an d "stats" are[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9061--9061 [] \T1/pcr/m/n/9 # both \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 base R\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and "Built" at same time[] [2071] [2072] Underfull \hbox (badness 10000) in paragraph at lines 9189--9194 []\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 "Status"[]\T1/ptm/m/n/10 , a fac-tor wit h lev-els []\T1/pcr/m/n/10 c("ok", "upgrade", Underfull \hbox (badness 10000) in paragraph at lines 9196--9199 []\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 "Status"[]\T1/ptm/m/n/10 , a fac-tor wit h lev-els []\T1/pcr/m/n/10 c("installed", "not [2073] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9311--9311 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9312--9312 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [2074] [2075] [2076] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9492--9492 [] \T1/pcr/m/n/9 "S original, "),[] [2077] [2078] Underfull \hbox (badness 1789) in paragraph at lines 9662--9664 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [2079] [2080] [2081] [2082] Underfull \hbox (badness 2600) in paragraph at lines 9886--9889 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the name of the help topic; de-faults to [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] Overfull \hbox (30.78088pt too wide) in paragraph at lines 10499--10499 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", " no.loss"),[] [2091] [2092] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10660--10660 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr anspose = TRUE)[] [2093] [2094] [2095] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10841--10841 []\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23 456 98 76 54[] [2096] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10927--10927 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"),[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 10928--10928 [] \T1/pcr/m/n/10 row.names, col.names, as.is = !stringsAsFactors, t ryLogical = TRUE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10930--10930 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 10935--10935 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski pNul = FALSE)[] [2097] Underfull \hbox (badness 2027) in paragraph at lines 11007--11010 []\T1/ptm/m/n/10 Using []\T1/pcr/m/n/10 row.names = NULL []\T1/ptm/m/n/10 force s row num-ber-ing. Miss-ing or []\T1/pcr/m/n/10 NULL [2098] Underfull \hbox (badness 2435) in paragraph at lines 11030--11034 []\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 de-ter-m in-ing if columns con-sist-ing en-tirely of []\T1/pcr/m/n/10 "F"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1824) in paragraph at lines 11030--11034 []\T1/pcr/m/n/10 "FALSE"[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 "TRUE" []\T1/pt m/m/n/10 should be con-verted to [][][]\T1/pcr/m/n/10 logical[][][][]\T1/ptm/m/ n/10 ; passed to [2099] [2100] [2101] Overfull \hbox (12.78088pt too wide) in paragraph at lines 11291--11291 []\T1/pcr/m/n/10 readRegistry(key, hive = c("HLM", "HCR", "HCU", "HU", "HCC", "HPD"), Overfull \hbox (6.78088pt too wide) in paragraph at lines 11292--11292 [] \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64- bit"))[] Underfull \hbox (badness 10000) in paragraph at lines 11299--11304 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are Underfull \hbox (badness 10000) in paragraph at lines 11299--11304 \T1/ptm/m/n/10 for []\T1/pcr/m/n/10 HKEY_LOCAL_MACHINE[]\T1/ptm/m/n/10 , []\T1/ pcr/m/n/10 HKEY_CLASSES_ROOT[]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 11299--11304 []\T1/pcr/m/n/10 HKEY_CURRENT_USER[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 HKEY_USER S[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 HKEY_CURRENT_CONFIG [2102] [2103] [2104] [2105] Overfull \hbox (18.78088pt too wide) in paragraph at lines 11531--11531 [] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c (1, 0))) [2106] [2107] [2108] [2109] Underfull \hbox (badness 10000) in paragraph at lines 11797--11801 \T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral s & oldid = 78252134$[][]\T1/ptm/m/n/10 . Overfull \hbox (20.58041pt too wide) in paragraph at lines 11815--11815 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni ng for "IIIIII"[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11820--11820 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [2110] [2111] Overfull \hbox (18.78088pt too wide) in paragraph at lines 11956--11956 []\T1/pcr/m/n/10 4. | \-base:::tryCatchOne(expr, names, parentenv, handler s[[1L]])[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 11957--11957 []\T1/pcr/m/n/10 5. | \-base:::doTryCatch(return(expr), name, parentenv, handler)[] [2112] [2113] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12092--12092 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [2114] [2115] Underfull \hbox (badness 1917) in paragraph at lines 12224--12227 []\T1/ptm/m/n/10 If `[]\T1/pcr/m/n/10 --default-packages[]\T1/ptm/m/n/10 ' is n ot used, then []\T1/pcr/m/n/10 Rscript []\T1/ptm/m/n/10 checks the en-vi-ron-me nt vari- Underfull \hbox (badness 4328) in paragraph at lines 12224--12227 \T1/ptm/m/n/10 able []\T1/pcr/m/n/10 R_SCRIPT_DEFAULT_PACKAGES[]\T1/ptm/m/n/10 . If this is set, then it takes prece-dence over Overfull \hbox (106.98032pt too wide) in paragraph at lines 12247--12247 []\T1/pcr/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 sessionInfo()\TS1/pcr/m/n/9 '[] [2116] [2117] Overfull \hbox (54.78088pt too wide) in paragraph at lines 12339--12339 [] \T1/pcr/m/n/10 restrict = c("functions", "descriptions", "news", "Rfunctions",[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 12340--12340 [] \T1/pcr/m/n/10 "Rmanuals", "READMEs", "views", "vig nettes"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 12342--12342 [] \T1/pcr/m/n/10 sortby = c("score", "date:late", "date:early", "s ubject",[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 12343--12343 [] \T1/pcr/m/n/10 "subject:descending", "size", "size:de scending"),[] Underfull \hbox (badness 6725) in paragraph at lines 12366--12374 \T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 score[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 date: late []\T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first, Underfull \hbox (badness 2662) in paragraph at lines 12366--12374 \T1/ptm/m/n/10 der, []\T1/pcr/m/n/10 subject:descending []\T1/ptm/m/n/10 for re -verse al-pha-bet-i-cal or-der, []\T1/pcr/m/n/10 size []\T1/ptm/m/n/10 or [2118] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12411--12411 []\T1/pcr/m/n/9 fullquery <- RSiteSearch("lattice", restrict = c("vignettes"," Rfunctions"))[] [2119] Underfull \hbox (badness 1377) in paragraph at lines 12467--12470 []\T1/ptm/m/n/10 Character string spec-i-fy-ing whether emacs style ([]\T1/pcr/ m/n/10 "etags"[]\T1/ptm/m/n/10 ) or vi style Underfull \hbox (badness 3646) in paragraph at lines 12502--12504 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software / [2120] Overfull \hbox (30.78088pt too wide) in paragraph at lines 12540--12540 [] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F ALSE, ...)[] [2121] [2122] Underfull \hbox (badness 10000) in paragraph at lines 12722--12726 []\T1/ptm/m/n/10 The de-fault for []\T1/pcr/m/n/10 stylepath []\T1/ptm/m/n/10 i s now taken from the en-vi-ron-ment vari-able [2123] Underfull \hbox (badness 10000) in paragraph at lines 12755--12761 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a Underfull \hbox (badness 2027) in paragraph at lines 12770--12776 []\T1/ptm/m/n/10 The use of fancy quotes (see [][][]\T1/pcr/m/n/10 sQuote[][][] []\T1/ptm/m/n/10 ) can cause prob-lems when set-ting \T1/phv/m/n/10 R \T1/ptm/m /n/10 out-put in [2124] [2125] Overfull \hbox (6.78088pt too wide) in paragraph at lines 12927--12927 [] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa rent")[] Underfull \hbox (badness 1009) in paragraph at lines 12945--12957 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If [2126] Underfull \hbox (badness 2600) in paragraph at lines 12985--12987 []\T1/ptm/m/n/10 The file `\T1/pcr/m/n/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ures the R GUI ([]\T1/pcr/m/n/10 Rgui[]\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows and Underfull \hbox (badness 1043) in paragraph at lines 13028--13033 []\T1/ptm/m/n/10 At the time of writ-ing `\T1/pcr/m/n/10 Rdevga\T1/ptm/m/n/10 ' con-fig-ured the map-ping of font num-bers to fonts, and [2127] [2128] [2129] [2130] [2131] Underfull \hbox (badness 1888) in paragraph at lines 13330--13333 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form \T1/phv/m/n/10 R \T1/ptm/m/n/10 was built un-der. Where Underfull \hbox (badness 10000) in paragraph at lines 13347--13350 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g Underfull \hbox (badness 10000) in paragraph at lines 13350--13353 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g [2132] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13396--13396 []\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at end of report[] [2133] Underfull \hbox (badness 2158) in paragraph at lines 13455--13458 []\T1/ptm/m/n/10 Repository `[]\T1/pcr/m/n/10 CRAN[]\T1/ptm/m/n/10 ' is treated spe-cially: the value is taken from the cur-rent set-ting of Overfull \hbox (0.78088pt too wide) in paragraph at lines 13503--13503 []\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf fix)) [2134] [2135] [2136] Underfull \hbox (badness 2302) in paragraph at lines 13660--13662 []\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t o the Win-dows API call [2137] Underfull \hbox (badness 3333) in paragraph at lines 13768--13770 []\T1/pcr/m/n/10 getSrcFilename []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 getSrcDir ectory []\T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file- [2138] [2139] [2140] Overfull \hbox (42.78088pt too wide) in paragraph at lines 13935--13935 [] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing = TRUE, ...))[] Underfull \hbox (badness 2012) in paragraph at lines 13959--13964 []\T1/ptm/m/n/10 logical; if []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 (de-fault), [][][]\T1/pcr/m/n/10 deparse[][][](control = ) []\T1/ptm/m/n/10 will not ha ve Underfull \hbox (badness 5970) in paragraph at lines 13968--13971 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive Underfull \hbox (badness 2600) in paragraph at lines 13968--13971 [][][]\T1/pcr/m/n/10 options[][][]("width")[]\T1/ptm/m/n/10 ; note that this ha s only a weak ef-fect, un-less Underfull \hbox (badness 1052) in paragraph at lines 13979--13988 []\T1/ptm/m/n/10 (see [][][]\T1/pcr/m/n/10 options[][][][]\T1/ptm/m/n/10 ) whic h de-faults to []\T1/pcr/m/n/10 "no" []\T1/ptm/m/n/10 for back com-pat-i-bil-it y rea-sons; [2141] Underfull \hbox (badness 1442) in paragraph at lines 13995--13999 []\T1/ptm/m/n/10 numeric or []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 as by de-fau lt, de-ter-min-ing the []\T1/pcr/m/n/10 nlines []\T1/ptm/m/n/10 ar-gu-ment to Overfull \hbox (36.7804pt too wide) in paragraph at lines 14041--14041 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification of binary numbers[] [2142] Overfull \hbox (15.18042pt too wide) in paragraph at lines 14068--14068 []\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo ng" non-ASCII:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 14075--14075 []\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of 2 in order to se e 1 (in UTF-8!):[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 14077--14077 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) # "1 is 1" here[] [2143] [2144] [2145] Underfull \hbox (badness 10000) in paragraph at lines 14243--14245 []\T1/ptm/m/n/10 Options other than []\T1/pcr/m/n/10 memory = "none" []\T1/ptm/ m/n/10 ap-ply only to files pro-duced by [2146] Underfull \hbox (badness 10000) in paragraph at lines 14353--14356 []\T1/ptm/m/n/10 further ar-gu-ments passed to the driver's setup func-tion. Se e Underfull \hbox (badness 1389) in paragraph at lines 14353--14356 [][][]\T1/pcr/m/n/10 RweaveLatexSetup[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/ m/n/10 RtangleSetup[][][][]\T1/ptm/m/n/10 , re-spec-tively, for the ar-gu- [2147] Underfull \hbox (badness 6300) in paragraph at lines 14401--14408 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 syntax = NULL []\T1/ptm/m/n/10 (the de-fau lt) then the avail-able syn-tax ob-jects are con-sulted in Underfull \hbox (badness 6252) in paragraph at lines 14401--14408 \T1/ptm/m/n/10 turn, and se-lected if their []\T1/pcr/m/n/10 extension []\T1/pt m/m/n/10 com-po-nent matches (as a reg-exp) the file Underfull \hbox (badness 4556) in paragraph at lines 14401--14408 \T1/ptm/m/n/10 name. Ob-jects []\T1/pcr/m/n/10 SweaveSyntaxNoweb []\T1/ptm/m/n/ 10 (with []\T1/pcr/m/n/10 extension = "[.][rsRS]nw$"[]\T1/ptm/m/n/10 ) and [2148] [2149] Underfull \hbox (badness 2020) in paragraph at lines 14565--14573 \T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `[]\T1/pcr/m/n/10 -h[]\T1/ptm/m/ n/10 ' (fol-low sym-bolic links, also `[]\T1/pcr/m/n/10 -L[]\T1/ptm/m/n/10 ' on some plat-forms), Underfull \hbox (badness 1194) in paragraph at lines 14565--14573 \T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 --acls[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 -- exclude-backups[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 --exclude-vcs[]\T1/ptm/m/n /10 ' (and sim-i-lar) and on Win-dows [2150] Underfull \hbox (badness 1622) in paragraph at lines 14574--14581 []\T1/ptm/m/n/10 A con-ve-nient and ro-bust way to set op-tions for GNU []\T1/p cr/m/n/10 tar []\T1/ptm/m/n/10 is via en-vi-ron-ment vari-able [2151] Underfull \hbox (badness 5022) in paragraph at lines 14714--14718 []\T1/ptm/m/n/10 When ar-gu-ment []\T1/pcr/m/n/10 tar []\T1/ptm/m/n/10 is set t o the com-mand []\T1/pcr/m/n/10 tar []\T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 14721--14724 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / pubs . Underfull \hbox (badness 10000) in paragraph at lines 14721--14724 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht ml # tag _ 20 _ 92 _ [2152] [2153] [2154] [2155] [2156] [2157] [2158] [2159] [2160] Overfull \hbox (6.78088pt too wide) in paragraph at lines 15339--15339 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 15345--15345 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] [2161] Underfull \hbox (badness 4467) in paragraph at lines 15366--15368 []\T1/ptm/m/n/10 Download method, see [][][]\T1/pcr/m/n/10 download.file[][][][ ]\T1/ptm/m/n/10 . Un-used if a non-[]\T1/pcr/m/n/10 NULL Underfull \hbox (badness 4660) in paragraph at lines 15381--15385 \T1/ptm/m/n/10 able at the repos-i-to-ries, or []\T1/pcr/m/n/10 NULL []\T1/ptm/ m/n/10 which makes an in-ter-nal call to Underfull \hbox (badness 1694) in paragraph at lines 15395--15399 []\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][][]\T1/pcr/m/n/10 ins talled.packages[][][](lib.loc = Underfull \hbox (badness 10000) in paragraph at lines 15401--15406 []\T1/ptm/m/n/10 Arguments such as []\T1/pcr/m/n/10 destdir []\T1/ptm/m/n/10 an d []\T1/pcr/m/n/10 dependencies []\T1/ptm/m/n/10 to be Underfull \hbox (badness 10000) in paragraph at lines 15401--15406 \T1/ptm/m/n/10 passed to [][][]\T1/pcr/m/n/10 install.packages[][][] []\T1/ptm/ m/n/10 and []\T1/pcr/m/n/10 ignore_repo_cache[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 15401--15406 []\T1/pcr/m/n/10 max_repo_cache_age []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 noCac he []\T1/ptm/m/n/10 to [][][]\T1/pcr/m/n/10 available.packages[][][] Underfull \hbox (badness 1052) in paragraph at lines 15407--15409 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See [2162] Underfull \hbox (badness 10000) in paragraph at lines 15437--15442 []\T1/pcr/m/n/10 available = NULL []\T1/ptm/m/n/10 make a call to []\T1/pcr/m/n /10 available.packages(contriburl = Underfull \hbox (badness 1226) in paragraph at lines 15437--15442 \T1/pcr/m/n/10 contriburl, method = method) []\T1/ptm/m/n/10 and hence by de-fa ult fil-ters on \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion, OS type Underfull \hbox (badness 10000) in paragraph at lines 15458--15463 []\T1/ptm/m/n/10 Take care when us-ing []\T1/pcr/m/n/10 dependencies []\T1/ptm/ m/n/10 (passed to [][][]\T1/pcr/m/n/10 install.packages[][][][]\T1/ptm/m/n/10 ) with Underfull \hbox (badness 10000) in paragraph at lines 15466--15469 [][][]\T1/pcr/m/n/10 install.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n /10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 download.pa ckages[][][][]\T1/ptm/m/n/10 , [2163] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15543--15543 []\T1/pcr/m/n/9 ## Not run: url.show("https://www.stats.ox.ac.uk/pub/datasets/ csb/ch3a.txt") [2164] [2165] [2166] Underfull \hbox (badness 2293) in paragraph at lines 15750--15753 [][][]\T1/pcr/m/n/10 browseVignettes[][][] []\T1/ptm/m/n/10 for an HTML-based v i-gnette browser; [][][]\T1/pcr/m/n/10 RShowDoc[][][](, [2167] Overfull \hbox (42.18039pt too wide) in paragraph at lines 15766--15766 []\T1/pcr/m/n/9 ## Note that \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 package = *\TS1/pcr /m/n/9 ' \T1/pcr/m/n/9 is much faster in the case of many installed packages:[] [2168] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15833--15833 [] \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d ata = DAT)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 15855--15855 [] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal), data = DD)))[] [2169] [2170] Underfull \hbox (badness 1297) in paragraph at lines 15987--15989 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i s se-lected, or [2171] Underfull \hbox (badness 4036) in paragraph at lines 16034--16036 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 winMenuDel []\T1/ptm/m/n/10 func-tion wil l delete a menu and all of its items and sub-menus. [2172] [2173] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16154--16154 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", [2174] Underfull \hbox (badness 1715) in paragraph at lines 16206--16209 []\T1/ptm/m/n/10 arguments to []\T1/pcr/m/n/10 write.table[]\T1/ptm/m/n/10 : [] \T1/pcr/m/n/10 append[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 col.names[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 sep[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 dec []\T1/ptm/m/n /10 and Underfull \hbox (badness 10000) in paragraph at lines 16251--16253 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion e.g. []\T1/pcr/m/n/10 file = [2175] [2176] [2177]) [2178] [2179] [2180] (./KernSmooth-pkg.tex Chapter 15. [2181] Overfull \hbox (24.78088pt too wide) in paragraph at lines 123--123 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat e = TRUE) [2182] [2183] [2184] [2185] [2186] Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun = 0.05, [2187] [2188] [2189] [2190]) (./MASS-pkg.tex Chapter 16. [2191] [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] [2200] [2201] Overfull \hbox (20.58041pt too wide) in paragraph at lines 776--776 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b eav2$hours/24))[] [2202] [2203] [2204] [2205] [2206] [2207] [2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218] [2219] [2220] [2221] [2222] [2223] [2224] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2422--2422 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2426--2426 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] [2225] [2226] [2227] [2228] Underfull \hbox (badness 6559) in paragraph at lines 2707--2710 []\T1/ptm/m/n/10 further ar-gu-ments for []\T1/pcr/m/n/10 plot []\T1/ptm/m/n/10 and graph-i-cal pa-ram-e-ters. Note that [2229] [2230] [2231] Underfull \hbox (badness 10000) in paragraph at lines 2877--2882 []\T1/pcr/m/n/10 "gamma"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "geometric"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "log-normal"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lo gnormal"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2877--2882 []\T1/pcr/m/n/10 "logistic"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "negative binomi al"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "normal"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n /10 "Poisson"[]\T1/ptm/m/n/10 , [2232] [2233] Underfull \hbox (badness 4686) in paragraph at lines 3049--3051 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [2234] [2235] [2236] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3249--3249 [] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL SE, ...)[] [2237] [2238] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3381--3381 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist = "exponential")[] [2239] [2240] [2241] [2242] [2243] [2244] [2245] [2246] [2247] [2248] [2249] Underfull \hbox (badness 1845) in paragraph at lines 4183--4185 []\T1/ptm/m/n/10 The va-ri-ety of bar-ley ([]\T1/pcr/m/n/10 "manchuria"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "svansota"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "velv et"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "trebi" []\T1/ptm/m/n/10 and [2250] [2251] [2252] [2253] [2254] [2255] [2256] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4677--4677 [] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n", ...)[] [2257] [2258] [2259] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4899--4899 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model = FALSE, [2260] [2261] [2262] [2263] [2264] [2265] [2266] [2267] [2268] [2269] [2270] [2271] [2272] [2273] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5954--5954 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP ACK = FALSE) [2274] Overfull \hbox (48.78088pt too wide) in paragraph at lines 6015--6015 []\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/ 10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log") [2275] [2276] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.npk}) has been already used, duplicate ignored \relax l.6175 ...sical N, P, K Factorial Experiment}{npk} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.npk.1}) h as been already used, duplicate ignored \relax l.6175 ...sical N, P, K Factorial Experiment}{npk} [2277] [2278] [2279] [2280] [2281] [2282] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6595--6595 [] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb ose = TRUE)))[] [2283] Overfull \hbox (18.78088pt too wide) in paragraph at lines 6683--6683 [] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr ellis"))[] [2284] [2285] [2286] [2287] [2288] [2289] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7122--7122 []\T1/pcr/m/n/9 nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100 , A=10, B=1))[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7139--7139 [] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c auchit"))[] [2290] Underfull \hbox (badness 3138) in paragraph at lines 7217--7223 []\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c mr/m/n/10 ) = [2291] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7287--7287 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da ta = housing)[] [2292] [2293] Underfull \hbox (badness 1389) in paragraph at lines 7396--7399 []\T1/ptm/m/n/10 the di-men-sion of the space to be used. If this is less than []\T1/pcr/m/n/10 min(p, [2294] [2295] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7526--7526 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam p = "exact")[] [2296] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7591--7591 [] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC V"), ...)[] [2297] [2298] [2299] [2300] [2301] [2302] Underfull \hbox (badness 4686) in paragraph at lines 8029--8031 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [2303] [2304] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8148--8148 [] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control = NULL)[] Underfull \hbox (badness 1590) in paragraph at lines 8172--8176 []\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if []\T1/pcr/m /n/10 NA[]\T1/ptm/m/n/10 s are found. The [2305] [2306] [2307] [2308] [2309] [2310] [2311] [2312] [2313] [2314] [2315] [2316] [2317] [2318] [2319] [2320] [2321] [2322] [2323] [2324] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9554--9554 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS E, ...)[] [2325] Underfull \hbox (badness 2035) in paragraph at lines 9666--9668 []\T1/ptm/m/n/10 ``Fold your arms! Which is on top'' (Fac-tor, with lev-els []\ T1/pcr/m/n/10 "R on L"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "L on R"[]\T1/ptm/m/n /10 , Underfull \hbox (badness 1158) in paragraph at lines 9681--9684 []\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els []\T1/pcr/m/n/ 10 "Heavy"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Regul" []\T1/ptm/m/n/10 (reg-u-l arly), [2326] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9763--9763 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub le.eps^0.25) Overfull \hbox (30.78088pt too wide) in paragraph at lines 9765--9765 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double .eps^0.25,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9768--9768 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub le.eps^0.25)[] [2327] [2328] [2329] [2330] [2331] [2332] [2333] [2334] [2335] [2336] [2337] [2338] [2339]) (./Matrix-pkg.tex [2340] Chapter 17. Underfull \hbox (badness 10000) in paragraph at lines 35--38 []\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec t to change, and if you Underfull \hbox (badness 10000) in paragraph at lines 35--38 \T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack- age main-tain-ers [2341] Underfull \hbox (badness 1769) in paragraph at lines 89--92 []\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o wn code. Please con-tact us [2342] Underfull \hbox (badness 2229) in paragraph at lines 154--157 []\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm /m/n/10 ob-jects; here, when the first is Underfull \hbox (badness 1147) in paragraph at lines 154--157 \T1/ptm/m/n/10 an []\T1/pcr/m/n/10 "[][]abIndex[][][]" []\T1/ptm/m/n/10 vec-tor , these ar-gu-ments will be con-cate-nated to a new pdfTeX warning (ext4): destination with the same identifier (name{Rfn.all.equal }) has been already used, duplicate ignored \relax l.184 ...{all.equal}{all.equal-methods}{all.equal} Underfull \hbox (badness 10000) in paragraph at lines 211--214 []\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing Underfull \hbox (badness 10000) in paragraph at lines 217--219 []\T1/ptm/m/n/10 There are more meth-ods, no-tably also for []\T1/pcr/m/n/10 "[ ][]sparseVector[][][]"[]\T1/ptm/m/n/10 's, see [2343] Underfull \hbox (badness 3098) in paragraph at lines 266--268 []\T1/ptm/m/n/10 optional ar-gu-ments passed to the de-fault method for generic func-tion [2344] [2345] [2346] Overfull \hbox (15.18042pt too wide) in paragraph at lines 500--500 [] \T1/pcr/m/n/9 band(sm5, -1, 1)# "dsyMatrix": symmetric band preserves sym metry property[] [2347] Underfull \hbox (badness 5119) in paragraph at lines 543--547 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class Underfull \hbox (badness 1668) in paragraph at lines 547--552 [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/ m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse Overfull \hbox (4.38043pt too wide) in paragraph at lines 578--578 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 580--580 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] [2348] Overfull \hbox (36.7804pt too wide) in paragraph at lines 589--589 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20, 1), rpois(20, 3))[ c(1:3, 2:3, 3:2)],[] [2349] Overfull \hbox (52.98038pt too wide) in paragraph at lines 705--705 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd iag() -- for the case of *many* (k x k) matrices:[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 706--706 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(, , ....., ) where each mat_j is a k x k \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 matrix\TS1/pcr/m/n/9 '[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 707--707 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @return a sparse (N*k x N*k) matrix of class \code{"\linkS4class{dgCMatrix}"}.[] [2350] Overfull \hbox (31.3804pt too wide) in paragraph at lines 720--720 [] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \ T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri x indexing), but elegant?[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 721--721 [] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len( N), each=k)]),[] [2351] Overfull \hbox (9.78043pt too wide) in paragraph at lines 888--888 []\T1/pcr/m/n/9 L. <- L; L.[1:2,1] <- TRUE; L.@x[1:2] <- FALSE; L. # has "zero s" to drop0()[] [2352] Underfull \hbox (badness 1635) in paragraph at lines 970--975 []\T1/pcr/m/n/10 new("pBunchKaufman", ...)[]\T1/ptm/m/n/10 , but they are more typ-i-cally ob-tained as the value of Underfull \hbox (badness 10000) in paragraph at lines 980--983 []\T1/pcr/m/n/10 signature(from = "BunchKaufman", to = "dtrMatrix")[]\T1/ptm/m/ n/10 : re-turns a Underfull \hbox (badness 10000) in paragraph at lines 983--986 []\T1/pcr/m/n/10 signature(from = "pBunchKaufman", to = "dtpMatrix")[]\T1/ptm/m /n/10 : re-turns a Underfull \hbox (badness 10000) in paragraph at lines 986--989 []\T1/pcr/m/n/10 signature(from = "p?BunchKaufman", logarithm = [2353] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1059--1059 []\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m atrix"), ...)[] [2354] Underfull \hbox (badness 10000) in paragraph at lines 1132--1137 []\T1/ptm/m/n/10 An ob-ject rep-re-sent-ing the fac-tor-iza-tion, in-her-it-ing from vir-tual class [2355] Overfull \hbox (3.02814pt too wide) in paragraph at lines 1188--1188 []\T1/pcr/m/n/9 stopifnot(all.equal(as(A, "matrix"), as(Reduce(\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 %*%\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 , e.bk.A), "matrix")))[] [2356] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cbind2.Rd ash.methods}) has been already used, duplicate ignored \relax l.1236 ... on cbind2/rbind2}{cbind2.Rdash.methods} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cbind2}) has been already used, duplicate ignored \relax l.1237 \aliasA{cbind2}{cbind2-methods}{cbind2} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rbind2}) has been already used, duplicate ignored \relax l.1246 \aliasA{rbind2}{cbind2-methods}{rbind2} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rbind2.Rd ash.methods}) has been already used, duplicate ignored \relax l.1255 ...s}{cbind2-methods}{rbind2.Rdash.methods} [2357] Underfull \hbox (badness 10000) in paragraph at lines 1318--1323 []\T1/ptm/m/n/10 Our class def-i-ni-tion help pages men-tion-ing []\T1/pcr/m/n/ 10 cbind2() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 rbind2() []\T1/ptm/m/n/10 met h-ods: Underfull \hbox (badness 10000) in paragraph at lines 1373--1380 []\T1/ptm/m/n/10 The im-ple-men-ta-tion of class []\T1/pcr/m/n/10 CHMfactor []\ T1/ptm/m/n/10 is based on CHOLMOD's C-level [2358] [2359] Underfull \hbox (badness 5008) in paragraph at lines 1535--1550 []\T1/pcr/m/n/10 signature(from = "CHMfactor", logarithm = "logical")[]\T1/ptm/ m/n/10 : be- Underfull \hbox (badness 10000) in paragraph at lines 1585--1587 []\T1/pcr/m/n/10 signature(update = ., C = ., object = "CHMfactor")[]\T1/ptm/m/ n/10 : see [2360] Underfull \hbox (badness 1917) in paragraph at lines 1593--1597 []\T1/ptm/m/n/10 The CHOLMOD source code; see [][]$\T1/pcr/m/n/10 https : / / g ithub . com / DrTimothyAldenDavis / Underfull \hbox (badness 8132) in paragraph at lines 1593--1597 \T1/pcr/m/n/10 SuiteSparse$[][]\T1/ptm/m/n/10 , no-tably the header file `\T1/p cr/m/n/10 CHOLMOD/Include/cholmod.h\T1/ptm/m/n/10 ' defin-ing Overfull \hbox (9.78043pt too wide) in paragraph at lines 1643--1643 []\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m atrix"), ...)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1651--1651 [] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(list( NULL), dn[2L]),[] [2361] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1660--1660 [] \T1/pcr/m/n/9 ae2(A[ch.A@perm + 1L, ch.A@perm + 1L], with(e.ch.A, L1 %*% D %*% L1.))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1661--1661 [] \T1/pcr/m/n/9 ae2(A[ch.A@perm + 1L, ch.A@perm + 1L], with(E.ch.A, L %*% L. ))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1671--1671 []\T1/pcr/m/n/9 u2 <- update(ch.A, t(M), mult = sqrt(2)) # updating with cross prod(M), not M[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol}) ha s been already used, duplicate ignored \relax l.1676 \aliasA{chol}{chol-methods}{chol} [2362] Underfull \hbox (badness 10000) in paragraph at lines 1781--1785 \T1/pcr/m/n/10 double / dpstrf . f$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 htt ps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and Underfull \hbox (badness 1917) in paragraph at lines 1786--1790 []\T1/ptm/m/n/10 The CHOLMOD source code; see [][]$\T1/pcr/m/n/10 https : / / g ithub . com / DrTimothyAldenDavis / Underfull \hbox (badness 8132) in paragraph at lines 1786--1790 \T1/pcr/m/n/10 SuiteSparse$[][]\T1/ptm/m/n/10 , no-tably the header file `\T1/p cr/m/n/10 CHOLMOD/Include/cholmod.h\T1/ptm/m/n/10 ' defin-ing [2363] [2364] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol2inv} ) has been already used, duplicate ignored \relax l.1905 ...sA{chol2inv}{chol2inv-methods}{chol2inv} [2365] [2366] Underfull \hbox (badness 1931) in paragraph at lines 2041--2046 []\T1/ptm/m/n/10 a nu-meric vec-tor of length []\T1/pcr/m/n/10 n*n []\T1/ptm/m/ n/10 ([]\T1/pcr/m/n/10 Cholesky[]\T1/ptm/m/n/10 ) or []\T1/pcr/m/n/10 n*(n+1)/2 []\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 pCholesky[]\T1/ptm/m/n/10 ), where Underfull \hbox (badness 1226) in paragraph at lines 2056--2059 []\T1/ptm/m/n/10 Class [][][]\T1/pcr/m/n/10 CholeskyFactorization[][][][]\T1/pt m/m/n/10 , di-rectly. Class [][][]\T1/pcr/m/n/10 MatrixFactorization[][][][]\T1 /ptm/m/n/10 , by class Underfull \hbox (badness 3000) in paragraph at lines 2062--2070 []\T1/ptm/m/n/10 Objects can be gen-er-ated di-rectly by calls of the form []\T 1/pcr/m/n/10 new("Cholesky", ...) []\T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 2079--2083 []\T1/pcr/m/n/10 signature(from = "pCholesky", to = "dtpMatrix")[]\T1/ptm/m/n/1 0 : re-turns a Underfull \hbox (badness 10000) in paragraph at lines 2083--2086 []\T1/pcr/m/n/10 signature(from = "p?Cholesky", logarithm = "logical")[]\T1/ptm /m/n/10 : Underfull \hbox (badness 10000) in paragraph at lines 2117--2121 \T1/pcr/m/n/10 double / dpstrf . f$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 htt ps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and [2367] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2164--2164 []\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m atrix"), ...)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2172--2172 [] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(list( NULL), dn[2L]),[] [2368] [2369] Underfull \hbox (badness 10000) in paragraph at lines 2303--2310 []\T1/ptm/m/n/10 a [][]fi-nite[][][] num-ber. The ma-trix that is fac-tor-ized is []\T1/pcr/m/n/10 A + Imult * Underfull \hbox (badness 1946) in paragraph at lines 2303--2310 \T1/pcr/m/n/10 - diag(abs(A))) []\T1/ptm/m/n/10 en-sures that []\T1/pcr/m/n/10 A + Imult * diag(nrow(A)) []\T1/ptm/m/n/10 is di- [2370] Underfull \hbox (badness 10000) in paragraph at lines 2350--2363 []\T1/ptm/m/n/10 An ob-ject rep-re-sent-ing the fac-tor-iza-tion, in-her-it-ing from vir-tual class Underfull \hbox (badness 10000) in paragraph at lines 2366--2370 \T1/pcr/m/n/10 double / dpstrf . f$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 htt ps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and Underfull \hbox (badness 1917) in paragraph at lines 2371--2375 []\T1/ptm/m/n/10 The CHOLMOD source code; see [][]$\T1/pcr/m/n/10 https : / / g ithub . com / DrTimothyAldenDavis / Underfull \hbox (badness 8132) in paragraph at lines 2371--2375 \T1/pcr/m/n/10 SuiteSparse$[][]\T1/ptm/m/n/10 , no-tably the header file `\T1/p cr/m/n/10 CHOLMOD/Include/cholmod.h\T1/ptm/m/n/10 ' defin-ing [2371] Underfull \vbox (badness 10000) has occurred while \output is active [2372] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2488--2488 [] \T1/pcr/m/n/9 list(simpl1 = Cholesky(A4, perm = TRUE, super = FALSE, L DL = TRUE),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2489--2489 [] \T1/pcr/m/n/9 simpl0 = Cholesky(A4, perm = TRUE, super = FALSE, L DL = FALSE),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2490--2490 [] \T1/pcr/m/n/9 super0 = Cholesky(A4, perm = TRUE, super = TRUE )),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2492--2492 [] \T1/pcr/m/n/9 list(simpl1 = Cholesky(A4, perm = FALSE, super = FALSE, L DL = TRUE),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2493--2493 [] \T1/pcr/m/n/9 simpl0 = Cholesky(A4, perm = FALSE, super = FALSE, L DL = FALSE),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2494--2494 [] \T1/pcr/m/n/9 super0 = Cholesky(A4, perm = FALSE, super = TRUE )))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2498--2498 []\T1/pcr/m/n/9 rapply2 <- function(object, f, ...) rapply(object, f, , , how = "list", ...)[] Underfull \vbox (badness 10000) has occurred while \output is active [2373] Overfull \hbox (42.18039pt too wide) in paragraph at lines 2565--2565 [] \T1/pcr/m/n/9 x = c(1, 6, 38, 10, 60, 103, -4, 6, -32, -247, -2, - 16, -128, -2, -67))[] [2374] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2661--2661 [] \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4), j=c(2:4,1), x = 2, dimnames=dns))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2665--2665 [] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE, dimnames=dns))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2672--2672 [] \T1/pcr/m/n/9 a. <- sparseMatrix(i=4:1, j=1:4, dimnames=list(n4, n4), repr ="T") # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[] [2375] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colMeans} ) has been already used, duplicate ignored \relax l.2747 ...asA{colMeans}{colSums-methods}{colMeans} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colSums}) has been already used, duplicate ignored \relax l.2755 \aliasA{colSums}{colSums-methods}{colSums} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowMeans} ) has been already used, duplicate ignored \relax l.2762 ...asA{rowMeans}{colSums-methods}{rowMeans} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowSums}) has been already used, duplicate ignored \relax l.2770 \aliasA{rowSums}{colSums-methods}{rowSums} [2376] Underfull \hbox (badness 2922) in paragraph at lines 2822--2826 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i n-her-it-ing from Underfull \hbox (badness 1728) in paragraph at lines 2822--2826 \T1/ptm/m/n/10 class [][][]\T1/pcr/m/n/10 sparseVector[][][][]\T1/ptm/m/n/10 . Only ap-pli-ca-ble when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 is in-her-it-ing fr om a Underfull \hbox (badness 1237) in paragraph at lines 2833--2836 [][][]\T1/pcr/m/n/10 dimnames[][][](x) []\T1/ptm/m/n/10 are only kept (as [][][ ]\T1/pcr/m/n/10 names[][][](v)[]\T1/ptm/m/n/10 ) when the re-sult-ing []\T1/pcr /m/n/10 v []\T1/ptm/m/n/10 is [][][]\T1/pcr/m/n/10 numeric[][][][]\T1/ptm/m/n/1 0 , since [2377] [2378] Underfull \hbox (badness 3547) in paragraph at lines 2994--2997 []\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when [2379] [2380] [2381] [2382] [2383] Underfull \hbox (badness 10000) in paragraph at lines 3402--3405 []\T1/pcr/m/n/10 signature(from = "denseLU", logarithm = "logical")[]\T1/ptm/m/ n/10 : com- [2384] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3457--3457 []\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m atrix"), ...)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 3464--3464 [] \T1/pcr/m/n/9 new( "pMatrix", Dim = c(n, n), Dimnames = c(dn[ 1L], list(NULL)),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3467--3467 [] \T1/pcr/m/n/9 new("dtrMatrix", Dim = c(n, n), Dimnames = list( NULL, NULL),[] [2385] Overfull \hbox (31.3804pt too wide) in paragraph at lines 3470--3470 [] \T1/pcr/m/n/9 new("dtrMatrix", Dim = c(n, n), Dimnames = c(lis t(NULL), dn[2L]),[] [2386] Underfull \hbox (badness 7379) in paragraph at lines 3598--3600 []\T1/pcr/m/n/10 signature(x = "dgCMatrix")[]\T1/ptm/m/n/10 : com-putes the LU de-com-po-si-tion of a square [2387] [2388] [2389] Underfull \hbox (badness 4846) in paragraph at lines 3819--3823 []\T1/ptm/m/n/10 Note that both []\T1/pcr/m/n/10 new(.) []\T1/ptm/m/n/10 and [] [][]\T1/pcr/m/n/10 spMatrix[][][] []\T1/ptm/m/n/10 con-struc-tors for []\T1/pcr /m/n/10 "dgTMatrix" []\T1/ptm/m/n/10 (and other Underfull \hbox (badness 2717) in paragraph at lines 3824--3828 []\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can be stored in more than one pos-si-ble [2390] Underfull \hbox (badness 5231) in paragraph at lines 3869--3874 []\T1/ptm/m/n/10 Construct a for-mally di-ag-o-nal [][][]\T1/pcr/m/n/10 Matrix[ ][][][]\T1/ptm/m/n/10 , i.e., an ob-ject in-her-it-ing from vir-tual class Overfull \hbox (84.78088pt too wide) in paragraph at lines 3880--3880 []\T1/pcr/m/n/10 .sparseDiagonal(n, x = NULL, uplo = "U", shape = "t", unitri = TRUE, kind, cols)[] [2391] Underfull \hbox (badness 10000) in paragraph at lines 3936--3939 []\T1/pcr/m/n/10 .trDiagonal() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 .symDiagon al() []\T1/ptm/m/n/10 are sim-ple wrap-pers, for Underfull \hbox (badness 6792) in paragraph at lines 3936--3939 []\T1/pcr/m/n/10 .sparseDiagonal(shape = "t") []\T1/ptm/m/n/10 and []\T1/pcr/m/ n/10 .sparseDiagonal(shape = "s")[]\T1/ptm/m/n/10 , re-spec- [2392] Underfull \hbox (badness 3646) in paragraph at lines 4013--4016 []\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 dimnames[][][][]\T1/ptm/m/n/10 , a [] [][]\T1/pcr/m/n/10 list[][][][]\T1/ptm/m/n/10 , see the [][][]\T1/pcr/m/n/10 Ma trix[][][] []\T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally Underfull \hbox (badness 6542) in paragraph at lines 4048--4052 []\T1/pcr/m/n/10 signature(x = "diagonalMatrix")[]\T1/ptm/m/n/10 : all these gr oup meth-ods re-turn a Underfull \hbox (badness 4518) in paragraph at lines 4057--4063 []\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")[]\T1/ptm/m/n/10 : the re-sult is from class [2393] Underfull \hbox (badness 10000) in paragraph at lines 4064--4068 []\T1/pcr/m/n/10 (object = "diagonalMatrix")[]\T1/ptm/m/n/10 : Re-turns an ob-j ect of S3 class Underfull \hbox (badness 2318) in paragraph at lines 4074--4078 [][][]\T1/pcr/m/n/10 Diagonal[][][]() []\T1/ptm/m/n/10 as con-struc-tor of thes e ma-tri-ces, and [][][]\T1/pcr/m/n/10 isDiagonal[][][][]\T1/ptm/m/n/10 . [][][ ]\T1/pcr/m/n/10 ddiMatrix[][][] []\T1/ptm/m/n/10 and [2394] [2395] [2396] Underfull \hbox (badness 10000) in paragraph at lines 4331--4333 []\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")[]\T1/ptm/m/n/10 : this group con-tains [2397] [2398] Overfull \hbox (69.18036pt too wide) in paragraph at lines 4475--4475 []\T1/pcr/m/n/9 stopifnot(all.equal(S9p0, S9p))# same as as default, but diffe rent from the random one[] [2399] Underfull \hbox (badness 2469) in paragraph at lines 4590--4593 []\T1/pcr/m/n/10 signature(x = "dpoMatrix")[]\T1/ptm/m/n/10 : Re-turns the [][] []\T1/pcr/m/n/10 determinant[][][] []\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 x[]\T1/ ptm/m/n/10 , via [2400] Underfull \hbox (badness 10000) in paragraph at lines 4613--4618 []\T1/ptm/m/n/10 Currently the va-lid-ity meth-ods for these classes such as Underfull \hbox (badness 2020) in paragraph at lines 4613--4618 [][][]\T1/pcr/m/n/10 getValidity[][][](getClass("dpoMatrix")) []\T1/ptm/m/n/10 for ef-fi-ciency rea-sons only check the di- Underfull \hbox (badness 1748) in paragraph at lines 4619--4628 \T1/pcr/m/n/10 error=identity), "error") []\T1/ptm/m/n/10 . In-deed, when \T1/p tm/m/it/10 co-erc-ing \T1/ptm/m/n/10 to these classes, a ver-sion Underfull \hbox (badness 1590) in paragraph at lines 4619--4628 \T1/ptm/m/n/10 of [][][]\T1/pcr/m/n/10 Cholesky[][][]() []\T1/ptm/m/n/10 or [][ ][]\T1/pcr/m/n/10 chol[][][]() []\T1/ptm/m/n/10 is typ-i-cally used, e.g., see []\T1/pcr/m/n/10 selectMethod("coerce", Underfull \hbox (badness 6675) in paragraph at lines 4675--4682 []\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 Matrix[][][][]\T1/ptm/m/n/10 , typ-i-ca lly in-her-it-ing from vir-tual class [][][]\T1/pcr/m/n/10 sparseMatrix[][][][] \T1/ptm/m/n/10 . Underfull \hbox (badness 6493) in paragraph at lines 4675--4682 [][][]\T1/pcr/m/n/10 denseMatrix[][][] []\T1/ptm/m/n/10 and tra-di-tional vec-t ors and ma-tri-ces are co-erced to [2401] Underfull \hbox (badness 10000) in paragraph at lines 4690--4698 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing if the re-sult must in-herit from vi r-tual class Underfull \hbox (badness 1365) in paragraph at lines 4690--4698 [][][]\T1/pcr/m/n/10 CsparseMatrix[][][][]\T1/ptm/m/n/10 . If []\T1/pcr/m/n/10 FALSE []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 in-her-its from [][][]\T1/pcr/m/n/10 RsparseMatrix[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4713--4716 []\T1/ptm/m/n/10 Function [][][]\T1/pcr/m/n/10 sparseMatrix[][][][]\T1/ptm/m/n/ 10 , for con-struct-ing ob-jects in-her-it-ing from vir-tual class [2402] Underfull \hbox (badness 10000) in paragraph at lines 4757--4761 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10 new("dsCMatrix", ...) []\T1/ptm/m/n/10 or Underfull \hbox (badness 2103) in paragraph at lines 4757--4761 []\T1/pcr/m/n/10 new("dsTMatrix", ...)[]\T1/ptm/m/n/10 , or au-to-mat-i-cally v ia e.g., []\T1/pcr/m/n/10 as(*, "symmetricMatrix")[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1571) in paragraph at lines 4807--4810 []\T1/pcr/m/n/10 signature(x = "dsCMatrix", pivot = "logical")[]\T1/ptm/m/n/10 : Re-turns (and stores) the [2403] [2404] Underfull \hbox (badness 10000) in paragraph at lines 4949--4954 []\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "dMatrix"[]\T1/ptm/m/n/10 , by class [] \T1/pcr/m/n/10 "dsparseMatrix"[]\T1/ptm/m/n/10 , class []\T1/pcr/m/n/10 "sparse Matrix"[]\T1/ptm/m/n/10 , by Underfull \hbox (badness 6961) in paragraph at lines 4949--4954 \T1/ptm/m/n/10 class []\T1/pcr/m/n/10 "dsparseMatrix" []\T1/ptm/m/n/10 or []\T1 /pcr/m/n/10 "RsparseMatrix"[]\T1/ptm/m/n/10 ; class []\T1/pcr/m/n/10 "compMatri x" []\T1/ptm/m/n/10 by class Underfull \hbox (badness 1400) in paragraph at lines 4961--4964 []\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")[]\T1/ptm/m/n/10 : if []\T1/pcr/m/n/10 uplo == [2405] Underfull \hbox (badness 10000) in paragraph at lines 5013--5015 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10 new("dsyMatrix", ...) []\T1/ptm/m/n/10 or Underfull \hbox (badness 1365) in paragraph at lines 5049--5052 []\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")[]\T1/ptm/m/n/10 , or []\T1/pcr/m/n/10 x = "dsyMatrix" [2406] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5095--5095 []\T1/pcr/m/n/9 stopifnot(all(S1 == S2)) # equal "seen as matrix", but differ internally :[] [2407] [2408] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5201--5201 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim = c(5L, 5L),[] Underfull \hbox (badness 3635) in paragraph at lines 5256--5260 []\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ddenseMatrix"[]\T1/ptm/m/n/10 , di-rec tly. Class []\T1/pcr/m/n/10 "triangularMatrix"[]\T1/ptm/m/n/10 , di-rectly. Cla ss Underfull \hbox (badness 10000) in paragraph at lines 5265--5268 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")[]\T1/ptm/m/n/10 : Ma-trix mul-ti-pli-ca-tion; Underfull \hbox (badness 10000) in paragraph at lines 5268--5272 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")[]\T1/ptm/m/n /10 : the [2409] [2410] [2411] [2412] Underfull \hbox (badness 10000) in paragraph at lines 5524--5526 []\T1/ptm/m/n/10 a ma-trix fac-tor-iza-tion, typ-i-cally in-her-it-ing from vir -tual class Overfull \hbox (29.27832pt too wide) in paragraph at lines 5543--5543 [] \T1/pcr/m/n/10 all.equal(as(x, "matrix"), as(Reduce(\TS1/cmtt/m/n/10 `\T 1/pcr/m/n/10 %*%\TS1/cmtt/m/n/10 `\T1/pcr/m/n/10 , expand2(y)), "matrix")) Overfull \hbox (37.71342pt too wide) in alignment at lines 5574--5574 [] [] [2413] Underfull \hbox (badness 7064) in paragraph at lines 5602--5619 []\T1/pcr/m/n/10 signature(x = "p?BunchKaufman")[]\T1/ptm/m/n/10 : ex-pands the fac-tor-iza-tion $\OML/cmm/m/it/10 A \OT1/cmr/m/n/10 = Underfull \hbox (badness 3000) in paragraph at lines 5631--5638 []\T1/pcr/m/n/10 signature(x = "denseLU")[]\T1/ptm/m/n/10 : ex-pands the fac-to r-iza-tion $\OML/cmm/m/it/10 A \OT1/cmr/m/n/10 = \OML/cmm/m/it/10 P[]LU$ \T1/pt m/m/n/10 as Underfull \hbox (badness 2735) in paragraph at lines 5647--5654 []\T1/pcr/m/n/10 signature(x = "CHMfactor")[]\T1/ptm/m/n/10 : as []\T1/pcr/m/n/ 10 expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/pcr/m/n/10 list(P, L)[]\T1/p tm/m/n/10 . Underfull \hbox (badness 1337) in paragraph at lines 5654--5669 []\T1/pcr/m/n/10 signature(x = "sparseLU")[]\T1/ptm/m/n/10 : as []\T1/pcr/m/n/1 0 expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/pcr/m/n/10 list(P, L, U, Underfull \hbox (badness 2680) in paragraph at lines 5654--5669 \T1/pcr/m/n/10 Q)[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 expand(x)[["Q"]] []\T1/ptm /m/n/10 and []\T1/pcr/m/n/10 expand2(x)[["P2."]] []\T1/ptm/m/n/10 rep-re-sent t he same per- Underfull \hbox (badness 5374) in paragraph at lines 5654--5669 \T1/ptm/m/n/10 mu-ta-tion ma-trix $\OML/cmm/m/it/10 P[]$ \T1/ptm/m/n/10 but hav e op-po-site []\T1/pcr/m/n/10 margin []\T1/ptm/m/n/10 slots and in-verted []\T1 /pcr/m/n/10 perm []\T1/ptm/m/n/10 slots. Underfull \hbox (badness 2073) in paragraph at lines 5669--5674 []\T1/pcr/m/n/10 signature(x = "denseLU")[]\T1/ptm/m/n/10 : as []\T1/pcr/m/n/10 expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/pcr/m/n/10 list(L, U, P)[]\T1/ ptm/m/n/10 . [2414] [2415] [2416] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5881--5881 []\T1/pcr/m/n/9 str(pores <- readMM(system.file("external/pores_1.mtx", packag e = "Matrix")))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5882--5882 []\T1/pcr/m/n/9 str(utm <- readHB(system.file("external/utm300.rua" , packag e = "Matrix")))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5883--5883 []\T1/pcr/m/n/9 str(lundA <- readMM(system.file("external/lund_a.mtx" , packag e = "Matrix")))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5884--5884 []\T1/pcr/m/n/9 str(lundA <- readHB(system.file("external/lund_a.rsa" , packag e = "Matrix")))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5885--5885 []\T1/pcr/m/n/9 ## https://math.nist.gov/MatrixMarket/data/Harwell-Boeing/coun terx/counterx.htm[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5886--5886 []\T1/pcr/m/n/9 str(jgl <- readMM(system.file("external/jgl009.mtx" , packag e = "Matrix")))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5892--5892 []\T1/pcr/m/n/9 u. <- url("https://www.cise.ufl.edu/research/sparse/RB/Boeing/ msc00726.tar.gz")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5897--5897 []\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary dir./folder:[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5900--5900 []\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[] [2417] Overfull \hbox (58.38037pt too wide) in paragraph at lines 5910--5910 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume nts to sparseMatrix():[] [2418] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5972--5972 [] \T1/pcr/m/n/9 all.equal(facmul(x, nm, y, trans = TRUE, left = TRUE), crossprod(L, y))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5973--5973 [] \T1/pcr/m/n/9 all.equal(facmul(x, nm, y, trans = TRUE, left = FALSE), t crossprod(y, L))[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6052--6052 []\T1/pcr/m/n/10 .diag2dense(from, kind = ".", shape = "t", packed = FALSE, up lo = "U")[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 6054--6054 []\T1/pcr/m/n/10 .m2dense(from, class = ".ge", uplo = "U", diag = "N", trans = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6057--6057 []\T1/pcr/m/n/10 .diag2sparse(from, kind = ".", shape = "t", repr = "C", uplo = "U")[] [2419] Overfull \hbox (18.78088pt too wide) in paragraph at lines 6059--6059 []\T1/pcr/m/n/10 .m2sparse(from, class = ".gC", uplo = "U", diag = "N", trans = FALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 6131--6133 []\T1/ptm/m/n/10 a string in []\T1/pcr/m/n/10 c("trace", "sumLog", "prod", "min ", "max", [2420] Underfull \hbox (badness 10000) in paragraph at lines 6206--6212 [][]\T1/pcr/m/n/10 .solve.dgC.*(a, b)[]\T1/ptm/b/n/10 : []\T1/pcr/m/n/10 .solv e.dgC.lu(a, b) []\T1/ptm/m/n/10 needs a square ma-trix []\T1/pcr/m/n/10 a[]\T1/ ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 6206--6212 []\T1/pcr/m/n/10 .solve.dgC.qr(a, b) []\T1/ptm/m/n/10 needs a ``long'' ma-trix []\T1/pcr/m/n/10 a[]\T1/ptm/m/n/10 , with []\T1/pcr/m/n/10 nrow(a) >= ncol(a)[] \T1/ptm/m/n/10 . [2421] Underfull \hbox (badness 10000) in paragraph at lines 6220--6229 [][]\T1/pcr/m/n/10 .updateCHMfactor(object, parent, mult)[]\T1/ptm/b/n/10 : [] \T1/pcr/m/n/10 .updateCHMfactor []\T1/ptm/m/n/10 up- Underfull \hbox (badness 10000) in paragraph at lines 6220--6229 \T1/ptm/m/n/10 dates []\T1/pcr/m/n/10 object []\T1/ptm/m/n/10 with the re-sult of Cholesky fac-tor-iz-ing []\T1/pcr/m/n/10 F(parent) + mult[1] * Underfull \hbox (badness 2443) in paragraph at lines 6220--6229 \T1/pcr/m/n/10 diag(nrow(parent))[]\T1/ptm/m/n/10 , i.e., []\T1/pcr/m/n/10 F(pa rent) []\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 mult[1] []\T1/ptm/m/n/10 times the iden-tity ma-trix, [2422] [2423] [2424] Underfull \hbox (badness 10000) in paragraph at lines 6486--6491 []\T1/ptm/m/n/10 Classes [][][]\T1/pcr/m/n/10 compMatrix[][][][]\T1/ptm/m/n/10 , and the non-general vir-tual classes: [][][]\T1/pcr/m/n/10 symmetricMatrix[][ ][][]\T1/ptm/m/n/10 , [2425] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.image}) h as been already used, duplicate ignored \relax l.6529 \aliasA{image}{image-methods}{image} [2426] [2427] Underfull \hbox (badness 4120) in paragraph at lines 6625--6628 []\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][ ][]\T1/pcr/m/n/10 dgTMatrix[][][] []\T1/ptm/m/n/10 class. Use Overfull \hbox (47.58038pt too wide) in paragraph at lines 6644--6644 []\T1/pcr/m/n/9 stopifnot(!is.null(leg <- imgC$legend), is.list(leg$right)) # failed for 2 days ..[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6664--6664 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col /row) indices:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 6670--6670 [] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, border.col=NA)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 6671--6671 [] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd =2, border.col=NA)[] Overfull \hbox (144.78027pt too wide) in paragraph at lines 6675--6675 []\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor der.col = adjustcolor("skyblue", 1/2))[] [2428] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6683--6683 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a nti-aliasing[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 6686--6686 [] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi ly zoom in and out[] [2429] Underfull \hbox (badness 10000) in paragraph at lines 6820--6823 []\T1/pcr/m/n/10 signature(x = "indMatrix", y = "Matrix") []\T1/ptm/m/n/10 and oth-ers listed by Underfull \hbox (badness 1286) in paragraph at lines 6820--6823 []\T1/pcr/m/n/10 showMethods("%*%", classes = "indMatrix")[]\T1/ptm/m/n/10 : ma -trix prod-ucts im-ple-mented Underfull \hbox (badness 10000) in paragraph at lines 6823--6826 []\T1/pcr/m/n/10 signature(from = "numeric", to = "indMatrix")[]\T1/ptm/m/n/10 : sup-port-ing typ-i-cal Underfull \hbox (badness 3375) in paragraph at lines 6826--6831 []\T1/pcr/m/n/10 signature(from = "list", to = "indMatrix")[]\T1/ptm/m/n/10 : s up-port-ing []\T1/pcr/m/n/10 indMatrix [2430] Underfull \hbox (badness 4156) in paragraph at lines 6837--6839 []\T1/pcr/m/n/10 signature(x = "indMatrix")[]\T1/ptm/m/n/10 : row and Underfull \hbox (badness 1337) in paragraph at lines 6843--6847 []\T1/pcr/m/n/10 signature(X = "indMatrix", Y = "indMatrix")[]\T1/ptm/m/n/10 : Kro-necker prod-uct of Underfull \hbox (badness 1776) in paragraph at lines 6853--6862 []\T1/ptm/m/n/10 Fabian Scheipl at `\T1/pcr/m/n/10 uni-muenchen.de\T1/ptm/m/n/1 0 ', build-ing on the ex-ist-ing class [][][]\T1/pcr/m/n/10 pMatrix[][][] []\T1 /ptm/m/n/10 af-ter Underfull \hbox (badness 1253) in paragraph at lines 6853--6862 \T1/ptm/m/n/10 a nice hike's con-ver-sa-tion with Mar-tin Maech-ler. Meth-ods f or [][][]\T1/pcr/m/n/10 crossprod[][][](x, y) []\T1/ptm/m/n/10 and [2431] Underfull \hbox (badness 1509) in paragraph at lines 6946--6948 []\T1/ptm/m/n/10 an in-te-ger off-set, in-di-cat-ing that the re-sult should be a per-mu-ta-tion of Underfull \hbox (badness 10000) in paragraph at lines 6973--6977 []\T1/pcr/m/n/10 invertPerm(p) []\T1/ptm/m/n/10 re-turns an in-te-ger vec-tor o f length []\T1/pcr/m/n/10 length(p) []\T1/ptm/m/n/10 such that Underfull \hbox (badness 4441) in paragraph at lines 6973--6977 []\T1/pcr/m/n/10 p[invertPerm(p)] []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 invertP erm(p)[p] []\T1/ptm/m/n/10 are both []\T1/pcr/m/n/10 seq_along(p)[]\T1/ptm/m/n/ 10 , i.e., the [2432] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7010--7010 []\T1/pcr/m/n/9 ## Product of transpositions (1 2)(2 1)(4 3)(6 8)(10 1) = (3 4 )(6 8)(1 10)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.anyNA}) h as been already used, duplicate ignored \relax l.7024 \aliasA{anyNA}{is.na-methods}{anyNA} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.finite }) has been already used, duplicate ignored \relax l.7031 ...asA{is.finite}{is.na-methods}{is.finite} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.infini te}) has been already used, duplicate ignored \relax l.7039 ...is.infinite}{is.na-methods}{is.infinite} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.na}) h as been already used, duplicate ignored \relax l.7047 \aliasA{is.na}{is.na-methods}{is.na} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.nan}) has been already used, duplicate ignored \relax l.7054 \aliasA{is.nan}{is.na-methods}{is.nan} [2433] [2434] [2435] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.isSymmetr ic}) has been already used, duplicate ignored \relax l.7213 ...etric}{isSymmetric-methods}{isSymmetric} Overfull \hbox (138.78088pt too wide) in paragraph at lines 7260--7260 []\T1/pcr/m/n/10 isSymmetric(object, checkDN = TRUE, tol = 100 * .Machine$doub le.eps, tol1 = 8 * tol, ...)[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 7262--7262 []\T1/pcr/m/n/10 isSymmetric(object, checkDN = TRUE, tol = 100 * .Machine$doub le.eps, ...)[] [2436] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7317--7317 []\T1/pcr/m/n/9 isSymmetric(as(M, "generalMatrix")) # still symmetric, even if not "formally"[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7321--7321 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs = TRUE) # includes S3 g eneric from base[] [2437] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7404--7404 []\T1/pcr/m/n/9 isTriangular(as(M, "generalMatrix")) # still triangular, even if not "formally"[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 7431--7431 []\T1/pcr/m/n/10 KhatriRao(X, Y = X, FUN = "*", sparseY = TRUE, make.dimnames = FALSE) [2438] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7507--7507 []\T1/pcr/m/n/9 stopifnot(all(K1 <- KhatriRao(nd, zm) == 0), identical(dim(K1) , c(12L, 4L)),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7508--7508 [] \T1/pcr/m/n/9 all(K2 <- KhatriRao(zm, nd) == 0), identical(dim(K2) , c(12L, 4L)))[] [2439] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7515--7515 [] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di mnames(Kmd)))[] [2440] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.kronecker }) has been already used, duplicate ignored \relax l.7589 ...kronecker}{kronecker-methods}{kronecker} Underfull \hbox (badness 1062) in paragraph at lines 7686--7689 []\T1/pcr/m/n/10 ldenseMatrix []\T1/ptm/m/n/10 is the vir-tual class of all den se \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both [2441] Underfull \hbox (badness 6063) in paragraph at lines 7712--7715 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-call y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2442 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.*,ndiMatr ix,Matrix.Rdash.method}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.7826 C lass \code{"\LinkA{sparseMatrix}{sparseMatrix.Rdash.class}"}, by cla... ] Underfull \hbox (badness 2635) in paragraph at lines 7873--7878 []\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ldenseMatrix"[]\T1/ptm/m/n/10 , di-rec tly. Class []\T1/pcr/m/n/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/ 10 "ldenseMatrix"[]\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 7873--7878 \T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "denseMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/10 "ldenseMatrix"[]\T1/ptm/m/n/10 . Class []\T1/pcr/m/n/10 "Matri x"[]\T1/ptm/m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 7881--7884 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ); use, e.g., [2443] Underfull \hbox (badness 10000) in paragraph at lines 7938--7948 []\T1/pcr/m/n/10 lsTMatrix[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 ltTMatrix[]\T 1/ptm/m/n/10 ) or in com-pressed column-oriented form (class Underfull \hbox (badness 1242) in paragraph at lines 7938--7948 [][][]\T1/pcr/m/n/10 CsparseMatrix[][][][]\T1/ptm/m/n/10 , sub-classes []\T1/pc r/m/n/10 lgCMatrix[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lsCMatrix[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 ltCMatrix[]\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\ T1/ptm/m/n/10 --in [2444] Underfull \hbox (badness 3179) in paragraph at lines 8020--8023 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cal ly equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2445] Underfull \hbox (badness 10000) in paragraph at lines 8105--8108 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ; use, e.g., [2446] Underfull \hbox (badness 10000) in paragraph at lines 8166--8169 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ; use, e.g., [2447] [2448] [2449] Underfull \hbox (badness 10000) in paragraph at lines 8404--8407 []\T1/ptm/m/n/10 vector of all non-zero en-tries of []\T1/pcr/m/n/10 x[]\T1/ptm /m/n/10 ; ex-ists \T1/ptm/b/n/10 only \T1/ptm/m/n/10 when []\T1/pcr/m/n/10 as(x , Underfull \hbox (badness 1490) in paragraph at lines 8426--8428 []\T1/pcr/m/n/10 mat2triplet() []\T1/ptm/m/n/10 is con-cep-tu-ally the \T1/ptm/ m/it/10 in-verse \T1/ptm/m/n/10 func-tion of [][][]\T1/pcr/m/n/10 spMatrix[][][ ] []\T1/ptm/m/n/10 and (one case of) [2450] pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rpcent.* .Rpcent.}) has been already used, duplicate ignored \relax l.8447 ...*\%}{matmult-methods}{.Rpcent.*.Rpcent.} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.crossprod }) has been already used, duplicate ignored \relax l.8521 ...A{crossprod}{matmult-methods}{crossprod} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tcrosspro d}) has been already used, duplicate ignored \relax l.8597 ...tcrossprod}{matmult-methods}{tcrossprod} Underfull \hbox (badness 1881) in paragraph at lines 8683--8689 \T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][][]\T1/ pcr/m/n/10 t[][][](.)[]\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn [2451] Underfull \hbox (badness 10000) in paragraph at lines 8752--8755 []\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")[]\T1/ptm/m/n/10 : Ma-trix mul-ti-pli-ca-tion; Underfull \hbox (badness 10000) in paragraph at lines 8755--8760 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and other sig-na-tures (use Underfull \hbox (badness 3557) in paragraph at lines 8755--8760 []\T1/pcr/m/n/10 showMethods("%*%", class="dtrMatrix")[]\T1/ptm/m/n/10 ): ma-tr ix mul-ti-pli-ca-tion. Mul-ti- Underfull \hbox (badness 6608) in paragraph at lines 8760--8764 \T1/ptm/m/n/10 sig-na-tures, use []\T1/pcr/m/n/10 showMethods("crossprod", clas s = "dgeMatrix")[]\T1/ptm/m/n/10 , ma-trix Underfull \hbox (badness 1552) in paragraph at lines 8770--8771 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and other sig-na- [2452] [2453] [2454] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det}) has been already used, duplicate ignored \relax l.8995 \aliasA{det}{Matrix-class}{det} Underfull \hbox (badness 1337) in paragraph at lines 9069--9072 []\T1/pcr/m/n/10 signature(x = "Matrix", value = "list")[]\T1/ptm/m/n/10 : set the []\T1/pcr/m/n/10 dimnames []\T1/ptm/m/n/10 to a Underfull \hbox (badness 10000) in paragraph at lines 9082--9085 [2455] Underfull \hbox (badness 10000) in paragraph at lines 9091--9093 []\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")[]\T1/ptm/m/n/10 : This re-lies on a cor-rect [2456] [2457] Underfull \hbox (badness 10000) in paragraph at lines 9260--9264 []\T1/pcr/m/n/10 CholeskyFactorization[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Bunch KaufmanFactorization[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 9283--9285 []\T1/pcr/m/n/10 signature(x = "MatrixFactorization", logarithm = Underfull \hbox (badness 10000) in paragraph at lines 9300--9303 []\T1/pcr/m/n/10 signature(obj = "MatrixFactorization")[]\T1/ptm/m/n/10 : re-tu rns []\T1/pcr/m/n/10 obj []\T1/ptm/m/n/10 with [2458] Underfull \hbox (badness 3019) in paragraph at lines 9312--9315 []\T1/ptm/m/n/10 Classes ex-tend-ing []\T1/pcr/m/n/10 CholeskyFactorization[]\T 1/ptm/m/n/10 , namely [][][]\T1/pcr/m/n/10 Cholesky[][][][]\T1/ptm/m/n/10 , [][ ][]\T1/pcr/m/n/10 pCholesky[][][][]\T1/ptm/m/n/10 , and Underfull \hbox (badness 10000) in paragraph at lines 9316--9318 []\T1/ptm/m/n/10 Classes ex-tend-ing []\T1/pcr/m/n/10 BunchKaufmanFactorization []\T1/ptm/m/n/10 , namely [][][]\T1/pcr/m/n/10 BunchKaufman[][][] []\T1/ptm/m/n /10 and Underfull \hbox (badness 10000) in paragraph at lines 9331--9334 []\T1/ptm/m/n/10 Generic func-tions [][][]\T1/pcr/m/n/10 expand1[][][] []\T1/pt m/m/n/10 and [][][]\T1/pcr/m/n/10 expand2[][][] []\T1/ptm/m/n/10 for con-struct -ing ma-trix fac-tors from Underfull \hbox (badness 1062) in paragraph at lines 9360--9363 []\T1/pcr/m/n/10 ndenseMatrix []\T1/ptm/m/n/10 is the vir-tual class of all den se \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both Underfull \hbox (badness 6063) in paragraph at lines 9392--9395 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-call y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2459] Underfull \hbox (badness 3312) in paragraph at lines 9449--9451 []\T1/ptm/m/n/10 logical in-di-cat-ing if []\T1/pcr/m/n/10 X <- (X + t(X))/2 [] \T1/ptm/m/n/10 should be done, af-ter []\T1/pcr/m/n/10 X <- [2460] [2461] Overfull \hbox (85.38034pt too wide) in paragraph at lines 9552--9552 [] \T1/pcr/m/n/9 all.equal(n.A.m, unname(as.matrix(n.A$mat)), tolerance = 1e -15)# seen rel.d.= 1.46e-16[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 9592--9592 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a ll in this example[] [2462] Underfull \hbox (badness 2635) in paragraph at lines 9645--9650 []\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ndenseMatrix"[]\T1/ptm/m/n/10 , di-rec tly. Class []\T1/pcr/m/n/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/ 10 "ndenseMatrix"[]\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 9645--9650 \T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "denseMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/10 "ndenseMatrix"[]\T1/ptm/m/n/10 . Class []\T1/pcr/m/n/10 "Matri x"[]\T1/ptm/m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 9653--9656 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ); use, e.g., [2463] Underfull \hbox (badness 2521) in paragraph at lines 9721--9727 []\T1/pcr/m/n/10 signature(from = "matrix", to = "nMatrix")[]\T1/ptm/m/n/10 : N ote that these co-er-cions [2464] Underfull \hbox (badness 1867) in paragraph at lines 9834--9836 []\T1/ptm/m/n/10 fast sim- [2465] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.norm}) ha s been already used, duplicate ignored \relax l.9876 \aliasA{norm}{norm-methods}{norm} [2466] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9971--9971 []\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9972--9972 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9973--9973 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Underfull \hbox (badness 2401) in paragraph at lines 10018--10028 []\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][][]\T1/pcr/m/n /10 TsparseMatrix[][][][]\T1/ptm/m/n/10 , sub-classes []\T1/pcr/m/n/10 ngTMatri x[]\T1/ptm/m/n/10 , [2467] Underfull \hbox (badness 3179) in paragraph at lines 10089--10092 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cal ly equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2468] Underfull \hbox (badness 10000) in paragraph at lines 10169--10172 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ; use, e.g., [2469] Underfull \hbox (badness 10000) in paragraph at lines 10233--10236 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ; use, e.g., [2470] [2471] Underfull \hbox (badness 10000) in paragraph at lines 10330--10332 []\T1/ptm/m/n/10 typically a []\T1/pcr/m/n/10 "packedMatrix"[]\T1/ptm/m/n/10 , though [2472] [2473] Underfull \hbox (badness 10000) in paragraph at lines 10547--10550 []\T1/pcr/m/n/10 signature(x = "pMatrix", y = "Matrix") []\T1/ptm/m/n/10 and ot h-ers listed by Underfull \hbox (badness 8189) in paragraph at lines 10547--10550 []\T1/pcr/m/n/10 showMethods("%*%", classes = "pMatrix")[]\T1/ptm/m/n/10 : ma-t rix prod-ucts im-ple-mented [2474] Underfull \hbox (badness 10000) in paragraph at lines 10550--10554 []\T1/pcr/m/n/10 signature(from = "numeric", to = "pMatrix")[]\T1/ptm/m/n/10 : sup-port-ing typ-i-cal Underfull \hbox (badness 2460) in paragraph at lines 10558--10564 []\T1/pcr/m/n/10 signature(a = "pMatrix", b = "missing")[]\T1/ptm/m/n/10 : the in-verse per-mu-ta-tion ma-trix, [2475] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10628--10628 [] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD iag = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10631--10631 []\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m ax.print")),[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10633--10633 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 10637--10637 []\T1/pcr/m/n/10 printSpMatrix2(x, digits = NULL, maxp = max(100L, getOption(" max.print")),[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10638--10638 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Underfull \hbox (badness 3989) in paragraph at lines 10663--10673 []\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of [] \T1/pcr/m/n/10 x []\T1/ptm/m/n/10 should Underfull \hbox (badness 10000) in paragraph at lines 10663--10673 \T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro m [2476] [2477] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr}) has been already used, duplicate ignored \relax l.10764 \aliasA{qr}{qr-methods}{qr} [2478] [2479] Overfull \hbox (25.98041pt too wide) in paragraph at lines 10896--10896 [] \T1/pcr/m/n/9 all.equal(qr.coef(qr.A1, b), drop(solve(crossprod(A1), cro ssprod(A1, b))))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10912--10912 [] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 qr.coef\TS1/pcr/m/n/9 ' \ T1/pcr/m/n/9 computes unique least squares solution of "nearby" problem[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10913--10913 [] \T1/pcr/m/n/9 ## Z x = b for some full rank Z ~ A, currently without war ning {FIXME} ![] Underfull \vbox (badness 10000) has occurred while \output is active [2480] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10956--10956 []\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m atrix"), ...)[] [2481] Underfull \hbox (badness 2005) in paragraph at lines 11008--11014 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of [][][]\T1/pcr/m/n/10 qr[][][](x, tol, Underfull \hbox (badness 10000) in paragraph at lines 11025--11028 []\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense []\T1/pcr/m/n/10 x[]\ T1/ptm/m/n/10 , it cor-re-sponds to [2482] Overfull \hbox (85.38034pt too wide) in paragraph at lines 11124--11124 []\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/ n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale free"[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 11140--11140 []\T1/pcr/m/n/9 sapply(meths, function(.m.) rankMatrix(M15, method = .m., tol = 1e-7)) # all 14[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 11147--11147 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # war ning+ ~1.5 sec (2013)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 11148--11148 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con siderably faster![] [2483] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h as been already used, duplicate ignored \relax l.11167 \aliasA{rcond}{rcond-methods}{rcond} [2484] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11283--11283 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not have full rank[] [2485] [2486] [2487] Underfull \hbox (badness 2150) in paragraph at lines 11476--11484 \T1/ptm/m/n/10 dices, if not []\T1/pcr/m/n/10 symmetric [][]sample.int[][][](nr ow*ncol, nnz)[]\T1/ptm/m/n/10 , then---if []\T1/pcr/m/n/10 rand.x []\T1/ptm/m/n /10 is not [2488] [2489] Underfull \hbox (badness 5147) in paragraph at lines 11633--11636 []\T1/ptm/m/n/10 Class [][][]\T1/pcr/m/n/10 SchurFactorization[][][][]\T1/ptm/m /n/10 , di-rectly. Class [][][]\T1/pcr/m/n/10 MatrixFactorization[][][][]\T1/pt m/m/n/10 , by class [2490] Underfull \hbox (badness 3179) in paragraph at lines 11648--11651 []\T1/pcr/m/n/10 signature(from = "Schur", logarithm = "logical")[]\T1/ptm/m/n/ 10 : com-putes [2491] [2492] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11813--11813 [] \T1/pcr/m/n/9 all.equal(e1, e3[order(Mod(e3), decreasing = TRUE)], toler ance = 1e-13)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solve}) h as been already used, duplicate ignored \relax l.11823 \aliasA{solve}{solve-methods}{solve} [2493] Overfull \hbox (90.78088pt too wide) in paragraph at lines 11947--11947 []\T1/pcr/m/n/10 solve(a, b, system = c("A", "LDLt", "LD", "DLt", "L", "Lt", " D", "P", "Pt"), ...)[] Underfull \hbox (badness 1147) in paragraph at lines 11959--11965 []\T1/ptm/m/n/10 a vec-tor, [][][]\T1/pcr/m/n/10 sparseVector[][][][]\T1/ptm/m/ n/10 , ma-trix, or [][][]\T1/pcr/m/n/10 Matrix[][][] []\T1/ptm/m/n/10 sat-is-fy -ing []\T1/pcr/m/n/10 NROW(b) == Underfull \hbox (badness 3460) in paragraph at lines 12009--12014 []\T1/ptm/m/n/10 Methods for dense []\T1/pcr/m/n/10 a []\T1/ptm/m/n/10 are buil t on 14 LA-PACK rou-tines: class []\T1/pcr/m/n/10 d..Matrix[]\T1/ptm/m/n/10 , w here [2494] Overfull \hbox (52.98038pt too wide) in paragraph at lines 12082--12082 []\T1/pcr/m/n/9 image(ia0 <- solve(a, tol = 0)) # checker board, dense [but re ally, a is singular!][] Overfull \hbox (25.98041pt too wide) in paragraph at lines 12086--12086 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] [2495] Underfull \hbox (badness 10000) in paragraph at lines 12109--12112 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, from a for-mu la and data frame Overfull \hbox (6.78088pt too wide) in paragraph at lines 12126--12126 [] \T1/pcr/m/n/10 drop.unused.levels = TRUE, repr = c("C", "R", "T"), giveCs parse)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 12128--12128 [] \T1/pcr/m/n/10 drop.unused.levels = TRUE, repr = c("C", "R", "T"), giveCs parse,[] Underfull \hbox (badness 1648) in paragraph at lines 12137--12139 []\T1/ptm/m/n/10 a data frame cre-ated with [][][]\T1/pcr/m/n/10 model.frame[][ ][][]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 10000) in paragraph at lines 12145--12148 []\T1/ptm/m/n/10 character string or []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or (co-er-ca-ble to) Underfull \hbox (badness 2591) in paragraph at lines 12145--12148 []\T1/pcr/m/n/10 "[][]sparseMatrix[][][]"[]\T1/ptm/m/n/10 , spec-i-fy-ing the c on-trasts to be ap-plied to the Underfull \hbox (badness 10000) in paragraph at lines 12156--12160 []\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for Underfull \hbox (badness 2828) in paragraph at lines 12156--12160 []\T1/pcr/m/n/10 sparse.model.matrix []\T1/ptm/m/n/10 has been changed to []\T1 /pcr/m/n/10 FALSE[]\T1/ptm/m/n/10 , 2010-07, for [2496] Underfull \hbox (badness 1668) in paragraph at lines 12171--12176 [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/ m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse Underfull \hbox (badness 3291) in paragraph at lines 12198--12203 []\T1/pcr/m/n/10 model.Matrix(sparse = TRUE) []\T1/ptm/m/n/10 from pack-age [][ ]\T1/ptm/b/n/10 Ma-trix-Mod-els[][] \T1/ptm/m/n/10 may be nowa-days be Underfull \hbox (badness 2073) in paragraph at lines 12198--12203 \T1/ptm/m/n/10 prefer-able to []\T1/pcr/m/n/10 sparse.model.matrix[]\T1/ptm/m/n /10 , as []\T1/pcr/m/n/10 model.Matrix []\T1/ptm/m/n/10 re-turns an ob-ject of class [2497] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12252--12252 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M) == c(0, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12253--12253 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M) == c(3, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12254--12254 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2498] Underfull \hbox (badness 2961) in paragraph at lines 12316--12319 []\T1/pcr/m/n/10 signature(from = "sparseLU", logarithm = "logical")[]\T1/ptm/m /n/10 : com- Overfull \hbox (9.78043pt too wide) in paragraph at lines 12359--12359 []\T1/pcr/m/n/9 A <- as(readMM(system.file("external", "pores_1.mtx", package = "Matrix")),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12370--12370 []\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m atrix"), ...)[] [2499] Overfull \hbox (20.58041pt too wide) in paragraph at lines 12377--12377 [] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(dn[1L ], list(NULL)),[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 12380--12380 [] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(list( NULL), dn[2L]),[] Underfull \hbox (badness 10000) in paragraph at lines 12405--12407 []\T1/ptm/m/n/10 This in-ter-face is rec-om-mended over di-rect con-struc-tion via calls such as Overfull \hbox (0.78088pt too wide) in paragraph at lines 12412--12412 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] [2500] Underfull \hbox (badness 2261) in paragraph at lines 12450--12456 \T1/ptm/m/n/10 of the sparse ma-trix re-sult, i.e., spec-i-fy-ing one of the vi r-tual classes [2501] Underfull \hbox (badness 10000) in paragraph at lines 12539--12542 []\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][][]\T1/pcr/m/n/10 xtabs[][][ ](*, sparse=TRUE)[]\T1/ptm/m/n/10 , for sparse ta-bles and Overfull \hbox (4.38043pt too wide) in paragraph at lines 12552--12552 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12556--12556 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12557--12557 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12562--12562 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims = c(10,20)))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12565--12565 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar e consistent[] [2502] Overfull \hbox (15.18042pt too wide) in paragraph at lines 12588--12588 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 12589--12589 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12615--12615 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep resentations.[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 12618--12618 [] \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack age = "SparseM"))) {[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12620--12620 [] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims = X@dimension)[] [2503] Underfull \hbox (badness 6842) in paragraph at lines 12710--12713 []\T1/pcr/m/n/10 (x = "sparseMatrix", logarithm=TRUE)[]\T1/ptm/m/n/10 : [][][]\ T1/pcr/m/n/10 determinant[][][]() []\T1/ptm/m/n/10 meth-ods Underfull \hbox (badness 10000) in paragraph at lines 12745--12749 [][][]\T1/pcr/m/n/10 sparseMatrix[][][][]\T1/ptm/m/n/10 , and its ref-er-ences, such as [][][]\T1/pcr/m/n/10 xtabs[][][](*, sparse=TRUE)[]\T1/ptm/m/n/10 , or [2504] [2505] Underfull \hbox (badness 2961) in paragraph at lines 12929--12932 []\T1/pcr/m/n/10 signature(from = "sparseQR", logarithm = "logical")[]\T1/ptm/m /n/10 : com- [2506] Underfull \hbox (badness 3229) in paragraph at lines 13007--13011 []\T1/ptm/m/n/10 The many aux-il-iary func-tions for QR fac-tor-iza-tions: [][] []\T1/pcr/m/n/10 qr.Q[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 qr.R[][][][] \T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 qr.X[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc r/m/n/10 qr.coef[][][][]\T1/ptm/m/n/10 , [2507] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13047--13047 []\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m atrix"), ...)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 13055--13055 [] \T1/pcr/m/n/9 new("pMatrix", Dim = c(m, m), Dimnames = c(dn[1L ], list(NULL)),[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 13058--13058 [] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(list( NULL), dn[2L]),[] Underfull \vbox (badness 10000) has occurred while \output is active [2508] Overfull \hbox (42.18039pt too wide) in paragraph at lines 13077--13077 [] \T1/pcr/m/n/9 ae2(qrc <- qr.coef (qr.A, b), with(e.qr.A, solve(R1 %*% P 2., t(qrQ)) %*% b))[] Underfull \hbox (badness 5036) in paragraph at lines 13112--13114 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a [2509] Underfull \hbox (badness 2970) in paragraph at lines 13232--13238 []\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class []\T1/pcr/m/ n/10 "sparseVector" []\T1/ptm/m/n/10 has the five ac- Underfull \hbox (badness 3679) in paragraph at lines 13232--13238 \T1/ptm/m/n/10 tual daugh-ter classes []\T1/pcr/m/n/10 "dsparseVector"[]\T1/ptm /m/n/10 , []\T1/pcr/m/n/10 "isparseVector"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 " lsparseVector"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13277--13280 []\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") []\T1/ptm/m/ n/10 co-erces sparse [2510] Underfull \hbox (badness 10000) in paragraph at lines 13317--13322 []\T1/pcr/m/n/10 (x = "nsparseVector")[]\T1/ptm/m/n/10 : re-turn [][][]\T1/pcr/ m/n/10 logical[][][] []\T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 13332--13334 [][][]\T1/pcr/m/n/10 sparseVector[][][]() []\T1/ptm/m/n/10 for friendly con-str uc-tion of sparse vec-tors (apart from []\T1/pcr/m/n/10 as(*, [2511] Underfull \vbox (badness 10000) has occurred while \output is active [2512] Overfull \hbox (24.78088pt too wide) in paragraph at lines 13432--13432 []\T1/pcr/m/n/10 spMatrix(nrow, ncol, i = integer(0L), j = integer(0L), x = do uble(0L)) Underfull \hbox (badness 2310) in paragraph at lines 13459--13465 [][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) []\T1/ptm/m/n/10 for the more usual con-struc-tor of such ma-tri-ces. Then, [2513] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.[<.Rdash. }) has been already used, duplicate ignored \relax l.13511 ...\Rdash{}}{Subassign-methods}{[<.Rdash.} Underfull \hbox (badness 6910) in paragraph at lines 13598--13600 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2514] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.[}) has b een already used, duplicate ignored \relax l.13647 \aliasA{[}{Subscript-methods}{[} [2515] [2516] Underfull \hbox (badness 2591) in paragraph at lines 13780--13785 \T1/ptm/m/n/10 Classes [][][]\T1/pcr/m/n/10 triangularMatrix[][][][]\T1/ptm/m/n /10 , and, e.g., [][][]\T1/pcr/m/n/10 dsyMatrix[][][] []\T1/ptm/m/n/10 for nu-m eric \T1/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or [2517] Underfull \hbox (badness 2057) in paragraph at lines 13856--13858 []\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe r-ent ma-trix classes, use e.g., Underfull \hbox (badness 6396) in paragraph at lines 13865--13869 []\T1/pcr/m/n/10 symmpart(x) []\T1/ptm/m/n/10 re-turns a sym-met-ric ma-trix, i n-her-it-ing from [][][]\T1/pcr/m/n/10 symmetricMatrix[][][] []\T1/ptm/m/n/10 o r Underfull \hbox (badness 7722) in paragraph at lines 13870--13875 []\T1/pcr/m/n/10 skewpart(x) []\T1/ptm/m/n/10 re-turns a skew-symmetric ma-trix , in-her-it-ing from [][][]\T1/pcr/m/n/10 generalMatrix[][][][]\T1/ptm/m/n/10 , [2518] Underfull \hbox (badness 6641) in paragraph at lines 13947--13950 []\T1/ptm/m/n/10 Currently, [][][]\T1/pcr/m/n/10 Schur[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 isSymmetric[][][] []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 as () []\T1/ptm/m/n/10 (i.e. [][][]\T1/pcr/m/n/10 coerce[][][][]\T1/ptm/m/n/10 ) h ave meth-ods with [2519] Underfull \hbox (badness 5133) in paragraph at lines 13983--13987 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 "TsparseMatrix" []\T1/ptm/m/n/10 class is the vir-tual class of all sparse ma-tri-ces coded in Underfull \hbox (badness 2818) in paragraph at lines 13983--13987 \T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c re-ated from it. See [2520] Underfull \hbox (badness 1668) in paragraph at lines 14113--14116 [][][]\T1/pcr/m/n/10 pack[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 unpac k[][][][]\T1/ptm/m/n/10 ; its vir-tual "com-ple-ment" []\T1/pcr/m/n/10 "[][]pac kedMatrix[][][]"[]\T1/ptm/m/n/10 ; its proper sub-classes [2521] [2522] Underfull \hbox (badness 10000) in paragraph at lines 14224--14230 []\T1/ptm/m/n/10 GAL lat-tice file `\T1/pcr/m/n/10 usc_q.GAL\T1/ptm/m/n/10 ' (r e-trieved in 2008 from [2523] [2524] [2525]) (./boot-pkg.tex [2526] Chapter 18. [2527] [2528] [2529] [2530] [2531] [2532] [2533] Overfull \hbox (12.78088pt too wide) in paragraph at lines 532--532 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f" , "w"), [2534] Underfull \hbox (badness 1325) in paragraph at lines 570--577 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r e-quired. Pos-si-ble Underfull \hbox (badness 1275) in paragraph at lines 585--590 []\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m ulti-sample prob- [2535] [2536] [2537] Underfull \hbox (badness 1881) in paragraph at lines 826--828 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 6493) in paragraph at lines 853--857 [][][]\T1/pcr/m/n/10 boot.array[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 bo ot.ci[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 censboot[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 empinf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 j ack.after.boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 tilt.boot[][][][]\T 1/ptm/m/n/10 , [2538] Overfull \hbox (4.38043pt too wide) in paragraph at lines 887--887 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, data = nuke)[] Underfull \vbox (badness 10000) has occurred while \output is active [2539] [2540] [2541] Underfull \hbox (badness 1496) in paragraph at lines 1084--1093 []\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari- ance of the Underfull \hbox (badness 2005) in paragraph at lines 1084--1093 \T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i n-ter-vals. If it Underfull \hbox (badness 2343) in paragraph at lines 1084--1093 \T1/ptm/m/n/10 is not sup-plied and []\T1/pcr/m/n/10 length(index) []\T1/ptm/m/ n/10 is 2 then []\T1/pcr/m/n/10 var.t0 []\T1/ptm/m/n/10 de-faults to Underfull \hbox (badness 2150) in paragraph at lines 1105--1111 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa ult value is [2542] [2543] [2544] [2545] Underfull \hbox (badness 1571) in paragraph at lines 1445--1447 []\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis- [2546] [2547] [2548] [2549] [2550] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1738--1738 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix( 1,n,2), [2551] [2552] [2553] Underfull \vbox (badness 10000) has occurred while \output is active [2554] Overfull \hbox (31.3804pt too wide) in paragraph at lines 2013--2013 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4) + strata(ulcer),[] [2555] Underfull \hbox (badness 6268) in paragraph at lines 2084--2086 []\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch an-ning House. [2556] [2557] [2558] Underfull \hbox (badness 1565) in paragraph at lines 2338--2343 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori g-i-nal data set [2559] Underfull \hbox (badness 4595) in paragraph at lines 2363--2368 \T1/ptm/m/n/10 are passed un-changed ev-ery time []\T1/pcr/m/n/10 boot.out$stat istic []\T1/ptm/m/n/10 is called. Underfull \hbox (badness 1881) in paragraph at lines 2432--2434 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 2057) in paragraph at lines 2440--2441 [][][]\T1/pcr/m/n/10 boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 empinf[] [][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 k3.linear[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 linear.approx[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 saddle.distn[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 smooth.spline[][][][] \T1/ptm/m/n/10 , [2560] [2561] Underfull \hbox (badness 1077) in paragraph at lines 2536--2540 []\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of []\T1/pcr/m /n/10 n/((n-1)*(n-2)) []\T1/ptm/m/n/10 where []\T1/pcr/m/n/10 n []\T1/ptm/m/n/1 0 is the sam-ple Underfull \hbox (badness 1112) in paragraph at lines 2536--2540 \T1/ptm/m/n/10 size, if []\T1/pcr/m/n/10 unbiased []\T1/ptm/m/n/10 is []\T1/pcr /m/n/10 FALSE []\T1/ptm/m/n/10 then a mul-ti-plier of []\T1/pcr/m/n/10 1/n []\T 1/ptm/m/n/10 is used. This is mul-ti-plied by [2562] [2563] [2564] [2565] [2566] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2895--2895 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25, Overfull \hbox (18.78088pt too wide) in paragraph at lines 2897--2897 []\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25,[] [2567] [2568] [2569] Underfull \hbox (badness 3861) in paragraph at lines 3105--3108 [][][]\T1/pcr/m/n/10 boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 boot.arr ay[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 boot.ci[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 control[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 jack .after.boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 linear.approx[][][][]\ T1/ptm/m/n/10 , [2570] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3158--3158 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1 :ncol(mat)) [2571] [2572] [2573] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3378--3378 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling [2574] [2575] [2576] [2577] [2578] [2579] [2580] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3838--3838 [] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q = NULL)[] [2581] [2582] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3977--3977 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 = grav.z0[3])[] [2583] [2584] [2585] [2586] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4259--4259 []\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz e data as in [2587] [2588] Underfull \hbox (badness 10000) in paragraph at lines 4362--4364 []\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o f Underfull \hbox (badness 1430) in paragraph at lines 4371--4375 \T1/ptm/m/n/10 If []\T1/pcr/m/n/10 t0 []\T1/ptm/m/n/10 is sup-plied but nei-the r []\T1/pcr/m/n/10 t []\T1/ptm/m/n/10 nor []\T1/pcr/m/n/10 L []\T1/ptm/m/n/10 a re sup-plied then []\T1/pcr/m/n/10 t0 []\T1/ptm/m/n/10 is set to [2589] [2590] [2591] [2592] [2593] [2594] [2595] [2596] [2597] Underfull \hbox (badness 3000) in paragraph at lines 4959--4962 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2598] [2599] [2600] [2601] Underfull \hbox (badness 2293) in paragraph at lines 5238--5241 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5238--5241 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2602] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5317--5317 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat a = grav1[, 2])[] [2603] [2604] [2605] [2606] [2607] [2608] [2609] [2610] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5866--5866 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c ity.sp1$spa[1][] [2611] Underfull \hbox (badness 1127) in paragraph at lines 5988--6006 []\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less than []\T1/pcr/m/n/10 min(alpha)/10[]\T1/ptm/m/n/10 , then [2612] Underfull \hbox (badness 2837) in paragraph at lines 6021--6024 []\T1/ptm/m/n/10 The re-turned value is an ob-ject of class []\T1/pcr/m/n/10 "s addle.distn"[]\T1/ptm/m/n/10 . See the help file for [2613] [2614] [2615] [2616] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6306--6306 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and Wright (1991). [2617] [2618] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6495--6495 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling Overfull \hbox (20.58041pt too wide) in paragraph at lines 6497--6497 []\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t ilting was used[] [2619] [2620] [2621] Underfull \hbox (badness 1596) in paragraph at lines 6742--6746 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m ent ex-pected by [2622] [2623] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6902--6902 [] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha = c(0.05, 0.95),[] [2624] [2625] [2626] [2627] [2628] [2629] [2630] [2631]) (./class-pkg.tex [2632] Chapter 19. [2633] [2634] [2635] [2636] [2637] [2638] [2639] [2640] [2641] [2642] [2643] [2644] [2645] [2646] Overfull \hbox (42.18039pt too wide) in paragraph at lines 1006--1006 [] \T1/pcr/m/n/9 alpha = list(seq(0.05, 0, length.out = 1e4), seq(0.02, 0, length.out = 1e5)),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1007--1007 [] \T1/pcr/m/n/9 radii = list(seq(8, 1, length.out = 1e4), seq(4, 1, length .out = 1e5)))[] [2647] [2648]) (./cluster-pkg.tex Chapter 20. [2649] [2650] [2651] Overfull \hbox (42.18039pt too wide) in paragraph at lines 253--253 [] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met hod = 0.5)[iC]) ,[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 254--254 [] \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, -.5))[iC]),[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 255--255 [] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, +.5))[iC]))[] [2652] [2653] [2654] [2655] Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519 [] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot = axes,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 523--523 [] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5, ...)[] [2656] [2657] Overfull \hbox (66.78088pt too wide) in paragraph at lines 638--638 [] \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c orrect.d = TRUE)[] [2658] Underfull \hbox (badness 3078) in paragraph at lines 692--695 []\T1/ptm/m/n/10 Setting this to []\T1/pcr/m/n/10 FALSE []\T1/ptm/m/n/10 saves mem-ory (and hence time), but dis-ables [2659] [2660] Underfull \hbox (badness 2941) in paragraph at lines 795--798 [][][]\T1/pcr/m/n/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-en ces; [][][]\T1/pcr/m/n/10 clara.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 pam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 partition.object[][][][]\ T1/ptm/m/n/10 , [2661] Overfull \hbox (9.78043pt too wide) in paragraph at lines 838--838 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo r this seed):[] Underfull \hbox (badness 10000) in paragraph at lines 885--887 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2662] Overfull \hbox (24.78088pt too wide) in paragraph at lines 950--950 [] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code =3), ...)[] [2663] Underfull \hbox (badness 4872) in paragraph at lines 996--998 []\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is Underfull \hbox (badness 1342) in paragraph at lines 1010--1014 []\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in 2012, [2664] Underfull \hbox (badness 10000) in paragraph at lines 1102--1104 [][][]$\T1/pcr/m/n/10 https : / / bioconductor . org / packages / 3 . 12 / bioc / html / SAGx . html$[][] \T1/ptm/m/n/10 Dep-re- [2665] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1126--1126 [] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE. factor = SEf)))[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 1143--1143 []\T1/pcr/m/n/9 ## You can manually set it before running this : doExtras < - TRUE # or FALSE[] Underfull \vbox (badness 10000) has occurred while \output is active [2666] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1181--1181 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap() ==> k = 1 clust er is optimal")[] Underfull \hbox (badness 4144) in paragraph at lines 1213--1217 []\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 does not have a []\T1 /pcr/m/n/10 diss []\T1/ptm/m/n/10 nor a []\T1/pcr/m/n/10 data []\T1/ptm/m/n/10 com-po-nent, e.g., for [2667] Overfull \hbox (60.78088pt too wide) in paragraph at lines 1289--1289 [] \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1, cex.txt = cex,[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1295--1295 [] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin t variability."),[] [2668] [2669] [2670] Underfull \hbox (badness 10000) in paragraph at lines 1482--1485 Underfull \hbox (badness 10000) in paragraph at lines 1499--1503 [][][]\T1/pcr/m/n/10 princomp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cmds cale[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pam[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 clara[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 daisy[][ ][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 par[][][][]\T1/ptm/m/n/10 , [][][]\T 1/pcr/m/n/10 identify[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cov.mve[][][ ][]\T1/ptm/m/n/10 , Overfull \hbox (31.3804pt too wide) in paragraph at lines 1523--1523 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a nd label ellipses[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1533--1533 [] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i dent. only points[] [2671] Underfull \hbox (badness 5741) in paragraph at lines 1573--1576 []\T1/pcr/m/n/10 coefHier() []\T1/ptm/m/n/10 di-rectly in-ter-faces to the un-d er-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only [2672] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1642--1642 [] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa rnType,[] [2673] Underfull \hbox (badness 1552) in paragraph at lines 1691--1693 []\T1/ptm/b/n/10 A\T1/ptm/m/n/10 symmetric bi-nary vari-able, aka []\T1/pcr/m/n /10 "A" []\T1/ptm/m/n/10 in re-sult []\T1/pcr/m/n/10 Types[]\T1/ptm/m/n/10 , se e Underfull \hbox (badness 1629) in paragraph at lines 1705--1709 []\T1/ptm/b/n/10 I\T1/ptm/m/n/10 nterval scaled -- the \T1/ptm/b/n/10 de-fault \T1/ptm/m/n/10 for all nu-meric Underfull \hbox (badness 3746) in paragraph at lines 1705--1709 \T1/ptm/m/n/10 (incl []\T1/pcr/m/n/10 integer[]\T1/ptm/m/n/10 ) columns of []\T 1/pcr/m/n/10 x[]\T1/ptm/m/n/10 , aka []\T1/pcr/m/n/10 "I" []\T1/ptm/m/n/10 in r e-sult []\T1/pcr/m/n/10 Types[]\T1/ptm/m/n/10 , see [2674] Underfull \hbox (badness 1540) in paragraph at lines 1781--1789 \T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1 0 w[]^^N[]$\T1/ptm/m/n/10 , where $\OML/cmm/m/it/10 w[]$[]\T1/pcr/m/n/10 = [2675] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1870--1870 []\T1/pcr/m/n/9 ## Example 2 in reference, extended --- different ways of "m ixed" / "gower":[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1874--1874 []\T1/pcr/m/n/9 summary(d0 <- daisy(flower)) # -> the first 3 {0,1} treate d as *N*ominal[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 1875--1875 []\T1/pcr/m/n/9 summary(dS123 <- daisy(flower, type = list(symm = 1:3))) # fi rst 3 treated as *S*ymmetric[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1876--1876 []\T1/pcr/m/n/9 stopifnot(dS123 == d0) # i.e., *S*ymmetric <==> *N*ominal {fo r 2-level factor}[] Overfull \hbox (106.98032pt too wide) in paragraph at lines 1880--1880 []\T1/pcr/m/n/9 summary(dA123 <- daisy(flowerN)) # .. all 3 logicals treated * A*symmetric binary (w/ warning)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1882--1882 []\T1/pcr/m/n/9 summary(dA13 <- daisy(flower, type = list(asymm = c(1, 3), ord ratio = 7)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1890--1890 []\T1/pcr/m/n/9 summary(dN <- daisy(Nflow)) # w/ warning: treated binary .. 1: 3 as interval[] Overfull \hbox (117.7803pt too wide) in paragraph at lines 1891--1891 []\T1/pcr/m/n/9 ## Still, using Euclidean/Manhattan distance for {0-1} *is* id entical to treating them as "N" :[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 1907--1907 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st and = FALSE, [2676] [2677] [2678] [2679] [2680] Underfull \hbox (badness 10000) in paragraph at lines 2228--2231 Underfull \hbox (badness 3179) in paragraph at lines 2242--2248 [][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] []\T1/ptm/m/n/10 which is also the [][][]\T1/pcr/m/n/10 predict[][][] []\T1/ptm/m/n/10 method for []\T1/pcr/m/n/1 0 ellipsoid []\T1/ptm/m/n/10 ob-jects. [2681] [2682] Underfull \hbox (badness 10000) in paragraph at lines 2400--2403 [][][]\T1/pcr/m/n/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-en ces; [][][]\T1/pcr/m/n/10 fanny.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 partition.object[][][][]\T1/ptm/m/n/10 , [2683] Underfull \hbox (badness 1292) in paragraph at lines 2468--2471 []\T1/ptm/m/n/10 named vec-tor with []\T1/pcr/m/n/10 iterations[]\T1/ptm/m/n/10 , the num-ber of it-er-a-tions needed and [2684] Underfull \hbox (badness 6675) in paragraph at lines 2477--2479 []\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl us-ter-ing, see Underfull \hbox (badness 10000) in paragraph at lines 2500--2503 [][][]\T1/pcr/m/n/10 fanny[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.f anny[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 dissimilarity.object[][][][]\ T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 partition.object[][][][]\T1/ptm/m/n/10 , [2685] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2575--2575 [] \T1/pcr/m/n/9 "4" = "red", "5" = "blue")[levels(f lowerN$color)][] Overfull \hbox (90.78033pt too wide) in paragraph at lines 2576--2576 []\T1/pcr/m/n/9 levels(flowerN$soil) <- c("1" = "dry", "2" = "normal", "3" = "wet")[levels(flowerN$soil)][] [2686] Overfull \hbox (48.78088pt too wide) in paragraph at lines 2639--2639 []\T1/pcr/m/n/10 medoids(x, clustering, diss = inherits(x, "dist"), USE.NAMES = FALSE, ...) [2687] Overfull \hbox (69.18036pt too wide) in paragraph at lines 2686--2686 [] \T1/pcr/m/n/9 stopifnot(length(cl.k) == nrow(votes.repub), 1 <= cl.k, cl.k <= k, table(cl.k) >= 2)[] [2688] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2791--2791 []\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/ 9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[] [2689] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2870--2870 [] \T1/pcr/m/n/10 variant = c("original", "o_1", "o_2", "f_3", "f_4", "f_5" , "faster"),[] [2690] [2691] [2692] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3099--3099 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro und (1, 16):[] [2693] [2694] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3202--3202 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co l.axis = "red")[] [2695] [2696] [2697] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3398--3398 [] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x $ac, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3399--3399 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2698] Underfull \hbox (badness 10000) in paragraph at lines 3466--3469 []\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via []\T1/pcr/m /n/10 pltree() []\T1/ptm/m/n/10 is pro-vided by []\T1/pcr/m/n/10 dg <- [2699] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3516--3516 [] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3517--3517 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2700] [2701] [2702] Underfull \hbox (badness 10000) in paragraph at lines 3702--3705 []\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 does not have a []\T1 /pcr/m/n/10 diss []\T1/ptm/m/n/10 com-po-nent as for [][][]\T1/pcr/m/n/10 pam[] [][](*, Underfull \hbox (badness 1448) in paragraph at lines 3702--3705 \T1/pcr/m/n/10 keep.diss=FALSE)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 dist []\T1/p tm/m/n/10 must be the dis-sim-i-lar-ity if a clus-plot is [2703] Underfull \hbox (badness 10000) in paragraph at lines 3765--3770 [][][]\T1/pcr/m/n/10 partition.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n /10 clusplot.partition[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 clusplot.de fault[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pam[][][][]\T1/ptm/m/n/10 , [2704] Underfull \hbox (badness 1748) in paragraph at lines 3827--3832 \T1/ptm/m/n/10 dis-patches to [][][]\T1/pcr/m/n/10 plot.hclust[][][](..)[]\T1/p tm/m/n/10 . If more flex-i-ble plots are needed, con-sider []\T1/pcr/m/n/10 xx <- Underfull \hbox (badness 6268) in paragraph at lines 3839--3842 [][][]\T1/pcr/m/n/10 agnes[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 agnes.o bject[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 diana[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 diana.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/1 0 hclust[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 par[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.agnes[][][][]\T1/ptm/m/n/10 , [2705] [2706] [2707] Underfull \hbox (badness 10000) in paragraph at lines 4024--4027 [][][]\T1/pcr/m/n/10 summary.agnes[][][] []\T1/ptm/m/n/10 pro-duc-ing more out- put; [][][]\T1/pcr/m/n/10 agnes[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 ag nes.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/ n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4055--4058 [][][]\T1/pcr/m/n/10 summary.clara[][][] []\T1/ptm/m/n/10 pro-duc-ing more out- put; [][][]\T1/pcr/m/n/10 clara[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cl ara.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/ n/10 , [2708] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4108--4108 [] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right = TRUE, ...)[] [2709] Underfull \hbox (badness 2035) in paragraph at lines 4119--4121 []\T1/ptm/m/n/10 a []\T1/pcr/m/n/10 dissimilarity []\T1/ptm/m/n/10 ob-ject or a []\T1/pcr/m/n/10 summary.dissimilarity []\T1/ptm/m/n/10 one for [2710] [2711] [2712] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4312--4312 [] \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w idth "* s[i]),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 4314--4314 [] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat = TRUE, ...)[] [2713] [2714] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4456--4456 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus ter-wise coloring[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4465--4465 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4467--4467 [] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma in")); frame()[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 4470--4470 []\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol denrod4", "gray20")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4472--4472 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE,[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4479--4479 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro wnames == indices[] [2715] [2716] [2717] [2718] [2719] [2720] [2721] Underfull \hbox (badness 10000) in paragraph at lines 4853--4859 []\T1/ptm/m/n/10 Our ver-sion of the []\T1/pcr/m/n/10 xclara []\T1/ptm/m/n/10 i s slightly more rounded than the one from Underfull \hbox (badness 10000) in paragraph at lines 4869--4871 []\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file `\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side Overfull \hbox (52.98038pt too wide) in paragraph at lines 4882--4882 []\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10 01:2000}, {2001:3000} Overfull \hbox (9.78043pt too wide) in paragraph at lines 4884--4884 []\T1/pcr/m/n/9 p.ID <- c(78, 1411, 2535) ## PAM\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s medoid indices == pam(xclara, 3)$id.med[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4894--4894 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o bservations:[] [2722] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4898--4898 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? - - Robust range:[] [2723]) (./codetools-pkg.tex [2724] Chapter 21. Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16 [] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17 [] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = !all,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18 [] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress Undefined,[] [2725] Underfull \hbox (badness 10000) in paragraph at lines 65--70 []\T1/pcr/m/n/10 checkUsageEnv []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 checkUsage Package []\T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply [2726] Overfull \hbox (18.78088pt too wide) in paragraph at lines 118--118 []\T1/pcr/m/n/10 makeConstantFolder(..., leaf, handler, call, exit, isLocal, f oldable,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 121--121 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e nterInternal,[] [2727] [2728] [2729]) (./foreign-pkg.tex [2730] Chapter 22. Underfull \hbox (badness 10000) in paragraph at lines 33--37 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of a Data Underfull \hbox (badness 10000) in paragraph at lines 33--37 \T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able as [][]$\T1/p cr/m/n/10 https : / / support . Underfull \hbox (badness 10000) in paragraph at lines 33--37 \T1/pcr/m/n/10 sas . com / content / dam / SAS / support / en / technical-[]pap ers / Overfull \hbox (74.28088pt too wide) in paragraph at lines 33--37 \T1/pcr/m/n/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[]s et-[]in-[]sas-[]transport-[]xport-[]format . [2731] Underfull \hbox (badness 1231) in paragraph at lines 67--70 []\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr om, or a [2732] [2733] Underfull \hbox (badness 3601) in paragraph at lines 237--245 []\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude []\T1/pcr/m /n/10 "datalabel"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "time.stamp"[]\T1/ptm/m/n/ 10 , [2734] Overfull \hbox (12.78088pt too wide) in paragraph at lines 295--295 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates = FALSE, [2735] [2736] [2737] Overfull \hbox (48.78088pt too wide) in paragraph at lines 461--461 [] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t o.data.frame,[] [2738] Overfull \hbox (30.78088pt too wide) in paragraph at lines 462--462 [] \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen d", "no"),[] Underfull \hbox (badness 2846) in paragraph at lines 505--514 []\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif- fer-ent lev- Underfull \hbox (badness 3746) in paragraph at lines 505--514 \T1/ptm/m/n/10 els. For []\T1/pcr/m/n/10 "append" []\T1/ptm/m/n/10 (the de-faul t), the first orig-i-nal value la-bel is Underfull \hbox (badness 2269) in paragraph at lines 505--514 \T1/ptm/m/n/10 kept while fur-ther du-pli-cated la-bels are re-named to []\T1/p cr/m/n/10 paste0(label, Underfull \hbox (badness 10000) in paragraph at lines 515--518 []\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with du- Underfull \hbox (badness 10000) in paragraph at lines 515--518 \T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault []\T1/pcr/m/n/10 "_dup licated_"[]\T1/ptm/m/n/10 ) if [2739] Underfull \hbox (badness 10000) in paragraph at lines 549--557 []\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 https : / / learn . microsoft . com / en-[]us / windows / win32 / intl / Underfull \hbox (badness 7613) in paragraph at lines 567--573 []\T1/ptm/m/n/10 There may be at-tributes []\T1/pcr/m/n/10 "label.table" []\T1/ ptm/m/n/10 and []\T1/pcr/m/n/10 "variable.labels"[]\T1/ptm/m/n/10 . At-tribute [2740] Overfull \hbox (20.58041pt too wide) in paragraph at lines 622--622 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg ument settings.[] Overfull \hbox (112.38031pt too wide) in paragraph at lines 623--623 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to R factor labels) are uncomplete,[] [2741] Overfull \hbox (9.78043pt too wide) in paragraph at lines 656--656 []\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ ate variables[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 660--660 []\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt h=w), "\n"))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 667--667 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, collapse="")[] [2742] [2743] Underfull \hbox (badness 10000) in paragraph at lines 811--812 Overfull \hbox (4.38043pt too wide) in paragraph at lines 821--821 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f oreign")[1])[] [2744] Underfull \hbox (badness 10000) in paragraph at lines 868--872 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of a Data Underfull \hbox (badness 10000) in paragraph at lines 868--872 \T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able at [][]$\T1/p cr/m/n/10 https : / / support . Underfull \hbox (badness 10000) in paragraph at lines 868--872 \T1/pcr/m/n/10 sas . com / content / dam / SAS / support / en / technical-[]pap ers / Overfull \hbox (74.28088pt too wide) in paragraph at lines 868--872 \T1/pcr/m/n/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[]s et-[]in-[]sas-[]transport-[]xport-[]format . [2745] Overfull \hbox (24.78088pt too wide) in paragraph at lines 899--899 [] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G lobalEnv) [2746] Overfull \hbox (0.78088pt too wide) in paragraph at lines 963--963 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute (x))) [2747] [2748] Underfull \hbox (badness 10000) in paragraph at lines 1075--1076 [][][]$\T1/pcr/m/n/10 https : / / www . clicketyclick . dk / databases / xbase / format / data _ types . Overfull \hbox (24.78088pt too wide) in paragraph at lines 1111--1111 [] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", "codes"))[] [2749] [2750] Underfull \hbox (badness 10000) in paragraph at lines 1268--1274 []\T1/ptm/m/n/10 The work for this func-tion is done by []\T1/pcr/m/n/10 foreig n:::writeForeignStata[]\T1/ptm/m/n/10 , [2751] Underfull \hbox (badness 2088) in paragraph at lines 1294--1297 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 package="SPSS"[]\T1/ptm/m/n/10 , as a sid e ef-fect, the dec-i-mal in-di-ca-tor is al-ways set by []\T1/pcr/m/n/10 SET [2752]) (./lattice-pkg.tex Chapter 23. [2753] Underfull \hbox (badness 2073) in paragraph at lines 117--121 \T1/ptm/m/n/10 pro-vide a holis-tic in-tro-duc-tion to the Trel-lis paradigm: [ ][]$\T1/pcr/m/n/10 http : / / web . archive . org / Underfull \hbox (badness 10000) in paragraph at lines 117--121 \T1/pcr/m/n/10 web / 20081020164041 / http : / / cm . bell-[]labs . com / cm / ms / departments / sia / [2754] [2755] Overfull \hbox (12.78088pt too wide) in paragraph at lines 291--291 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 295--295 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .xyplot"),[] [2756] Overfull \hbox (42.78088pt too wide) in paragraph at lines 306--306 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul t.dotplot"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 316--316 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.barchart"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 327--327 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.stripplot"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 351--351 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Underfull \vbox (badness 10000) has occurred while \output is active [2757] Overfull \hbox (30.78088pt too wide) in paragraph at lines 355--355 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .bwplot"),[] [2758] [2759] [2760] Underfull \hbox (badness 1221) in paragraph at lines 676--679 []\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as ar-gu-ments to [2761] [2762] [2763] [2764] Underfull \hbox (badness 2005) in paragraph at lines 1014--1026 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of fac-tors will be Underfull \hbox (badness 1199) in paragraph at lines 1014--1026 \T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a use-ful lay-out. [2765] [2766] Underfull \hbox (badness 1661) in paragraph at lines 1127--1133 []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 y []\T1/ptm/m/n/10 sho uld be num-bers be-tween 0 and 1, giv-ing co-or-di-nates [2767] Underfull \hbox (badness 1097) in paragraph at lines 1253--1255 []\T1/ptm/m/n/10 Logical flag, whether leg-end should have a Underfull \hbox (badness 1917) in paragraph at lines 1267--1268 []\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to [2768] [2769] [2770] Underfull \hbox (badness 1540) in paragraph at lines 1507--1513 []\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][][]\T1/pcr/m/ n/10 plot.trellis[][][][]\T1/ptm/m/n/10 , [2771] Underfull \hbox (badness 10000) in paragraph at lines 1594--1611 [][][]\T1/pcr/m/n/10 panel.dotplot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.stripplot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.superpose[] [][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.loess[][][][]\T1/ptm/m/n/10 , [2772] Underfull \vbox (badness 10000) has occurred while \output is active [2773] Overfull \hbox (36.7804pt too wide) in paragraph at lines 1682--1682 [] \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar dSprays$rowpos))),[] [2774] Underfull \hbox (badness 2012) in paragraph at lines 1736--1738 []\T1/ptm/m/n/10 additional ar-gu-ments passed to [][][]\T1/pcr/m/n/10 xyplot[] [][][]\T1/ptm/m/n/10 , which may pass them on to Underfull \hbox (badness 6808) in paragraph at lines 1766--1770 []\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p assed to Underfull \hbox (badness 10000) in paragraph at lines 1783--1786 []\T1/ptm/m/n/10 style set-tings be-yond the stan-dard []\T1/pcr/m/n/10 col[]\T 1/ptm/m/n/10 , []\T1/pcr/m/n/10 lty[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lwd[]\T1 /ptm/m/n/10 , etc; see [2775] Underfull \hbox (badness 10000) in paragraph at lines 1836--1838 []\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix An-drews [2776] [2777] [2778] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2077--2077 [] \T1/pcr/m/n/10 auto.key = lattice.getOption("default.args")$auto .key,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2090--2090 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl ot"),[] Underfull \vbox (badness 10000) has occurred while \output is active [2779] Underfull \hbox (badness 10000) in paragraph at lines 2169--2172 []\T1/ptm/m/n/10 When []\T1/pcr/m/n/10 breaks []\T1/ptm/m/n/10 is un-spec-i-fie d, the value of Underfull \hbox (badness 1320) in paragraph at lines 2169--2172 []\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") []\T1/ptm/m/n/10 is firs t checked. If [2780] [2781] [2782] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2374--2374 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2378--2378 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .qqmath"),[] [2783] [2784] [2785] [2786] [2787] Overfull \hbox (60.78088pt too wide) in paragraph at lines 2737--2737 [] \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev elplot.raster")[] [2788] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2769--2769 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl ot"),[] Underfull \vbox (badness 10000) has occurred while \output is active [2789] Underfull \hbox (badness 2913) in paragraph at lines 2848--2853 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when []\T1/ pcr/m/n/10 x []\T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 2848--2853 []\T1/pcr/m/n/10 row.values []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 column.values []\T1/ptm/m/n/10 must have the same lengths as [2790] [2791] Underfull \hbox (badness 6758) in paragraph at lines 2976--2980 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be Underfull \hbox (badness 7576) in paragraph at lines 2976--2980 \T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][][]\T1/pcr/m/n/10 grid.ra ster[][][][]\T1/ptm/m/n/10 . See also Underfull \hbox (badness 10000) in paragraph at lines 2982--2984 []\T1/ptm/m/n/10 Logical flag, passed to [][][]\T1/pcr/m/n/10 rasterGrob[][][] []\T1/ptm/m/n/10 when Underfull \hbox (badness 1609) in paragraph at lines 3034--3040 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti ons should be used, Underfull \hbox (badness 2772) in paragraph at lines 3034--3040 \T1/ptm/m/n/10 both for the false color im-age and the color key (if present). Ef- Underfull \hbox (badness 1400) in paragraph at lines 3034--3040 \T1/ptm/m/n/10 fec-tively, set-ting this to []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n /10 changes the de-fault panel func-tion from Underfull \hbox (badness 2486) in paragraph at lines 3058--3062 []\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for the de-fault panel func-tion [2792] [2793] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3163--3163 [] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3164--3164 [] \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3165--3165 [] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite = TRUE),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3176--3176 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. cloud"),[] [2794] Overfull \hbox (66.78088pt too wide) in paragraph at lines 3191--3191 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.wireframe"),[] [2795] Underfull \hbox (badness 2913) in paragraph at lines 3256--3261 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when []\T1/ pcr/m/n/10 x []\T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 3256--3261 []\T1/pcr/m/n/10 row.values []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 column.values []\T1/ptm/m/n/10 must have the same lengths as [2796] [2797] [2798] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.parallel} ) has been already used, duplicate ignored \relax l.3545 \aliasA{parallel}{B\_08\_splom}{parallel} [2799] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3587--3587 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. splom"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3610--3610 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.parallel"),[] Underfull \vbox (badness 10000) has occurred while \output is active [2800] [2801] [2802] [2803] [2804] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3947--3947 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt( var(x))) [2805] Underfull \hbox (badness 2277) in paragraph at lines 4033--4037 []\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault set-tings by Underfull \hbox (badness 2435) in paragraph at lines 4033--4037 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2806] [2807] Overfull \hbox (120.78088pt too wide) in paragraph at lines 4130--4130 [] \T1/pcr/m/n/10 symbol = palette.colors(palette = "Okabe-Ito") [c(6, 2, 4, 7, 3, 5, 8)],[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 4132--4132 [] \T1/pcr/m/n/10 region = hcl.colors(14, palette = "YlGnBu", re v = TRUE),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4139--4139 [] \T1/pcr/m/n/10 reference = "gray90", bg = "transparent", fg = " black",[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 4140--4140 [] \T1/pcr/m/n/10 strip.bg = rep("gray95", 7), strip.fg = rep("gra y70", 7),[] [2808] [2809] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4283--4283 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict = FALSE) Underfull \hbox (badness 1173) in paragraph at lines 4292--4296 []\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un- spec-i-fied in Underfull \hbox (badness 3219) in paragraph at lines 4319--4321 []\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i s-sued when Underfull \hbox (badness 1728) in paragraph at lines 4336--4340 []\T1/pcr/m/n/10 theme[]\T1/ptm/m/n/10 ). These are used to mod-ify the cur-ren t set-tings (ob-tained by [2810] Underfull \hbox (badness 5161) in paragraph at lines 4401--4405 []\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in []\T1/pcr/m/n/10 trell is.settings []\T1/ptm/m/n/10 has not been fi-nal-ized, Underfull \hbox (badness 4913) in paragraph at lines 4401--4405 \T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca n be ob-tained by [2811] [2812] Underfull \hbox (badness 1067) in paragraph at lines 4519--4529 []\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. []\T1/pcr/m/n/10 col []\T1/ptm/m/n/ 10 is used for com-po-nents []\T1/pcr/m/n/10 "plot.symbol"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4519--4529 []\T1/pcr/m/n/10 "plot.line"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "plot.polygon"[ ]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "superpose.symbol"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1735) in paragraph at lines 4519--4529 []\T1/pcr/m/n/10 "superpose.line"[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 "super pose.polygon"[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 col.points Underfull \hbox (badness 10000) in paragraph at lines 4519--4529 []\T1/ptm/m/n/10 over-rides []\T1/pcr/m/n/10 col[]\T1/ptm/m/n/10 , but is used only for []\T1/pcr/m/n/10 "plot.symbol" []\T1/ptm/m/n/10 and Underfull \hbox (badness 5231) in paragraph at lines 4519--4529 []\T1/pcr/m/n/10 "superpose.symbol"[]\T1/ptm/m/n/10 . Sim-i-larly, []\T1/pcr/m/ n/10 col.line []\T1/ptm/m/n/10 over-rides []\T1/pcr/m/n/10 col []\T1/ptm/m/n/10 for Underfull \hbox (badness 1701) in paragraph at lines 4544--4547 []\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents []\T1/pcr/m/n/10 pl ot.symbol[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 plot.polygon[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4547--4549 []\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents []\T1/pcr/m/n/10 plot.polygon []\T1/ptm/m/n/10 and [2813] [2814] Underfull \hbox (badness 2932) in paragraph at lines 4690--4695 []\T1/pcr/m/n/10 auto.key[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 aspect[]\T1/ptm/m/ n/10 , []\T1/pcr/m/n/10 between[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 grid[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 skip[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 strip[]\T1/ ptm/m/n/10 , []\T1/pcr/m/n/10 xscale.components[]\T1/ptm/m/n/10 , [2815] [2816] [2817] [2818] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4966--4966 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab = "Height")[] [2819] [2820] [2821] Underfull \hbox (badness 10000) in paragraph at lines 5153--5156 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 trellis[]\T1/ptm/m/n/10 , by de-fault plot-ted by []\T1/pcr/m/n/10 print.trellis[]\T1/ptm/m/n/10 . [2822] Underfull \hbox (badness 1442) in paragraph at lines 5285--5288 []\T1/pcr/m/n/10 plot.shingle []\T1/ptm/m/n/10 dis-plays the ranges of shin-gle s via rect-an-gles. []\T1/pcr/m/n/10 print.shingle []\T1/ptm/m/n/10 and [2823] [2824] [2825] [2826] [2827] [2828] Underfull \hbox (badness 3646) in paragraph at lines 5624--5627 [][][]\T1/pcr/m/n/10 Lattice[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 draw. key[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 trellis.par.get[][][][]\T1/ptm /m/n/10 , and [][][]\T1/pcr/m/n/10 xyplot[][][][]\T1/ptm/m/n/10 , specif-i-call y the en-try for Overfull \hbox (36.78088pt too wide) in paragraph at lines 5654--5654 [] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh ich.given],[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5655--5655 [] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which .given],[] [2829] Underfull \hbox (badness 10000) in paragraph at lines 5743--5746 []\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i -zon-tal. Underfull \hbox (badness 2103) in paragraph at lines 5743--5746 []\T1/pcr/m/n/10 horizontal=FALSE []\T1/ptm/m/n/10 is use-ful for strips on the left of pan-els us-ing [2830] Underfull \hbox (badness 1635) in paragraph at lines 5769--5774 []\T1/pcr/m/n/10 strip.default []\T1/ptm/m/n/10 is called for its side-effect, which is to draw a strip ap-pro-pri-ate for [2831] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5920--5920 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la bels,[] [2832] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5934--5934 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose "), ...)[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5935--5935 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos e"), ...)[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5938--5938 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location" , "toplevel",[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5941--5941 [] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig ht", "page"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 5943--5943 [] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in side"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5949--5949 [] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi ch.given",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5950--5950 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5951--5951 [] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi ch.panel",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5952--5952 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5953--5953 [] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co lumn",[] Underfull \hbox (badness 10000) in paragraph at lines 5969--5971 []\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of Underfull \hbox (badness 2376) in paragraph at lines 5980--5982 []\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point. De-faults to [2833] [2834] Underfull \hbox (badness 2538) in paragraph at lines 6105--6109 \T1/ptm/m/n/10 For []\T1/pcr/m/n/10 trellis.focus[]\T1/ptm/m/n/10 , the de-faul t is []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 in in-ter-ac-tive mode, and Underfull \hbox (badness 4205) in paragraph at lines 6116--6123 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 panel.identify.qqmath[]\T1/ptm/m/n/10 , e x-tra pa-ram-e-ters are passed on to Underfull \hbox (badness 4792) in paragraph at lines 6116--6123 []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 trellis.switchFocus[]\T1/ptm/m/n/10 , the se are used (in com-bi-na-tion with [2835] [2836] Underfull \hbox (badness 10000) in paragraph at lines 6269--6273 [][][]\T1/pcr/m/n/10 identify[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Latt ice[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.trellis[][][][]\T1/ptm/m /n/10 , [][][]\T1/pcr/m/n/10 trellis.currentLayout[][][][]\T1/ptm/m/n/10 , [2837] [2838] Underfull \hbox (badness 4242) in paragraph at lines 6416--6421 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- [2839] [2840] Underfull \hbox (badness 3601) in paragraph at lines 6532--6537 []\T1/ptm/m/n/10 Creates Box and Whisker plot of []\T1/pcr/m/n/10 x []\T1/ptm/m /n/10 for ev-ery level of []\T1/pcr/m/n/10 y []\T1/ptm/m/n/10 (or the other way round Underfull \hbox (badness 2486) in paragraph at lines 6532--6537 \T1/ptm/m/n/10 if []\T1/pcr/m/n/10 horizontal=FALSE[]\T1/ptm/m/n/10 ). By de-fa ult, the ac-tual box-plot statis-tics are cal-cu-lated us-ing [2841] Overfull \hbox (60.78088pt too wide) in paragraph at lines 6620--6620 [] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co lors")$palette,[] [2842] [2843] [2844] Underfull \hbox (badness 10000) in paragraph at lines 6819--6823 []\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The Underfull \hbox (badness 10000) in paragraph at lines 6824--6826 []\T1/ptm/m/n/10 numeric, be-tween 0 and 1, giv-ing a min-i-mum sat-u-ra-tion i n [2845] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6920--6920 [] \T1/pcr/m/n/9 shade.colors.palette = makeShadePalette(hcl.colors(1 0, "Inferno"),[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6923--6923 [] \T1/pcr/m/n/9 shade.colors.palette = makeShadePalette(hcl.colors(1 0, "Dark Mint"),[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6926--6926 [] \T1/pcr/m/n/9 shade.colors.palette = makeShadePalette(hcl.colors(1 0, "Harmonic"),[] [2846] [2847] [2848] [2849] [2850] [2851] Underfull \hbox (badness 1320) in paragraph at lines 7288--7295 []\T1/pcr/m/n/10 panel.levelplot.raster []\T1/ptm/m/n/10 is an al-ter-na-tive p anel func-tion that uses the raster draw- Underfull \hbox (badness 1715) in paragraph at lines 7288--7295 \T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more ef-fi-cient. When us-ing [2852] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7363--7363 [] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = NULL,[] [2853] Underfull \hbox (badness 10000) in paragraph at lines 7393--7397 []\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments to Underfull \hbox (badness 1584) in paragraph at lines 7393--7397 []\T1/pcr/m/n/10 diag.panel.splom []\T1/ptm/m/n/10 to know what ar-gu-ments thi s func-tion is passed [2854] Underfull \hbox (badness 10000) in paragraph at lines 7498--7501 \T1/ptm/m/n/10 and []\T1/pcr/m/n/10 diag.panel []\T1/ptm/m/n/10 from []\T1/pcr/ m/n/10 panel.pairs[]\T1/ptm/m/n/10 . Cur-rently ig-nored by Overfull \hbox (101.58032pt too wide) in paragraph at lines 7523--7523 [] \T1/pcr/m/n/9 function(i,j) hcl.colors(11)[i+j-1]) ## rainbow( 11, start=.12, end=.5)[i+j-1])[] [2855] [2856] Underfull \hbox (badness 2012) in paragraph at lines 7664--7667 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2857] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7710--7710 [] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta ils.n = 50))[] [2858] [2859] [2860] Underfull \hbox (badness 1939) in paragraph at lines 7899--7907 []\T1/pcr/m/n/10 "lm" []\T1/ptm/m/n/10 adds a lin-ear re-gres-sion line (same a s [][][]\T1/pcr/m/n/10 panel.lmline[][][][]\T1/ptm/m/n/10 , ex-cept Underfull \hbox (badness 1163) in paragraph at lines 7899--7907 \T1/ptm/m/n/10 for de-fault graph-i-cal pa-ram-e-ters). []\T1/pcr/m/n/10 "loess " []\T1/ptm/m/n/10 adds a loess fit (same as Underfull \hbox (badness 2772) in paragraph at lines 7922--7925 []\T1/ptm/m/n/10 Most gen-er-ally, []\T1/pcr/m/n/10 grid []\T1/ptm/m/n/10 can b e a list of ar-gu-ments to be sup-plied to [2861] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7993--7993 [] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y = c(1/6, 4/6)),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8003--8003 [] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d raw = FALSE),[] [2862] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8088--8088 [] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam e.type)[] [2863] Overfull \hbox (84.78088pt too wide) in paragraph at lines 8107--8107 [] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ide ntifier, name.type)[] [2864] [2865] Overfull \hbox (63.78036pt too wide) in paragraph at lines 8246--8246 []\T1/pcr/m/n/9 xyplot(y ~ x, d, panel = panel.rect, col = 4, alpha = 0.5, wid th = 0.1, height = 0.1)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8253--8253 []\T1/pcr/m/n/9 xyplot(y ~ x, d, panel = panel.polygon, col = 4, alpha = 0.5, rule = "evenodd")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8255--8255 []\T1/pcr/m/n/9 ## Example adapted from https://journal.r-project.org/articles /RJ-2012-017/[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8259--8259 []\T1/pcr/m/n/9 xyplot(y ~ x, data = d, panel = panel.polygon, rule = "none", col = "grey")[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8260--8260 []\T1/pcr/m/n/9 xyplot(y ~ x, data = d, panel = panel.polypath, rule = "windin g", col = "grey")[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8261--8261 []\T1/pcr/m/n/9 xyplot(y ~ x, data = d, panel = panel.polypath, rule = "evenod d", col = "grey")[] [2866] Overfull \hbox (66.78088pt too wide) in paragraph at lines 8324--8324 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden tifier = "grid")[] [2867] Underfull \hbox (badness 1436) in paragraph at lines 8379--8385 []\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c al pa-ram-e-ters for [2868] Overfull \hbox (42.18039pt too wide) in paragraph at lines 8509--8509 [] \T1/pcr/m/n/9 panel.superpose(x, y, ..., panel.groups = panel.ave rage, grid = FALSE,[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8523--8523 [] \T1/pcr/m/n/9 args = list(mean = mean(x), sd = sd(x)), ...)[] [2869] [2870] [2871] [2872] [2873] [2874] [2875] Underfull \hbox (badness 10000) in paragraph at lines 8948--8951 []\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to []\T1/pcr/m/n/10 panel.super pose Underfull \hbox (badness 10000) in paragraph at lines 8948--8951 []\T1/ptm/m/n/10 from []\T1/pcr/m/n/10 panel.superpose.2[]\T1/ptm/m/n/10 , and to []\T1/pcr/m/n/10 panel.groups []\T1/ptm/m/n/10 from [2876] [2877] Overfull \hbox (24.78088pt too wide) in paragraph at lines 9123--9123 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st ack, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9124--9124 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin t, ...)[] [2878] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9136--9136 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr ipts, ...)[] Underfull \hbox (badness 3118) in paragraph at lines 9155--9158 []\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. []\T1/pcr/m/n/10 type [ ]\T1/ptm/m/n/10 has a dif-fer-ent mean-ing in [2879] Underfull \hbox (badness 1515) in paragraph at lines 9231--9235 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2880] [2881] Underfull \hbox (badness 6316) in paragraph at lines 9337--9342 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in [2882] Overfull \hbox (47.58038pt too wide) in paragraph at lines 9447--9447 [] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b ottom$labels$labels)[] [2883] [2884] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9586--9586 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su nspot.year)),[] [2885] Underfull \hbox (badness 1028) in paragraph at lines 9645--9649 \T1/pcr/m/n/10 condition []\T1/ptm/m/n/10 for 2-D, and []\T1/pcr/m/n/10 left, r ight.x, right.y, left.name, right.x.name, [2886] [2887] [2888] [2889] [2890] [2891] [2892] Underfull \hbox (badness 7238) in paragraph at lines 10109--10113 []\T1/ptm/m/n/10 Factor with lev-els []\T1/pcr/m/n/10 "Svansota"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "No. 462"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Manchuria"[] \T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "No. 475"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10109--10113 []\T1/pcr/m/n/10 "Velvet"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Peatland"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "Glabron"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "No. 4 57"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Wisconsin No. 38"[]\T1/ptm/m/n/10 , [2893] [2894] [2895] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma} ) has been already used, duplicate ignored \relax l.10340 \aliasA{melanoma}{H\_melanoma}{melanoma} [2896] [2897] [2898] Underfull \hbox (badness 10000) in paragraph at lines 10502--10507 \T1/pcr/m/n/10 diseases[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Diabetes[]\T1/ptm/m/ n/10 , []\T1/pcr/m/n/10 Flu and pneumonia[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 He art disease[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Lower Overfull \hbox (9.78043pt too wide) in paragraph at lines 10575--10575 [] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list( columns = 2),[] [2899] [2900]) (./mgcv-pkg.tex Chapter 24. [2901] [2902] Overfull \hbox (6.78088pt too wide) in paragraph at lines 160--160 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL, Overfull \hbox (18.78088pt too wide) in paragraph at lines 163--163 [] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret e=FALSE,[] [2903] Overfull \hbox (48.78088pt too wide) in paragraph at lines 165--165 [] \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in tercept=NULL,[] Underfull \hbox (badness 1142) in paragraph at lines 185--189 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 210--215 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2904] [2905] [2906] [2907] Underfull \hbox (badness 10000) in paragraph at lines 379--386 [][][]\T1/pcr/m/n/10 mgcv.parallel[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gamObject[][][][]\T1 /ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/ptm/m/n/10 , [][][]\T1 /pcr/m/n/10 smooth.terms[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 379--386 [][][]\T1/pcr/m/n/10 linear.functional.terms[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][] [][]predict. gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 379--386 [][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 g am.side[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.selection[][][][]\T1/p tm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][][]\T1/ptm /m/n/10 , [2908] Overfull \hbox (4.38043pt too wide) in paragraph at lines 422--422 []\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2 ,bs=bs,k=k)+[] [2909] [2910] [2911] Underfull \hbox (badness 2922) in paragraph at lines 634--635 []\T1/ptm/m/n/10 The link func-tion: one of []\T1/pcr/m/n/10 "logit"[]\T1/ptm/m /n/10 , []\T1/pcr/m/n/10 "probit"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cloglog" []\T1/ptm/m/n/10 and [2912] [2913] Underfull \hbox (badness 1406) in paragraph at lines 704--705 []\T1/ptm/m/n/10 The MKL BLAS is mut-lithreaded by de-fault. Un-der linux set-t ing en-vi-ron-ment vari-able [2914] [2915] Underfull \hbox (badness 1158) in paragraph at lines 814--816 []\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe n us-ing pe-nal-ized re-gres-sion [2916] Underfull \hbox (badness 1259) in paragraph at lines 877--878 []\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro -duc-tion with R (2nd edi-tion). [2917] Underfull \vbox (badness 10000) has occurred while \output is active [2918] [2919] [2920] [2921] [2922] [2923] [2924] [2925] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1337--1337 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1338--1338 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1355--1355 [] \T1/pcr/m/n/9 plot(b$y[oy],rs[oy,ii[1]],ylim=c(-3,3),type="l",ylab="scor e residuals",[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1367--1367 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor +rx+obstruct[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1376--1376 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in d]),type="l",[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1378--1378 [] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind]) ,lwd=2,col=i)[] Underfull \vbox (badness 10000) has occurred while \output is active [2926] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1409--1409 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights= d,data=surv)[] Underfull \vbox (badness 10000) has occurred while \output is active [2927] [2928] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1492--1492 [] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid), initial = 0,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1503--1503 [] \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][ nrow(um)] <- 1[] Underfull \vbox (badness 10000) has occurred while \output is active [2929] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1542--1542 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter polate to te[] [2930] [2931] [2932] [2933] [2934] [2935] [2936] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1939--1939 []\T1/pcr/m/n/9 bd <- bam(y~s(x0)+ s(x1) + s(x1,fac,bs="sz",k=5)+s(x2,k=20),di screte=TRUE)[] [2937] [2938] [2939] [2940] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2174--2174 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str ict=FALSE) [2941] [2942] [2943] [2944] [2945] [2946] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2579--2579 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL,[] Underfull \hbox (badness 1728) in paragraph at lines 2591--2594 []\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][][]\T1/pcr/m/n /10 formula.gam[][][] []\T1/ptm/m/n/10 and also Underfull \hbox (badness 1142) in paragraph at lines 2604--2608 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2947] Underfull \hbox (badness 1043) in paragraph at lines 2630--2636 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2948] [2949] [2950] Underfull \hbox (badness 1043) in paragraph at lines 2795--2801 \T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v en-tion mech-a-nism de-scribed in [2951] [2952] Underfull \hbox (badness 10000) in paragraph at lines 2933--2939 [][][]\T1/pcr/m/n/10 mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gamObject[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/pt m/m/n/10 , [][][]\T1/pcr/m/n/10 smooth.terms[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2933--2939 [][][]\T1/pcr/m/n/10 linear.functional.terms[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][] [][]predict. gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2933--2939 [][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 g am.side[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.selection[][][][]\T1/p tm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][][]\T1/ptm /m/n/10 , [2953] Underfull \vbox (badness 10000) has occurred while \output is active [2954] Underfull \vbox (badness 10000) has occurred while \output is active [2955] [2956] [2957] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3250--3250 []\T1/pcr/m/n/10 gam.control(nthreads=1,ncv.threads=1,irls.reg=0.0,epsilon = 1 e-07, [2958] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3251--3251 [] \T1/pcr/m/n/10 maxit = 200,mgcv.tol=1e-7,mgcv.half=15, trace = F ALSE,[] [2959] [2960] [2961] [2962] [2963] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3591--3591 [] \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco l(x)),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3594--3594 [] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol (x)),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3595--3595 [] \T1/pcr/m/n/10 pearson.extra=0,dev.extra=0,n.true=-1,Sl=NULL,nei=NU LL,...)[] [2964] [2965] [2966] [2967] [2968] [2969] [2970] [2971] Underfull \hbox (badness 5189) in paragraph at lines 4073--4077 []\T1/ptm/m/n/10 Random ef-fects can be added to []\T1/pcr/m/n/10 gam []\T1/ptm /m/n/10 mod-els us-ing []\T1/pcr/m/n/10 s(...,bs="re") []\T1/ptm/m/n/10 terms ( see [2972] [2973] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4190--4190 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Underfull \vbox (badness 10000) has occurred while \output is active [2974] [2975] [2976] Underfull \hbox (badness 1184) in paragraph at lines 4360--4364 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2977] [2978] [2979] [2980] [2981] [2982] [2983] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4806--4806 [] \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i d=1)+s(x1,id=1)+[] [2984] [2985] [2986] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4956--4956 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, d1b = 0, [2987] [2988] Underfull \hbox (badness 1142) in paragraph at lines 5083--5087 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2989] Underfull \hbox (badness 10000) in paragraph at lines 5155--5164 []\T1/ptm/m/n/10 In the event of []\T1/pcr/m/n/10 lme []\T1/ptm/m/n/10 con-ver- gence fail-ures, con-sider mod-i-fy-ing [2990] [2991] Underfull \hbox (badness 5970) in paragraph at lines 5272--5278 [][][]\T1/pcr/m/n/10 magic[][][] []\T1/ptm/m/n/10 for an al-ter-na-tive for cor -re-lated data, [][][]\T1/pcr/m/n/10 te[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.gam[][][][]\T1/ptm /m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 1418) in paragraph at lines 5272--5278 [][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 n egbin[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 vis.gam[][][][]\T1/ptm/m/n/1 0 ,[][][]\T1/pcr/m/n/10 pdTens[][][][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 gamm4 [ ]\T1/ptm/m/n/10 ( [][]$\T1/pcr/m/n/10 https : / / cran . r-[]project . [2992] Underfull \vbox (badness 10000) has occurred while \output is active [2993] [2994] [2995] [2996] Underfull \hbox (badness 1577) in paragraph at lines 5622--5625 []\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see [] [][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 ar-gu-ment Underfull \hbox (badness 2181) in paragraph at lines 5629--5630 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2997] [2998] [2999] [3000] [3001] [3002] [3003] [3004] [3005] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6127--6127 []\T1/pcr/m/n/10 ginla(G,A=NULL,nk=16,nb=100,J=1,interactive=FALSE,integ=0,app rox=0) Underfull \hbox (badness 6708) in paragraph at lines 6133--6134 []\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by []\T1/pcr/m/n/10 gam(.. .,fit=FALSE) []\T1/ptm/m/n/10 or [3006] [3007] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6182--6182 [] \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d ata. A simple[] [3008] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6207--6207 [] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j] ,lty=lty[j])[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6236--6236 [] \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo r comparison[] [3009] [3010] [3011] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6358--6358 [] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r norm(100)*.4[] [3012] [3013] [3014] [3015] [3016] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6695--6695 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n a.action, Overfull \hbox (36.78088pt too wide) in paragraph at lines 6697--6697 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona lize=FALSE)[] Underfull \hbox (badness 1142) in paragraph at lines 6718--6722 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [3017] [3018] [3019] [3020] [3021] [3022] [3023] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7037--7037 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999, all.derivs=FALSE) [3024] [3025] [3026] Underfull \vbox (badness 10000) has occurred while \output is active [3027] Underfull \vbox (badness 10000) has occurred while \output is active [3028] [3029] [3030] Overfull \hbox (52.98038pt too wide) in paragraph at lines 7469--7469 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want to rule the world.",[] [3031] Overfull \hbox (36.78088pt too wide) in paragraph at lines 7496--7496 [] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y), nthreads=1)[] [3032] [3033] [3034] [3035] [3036] [3037] Underfull \vbox (badness 4805) has occurred while \output is active [3038] [3039] [3040] Underfull \hbox (badness 1242) in paragraph at lines 8050--8051 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [3041] [3042] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8137--8137 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt ion with bam...[] [3043] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8200--8200 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate d covariates[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8219--8219 [] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]] ,na.rm=TRUE)[] [3044] [3045] [3046] [3047] [3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055] [3056] [3057] [3058] [3059] [3060] [3061] [3062] [3063] [3064] Underfull \vbox (badness 10000) has occurred while \output is active [3065] [3066] Underfull \hbox (badness 10000) in paragraph at lines 9538--9541 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: []\T1/pcr/m/n/10 Dim .pdIndot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 coef.pdIdnot[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 9538--9541 []\T1/pcr/m/n/10 corMatrix.pdIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 logDet.pd Idnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdConstruct.pdIdnot[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3118) in paragraph at lines 9538--9541 []\T1/pcr/m/n/10 pdFactor.pdIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdMatrix.p dIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 solve.pdIdnot[]\T1/ptm/m/n/10 , []\T1 /pcr/m/n/10 summary.pdIdnot[]\T1/ptm/m/n/10 . [3067] Underfull \hbox (badness 10000) in paragraph at lines 9594--9597 []\T1/ptm/m/n/10 These func-tions ([]\T1/pcr/m/n/10 pdTens[]\T1/ptm/m/n/10 , [] \T1/pcr/m/n/10 pdConstruct.pdTens[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdFactor.p dTens[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3108) in paragraph at lines 9594--9597 []\T1/pcr/m/n/10 pdMatrix.pdTens[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 coef.pdTens []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 summary.pdTens[]\T1/ptm/m/n/10 ) would n ot nor-mally be [3068] [3069] [3070] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9814--9814 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s cale=-1,[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 9818--9818 [] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi ds=FALSE,[] [3071] [3072] [3073] Underfull \hbox (badness 1629) in paragraph at lines 9974--9979 []\T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is some-times to clone the [3074] [3075] [3076] [3077] Overfull \hbox (84.78088pt too wide) in paragraph at lines 10186--10186 [] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread s=1,gc.level=0,...)[] Underfull \hbox (badness 1062) in paragraph at lines 10223--10227 []\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 type=="terms" []\T1/ptm/m/n/10 or []\T1/pc r/m/n/10 type="iterms" []\T1/ptm/m/n/10 then terms (smooth or para- [3078] [3079] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10356--10356 [] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL L,...)[] [3080] [3081] [3082] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10517--10517 []\T1/pcr/m/n/9 x1 <- seq(.2,.8,length=m1);x2 <- seq(.2,.8,length=m2) ## margi nal grid points[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10518--10518 []\T1/pcr/m/n/9 df <- data.frame(x0=rep(.5,n),x1=rep(x1,m2),x2=rep(x2,each=m1) ,x3=rep(0,n))[] [3083] Underfull \vbox (badness 10000) has occurred while \output is active [3084] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10637--10637 [] \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s mooth deriv i[] [3085] Underfull \hbox (badness 1205) in paragraph at lines 10675--10676 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 10675--10676 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for Underfull \hbox (badness 1975) in paragraph at lines 10681--10686 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [3086] Underfull \hbox (badness 1205) in paragraph at lines 10765--10766 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 10765--10766 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [3087] Underfull \hbox (badness 10000) in paragraph at lines 10834--10837 []\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from Underfull \hbox (badness 2057) in paragraph at lines 10834--10837 [][][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][][]\T1/ptm/m/n/10 , al -though el-e-ments []\T1/pcr/m/n/10 X []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 S [ ]\T1/ptm/m/n/10 are not needed, [3088] [3089] [3090] Underfull \hbox (badness 1253) in paragraph at lines 10964--10966 []\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion cri-te-rion re-ported is one of GCV, [3091] [3092] [3093] [3094] [3095] Underfull \hbox (badness 1946) in paragraph at lines 11217--11224 []\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef- fects in a GAM in the same Underfull \hbox (badness 2221) in paragraph at lines 11217--11224 \T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre s-sion terms. This method Underfull \hbox (badness 2042) in paragraph at lines 11217--11224 \T1/ptm/m/n/10 can be used with [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 by mak-ing use of []\T1/pcr/m/n/10 s(...,bs="re") []\T1/ptm/m/n/10 terms in a model: see Underfull \hbox (badness 2846) in paragraph at lines 11225--11228 []\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the []\T1/pcr/m/n /10 paraPen []\T1/ptm/m/n/10 ar-gu-ment to [][][]\T1/pcr/m/n/10 gam[][][] []\T1 /ptm/m/n/10 can be used: Underfull \hbox (badness 5862) in paragraph at lines 11225--11228 \T1/ptm/m/n/10 see [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/ptm/m/n/10 . If s mooth-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g. [3096] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11291--11291 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11301--11301 []\T1/pcr/m/n/9 ## The effect of the new factor levels (or any interaction inv olving them)[] [3097] Underfull \hbox (badness 10000) in paragraph at lines 11332--11335 []\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of []\T1/pcr/m/n/ 10 "deviance"[]\T1/ptm/m/n/10 , [3098] [3099] [3100] [3101] [3102] Overfull \hbox (36.78088pt too wide) in paragraph at lines 11634--11634 []\T1/pcr/m/n/10 s(..., k=-1,fx=FALSE,bs="tp",m=NA,by=NA,xt=NULL,id=NULL,sp=NU LL,pc=NULL) [3103] [3104] [3105] [3106] [3107] [3108] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12007--12007 [] \T1/pcr/m/n/9 true <- mu + (del * sigma) * sinh((1/del) * asinh(qnorm(qq)) + (eps/del))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12021--12021 []\T1/pcr/m/n/9 b <- gam(list(accel~s(times, k=20, bs = "ad"), ~s(times, k = 1 0), ~1, ~1),[] Underfull \vbox (badness 10000) has occurred while \output is active [3109] [3110] Underfull \hbox (badness 3861) in paragraph at lines 12123--12126 []\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to model ma-trix X, or, if Overfull \hbox (36.78088pt too wide) in paragraph at lines 12132--12132 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, cov = TRUE,[] [3111] Underfull \hbox (badness 10000) in paragraph at lines 12149--12153 []\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 inverse==TRUE []\T1/ptm/m/n/10 and []\T1/p cr/m/n/10 both.sides==FALSE []\T1/ptm/m/n/10 then the re- Underfull \hbox (badness 10000) in paragraph at lines 12189--12193 []\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 inverse==TRUE []\T1/ptm/m/n/10 and []\T1/p cr/m/n/10 both.sides==FALSE []\T1/ptm/m/n/10 then the re- [3112] [3113] [3114] Overfull \hbox (20.58041pt too wide) in paragraph at lines 12333--12333 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$ vectors[,ind]))[] Underfull \hbox (badness 1975) in paragraph at lines 12344--12349 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [3115] Underfull \hbox (badness 1803) in paragraph at lines 12421--12425 \T1/ptm/m/n/10 The last en-try will be the []\T1/pcr/m/n/10 by []\T1/ptm/m/n/10 vari-able, if []\T1/pcr/m/n/10 object$by []\T1/ptm/m/n/10 is not []\T1/pcr/m/n /10 "NA"[]\T1/ptm/m/n/10 . Underfull \hbox (badness 1502) in paragraph at lines 12433--12445 []\T1/pcr/m/n/10 cs.smooth.spec []\T1/ptm/m/n/10 (cu-bic re-gres-sion splines w ith shrinkage-to-zero); []\T1/pcr/m/n/10 cc.smooth.spec [3116] Underfull \hbox (badness 2401) in paragraph at lines 12450--12454 []\T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able . Plot meth-ods can be Underfull \hbox (badness 2970) in paragraph at lines 12450--12454 \T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for []\T1/pc r/m/n/10 mgcv:::plot.sos.smooth[]\T1/ptm/m/n/10 , [3117] [3118] [3119] Underfull \hbox (badness 6876) in paragraph at lines 12645--12651 [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use adap-tive smooths of on e or two vari-ables, spec-i-fied via terms like [3120] Underfull \hbox (badness 10000) in paragraph at lines 12686--12687 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3121] [3122] Underfull \hbox (badness 10000) in paragraph at lines 12804--12805 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3123] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12858--12858 [] \T1/pcr/m/n/9 b <- gam(y~s(x0,bs=bs,m=c(4,2))+s(x1,bs=bs)+s(x2,k=15,bs=bs, m=c(4,3,0))+[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12870--12870 [] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5, 1.5) (black)[] [3124] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12882--12882 [] \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions and intervals[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12887--12887 [] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i ntervals away[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12893--12893 [] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w ild and wide[] Overfull \hbox (3.70428pt too wide) in paragraph at lines 12894--12894 [] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/cmtt/m/n/9 `\T1 /pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] [3125] Underfull \hbox (badness 10000) in paragraph at lines 12963--12965 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a Underfull \hbox (badness 10000) in paragraph at lines 12963--12965 \T1/ptm/m/n/10 term []\T1/pcr/m/n/10 s(...,bs="cr",...)[]\T1/ptm/m/n/10 , []\T1 /pcr/m/n/10 s(...,bs="cs",...) []\T1/ptm/m/n/10 or [3126] [3127] Underfull \hbox (badness 10000) in paragraph at lines 13093--13094 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3128] [3129] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13174--13174 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first deriv penalty[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13175--13175 []\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi ed 2nd deriv[] [3130] [3131] Underfull \hbox (badness 10000) in paragraph at lines 13328--13329 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3132] [3133] [3134] [3135] [3136] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13578--13578 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m ethod="REML")[] [3137] Underfull \hbox (badness 10000) in paragraph at lines 13639--13641 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3138] [3139] Underfull \hbox (badness 10000) in paragraph at lines 13798--13801 []\T1/ptm/m/n/10 For the []\T1/pcr/m/n/10 smooth.construct []\T1/ptm/m/n/10 met hod a smooth spec-i-fi-ca-tion ob- Underfull \hbox (badness 3312) in paragraph at lines 13798--13801 \T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term []\T1/pcr/m/n/10 s(x,...,bs ="re",)[]\T1/ptm/m/n/10 . For the Underfull \hbox (badness 7099) in paragraph at lines 13798--13801 []\T1/pcr/m/n/10 predict.Matrix []\T1/ptm/m/n/10 method an ob-ject of class []\ T1/pcr/m/n/10 "random.effect" [3140] [3141] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13884--13884 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with 2 variances[] [3142] Underfull \hbox (badness 10000) in paragraph at lines 13929--13935 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a Underfull \hbox (badness 7832) in paragraph at lines 13929--13935 []\T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) []\T1/ptm/m/n/10 term in a []\T1/pcr/m/n/10 gam []\T1/ptm/m/n/10 for- [3143] [3144] [3145] Overfull \hbox (36.7804pt too wide) in paragraph at lines 14144--14144 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] Underfull \vbox (badness 10000) has occurred while \output is active [3146] Underfull \vbox (badness 10000) has occurred while \output is active [3147] Underfull \hbox (badness 10000) in paragraph at lines 14247--14255 [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths on th e sphere, via terms like Underfull \hbox (badness 10000) in paragraph at lines 14273--14274 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3148] [3149] [3150] Underfull \hbox (badness 7613) in paragraph at lines 14418--14421 []\T1/ptm/m/n/10 method an ob-ject of class []\T1/pcr/m/n/10 "sz.interaction" [ ]\T1/ptm/m/n/10 pro-duced by the [3151] Underfull \hbox (badness 1546) in paragraph at lines 14439--14440 []\T1/ptm/m/n/10 The terms can have a smooth-ing pa-ram-e-ter per smooth, or a sin-gle smooth-ing pa-ram-e- Overfull \hbox (128.58029pt too wide) in paragraph at lines 14485--14485 []\T1/pcr/m/n/9 b <- gam(y ~ s(x)+s(f1,x,bs="sz")+s(f2,x,bs="sz")+s(f1,f2,x,bs ="sz",id=1),data=dat,method="REML")[] [3152] [3153] [3154] Underfull \hbox (badness 3396) in paragraph at lines 14631--14634 [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths of an y num-ber of vari-ables, spec-i-fied via terms like Underfull \hbox (badness 10000) in paragraph at lines 14676--14678 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3155] [3156] [3157] [3158] [3159] [3160] Underfull \hbox (badness 10000) in paragraph at lines 14967--14969 []\T1/pcr/m/n/10 bs="fs" []\T1/ptm/m/n/10 A spe-cial smoother class (see [3161] Underfull \hbox (badness 10000) in paragraph at lines 15001--15005 [][][]\T1/pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][][]\ T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 t2[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 tprs[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Duchon.spline[][][][]\T 1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cubic.regression.spline[][][][]\T1/ptm/m/n/ 10 , Underfull \hbox (badness 10000) in paragraph at lines 15001--15005 [][][]\T1/pcr/m/n/10 p.spline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 d.sp line[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 mrf[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 soap[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Spherical .Spline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 adaptive.smooth[][][][]\T1 /ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 15001--15005 [][][]\T1/pcr/m/n/10 user.defined.smooth[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/ m/n/10 smooth.construct.re.smooth.spec[][][][]\T1/ptm/m/n/10 , [3162] [3163] [3164] [3165] [3166] Underfull \hbox (badness 2158) in paragraph at lines 15291--15291 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [3167] Overfull \hbox (48.78088pt too wide) in paragraph at lines 15370--15370 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0, centre=FALSE)[] [3168] [3169] Overfull \hbox (12.78088pt too wide) in paragraph at lines 15504--15504 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars "),...)[] [3170] [3171] Underfull \hbox (badness 4846) in paragraph at lines 15635--15638 []\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or es-ti-ma-tors if [3172] [3173] [3174] [3175] [3176] [3177] [3178] [3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186] [3187] [3188] [3189] [3190] [3191] Overfull \hbox (120.78088pt too wide) in paragraph at lines 16853--16853 []\T1/pcr/m/n/10 vcov(object, sandwich=FALSE, freq = FALSE, dispersion = NULL, unconditional=FALSE, ...)[] [3192] Underfull \hbox (badness 1715) in paragraph at lines 16875--16876 []\T1/ptm/m/n/10 Basically, just ex-tracts []\T1/pcr/m/n/10 object$Ve[]\T1/ptm/ m/n/10 , []\T1/pcr/m/n/10 object$Vp []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 object $Vc []\T1/ptm/m/n/10 (if avail-able) from a [3193] [3194] [3195] Overfull \hbox (54.78088pt too wide) in paragraph at lines 17065--17065 []\T1/pcr/m/n/10 XWXd(X,w,k,ks,ts,dt,v,qc,nthreads=1,drop=NULL,ar.stop=-1,ar.r ow=-1,ar.w=-1, Overfull \hbox (48.78088pt too wide) in paragraph at lines 17067--17067 []\T1/pcr/m/n/10 XWyd(X,w,y,k,ks,ts,dt,v,qc,drop=NULL,ar.stop=-1,ar.row=-1,ar. w=-1,lt=NULL)[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17069--17069 []\T1/pcr/m/n/10 diagXVXd(X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,rt= NULL)[] [3196] Underfull \hbox (badness 10000) in paragraph at lines 17089--17090 []\T1/ptm/m/n/10 Negative to ig-nore. Oth-er-wise sum rows Underfull \hbox (badness 1668) in paragraph at lines 17089--17090 []\T1/pcr/m/n/10 (ar.stop[i-1]+1):ar.stop[i] []\T1/ptm/m/n/10 of the rows se-le cted by []\T1/pcr/m/n/10 ar.row [3197] Underfull \vbox (badness 10000) has occurred while \output is active [3198] [3199] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17277--17277 []\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li near predictor,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17278--17278 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun ded in regions[] [3200] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17290--17290 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val ues, to check we[] [3201] [3202] [3203]) (./nlme-pkg.tex [3204] Chapter 25. [3205] Underfull \hbox (badness 1009) in paragraph at lines 84--93 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3206] Underfull \hbox (badness 1009) in paragraph at lines 174--183 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3207] [3208] [3209] [3210] [3211] Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454 [] \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [3212] [3213] Overfull \hbox (20.58041pt too wide) in paragraph at lines 595--595 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 --------------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 611--611 []\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n on-sensical!)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 614--614 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 --------------------------- ---------------[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 621--621 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 --------------------------- ---------------[] [3214] [3215] [3216] [3217] [3218] [3219] [3220] [3221] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1085--1085 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil lary fissure"),[] [3222] Underfull \hbox (badness 5446) in paragraph at lines 1147--1149 []\T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel .htm[]\T1/ptm/m/n/10 ', the first edi-tion of [3223] [3224] [3225] [3226] [3227] [3228] [3229] Underfull \hbox (badness 10000) in paragraph at lines 1626--1629 [][][]\T1/pcr/m/n/10 lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fixed. effects.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 ranef.lmList[][][][ ]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.ranef.lmList[][][][]\T1/ptm/m/n/10 , [3230] Underfull \hbox (badness 3780) in paragraph at lines 1643--1645 []\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a ted with each com-po-nent of the [3231] [3232] [3233] [3234] [3235] Underfull \hbox (badness 2042) in paragraph at lines 1992--1998 \T1/ptm/m/n/10 is in-ner to the []\T1/pcr/m/n/10 displayLevel []\T1/ptm/m/n/10 group-ing fac-tor. If equal to []\T1/pcr/m/n/10 TRUE[]\T1/ptm/m/n/10 , [3236] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2054--2054 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla pse = "Dog")[] [3237] Underfull \hbox (badness 1132) in paragraph at lines 2143--2145 []\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac ted us-ing the [3238] [3239] Underfull \hbox (badness 4168) in paragraph at lines 2254--2260 [][][]\T1/pcr/m/n/10 ACF.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corAR MA[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/pcr/m/n/10 Dim.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 , [3240] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2279--2279 [] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [3241] [3242] [3243] [3244] [3245] [3246] [3247] [3248] Underfull \hbox (badness 10000) in paragraph at lines 2845--2849 [][][]\T1/pcr/m/n/10 corFactor[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cor Matrix.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 recalc.corStruct[ ][][][]\T1/ptm/m/n/10 , [3249] [3250] [3251] [3252] [3253] [3254 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.corMatrix .corCompSymm}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.3188 ...trix(cs1, covariate = 1:4, corr = FALSE) ] [3255] [3256] [3257] [3258] [3259] [3260] Underfull \hbox (badness 6493) in paragraph at lines 3580--3588 [][][]\T1/pcr/m/n/10 corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corGau s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corLin[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 corRatio[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corSp her[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][][]\T 1/ptm/m/n/10 , [3261] [3262] [3263] [3264] [3265] [3266] [3267] [3268] [3269] [3270] [3271] [3272] [3273] [3274] [3275] [3276] [3277] [3278] [3279] [3280] [3281] [3282] [3283] [3284] Underfull \hbox (badness 10000) in paragraph at lines 5160--5164 [][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/p cr/m/n/10 getCovariate.data.frame[][][][]\T1/ptm/m/n/10 , [3285] [3286] [3287] [3288] [3289] [3290] [3291] Underfull \hbox (badness 10000) in paragraph at lines 5592--5595 [][][]\T1/pcr/m/n/10 getGroupsFormula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n /10 getGroups.data.frame[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 getGroups .gls[][][][]\T1/ptm/m/n/10 , [3292] [3293] [3294] [3295] [3296] [3297] [3298] [3299] [3300] Underfull \hbox (badness 2799) in paragraph at lines 6098--6104 \T1/ptm/m/n/10 covariance ma-trix, ei-ther []\T1/pcr/m/n/10 "random.effects" [] \T1/ptm/m/n/10 for the random-effects [3301] Underfull \hbox (badness 7133) in paragraph at lines 6159--6163 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in [ ]\T1/pcr/m/n/10 model[]\T1/ptm/m/n/10 , [3302] Underfull \hbox (badness 2057) in paragraph at lines 6248--6259 [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gl sControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 glsObject[][][][]\T1/ptm/ m/n/10 , [][][]\T1/pcr/m/n/10 glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 plot.gls[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.gls[][][][] \T1/ptm/m/n/10 , [3303] Underfull \hbox (badness 10000) in paragraph at lines 6312--6314 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3304] [3305] [3306] [3307] Underfull \hbox (badness 7133) in paragraph at lines 6560--6564 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in [ ]\T1/pcr/m/n/10 model[]\T1/ptm/m/n/10 , [3308] Underfull \hbox (badness 10000) in paragraph at lines 6659--6665 [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gn lsControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gnlsObject[][][][]\T1/pt m/m/n/10 , [][][]\T1/pcr/m/n/10 gnlsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc r/m/n/10 predict.gnls[][][][]\T1/ptm/m/n/10 , Overfull \hbox (54.78088pt too wide) in paragraph at lines 6686--6686 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min Scale = 0.001, [3309] Underfull \hbox (badness 10000) in paragraph at lines 6724--6726 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3310] [3311] [3312] [3313] Underfull \hbox (badness 10000) in paragraph at lines 6995--7002 [][][]\T1/pcr/m/n/10 formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gappl y[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gsummary[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.nff GroupedData[][][][]\T1/ptm/m/n/10 , [3314] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7013--7013 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla ry fissure" ),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7018--7018 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted from object[] Underfull \hbox (badness 2875) in paragraph at lines 7040--7042 []\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a []\T1/pcr/m/n/10 gr oupedData []\T1/ptm/m/n/10 ob-ject or a [3315] [3316] [3317] Underfull \hbox (badness 10000) in paragraph at lines 7255--7260 [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr /m/n/10 Initialize.lmeStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initi alize.glsStruct[][][][]\T1/ptm/m/n/10 , [3318] [3319] [3320] Underfull \hbox (badness 1997) in paragraph at lines 7406--7414 []\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial -iza-tion and op-ti- Underfull \hbox (badness 2205) in paragraph at lines 7406--7414 \T1/ptm/m/n/10 miza-tion al-go-rithms used in []\T1/pcr/m/n/10 lme[]\T1/ptm/m/n /10 . De-faults to []\T1/pcr/m/n/10 list(niterEM=20, Underfull \hbox (badness 3118) in paragraph at lines 7429--7432 [][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initializ e.reStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.corStruct[][ ][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.varFunc[][][][]\T1/ptm/m/ n/10 , [3321] [3322] [3323] Underfull \hbox (badness 3354) in paragraph at lines 7645--7647 []\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when []\T1/pcr/m/n/ 10 which []\T1/ptm/m/n/10 is not equal to [3324] [3325] [3326] [3327] [3328] [3329] [3330] [3331] Underfull \hbox (badness 10000) in paragraph at lines 8173--8190 [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lm e.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lme.groupedData[][][][]\T 1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lmeControl[][][][]\T1/ptm/m/n/10 , [][][]\T 1/pcr/m/n/10 lmeObject[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8173--8190 [][][]\T1/pcr/m/n/10 lmeStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lmL ist[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/pcr/m/n/10 plot.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 qqnorm.lme[][][][]\T1/ ptm/m/n/10 , [3332] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8216--8216 [] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data = TRUE)[] Underfull \hbox (badness 1642) in paragraph at lines 8225--8247 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3333] [3334] [3335] [3336] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8490--8490 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni terEM = 25, [3337] Underfull \hbox (badness 10000) in paragraph at lines 8538--8540 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Overfull \hbox (9.78043pt too wide) in paragraph at lines 8582--8582 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3338] [3339] [3340] [3341] [3342] [3343] [3344] [3345] [3346] [3347] [3348] [3349] Underfull \hbox (badness 10000) in paragraph at lines 9345--9352 [][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 ,[][][]\T1/pcr/m/n/10 gls[][][][ ]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logLik.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logLik.glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 logLik.lmeStruct[][][][]\T1/ptm/m/n/10 , Overfull \hbox (4.38043pt too wide) in paragraph at lines 9356--9356 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me thod = "ML") [3350] [3351] [3352] [3353] [3354] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9707 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Matrix.1} ) has been already used, duplicate ignored \relax l.9707 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3355] Underfull \hbox (badness 10000) in paragraph at lines 9727--9730 []\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a s Underfull \hbox (badness 3108) in paragraph at lines 9771--9774 []\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive -definite Underfull \hbox (badness 2521) in paragraph at lines 9771--9774 \T1/ptm/m/n/10 ma-trix rep-re-sented by []\T1/pcr/m/n/10 object[]\T1/ptm/m/n/10 . Must have the same di-men-sions as [3356] [3357] [3358] [3359] [3360] [3361] [3362] [3363] [3364] [3365] [3366] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10451--10451 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights, [3367] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10455--10455 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights,[] Underfull \hbox (badness 1596) in paragraph at lines 10484--10510 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3368] [3369] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10638--10638 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights,[] [3370] [3371] [3372] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10789--10789 [] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma = NULL, ...)[] Underfull \hbox (badness 2213) in paragraph at lines 10800--10805 []\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][][]\T1/pcr/m/n/10 nlmi nb[][][] []\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 iter.max[]\T1/ptm/m/n/10 ) or the [ ][][]\T1/pcr/m/n/10 nlm[][][] Underfull \hbox (badness 6961) in paragraph at lines 10822--10826 []\T1/ptm/m/n/10 a log-i-cal value passed as the []\T1/pcr/m/n/10 trace []\T1/p tm/m/n/10 to [][][]\T1/pcr/m/n/10 nlminb[][][](.., control= [3373] Underfull \hbox (badness 10000) in paragraph at lines 10841--10843 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3374] [3375] [3376] [3377] Overfull \hbox (96.18033pt too wide) in paragraph at lines 11137--11137 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* message instead of one *each*[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 11138--11138 []\T1/pcr/m/n/9 mat.class <- class(matrix(1)) # ("matrix", "array") for R >= 4 .0.0; ("matrix" in older R)[] [3378] [3379] [3380] [3381] [3382] [3383] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11528--11528 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo nt)), .. lme(*)) [3384] [3385] [3386] [3387] [3388] [3389] Underfull \hbox (badness 6268) in paragraph at lines 11915--11925 [][][]\T1/pcr/m/n/10 pdBlocked[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdC ompSymm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdDiag[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 pdFactor[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdIdent[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 pdMatrix[][][][]\T1/ptm/m/n/10 , [3390] [3391] [3392] [3393] Underfull \hbox (badness 10000) in paragraph at lines 12176--12182 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 coef.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdBlocked[][][][]\T1 /ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 pdConstruct[][][][]\T1/ptm/m/n/10 , [3394] [3395] [3396] [3397] [3398] Underfull \hbox (badness 6876) in paragraph at lines 12498--12500 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 value []\T1/ptm/m/n/10 is an \T1/ptm/m/it/ 10 ini-tial-ized []\T1/pcr/m/n/10 pdMat []\T1/ptm/m/n/10 ob-ject, []\T1/pcr/m/n /10 object []\T1/ptm/m/n/10 will be con-structed from [3399] [3400] Underfull \hbox (badness 2452) in paragraph at lines 12654--12661 [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdC ompSymm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdDiag[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 pdIdent[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdNatural[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdSymm[][][][]\T1/ptm/m/ n/10 , [][][]\T1/pcr/m/n/10 reStruct[][][][]\T1/ptm/m/n/10 , [3401] Underfull \hbox (badness 10000) in paragraph at lines 12720--12726 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdFactor[][][][]\T1/p tm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 pdMatrix.reStruct[][][][]\T1/ptm/m/n/10 , [3402] [3403] [3404] [3405] [3406] [3407] [3408] [3409] [3410] Overfull \hbox (25.98041pt too wide) in paragraph at lines 13309--13309 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo nt)), .. lme(*)) [3411] [3412] [3413] [3414] [3415] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13674--13674 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 0, id = 0.05)[] [3416] Underfull \hbox (badness 10000) in paragraph at lines 13701--13704 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nffGroupe dData[]\T1/ptm/m/n/10 , rep-re-sent-ing a [3417] Underfull \hbox (badness 1838) in paragraph at lines 13744--13751 []\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If []\T1/pcr/m/ n/10 TRUE []\T1/ptm/m/n/10 and ei-ther []\T1/pcr/m/n/10 inner Underfull \hbox (badness 3713) in paragraph at lines 13744--13751 []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 innerGroups []\T1/ptm/m/n/10 are non-[]\T1 /pcr/m/n/10 NULL[]\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent []\T1/pcr/m/n/ 10 inner Overfull \hbox (12.78088pt too wide) in paragraph at lines 13801--13801 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect, panel,[] [3418] Underfull \hbox (badness 10000) in paragraph at lines 13808--13811 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nfnGroupe dData[]\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 2469) in paragraph at lines 13808--13811 []\T1/pcr/m/n/10 groupedData []\T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-vari-ate and a sin-gle [3419] Underfull \hbox (badness 10000) in paragraph at lines 13916--13919 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nmGrouped Data[]\T1/ptm/m/n/10 , rep-re-sent-ing a [3420] [3421] Underfull \hbox (badness 10000) in paragraph at lines 14010--14012 [][][]\T1/pcr/m/n/10 groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 c ollapse.groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.nfnGroupe dData[][][][]\T1/ptm/m/n/10 , [3422] [3423] [3424] [3425] [3426] [3427] [3428] [3429] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14534--14534 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female", "Male","Male"),[] [3430] [3431] [3432] [3433] [3434] [3435] [3436] [3437] [3438] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.random.ef fects}) has been already used, duplicate ignored \relax l.15187 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.random.ef fects.1}) has been already used, duplicate ignored \relax l.15187 ...Extract Random Effects}{random.effects} [3439] [3440] [3441] [3442] [3443] [3444] [3445] [3446] [3447] [3448] Underfull \hbox (badness 2126) in paragraph at lines 15826--15830 []\T1/ptm/m/n/10 Charles F. Minto, Thomas W. Schnider and Steven L. Shafer (199 7). Phar-ma-coki-net- [3449] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15834--15834 []\T1/pcr/m/n/9 plot(Remifentanil, type = "l", lwd = 2) # shows the 65 patient s\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 remi profiles Overfull \hbox (31.3804pt too wide) in paragraph at lines 15853--15853 [] \T1/pcr/m/n/9 stopifnot(all.equal(BSA, Wt^{0.425} * Ht^{0.725} * 0.00718 4, tol = 1.5e-5),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15854--15854 [] \T1/pcr/m/n/9 all.equal(LBM, LBMfn(Wt, Ht, Sex), tol = 7e-7)[] [3450] Underfull \hbox (badness 1009) in paragraph at lines 15884--15893 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3451] [3452] Overfull \hbox (66.78088pt too wide) in paragraph at lines 16031--16031 [] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi st = FALSE, ...)[] [3453] [3454] [3455] [3456] [3457] Underfull \hbox (badness 10000) in paragraph at lines 16366--16372 [][][]\T1/pcr/m/n/10 groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 l me[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 solve.reStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 summary.reStruct[][][][]\T1/ptm/m/n/10 , [3458] Overfull \hbox (18.78088pt too wide) in paragraph at lines 16398--16398 [] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG en, ...)[] [3459] [3460] [3461] [3462] [3463] [3464] [3465] Underfull \hbox (badness 1728) in paragraph at lines 16885--16888 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3466] [3467] [3468] [3469] [3470] Underfull \hbox (badness 1803) in paragraph at lines 17219--17228 \T1/pcr/m/n/10 of an Identity" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pdIdent[]\ T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "General Positive-Definite, Underfull \hbox (badness 10000) in paragraph at lines 17219--17228 \T1/pcr/m/n/10 Natural Parametrization" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 p dNatural[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "General Underfull \hbox (badness 7888) in paragraph at lines 17219--17228 \T1/pcr/m/n/10 Positive-Definite" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pdSymm[ ]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 data.class(object) [3471] Underfull \hbox (badness 10000) in paragraph at lines 17290--17291 []\T1/pcr/m/n/10 "Constant plus power of variance Underfull \hbox (badness 10000) in paragraph at lines 17291--17292 []\T1/pcr/m/n/10 "Constant plus proportion of variance [3472] [3473] [3474] [3475] Underfull \hbox (badness 10000) in paragraph at lines 17541--17549 [][][]\T1/pcr/m/n/10 varComb[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varCo nstPower[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varConstProp[][][][]\T1/p tm/m/n/10 , [][][]\T1/pcr/m/n/10 varExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 varFixed[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varIdent[][][][]\T1 /ptm/m/n/10 , [3476] [3477] [3478] [3479] Overfull \hbox (4.38043pt too wide) in paragraph at lines 17813--17813 []\T1/pcr/m/n/9 # Generate some synthetic data using the two-component error m odel and use Overfull \hbox (25.98041pt too wide) in paragraph at lines 17815--17815 []\T1/pcr/m/n/9 # overparameterisation in the case of a constant term in the v ariance function[] [3480] [3481] [3482] [3483] [3484] [3485] Underfull \hbox (badness 10000) in paragraph at lines 18251--18261 [][][]\T1/pcr/m/n/10 Variogram.corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n /10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.co rLin[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18251--18261 [][][]\T1/pcr/m/n/10 Variogram.corRatio[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 Variogram.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogr am.corSpher[][][][]\T1/ptm/m/n/10 , [3486] Underfull \hbox (badness 3579) in paragraph at lines 18289--18294 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3487] Underfull \hbox (badness 3579) in paragraph at lines 18353--18358 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3488] Underfull \hbox (badness 3579) in paragraph at lines 18416--18421 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3489] Underfull \hbox (badness 1577) in paragraph at lines 18477--18479 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 "[][]corR atio[][][]"[]\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal Underfull \hbox (badness 3579) in paragraph at lines 18479--18484 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3490] Underfull \hbox (badness 3579) in paragraph at lines 18542--18547 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence Underfull \hbox (badness 10000) in paragraph at lines 18575--18584 [][][]\T1/pcr/m/n/10 corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Va riogram[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.default[][][][]\ T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.corExp[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18575--18584 [][][]\T1/pcr/m/n/10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 Variogram.corLin[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.co rRatio[][][][]\T1/ptm/m/n/10 , [3491] Underfull \hbox (badness 3579) in paragraph at lines 18614--18619 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3492] [3493] Underfull \hbox (badness 1009) in paragraph at lines 18760--18769 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3494] [3495] Underfull \hbox (badness 1009) in paragraph at lines 18892--18901 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3496] [3497] [3498] [3499] [3500] [3501] [3502] [3503] [3504]) (./nnet-pkg.tex Chapter 26. pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom} ) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom. 1}) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} [3505] Overfull \hbox (12.78088pt too wide) in paragraph at lines 71--71 [] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored = FALSE,[] [3506] [3507] [3508] Overfull \hbox (15.18042pt too wide) in paragraph at lines 371--371 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3509] Overfull \hbox (4.38043pt too wide) in paragraph at lines 428--428 []\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c( 0,0,1),50)),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 431--431 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay =5e-4, maxit=200)[] [3510] [3511] Overfull \hbox (15.18042pt too wide) in paragraph at lines 511--511 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3512]) (./rpart-pkg.tex Chapter 27. [3513] [3514] [3515] [3516] Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse = TRUE, ...)[] [3517] Underfull \hbox (badness 2351) in paragraph at lines 349--353 \T1/ptm/m/n/10 age: []\T1/pcr/m/n/10 pretty = 0 []\T1/ptm/m/n/10 im-plies []\T1 /pcr/m/n/10 minlength = 0L[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pretty = NULL []\ T1/ptm/m/n/10 im-plies [3518] [3519] [3520] Underfull \hbox (badness 1442) in paragraph at lines 592--598 []\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 FALSE[]\T1/ptm/m/n/10 , the leaf nodes wil l be at the hor-i-zon-tal plot co-or-di-nates of [3521] [3522] Overfull \hbox (0.78088pt too wide) in paragraph at lines 738--738 [] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep = ""),[] Underfull \hbox (badness 10000) in paragraph at lines 771--775 []\T1/ptm/m/n/10 Logical. If []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 (de-fault), adds to the la-bel Underfull \hbox (badness 1142) in paragraph at lines 771--775 \T1/pcr/m/n/10 #events level1/ #events level2/ \T1/ptm/m/n/10 etc. for method [ ]\T1/pcr/m/n/10 class[]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 n [3523] [3524] [3525] Overfull \hbox (25.98041pt too wide) in paragraph at lines 915--915 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie s, probabilities[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 934--934 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d igits"),[] [3526] [3527] [3528] [3529] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1180--1180 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m ethod, Overfull \hbox (12.78088pt too wide) in paragraph at lines 1181--1181 [] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos t, ...)[] Underfull \hbox (badness 2846) in paragraph at lines 1243--1245 []\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the []\T1/pcr/m/n /10 rpart []\T1/ptm/m/n/10 al-go-rithm. See [3530] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1287--1287 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the text is clipped[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1303--1303 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c p = 0.01, Overfull \hbox (60.78088pt too wide) in paragraph at lines 1304--1304 [] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,[] [3531] [3532] [3533] [3534] [3535] [3536] [3537] Underfull \hbox (badness 1565) in paragraph at lines 1760--1763 []\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val- ues are `[]\T1/pcr/m/n/10 diploid[]\T1/ptm/m/n/10 ', [3538] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1854--1854 [] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,[] [3539] [3540] [3541]) (./spatial-pkg.tex [3542] Chapter 28. [3543] [3544] [3545] [3546] [3547] [3548] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3549] [3550] [3551] [3552] [3553] [3554] [3555] [3556] [3557] [3558] [3559] [3560] [3561]) (./survival-pkg.tex [3562] Chapter 29. [3563] [3564] Overfull \hbox (31.3804pt too wide) in paragraph at lines 173--173 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data = lung, nmin = 1[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 192--192 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t he last point[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 195--195 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a nd Grambsch.[] [3565] [3566] Underfull \hbox (badness 6412) in paragraph at lines 284--286 []\T1/ptm/m/n/10 an op-tional list or vec-tor of group-ing el-e-ments, each as long as [3567] [3568] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has been already used, duplicate ignored \relax l.384 ... Myelogenous Leukemia survival data}{aml} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml.1}) h as been already used, duplicate ignored \relax l.384 ... Myelogenous Leukemia survival data}{aml} [3569] Overfull \hbox (9.78043pt too wide) in paragraph at lines 485--485 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da ta = ovarian) Overfull \hbox (4.38043pt too wide) in paragraph at lines 487--487 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d ata=ovarian)[] [3570] Overfull \hbox (6.78088pt too wide) in paragraph at lines 525--525 [] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog), lung)[] [3571] [3572] [3573] [3574] Overfull \hbox (20.58041pt too wide) in paragraph at lines 773--773 []\T1/pcr/m/n/9 py <- pseudo(survfit(Surv(time, status) ~1, lung), time=730) # 2 year survival Overfull \hbox (30.78088pt too wide) in paragraph at lines 789--789 []\T1/pcr/m/n/10 brier(fit, times, newdata, ties = TRUE, detail = FALSE, timef ix = TRUE, [3575] [3576] Overfull \hbox (48.78088pt too wide) in paragraph at lines 872--872 [] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan", "II.Borgan"),[] [3577] [3578] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1015--1015 [] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz e=stratsizes,[] [3579] [3580] Underfull \hbox (badness 1097) in paragraph at lines 1186--1188 []\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi al and negative-binomial data. [3581] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1206--1206 []\T1/pcr/m/n/9 ppois(4, 10.24153) #chance of seeing 4 or fewer events wit h large rate[] [3582] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1321--1321 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat um), data=infert) [3583] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1382--1382 []\T1/pcr/m/n/9 marginal.model <- coxph(Surv(time, status) ~ rx, data= rats, c luster=litter, pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colon}) h as been already used, duplicate ignored \relax l.1388 ...erapy for Stage B/C colon cancer}{colon} [3584] [3585] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1488--1488 [] \T1/pcr/m/n/10 influence=0, ranks = FALSE, reverse=FALSE, timefix=TRUE, ke epstrata=10, ...)[] [3586] [3587] [3588] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1714--1714 []\T1/pcr/m/n/9 options(na.action = na.exclude) # predict all 1384 obs, incl uding missing[] [3589] [3590] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1808--1808 []\T1/pcr/m/n/10 cox.zph(fit, transform="km", terms=TRUE, singledf=FALSE, glob al=TRUE) [3591] [3592] [3593] [3594] Underfull \hbox (badness 10000) in paragraph at lines 2124--2139 []\T1/ptm/m/n/10 One user mis-take that has re-cently arisen is to slav-ishly f ol-low the ad-vice of Underfull \hbox (badness 7486) in paragraph at lines 2124--2139 \T1/ptm/m/n/10 some cod-ing guides and prepend []\T1/pcr/m/n/10 survival:: []\T 1/ptm/m/n/10 onto ev-er-thing, in-clud-ing the spe- Underfull \hbox (badness 10000) in paragraph at lines 2124--2139 \T1/ptm/m/n/10 cial terms, e.g., []\T1/pcr/m/n/10 survival::coxph(survival:Surv (time, status) ~ age + [3595] Underfull \hbox (badness 3861) in paragraph at lines 2219--2223 [][][]\T1/pcr/m/n/10 coxph.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 coxphms.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 coxph.control[][][] []\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cluster[][][][]\T1/ptm/m/n/10 , [][][]\ T1/pcr/m/n/10 strata[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Surv[][][][]\ T1/ptm/m/n/10 , [3596] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2274--2274 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix =TRUE)[] [3597] [3598] [3599] [3600] [3601] [3602] [3603] [3604] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2902--2902 [] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" " exponential"[] [3605] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2943--2943 []\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass, etype, [3606] [3607] [3608] [3609] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3187--3187 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t df = 5,[] [3610] [3611] [3612] [3613] Underfull \hbox (badness 1019) in paragraph at lines 3449--3451 []\T1/ptm/m/n/10 outcome: []\T1/pcr/m/n/10 censor[]\T1/ptm/m/n/10 , []\T1/pcr/m /n/10 thymic lymphoma[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 reticulum cell sarcoma other [3614] [3615] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3593--3593 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt y(id), kidney) [3616] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3628--3628 [] \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre ssion", "death")))[] Underfull \hbox (badness 1389) in paragraph at lines 3642--3644 []\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan -Meier plot gen-er-ated with Overfull \hbox (12.78088pt too wide) in paragraph at lines 3653--3653 [] \T1/pcr/m/n/10 conf.type = c("log", "log-log", "plain", "logit", "ar csin"),[] [3617] [3618] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3787--3787 [] \T1/pcr/m/n/9 rmap=list(sex=sex, age=age*365.35, year=as.Da te(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/01/01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3619] [3620] Overfull \hbox (467.89665pt too wide) in alignment at lines 3928--3928 [] [] [3621] [3622] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4050--4050 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential ly the same.[] [3623] [3624] [3625] [3626] [3627] [3628] [3629] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4496--4496 [] \T1/pcr/m/n/9 entry.dt = as.Date(paste("2011", 1:10, "5" , sep=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 -\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3630] [3631] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4646--4646 []\T1/pcr/m/n/9 tdata <- data.frame(x= lung$age, y = 10*log(lung$age-35) + rno rm(228, 0, 2))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4651--4651 []\T1/pcr/m/n/9 knots <- unlist(attributes(fit1$model[[2]])[c(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Boundary.knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )])[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4655--4655 []\T1/pcr/m/n/9 unname(coef(fit1)[-1] - coef(fit1)[1]) # differences: yhat[2: 4] - yhat[1][] [3632] [3633] [3634] [3635] [3636] [3637] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4986--4986 [] \T1/pcr/m/n/10 xlab="Time", ylab, lty=1:2, col=1, lwd=1, hr=FALSE, p lot=TRUE, ...)[] [3638] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5075--5075 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca le=1,[] [3639] [3640] [3641] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5305--5305 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), collapse,[] [3642] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5431--5431 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] [3643] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5439--5439 [] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means , na.rm=TRUE)[] [3644] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5525--5525 []\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival is at +infinity[] [3645] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5603--5603 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars"), expand=FALSE , ...)[] [3646] Underfull \hbox (badness 1852) in paragraph at lines 5675--5677 []\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.survfit"[]\T1/pt m/m/n/10 , which is the re-sult of the [3647] [3648] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5801--5801 []\T1/pcr/m/n/10 pseudo(fit, times, type, addNA=TRUE, data.frame=FALSE, minus1 =FALSE, ...) [3649] [3650] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5912--5912 []\T1/pcr/m/n/9 rhat <- predict(rfit, newdata=expand.grid(ph.ecog=0:3, sex=1:2 ), se.fit=TRUE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5924--5924 []\T1/pcr/m/n/9 # the estimate for ph.ecog=3 is very unstable (n=1), pseudoval ues smooth it.[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5926--5926 []\T1/pcr/m/n/9 # In all the above we should be using the robust variance, e.g ., svyglm, but[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5950--5950 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me thod, Overfull \hbox (36.78088pt too wide) in paragraph at lines 5951--5951 [] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co mbine, ...)[] [3651] [3652] [3653] Overfull \hbox (30.78088pt too wide) in paragraph at lines 6114--6114 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] [3654] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6216--6216 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age + sex, mgus,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6237--6237 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50 ,60,70,100)) +[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6239--6239 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5 0,60,70,100)) +[] [3655] [3656] [3657] [3658] [3659] [3660] [3661] Overfull \hbox (42.78088pt too wide) in paragraph at lines 6705--6705 [] \T1/pcr/m/n/10 collapse=FALSE, weighted= (type %in% c("dfbeta", "dfbe tas")), ...)[] [3662] [3663] [3664] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6887--6887 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb etas",[] Underfull \hbox (badness 1043) in paragraph at lines 6899--6902 []\T1/pcr/m/n/10 "dfbetas"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "working"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "ldcase"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lsresp "[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ldshape"[]\T1/ptm/m/n/10 , and [3665] [3666] [3667] [3668] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7206--7206 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the ta=5), lung)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7207--7207 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog , theta=1), lung)[] [3669] [3670] [3671] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7391--7391 []\T1/pcr/m/n/10 rttright(formula, data, weights, subset, na.action, times, id , timefix = TRUE, [3672] Overfull \hbox (42.18039pt too wide) in paragraph at lines 7474--7474 []\T1/pcr/m/n/9 cdf <- cdf[!duplicated(aml$time[index], fromLast=TRUE)] # rem ove duplicate times[] [3673] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7478--7478 []\T1/pcr/m/n/9 wt2 <- rttright(Surv(dtime, death) ~ hormon, rotterdam, times= 365*c(3, 5))[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) has been already used, duplicate ignored \relax l.7482 ...ata from a soldering experiment}{solder} [3674] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7588--7588 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1, col = 1, [3675] [3676] [3677] [3678] [3679] [3680] Overfull \hbox (42.78088pt too wide) in paragraph at lines 7954--7954 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r r =expected,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 7955--7955 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli ne = FALSE,[] [3681] [3682] [3683] [3684] Overfull \hbox (54.78088pt too wide) in paragraph at lines 8272--8272 [] \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/ 10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/ n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[] [3685] [3686] [3687] [3688] Underfull \hbox (badness 1253) in paragraph at lines 8561--8564 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 median[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 quantile []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 plot []\T1/ptm/m/n/10 meth-ods first con-struct a sur-vival curve us-ing [3689] [3690] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8691--8691 []\T1/pcr/m/n/10 survcheck(formula, data, subset, na.action, id, istate, istat e0="(s0)", [3691] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8814--8814 []\T1/pcr/m/n/10 survcondense(formula, data, subset, weights, na.action= na.pa ss, id, [3692] [3693] [3694] Overfull \hbox (36.7804pt too wide) in paragraph at lines 9013--9013 [] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1 , year=accept.dt),[] [3695] Overfull \hbox (24.78088pt too wide) in paragraph at lines 9038--9038 [] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv idual.h",[] Underfull \hbox (badness 1038) in paragraph at lines 9080--9086 []\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre -dicted sur-vival [3696] Overfull \hbox (48.78088pt too wide) in paragraph at lines 9132--9132 [] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d t-entry.dt)),[] [3697] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9218--9218 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival by 1/2 years[] [3698] [3699] [3700] Underfull \hbox (badness 10000) in paragraph at lines 9438--9443 [][][]\T1/pcr/m/n/10 survfit.formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 survfit.coxph[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 survfit.object[][ ][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.survfit[][][][]\T1/ptm/m/n/10 , Overfull \hbox (12.78088pt too wide) in paragraph at lines 9458--9458 [] \T1/pcr/m/n/10 se.fit=TRUE, conf.int=.95, individual=FALSE, stype=2, ctype,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9459--9459 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] [3701] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9464--9464 [] \T1/pcr/m/n/10 se.fit=FALSE, conf.int=.95, individual=FALSE, stype=2 , ctype,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9465--9465 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] [3702] [3703] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9688--9688 [] \T1/pcr/m/n/10 stype=1, ctype=1, id, cluster, robust, istate, timefi x=TRUE,[] [3704] [3705] Underfull \hbox (badness 2653) in paragraph at lines 9822--9827 \T1/pcr/m/n/10 ctype=1[]\T1/ptm/m/n/10 , "fleming-harrington" which is equiv-a- lent to []\T1/pcr/m/n/10 stype=2, [3706] [3707] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9962--9962 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3708] [3709] [3710] [3711] [3712] Overfull \hbox (30.78088pt too wide) in paragraph at lines 10349--10349 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, Underfull \hbox (badness 1354) in paragraph at lines 10390--10394 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3713] Overfull \hbox (60.78088pt too wide) in paragraph at lines 10436--10436 []\T1/pcr/m/n/10 survConcordance(formula, data, weights, subset, na.action) # use concordance [3714] [3715] Underfull \hbox (badness 2035) in paragraph at lines 10600--10607 \T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][][]\T1/pcr/m/n/10 su rvreg.distributions[][][][]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 10600--10607 \T1/ptm/m/n/10 These in-clude []\T1/pcr/m/n/10 "weibull"[]\T1/ptm/m/n/10 , []\T 1/pcr/m/n/10 "exponential"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "gaussian"[]\T1/p tm/m/n/10 , Underfull \hbox (badness 1297) in paragraph at lines 10600--10607 []\T1/pcr/m/n/10 "logistic"[]\T1/ptm/m/n/10 ,[]\T1/pcr/m/n/10 "lognormal" []\T1 /ptm/m/n/10 and []\T1/pcr/m/n/10 "loglogistic"[]\T1/ptm/m/n/10 . Oth-er-wise, i t is [3716] [3717] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10690--10690 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3718] [3719] Overfull \hbox (31.3804pt too wide) in paragraph at lines 10847--10847 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3720] [3721] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10979--10979 [] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x ^2*temp -1))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 10982--10982 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3722] [3723] [3724] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11158--11158 []\T1/pcr/m/n/9 pfit2 <- pyears(Surv(years, death) ~ fgrp + agegrp, scale =100 0, data=test)[] [3725] [3726] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11316--11316 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic al trial plus[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11317--11317 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11323--11323 [] \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day , alk.phos))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 11325--11325 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil i), data=pbc2)[] [3727] [3728] [3729] [3730] [3731] [3732] [3733] Overfull \hbox (12.78088pt too wide) in paragraph at lines 11766--11766 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l inear",[] [3734] [3735] [3736]) (./fullrefman.ind [3737] [3738] [3739] [3740] [3741] [3742] [3743] [3744] [3745] [3746] [3747] [3748] [3749] [3750] [3751] [3752] [3753] [3754] [3755] [3756] [3757] [3758] [3759] [3760] [3761] [3762] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2691--2693 []| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2693--2695 []| \T1/pcr/m/n/10 smooth.construct.bs.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2695--2697 []| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2697--2699 []| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2699--2701 []| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2701--2703 []| \T1/pcr/m/n/10 smooth.construct.gp.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (25.3567pt too wide) in paragraph at lines 2703--2705 []| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2705--2707 []| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 , 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paragraph at lines 3355--3357 []| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 3357--3359 []| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 3359--3361 []| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (25.3567pt too wide) in paragraph at lines 3361--3363 []| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 3363--3365 []| \T1/pcr/m/n/10 smooth.construct.sz.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 3365--3367 []| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (43.3567pt too wide) in paragraph at lines 3367--3369 []| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 3369--3371 []| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , [3769] [3770] Overfull \hbox (19.3567pt too wide) in paragraph at lines 3525--3527 []| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , [3771] [3772] [3773] [3774] [3775] [3776] [3777] [3778] [3779] Overfull \hbox (20.8567pt too wide) in paragraph at lines 4759--4761 []\T1/pcr/m/n/10 [,Matrix,index,index,logical-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 4761--4763 []\T1/pcr/m/n/10 [,Matrix,index,index,missing-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 4763--4765 []\T1/pcr/m/n/10 [,Matrix,index,missing,logical-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 4765--4767 []\T1/pcr/m/n/10 [,Matrix,index,missing,missing-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 4767--4769 []\T1/pcr/m/n/10 [,Matrix,lMatrix,missing,missing-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 4769--4771 []\T1/pcr/m/n/10 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Arith,sparseVector,ddenseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 6162--6164 []\T1/pcr/m/n/10 Arith,sparseVector,dgeMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 6164--6166 []\T1/pcr/m/n/10 Arith,sparseVector,sparseVector-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 6166--6168 []\T1/pcr/m/n/10 Arith,triangularMatrix,diagonalMatrix-method [3790] [3791] [3792] Overfull \hbox (32.8567pt too wide) in paragraph at lines 6667--6669 []\T1/pcr/m/n/10 aspell_write_personal_dictionary_file [3793] Overfull \hbox (46.01662pt too wide) in paragraph at lines 6852--6854 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [3794] [3795] Overfull \hbox (10.01662pt too wide) in paragraph at lines 7299--7301 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3796] [3797] Overfull \hbox (2.8567pt too wide) in paragraph at lines 7773--7775 []\T1/pcr/m/n/10 chol2inv,triangularMatrix-method [3798] Overfull \hbox (2.8567pt too wide) in paragraph at lines 7818--7820 []\T1/pcr/m/n/10 Cholesky,triangularMatrix-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 7825--7827 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3799] [3800] [3801] Overfull \hbox (50.8567pt too wide) in paragraph at lines 8331--8333 []\T1/pcr/m/n/10 coerce,atomicVector,dsparseVector-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 8333--8335 []\T1/pcr/m/n/10 coerce,atomicVector,sparseVector-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 8335--8337 []\T1/pcr/m/n/10 coerce,BunchKaufman,dtrMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 8337--8339 []\T1/pcr/m/n/10 coerce,CHMsimpl,dtCMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 8339--8341 []\T1/pcr/m/n/10 coerce,CHMsuper,dgCMatrix-method Overfull \hbox (2.8567pt too 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coerce,matrix,CsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8405--8407 []\T1/pcr/m/n/10 coerce,Matrix,ddenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8407--8409 []\T1/pcr/m/n/10 coerce,matrix,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 8409--8411 []\T1/pcr/m/n/10 coerce,Matrix,denseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 8411--8413 []\T1/pcr/m/n/10 coerce,matrix,denseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 8415--8417 []\T1/pcr/m/n/10 coerce,Matrix,diagonalMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 8417--8419 []\T1/pcr/m/n/10 coerce,matrix,diagonalMatrix-method [3802] Overfull \hbox (14.8567pt too wide) in paragraph at lines 8431--8433 []\T1/pcr/m/n/10 coerce,Matrix,dsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8433--8435 []\T1/pcr/m/n/10 coerce,matrix,dsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8435--8437 []\T1/pcr/m/n/10 coerce,Matrix,generalMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8437--8439 []\T1/pcr/m/n/10 coerce,matrix,generalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8447--8449 []\T1/pcr/m/n/10 coerce,Matrix,ldenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8449--8451 []\T1/pcr/m/n/10 coerce,matrix,ldenseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8455--8457 []\T1/pcr/m/n/10 coerce,Matrix,lsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8457--8459 []\T1/pcr/m/n/10 coerce,matrix,lsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8469--8471 []\T1/pcr/m/n/10 coerce,Matrix,ndenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8471--8473 []\T1/pcr/m/n/10 coerce,matrix,ndenseMatrix-method 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paragraph at lines 8501--8503 []\T1/pcr/m/n/10 coerce,Matrix,sparseVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8503--8505 []\T1/pcr/m/n/10 coerce,matrix,sparseVector-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 8505--8507 []\T1/pcr/m/n/10 coerce,Matrix,symmetricMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 8507--8509 []\T1/pcr/m/n/10 coerce,matrix,symmetricMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 8509--8511 []\T1/pcr/m/n/10 coerce,Matrix,triangularMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 8511--8513 []\T1/pcr/m/n/10 coerce,matrix,triangularMatrix-method [3803] Overfull \hbox (14.8567pt too wide) in paragraph at lines 8513--8515 []\T1/pcr/m/n/10 coerce,Matrix,TsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8515--8517 []\T1/pcr/m/n/10 coerce,matrix,TsparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 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[]\T1/pcr/m/n/10 coerce,matrix.csc,CsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8537--8539 []\T1/pcr/m/n/10 coerce,matrix.csc,dgCMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 8541--8543 []\T1/pcr/m/n/10 coerce,matrix.csc,RsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 8543--8545 []\T1/pcr/m/n/10 coerce,matrix.csc,sparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 8545--8547 []\T1/pcr/m/n/10 coerce,matrix.csc,TsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 8547--8549 []\T1/pcr/m/n/10 coerce,matrix.csr,CsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8549--8551 []\T1/pcr/m/n/10 coerce,matrix.csr,dgCMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8551--8553 []\T1/pcr/m/n/10 coerce,matrix.csr,dgRMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 8555--8557 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coerce,sparseVector,CsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 8587--8589 []\T1/pcr/m/n/10 coerce,sparseVector,denseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8589--8591 []\T1/pcr/m/n/10 coerce,sparseVector,dsparseVector-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8591--8593 []\T1/pcr/m/n/10 coerce,sparseVector,generalMatrix-method [3804] Overfull \hbox (50.8567pt too wide) in paragraph at lines 8593--8595 []\T1/pcr/m/n/10 coerce,sparseVector,isparseVector-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8595--8597 []\T1/pcr/m/n/10 coerce,sparseVector,lsparseVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8597--8599 []\T1/pcr/m/n/10 coerce,sparseVector,Matrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8599--8601 []\T1/pcr/m/n/10 coerce,sparseVector,nsparseVector-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8601--8603 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coerce,vector,ndenseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8643--8645 []\T1/pcr/m/n/10 coerce,vector,nsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8645--8647 []\T1/pcr/m/n/10 coerce,vector,nsparseVector-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8647--8649 []\T1/pcr/m/n/10 coerce,vector,RsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8649--8651 []\T1/pcr/m/n/10 coerce,vector,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8651--8653 []\T1/pcr/m/n/10 coerce,vector,sparseVector-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8653--8655 []\T1/pcr/m/n/10 coerce,vector,TsparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 8655--8657 []\T1/pcr/m/n/10 coerce,vector,unpackedMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8657--8659 []\T1/pcr/m/n/10 coerce,vector,zsparseVector-method [3805] Overfull \hbox (62.8567pt too wide) in paragraph at lines 8782--8784 []\T1/pcr/m/n/10 Compare,CsparseMatrix,CsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8788--8790 []\T1/pcr/m/n/10 Compare,lgeMatrix,lgeMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8800--8802 []\T1/pcr/m/n/10 Compare,ngeMatrix,ngeMatrix-method Overfull \hbox (86.8567pt too wide) in paragraph at lines 8814--8816 []\T1/pcr/m/n/10 Compare,triangularMatrix,diagonalMatrix-method [3806] [3807] [3808] Overfull \hbox (8.8567pt too wide) in paragraph at lines 9351--9353 []\T1/pcr/m/n/10 crossprod,ANY,sparseVector-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 9353--9355 []\T1/pcr/m/n/10 crossprod,CsparseMatrix,CsparseMatrix-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 9355--9357 []\T1/pcr/m/n/10 crossprod,CsparseMatrix,denseMatrix-method Overfull \hbox (80.8567pt too wide) in paragraph at lines 9357--9359 []\T1/pcr/m/n/10 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[]\T1/pcr/m/n/10 derivedDefaultMethodWithTrace-class Overfull \hbox (44.8567pt too wide) in paragraph at lines 9972--9974 []\T1/pcr/m/n/10 determinant,BunchKaufman,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 9974--9976 []\T1/pcr/m/n/10 determinant,CHMfactor,logical-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 9976--9978 []\T1/pcr/m/n/10 determinant,Cholesky,logical-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 9978--9980 []\T1/pcr/m/n/10 determinant,denseLU,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 9980--9982 []\T1/pcr/m/n/10 determinant,dgCMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 9982--9984 []\T1/pcr/m/n/10 determinant,dgeMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 9984--9986 []\T1/pcr/m/n/10 determinant,dgRMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 9986--9988 []\T1/pcr/m/n/10 determinant,dgTMatrix,logical-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 9988--9990 []\T1/pcr/m/n/10 determinant,diagonalMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 9990--9992 []\T1/pcr/m/n/10 determinant,dpoMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 9992--9994 []\T1/pcr/m/n/10 determinant,dppMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 9994--9996 []\T1/pcr/m/n/10 determinant,dsCMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 9996--9998 []\T1/pcr/m/n/10 determinant,dspMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 9998--10000 []\T1/pcr/m/n/10 determinant,dsRMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 10000--10002 []\T1/pcr/m/n/10 determinant,dsTMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 10002--10004 []\T1/pcr/m/n/10 determinant,dsyMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 10004--10006 []\T1/pcr/m/n/10 determinant,indMatrix,logical-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 10006--10008 []\T1/pcr/m/n/10 determinant,Matrix,logical-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 10008--10010 []\T1/pcr/m/n/10 determinant,Matrix,missing-method [3812] Overfull \hbox (86.8567pt too wide) in paragraph at lines 10010--10012 []\T1/pcr/m/n/10 determinant,MatrixFactorization,missing-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 10010--10012 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , Overfull \hbox (50.8567pt too wide) in paragraph at lines 10012--10014 []\T1/pcr/m/n/10 determinant,pBunchKaufman,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 10014--10016 []\T1/pcr/m/n/10 determinant,pCholesky,logical-method Overfull \hbox (14.8567pt too wide) 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MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , Overfull \hbox (8.8567pt too wide) in paragraph at lines 10392--10394 []\T1/pcr/m/n/10 dimnames<-,compMatrix,list-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 10394--10396 []\T1/pcr/m/n/10 dimnames<-,compMatrix,NULL-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 10400--10402 []\T1/pcr/m/n/10 dimnames<-,MatrixFactorization,list-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 10400--10402 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3814] Overfull \hbox (62.8567pt too wide) in paragraph at lines 10402--10404 []\T1/pcr/m/n/10 dimnames<-,MatrixFactorization,NULL-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 10402--10404 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3815] Overfull \hbox (46.01662pt too wide) in paragraph at lines 10753--10755 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [3816] [3817] [3818] [3819] [3820] Overfull \hbox (80.8567pt too wide) in paragraph at lines 11720--11722 []\T1/pcr/m/n/10 forceSymmetric,CsparseMatrix,character-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 11722--11724 []\T1/pcr/m/n/10 forceSymmetric,CsparseMatrix,missing-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 11724--11726 []\T1/pcr/m/n/10 forceSymmetric,denseMatrix,character-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 11726--11728 []\T1/pcr/m/n/10 forceSymmetric,denseMatrix,missing-method Overfull \hbox (86.8567pt too wide) in paragraph at lines 11728--11730 []\T1/pcr/m/n/10 forceSymmetric,diagonalMatrix,character-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 11730--11732 []\T1/pcr/m/n/10 forceSymmetric,diagonalMatrix,missing-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 11732--11734 []\T1/pcr/m/n/10 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kronecker,TsparseMatrix,Matrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 14358--14360 []\T1/pcr/m/n/10 kronecker,TsparseMatrix,TsparseMatrix-method [3834] Overfull \hbox (8.8567pt too wide) in paragraph at lines 14569--14571 []\T1/pcr/m/n/10 length,MatrixFactorization-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 14569--14571 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3835] [3836] [3837] Overfull \hbox (50.8567pt too wide) in paragraph at lines 15190--15192 []\T1/pcr/m/n/10 Logic,CsparseMatrix,CsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15196--15198 []\T1/pcr/m/n/10 Logic,dMatrix,sparseVector-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 15198--15200 []\T1/pcr/m/n/10 Logic,ldenseMatrix,lsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 15200--15202 []\T1/pcr/m/n/10 Logic,lgCMatrix,lgCMatrix-method Overfull \hbox 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wide) in paragraph at lines 15232--15234 []\T1/pcr/m/n/10 Logic,ngeMatrix,ngeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15242--15244 []\T1/pcr/m/n/10 Logic,nMatrix,sparseVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15250--15252 []\T1/pcr/m/n/10 Logic,sparseVector,dMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15252--15254 []\T1/pcr/m/n/10 Logic,sparseVector,lMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15254--15256 []\T1/pcr/m/n/10 Logic,sparseVector,nMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 15256--15258 []\T1/pcr/m/n/10 Logic,sparseVector,sparseVector-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 15258--15260 []\T1/pcr/m/n/10 Logic,triangularMatrix,diagonalMatrix-method [3838] [3839] Overfull \hbox (10.01662pt too wide) in paragraph at lines 15563--15565 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3840] [3841] [3842] Overfull \hbox (52.01662pt too wide) in paragraph at lines 16340--16342 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , [3843] [3844] [3845] Overfull \hbox (8.8567pt too wide) in paragraph at lines 16944--16946 []\T1/pcr/m/n/10 nonstandardGenericWithTrace-class Overfull \hbox (8.8567pt too wide) in paragraph at lines 16965--16967 []\T1/pcr/m/n/10 norm,denseMatrix,character-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 16967--16969 []\T1/pcr/m/n/10 norm,diagonalMatrix,character-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 16973--16975 []\T1/pcr/m/n/10 norm,sparseMatrix,character-method [3846] Overfull \hbox (26.8567pt too wide) in paragraph at lines 17252--17254 []\T1/pcr/m/n/10 Ops,atomicVector,sparseVector-method [3847] Overfull \hbox (8.8567pt too wide) in paragraph at lines 17270--17272 []\T1/pcr/m/n/10 Ops,ddiMatrix,sparseMatrix-method Overfull \hbox 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Ops,sparseVector,atomicVector-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 17398--17400 []\T1/pcr/m/n/10 Ops,sparseVector,sparseVector-method [3849] Overfull \hbox (46.01662pt too wide) in paragraph at lines 17607--17609 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (77.3567pt too wide) in paragraph at lines 17639--17641 []\T1/pcr/m/n/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , [3850] [3851] [3852] [3853] [3854] [3855] Overfull \hbox (46.01662pt too wide) in paragraph at lines 18982--18984 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 18985--18987 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 18987--18989 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 18989--18991 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 18991--18993 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.fs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 18993--18995 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (52.01662pt too wide) in paragraph at lines 18995--18997 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 18997--18999 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 18999--19001 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.re.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19001--19003 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (52.01662pt too wide) in paragraph at lines 19005--19007 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19007--19009 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 19009--19011 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.sz.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19011--19013 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19013--19015 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19015--19017 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19017--19019 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [3856] [3857] Overfull \hbox (4.01662pt too wide) in paragraph at lines 19367--19369 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19441--19443 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [3858] [3859] [3860] Overfull \hbox (10.01662pt too wide) in paragraph at lines 19913--19915 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , Overfull \hbox (8.8567pt too wide) in paragraph at lines 19919--19921 []\T1/pcr/m/n/10 qr.coef,sparseQR,dgeMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 19929--19931 []\T1/pcr/m/n/10 qr.fitted,sparseQR,dgeMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19931--19933 []\T1/pcr/m/n/10 qr.fitted,sparseQR,Matrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19933--19935 []\T1/pcr/m/n/10 qr.fitted,sparseQR,matrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19935--19937 []\T1/pcr/m/n/10 qr.fitted,sparseQR,vector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19945--19947 []\T1/pcr/m/n/10 qr.qty,sparseQR,dgeMatrix-method [3861] Overfull \hbox (14.8567pt too wide) in paragraph at lines 19970--19972 []\T1/pcr/m/n/10 qr.resid,sparseQR,dgeMatrix-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 20105--20107 []\T1/pcr/m/n/10 R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE [3862] [3863] Overfull \hbox (14.8567pt too wide) in paragraph at lines 20383--20385 []\T1/pcr/m/n/10 rcond,denseMatrix,character-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 20385--20387 []\T1/pcr/m/n/10 rcond,diagonalMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20387--20389 []\T1/pcr/m/n/10 rcond,indMatrix,character-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 20391--20393 []\T1/pcr/m/n/10 rcond,sparseMatrix,character-method [3864] [3865] [3866] [3867] [3868] Overfull \hbox (10.01662pt too wide) in paragraph at lines 21396--21398 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3869] Overfull \hbox (32.8567pt too wide) in paragraph at lines 21765--21767 []\T1/pcr/m/n/10 show,BunchKaufmanFactorization-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 21765--21767 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , Overfull \hbox (8.8567pt too wide) in paragraph at lines 21767--21769 []\T1/pcr/m/n/10 show,CholeskyFactorization-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 21767--21769 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , Overfull \hbox (26.8567pt too wide) in paragraph at lines 21781--21783 []\T1/pcr/m/n/10 show,genericFunctionWithTrace-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 21783--21785 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , Overfull \hbox (10.01662pt too wide) in paragraph at lines 21785--21787 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , Overfull \hbox (32.8567pt too wide) in paragraph at lines 21789--21791 []\T1/pcr/m/n/10 show,MethodDefinitionWithTrace-method [3870] Overfull \hbox (20.8567pt too wide) in paragraph at lines 21793--21795 []\T1/pcr/m/n/10 show,MethodWithNextWithTrace-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 21799--21801 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , Overfull \hbox (14.8567pt too wide) in paragraph at lines 21801--21803 []\T1/pcr/m/n/10 show,refClassRepresentation-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 21807--21809 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3871] Overfull \hbox (46.01662pt too wide) in paragraph at lines 22049--22051 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 22051--22053 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 22054--22056 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (5.3567pt too wide) in paragraph at lines 22062--22063 []\T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 22071--22073 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (5.3567pt too wide) in paragraph at lines 22075--22076 []\T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 22076--22078 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (23.3567pt too wide) in paragraph at lines 22083--22087 []\T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 22088--22090 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.tp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [3872] Overfull \hbox (46.01662pt too wide) in paragraph at lines 22139--22141 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10 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[3] [4] Underfull \hbox (badness 6741) in paragraph at lines 137--143 []\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber []\T1/pcr/m/n/ 10 x []\T1/ptm/m/n/10 such that []\T1/pcr/m/n/10 1 + x != 1[]\T1/ptm/m/n/10 . Underfull \hbox (badness 4805) in paragraph at lines 137--143 \T1/ptm/m/n/10 It equals []\T1/pcr/m/n/10 double.base ^ ulp.digits []\T1/ptm/m/ n/10 if ei-ther []\T1/pcr/m/n/10 double.base []\T1/ptm/m/n/10 is Underfull \hbox (badness 4316) in paragraph at lines 137--143 \T1/ptm/m/n/10 2 or []\T1/pcr/m/n/10 double.rounding []\T1/ptm/m/n/10 is 0; oth -er-wise, it is []\T1/pcr/m/n/10 (double.base ^ Underfull \hbox (badness 4454) in paragraph at lines 143--151 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber []\T1/pcr/m/n/10 x [ ]\T1/ptm/m/n/10 such that []\T1/pcr/m/n/10 1 - x != 1[]\T1/ptm/m/n/10 . It Underfull \hbox (badness 1028) in paragraph at lines 143--151 \T1/ptm/m/n/10 equals []\T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits []\T 1/ptm/m/n/10 if []\T1/pcr/m/n/10 double.base Underfull \hbox (badness 2980) in paragraph at lines 143--151 []\T1/ptm/m/n/10 is 2 or []\T1/pcr/m/n/10 double.rounding []\T1/ptm/m/n/10 is 0 ; oth-er-wise, it is []\T1/pcr/m/n/10 (double.base Underfull \hbox (badness 1394) in paragraph at lines 143--151 \T1/pcr/m/n/10 ^ double.neg.ulp.digits) / 2[]\T1/ptm/m/n/10 . Nor-mally []\T1/p cr/m/n/10 1.110223e-16[]\T1/ptm/m/n/10 . As [5] Underfull \hbox (badness 1142) in paragraph at lines 215--220 []\T1/ptm/m/n/10 the num-ber of \T1/ptm/m/it/10 bytes \T1/ptm/m/n/10 in the C [ ]\T1/pcr/m/n/10 time_t []\T1/ptm/m/n/10 type: a 64-bit []\T1/pcr/m/n/10 time_t []\T1/ptm/m/n/10 (value Underfull \hbox (badness 1478) in paragraph at lines 215--220 []\T1/pcr/m/n/10 8[]\T1/ptm/m/n/10 ) is much pre-ferred these days. Note that t his is the type used by Underfull \hbox (badness 3009) in paragraph at lines 231--243 []\T1/pcr/m/n/10 *.exponent[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 *.min.exp[]\T1/p tm/m/n/10 , and []\T1/pcr/m/n/10 *.max.exp[]\T1/ptm/m/n/10 , com-puted en-tirel y anal-o-gously to their [6] [7] Underfull \hbox (badness 10000) in paragraph at lines 374--378 [][][]\T1/pcr/m/n/10 R.version[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 Sys.info[][][] []\T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-l ar, [8] [9] [10] Underfull \hbox (badness 1072) in paragraph at lines 571--577 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[] \T1/pcr/m/n/10 insertions[]\T1/ptm/m/n/10 ', [11] Overfull \hbox (4.38043pt too wide) in paragraph at lines 639--639 []\T1/pcr/m/n/9 agrep("laysy", c("1 lazy", "1", "1 LAZY"), max.distance = 2, v alue = TRUE)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 640--640 []\T1/pcr/m/n/9 agrep("laysy", c("1 lazy", "1", "1 LAZY"), max.distance = 2, i gnore.case = TRUE)[] [12] [13] (/usr/share/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [14] [15] Overfull \hbox (4.38043pt too wide) in paragraph at lines 920--920 []\T1/pcr/m/n/9 all.equal(tan(d45), one, tolerance = 0, scale = 1+(-2:2)/1e9) # "absolute"[] [16] Overfull \hbox (4.38043pt too wide) in paragraph at lines 941--941 []\T1/pcr/m/n/9 mtext(paste("mean(all.equal(x1, x2*(1 + eps_k))) {100 x} Mean rel.diff.=",[] [17] Overfull \hbox (0.78088pt too wide) in paragraph at lines 990--990 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE) [18] [19] [20] [21] [22] [23] [24] (/usr/share/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texmf-dist/tex/latex/base/ts1cmtt.fd) [25{/usr/share/texmf-dist/fon ts/enc/dvips/cm-super/cm-super-ts1.enc}] Underfull \hbox (badness 1221) in paragraph at lines 1523--1529 []\T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion, where \T1/phv/m/n/10 R \T1/p tm/m/n/10 uses ``floored'' in-te-ger di-vi-sion, i.e., []\T1/pcr/m/n/10 q <- x %/% y := [26] Underfull \hbox (badness 10000) in paragraph at lines 1611--1617 Underfull \hbox (badness 10000) in paragraph at lines 1624--1626 []\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac le . com / cd / E19957-[]01 / 806-[]3568 / ncg _ [27] [28] [29] [30] Underfull \vbox (badness 10000) has occurred while \output is active [31] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1966--1966 [] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em pty.names = TRUE,[] Underfull \hbox (badness 1303) in paragraph at lines 1998--2001 []\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more than 256 (or [32] Underfull \hbox (badness 1325) in paragraph at lines 2027--2031 []\T1/ptm/m/n/10 Direct calls to []\T1/pcr/m/n/10 as.data.frame.() []\T1 /ptm/m/n/10 are still pos-si-ble (base pack-age!), for 12 Underfull \hbox (badness 3568) in paragraph at lines 2027--2031 \T1/ptm/m/n/10 atomic base classes, but will dep-re-cated (al-ready vis-i-bly b y set-ting en-vi-ron-ment vari- Underfull \hbox (badness 4144) in paragraph at lines 2027--2031 \T1/ptm/m/n/10 able []\T1/pcr/m/n/10 _R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_ [] \T1/ptm/m/n/10 to non-empty) where call-ing [33] [34] [35] Overfull \hbox (112.38031pt too wide) in paragraph at lines 2267--2267 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [36] Underfull \hbox (badness 10000) in paragraph at lines 2305--2307 []\T1/ptm/m/n/10 If [][][]\T1/pcr/m/n/10 is.object[][][](x) []\T1/ptm/m/n/10 is true and it has a [][][]\T1/pcr/m/n/10 class[][][] []\T1/ptm/m/n/10 for which an [37] [38] [39] [40] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2579--2579 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla ss "POSIXlt"[] [41] [42] [43] Underfull \hbox (badness 1107) in paragraph at lines 2783--2785 []\T1/ptm/m/n/10 There are no re-stric-tions on the name given as []\T1/pcr/m/n /10 x[]\T1/ptm/m/n/10 : it can be a non-syntactic name (see [44] [45] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2950--2950 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse1(substitute(what), back tick=FALSE), [46] [47] [48] [49] [50] [51] [52] Underfull \hbox (badness 10000) in paragraph at lines 3413--3416 []\T1/pcr/m/n/10 unCfillPOSIXlt(x) []\T1/ptm/m/n/10 is a fast [][]prim-i-tive[] [][] ver-sion of []\T1/pcr/m/n/10 balancePOSIXlt(x, [53] [54] [55] [56] Overfull \hbox (31.3804pt too wide) in paragraph at lines 3718--3718 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2, lwd = 1, bty="n")[] [57] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3749--3749 []\T1/pcr/m/n/9 plot(range(x0), c(1e-40, 1), log = "xy", xlab = "x", ylab = "" , type = "n",[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3750--3750 [] \T1/pcr/m/n/9 main = "Bessel Functions J_nu(x) near 0\n log - log sc ale") ; axis(2, at=1)[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3757--3757 []\T1/pcr/m/n/9 plot(range(x0), 10^c(-100, 80), log = "xy", xlab = "x", ylab = "", type = "n",[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3758--3758 [] \T1/pcr/m/n/9 main = "Bessel Functions K_nu(x) near 0\n log - log sc ale") ; axis(2, at=1)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3761--3761 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5, sep = ", ")),[] Underfull \vbox (badness 10000) has occurred while \output is active [58] [59] [60] [61] [62] [63] [64] Underfull \hbox (badness 10000) in paragraph at lines 4209--4211 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [65] [66] [67] [68] [69] [70] [71] Underfull \hbox (badness 4927) in paragraph at lines 4714--4718 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an ob-ject Underfull \hbox (badness 2012) in paragraph at lines 4714--4718 \T1/ptm/m/n/10 of class []\T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"[]\T1/ptm/ m/n/10 , []\T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" []\T1/ptm/m/n/10 o r [72] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4798--4798 [] \T1/pcr/m/n/10 Xchk = any(nas %in% c("X11", "jpeg", "png", "tif f")))[] [73] Underfull \hbox (badness 4595) in paragraph at lines 4872--4875 []\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par -i-son[][][] and [74] [75] [76] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5035--5035 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{ ", 1:10, "}:"))[] Underfull \hbox (badness 1199) in paragraph at lines 5064--5070 []\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na med ar-gu- Underfull \hbox (badness 2573) in paragraph at lines 5076--5079 []\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu e and valid [77] [78] [79] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5249--5249 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna mes (default)[] [80] [81] [82] Underfull \hbox (badness 2521) in paragraph at lines 5506--5508 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [83] [84] [85] [86] [87] [88] [89] [90] Underfull \hbox (badness 1270) in paragraph at lines 5998--6006 []\T1/ptm/m/n/10 When a generic func-tion []\T1/pcr/m/n/10 fun []\T1/ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute []\T1/pcr/m/n/10 c("first", [91] [92] [93] [94] [95] [96] [97] [98] Underfull \hbox (badness 1796) in paragraph at lines 6572--6580 []\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i n-tro-duc-tion see [][]$\T1/pcr/m/n/10 https : / / [99] [100] [101] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6769--6769 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile r, math-library:[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 6771--6771 []\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6772--6772 []\T1/pcr/m/n/9 showC(NpNA)# but not always is {shows \TS1/pcr/m/n/9 '\T1/pcr /m/n/9 (R = NaN, I = NA)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 on some platforms}[] [102] [103] Underfull \hbox (badness 1635) in paragraph at lines 6974--6977 []\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class []\T1/pcr/m/n /10 interrupt []\T1/ptm/m/n/10 that in-her-its di-rectly from class Underfull \hbox (badness 3009) in paragraph at lines 6978--6981 []\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols. They can be es-tab-lished us-ing [104] Underfull \hbox (badness 1308) in paragraph at lines 7021--7029 []\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i s []\T1/pcr/m/n/10 interactive[]\T1/ptm/m/n/10 . This should [105] [106] Overfull \hbox (30.78088pt too wide) in paragraph at lines 7185--7185 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e ncoding"))[] [107] Underfull \hbox (badness 4505) in paragraph at lines 7237--7240 []\T1/ptm/m/n/10 character string, par-tially matched to []\T1/pcr/m/n/10 c("de fault", "internal", [108] [109] Underfull \hbox (badness 1997) in paragraph at lines 7374--7379 []\T1/pcr/m/n/10 file[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pipe[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 fifo[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 url[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 gzfile[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 bzfile[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 xzfile[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 unz[]\T1/ptm/m /n/10 , []\T1/pcr/m/n/10 socketConnection[]\T1/ptm/m/n/10 , [110] [111] [112] Underfull \hbox (badness 10000) in paragraph at lines 7622--7624 []\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in g from Underfull \hbox (badness 3302) in paragraph at lines 7664--7671 []\T1/pcr/m/n/10 file []\T1/ptm/m/n/10 can be used with []\T1/pcr/m/n/10 descri ption = "clipboard" []\T1/ptm/m/n/10 in mode []\T1/pcr/m/n/10 "r" []\T1/ptm/m/n /10 only. This Underfull \hbox (badness 6592) in paragraph at lines 7664--7671 \T1/ptm/m/n/10 reads the X11 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http s : / / specifications . freedesktop . Underfull \hbox (badness 1735) in paragraph at lines 7664--7671 []\T1/pcr/m/n/10 "X11_primary" []\T1/ptm/m/n/10 and the sec-ondary se-lec-tion as []\T1/pcr/m/n/10 "X11_secondary"[]\T1/ptm/m/n/10 . On most sys- [113] [114] [115] Underfull \vbox (badness 10000) has occurred while \output is active [116] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7879--7879 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE")) ; close(con)[] [117] [118] [119] [120] Underfull \hbox (badness 10000) in paragraph at lines 8212--8214 []\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th e call to [121] [122] [123] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8370--8370 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect s to https://[] [124] [125] [126] [127] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8604--8604 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng th.out = 24)[] [128] Underfull \hbox (badness 10000) in paragraph at lines 8720--8730 []\T1/pcr/m/n/10 data.frame []\T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing Underfull \hbox (badness 1975) in paragraph at lines 8720--8730 [][][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)[]\T1/ptm/m/n/10 . As that is a generic func-tion, meth-ods can be [129] [130] [131] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8888--8888 [] \T1/pcr/m/n/9 c = seq(as.Date("2004-01-01"), by = "week", l ength.out = 3),[] [132] [133] [134] [135] Underfull \hbox (badness 10000) in paragraph at lines 9216--9228 \T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") []\T1/ptm/m /n/10 may give []\T1/pcr/m/n/10 NA[]\T1/ptm/m/n/10 , and [136] [137] [138] [139] [140] [141] [142] Underfull \hbox (badness 10000) in paragraph at lines 9760--9764 []\T1/pcr/m/n/10 .Defunct []\T1/ptm/m/n/10 is called from de-funct func-tions. Func-tions should be listed in [143] [144] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9851--9851 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: -------- -------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9853--9853 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO !\n"); pi+2})[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9881--9881 [] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "( ", "function"),[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9882--9882 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh owAttributes"),[] [145] [146] Underfull \hbox (badness 5403) in paragraph at lines 10013--10015 []\T1/pcr/m/n/10 ..deparseOpts []\T1/ptm/m/n/10 is the [][][]\T1/pcr/m/n/10 cha racter[][][] []\T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used b y Underfull \hbox (badness 6063) in paragraph at lines 10032--10034 []\T1/ptm/m/n/10 Surround un-eval-u-ated ex-pres-sions, but not [][][]\T1/pcr/m /n/10 formula[][][][]\T1/ptm/m/n/10 s, with [147] [148] [149] Underfull \hbox (badness 1603) in paragraph at lines 10263--10266 []\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t er-mi-nant if [150] [151] [152] [153] [154] [155] [156] Overfull \hbox (12.78088pt too wide) in paragraph at lines 10728--10728 [] \T1/pcr/m/n/10 z <- as.POSIXct(c("2016-12-31 23:59:59", "2017-01-01 00:0 0:01"))[] [157] [158] Underfull \hbox (badness 1917) in paragraph at lines 10892--10897 []\T1/pcr/m/n/10 provideDimnames(x) []\T1/ptm/m/n/10 pro-vides []\T1/pcr/m/n/10 dimnames []\T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has [159] Overfull \hbox (36.7804pt too wide) in paragraph at lines 10947--10947 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE RS)))) # recycling[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10948--10948 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling on both levels[] [160] [161] Underfull \hbox (badness 1168) in paragraph at lines 11050--11055 []\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of []\ T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . Cur-rently this is only used by [162] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11152--11152 []\T1/pcr/m/n/9 ## From R 4.1.0 to 4.1.2, ...names() sometimes did not match n ames(list(...));[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 11154--11154 []\T1/pcr/m/n/9 chk.n2 <- function(...) stopifnot(identical(print(...names()), names(list(...))))[] [163] [164] Underfull \hbox (badness 2828) in paragraph at lines 11273--11278 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19 85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Underfull \hbox (badness 10000) in paragraph at lines 11273--11278 \T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr /m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ Underfull \hbox (badness 10000) in paragraph at lines 11273--11278 \T1/pcr/m/n/10 754-[]2019$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ pcr/m/n/10 https : Overfull \hbox (42.78088pt too wide) in paragraph at lines 11304--11304 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA ttributes"))[] [165] Overfull \hbox (15.18042pt too wide) in paragraph at lines 11378--11378 []\T1/pcr/m/n/9 ## Write an ASCII version of the \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 base\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 function mean() to our temp file, ..[] [166] [167] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11527--11527 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon th.abb[5:9])) [168] [169] [170] Underfull \hbox (badness 6396) in paragraph at lines 11725--11733 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for Underfull \hbox (badness 10000) in paragraph at lines 11734--11736 []\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) []\T1/ptm/m/n/10 is equiv-a-len t to but faster than [171] [172] [173] Underfull \hbox (badness 10000) in paragraph at lines 11951--11954 []\T1/ptm/m/n/10 Do not use []\T1/pcr/m/n/10 dyn.unload []\T1/ptm/m/n/10 on a D LL loaded by [][][]\T1/pcr/m/n/10 library.dynam[][][][]\T1/ptm/m/n/10 : use [174] [175] [176] [177] [178] [179] Underfull \hbox (badness 2744) in paragraph at lines 12398--12400 []\T1/ptm/m/n/10 Changing the cur-rent en-cod-ing from a run-ning R ses-sion ma y lead to con-fu-sion (see [180] Overfull \hbox (20.58041pt too wide) in paragraph at lines 12421--12421 []\T1/pcr/m/n/9 Encoding(x.) # "unknown" (UTF-8 loc.) | "latin1" (8859-1/CP-12 52 loc.) | ....[] [181] [182] [183] Underfull \hbox (badness 5288) in paragraph at lines 12673--12675 []\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val ue of Underfull \hbox (badness 3039) in paragraph at lines 12683--12688 []\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][][]\T1/pcr/m/n/1 0 dev2bitmap[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 bitmap[][][] []\T1/pt m/m/n/10 and [184] Underfull \hbox (badness 10000) in paragraph at lines 12740--12743 []\T1/ptm/m/n/10 The path to HTML []\T1/pcr/m/n/10 tidy[]\T1/ptm/m/n/10 . Used by []\T1/pcr/m/n/10 R CMD check []\T1/ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 12758--12760 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [185] [186] [187] [188] Underfull \hbox (badness 10000) in paragraph at lines 13008--13010 []\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing []\T1/pc r/m/n/10 where []\T1/ptm/m/n/10 as Underfull \hbox (badness 5970) in paragraph at lines 13051--13053 []\T1/pcr/m/n/10 get0(): []\T1/ptm/m/n/10 The object---as from [][][]\T1/pcr/m/ n/10 get[][][](x, *)[]\T1/ptm/m/n/10 --- if []\T1/pcr/m/n/10 exists(x, *) []\T1 /ptm/m/n/10 is true, oth-er-wise [189] [190] [191] [192] [193] [194] [195] [196] [197] [198] [199] [200] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13874--13874 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide a constructor[] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] Underfull \hbox (badness 2253) in paragraph at lines 14602--14604 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see Underfull \hbox (badness 1490) in paragraph at lines 14637--14640 []\T1/ptm/m/n/10 Junction points and sym-bolic links are fol-lowed, so in-for-m a-tion is given about the [211] [212] Underfull \hbox (badness 2573) in paragraph at lines 14770--14772 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as []\T1/pcr /m/n/10 PATH []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 R_LIBS []\T1/ptm/m/n/10 with []\T1/pcr/m/n/10 fsep = [213] [214] Underfull \hbox (badness 10000) in paragraph at lines 14929--14931 []\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See [215] [216] Underfull \hbox (badness 10000) in paragraph at lines 15050--15054 [][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil e.access[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.path[][][][]\T1/ptm/ m/n/10 , [][][]\T1/pcr/m/n/10 file.show[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 list.files[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 unlink[][][][]\T1 /ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 15061--15064 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Overfull \hbox (47.58038pt too wide) in paragraph at lines 15082--15082 [] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B as it exists already[] [217] Overfull \hbox (30.78088pt too wide) in paragraph at lines 15107--15107 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [218] Underfull \hbox (badness 10000) in paragraph at lines 15204--15207 [][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil e.exists[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.path[][][][]\T1/ptm/ m/n/10 , [][][]\T1/pcr/m/n/10 list.files[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/ m/n/10 unlink[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 basename[][][][]\T1/ ptm/m/n/10 , Overfull \hbox (9.78043pt too wide) in paragraph at lines 15214--15214 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu rsive = TRUE)[] [219] Underfull \hbox (badness 10000) in paragraph at lines 15280--15283 []\T1/pcr/m/n/10 packageNotFoundError []\T1/ptm/m/n/10 cre-ates an er-ror con-d i-tion ob-ject of class Overfull \hbox (20.58041pt too wide) in paragraph at lines 15297--15297 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio ns it is found:[] [220] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15326--15326 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE, Underfull \hbox (badness 3965) in paragraph at lines 15358--15362 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [221] [222] [223] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15522--15522 [] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING) Overfull \hbox (0.78088pt too wide) in paragraph at lines 15523--15523 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING)[] [224] [225] [226] [227] Overfull \hbox (63.78036pt too wide) in paragraph at lines 15765--15765 []\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have type symbol (aka name).[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15768--15768 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co mbination with[] [228] Underfull \hbox (badness 1168) in paragraph at lines 15854--15858 []\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real or com-plex vec- Underfull \hbox (badness 2012) in paragraph at lines 15854--15858 \T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger penalty (see [229] Underfull \hbox (badness 6944) in paragraph at lines 15951--15954 [][][]\T1/pcr/m/n/10 formatC[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 paste [][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 as.character[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/pcr/m/n/10 sprintf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 p rint[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 prettyNum[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 toString[][][][]\T1/ptm/m/n/10 , [230] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15976--15976 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1 0,100,1000),[] [231] [232] Underfull \hbox (badness 10000) in paragraph at lines 16114--16116 []\T1/pcr/m/n/10 prettyNum() []\T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (p os-si-bly for-mat-ted) num-bers, also in Overfull \hbox (48.78088pt too wide) in paragraph at lines 16134--16134 [] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = decimal.mark,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16140--16140 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric (x)),[] Underfull \hbox (badness 2790) in paragraph at lines 16147--16150 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] []\T1/pcr/m/n/10 complex[][][] []\T1/ptm/m/n/10 only for [233] Underfull \hbox (badness 1024) in paragraph at lines 16178--16185 []\T1/pcr/m/n/10 "f" []\T1/ptm/m/n/10 gives num-bers in the usual []\T1/pcr/m/n /10 xxx.xxx []\T1/ptm/m/n/10 for-mat; []\T1/pcr/m/n/10 "e" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "E" []\T1/ptm/m/n/10 give [234] Underfull \hbox (badness 10000) in paragraph at lines 16253--16255 []\T1/ptm/m/n/10 This works via []\T1/pcr/m/n/10 prettyNum()[]\T1/ptm/m/n/10 , which calls []\T1/pcr/m/n/10 .format.zeros(*, Underfull \hbox (badness 10000) in paragraph at lines 16275--16280 []\T1/ptm/m/n/10 For num-bers, []\T1/pcr/m/n/10 formatC() []\T1/ptm/m/n/10 call s []\T1/pcr/m/n/10 prettyNum() []\T1/ptm/m/n/10 when needed which it-self calls Underfull \hbox (badness 2426) in paragraph at lines 16281--16283 []\T1/ptm/m/n/10 If you set []\T1/pcr/m/n/10 format []\T1/ptm/m/n/10 it over-ri des the set-ting of []\T1/pcr/m/n/10 mode[]\T1/ptm/m/n/10 , so []\T1/pcr/m/n/10 formatC(123.45, mode = Underfull \hbox (badness 10000) in paragraph at lines 16292--16300 []\T1/pcr/m/n/10 prettyNum []\T1/ptm/m/n/10 is the util-ity func-tion for pret- ti-fy-ing []\T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 x []\T1/ptm/m/n /10 can be com-plex (or [235] [236] Overfull \hbox (4.38043pt too wide) in paragraph at lines 16400--16400 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big .mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 16422--16422 []\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you want see the effect[] Underfull \vbox (badness 10000) has occurred while \output is active [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17256--17256 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil l a DLLInfoList[] [249] [250] Underfull \hbox (badness 2418) in paragraph at lines 17365--17369 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing [ ]\T1/pcr/m/n/10 CRoutine[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 CallRoutine[]\T1/pt m/m/n/10 , Underfull \hbox (badness 6510) in paragraph at lines 17372--17375 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 name []\T1/ptm/m/n/10 con-tains only one s ym-bol name and []\T1/pcr/m/n/10 unlist []\T1/ptm/m/n/10 is []\T1/pcr/m/n/10 TR UE[]\T1/ptm/m/n/10 , then the sin-gle Underfull \hbox (badness 2326) in paragraph at lines 17407--17414 [][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][][]\T1/ptm/m/n/10 , [][][]\T1 /pcr/m/n/10 is.loaded[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .C[][][][]\T 1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .Fortran[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 .External[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .Call[][][][] \T1/ptm/m/n/10 , [251] [252] Underfull \hbox (badness 10000) in paragraph at lines 17513--17517 []\T1/ptm/m/n/10 The spe-cial case []\T1/pcr/m/n/10 bindtextdomain(NULL) []\T1/ ptm/m/n/10 calls C level Underfull \hbox (badness 3302) in paragraph at lines 17513--17517 []\T1/pcr/m/n/10 textdomain(textdomain(NULL)) []\T1/ptm/m/n/10 for the pur-pose of flush-ing (i.e., emp-ty-ing) the [253] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17580--17580 []\T1/pcr/m/n/9 if(is.na(thisLang) || !nzchar(thisLang)) thisLang <- "en" # "f actory" default[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 17583--17583 []\T1/pcr/m/n/9 gettext(enT, domain="R-stats")# "leeres Modell angegeben" (if translation works)[] Underfull \vbox (badness 10000) has occurred while \output is active [254] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17614--17614 []\T1/pcr/m/n/9 ## Here, we reset to the *original* setting before the full ex ample started:[] [255] [256] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17751--17751 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE, Underfull \hbox (badness 1867) in paragraph at lines 17779--17786 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [257] [258] [259] [260] [261] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18097--18097 [] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around "checking hack"[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 18126--18126 []\T1/pcr/m/n/9 name.rex <- "(?[[:upper:]][[:lower:]]+) (?[[:uppe r:]][[:lower:]]+)"[] Underfull \vbox (badness 10000) has occurred while \output is active [262] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18182--18182 [] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F ALSE)[] [263] [264] [265] [266] [267] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18575--18575 []\T1/pcr/m/n/9 (ii <- grouping(x <- c(1, 1, 3:1, 1:4, 3), y <- c(9, 9:1), z < - c(2, 1:9))) [268] Overfull \hbox (4.38043pt too wide) in paragraph at lines 18640--18640 []\T1/pcr/m/n/9 z <- gzcon(url("https://www.stats.ox.ac.uk/pub/datasets/csb/ch 12.dat.gz"))[] [269] [270] [271] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18853--18853 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F ALSE) [272] [273] Underfull \hbox (badness 1360) in paragraph at lines 19017--19022 []\T1/ptm/m/n/10 The most portable name for the ISO 8859-15 en-cod-ing, com-mon ly known as `Latin 9', Underfull \hbox (badness 1953) in paragraph at lines 19017--19022 \T1/ptm/m/n/10 is []\T1/pcr/m/n/10 "iso885915"[]\T1/ptm/m/n/10 : most plat-form s sup-port both []\T1/pcr/m/n/10 "latin-9" []\T1/ptm/m/n/10 and[]\T1/pcr/m/n/10 "latin9" []\T1/ptm/m/n/10 but GNU [274] [275] [276] Underfull \hbox (badness 1163) in paragraph at lines 19233--19235 []\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1 0 https : / / unicode-[]org . github . io / icu / Overfull \hbox (9.78043pt too wide) in paragraph at lines 19241--19241 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s ettings, we can only reset to the default.[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 19271--19271 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE, [277] [278] Overfull \hbox (30.78088pt too wide) in paragraph at lines 19365--19365 [] \T1/pcr/m/n/10 num.eq = FALSE, single.NA = FALSE, attrib.as.se t = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19366--19366 [] \T1/pcr/m/n/10 ignore.bytecode = FALSE, ignore.environment = F ALSE,[] [279] Overfull \hbox (25.98041pt too wide) in paragraph at lines 19419--19419 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------ ----------------[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 19425--19425 []\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is ignored by default[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 19428--19428 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share an environment:[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19434--19434 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi ng "srcref" :[] [280] [281] Overfull \hbox (4.38043pt too wide) in paragraph at lines 19561--19561 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u se ifelse(),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19569--19569 []\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[] [282] [283] [284] Underfull \hbox (badness 10000) in paragraph at lines 19774--19776 []\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][][]\T 1/pcr/m/n/10 stop[][][] []\T1/ptm/m/n/10 and [285] [286] [287] [288] [289] Underfull \hbox (badness 10000) in paragraph at lines 20114--20120 Underfull \hbox (badness 10000) in paragraph at lines 20127--20129 []\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac le . com / cd / E19957-[]01 / 806-[]3568 / ncg _ [290] [291] [292] [293] Underfull \hbox (badness 4699) in paragraph at lines 20371--20374 []\T1/pcr/m/n/10 is.atomic []\T1/ptm/m/n/10 is true for the [][]atomic[][][] ty pes ([]\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "integer"[]\ T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "numeric"[]\T1/ptm/m/n/10 , [294] [295] Overfull \hbox (0.78088pt too wide) in paragraph at lines 20499--20499 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [296] [297] Underfull \hbox (badness 4739) in paragraph at lines 20634--20636 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [298] Overfull \hbox (36.7804pt too wide) in paragraph at lines 20683--20683 []\T1/pcr/m/n/9 isSymmetric(D3) # FALSE (as row and co lumn names differ)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20684--20684 []\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE (as names are not checked)[] [299] [300] Underfull \hbox (badness 2961) in paragraph at lines 20861--20864 []\T1/ptm/m/n/10 LAPACK and LIN-PACK are from [][]$\T1/pcr/m/n/10 https : / / n etlib . org / lapack/$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / [301] [302] [303] [304] [305] [306] [307] Underfull \hbox (badness 1975) in paragraph at lines 21302--21305 []\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to [308] [309] [310] [311] [312] [313] Underfull \hbox (badness 1077) in paragraph at lines 21718--21723 []\T1/ptm/m/n/10 In late 2017 a []\T1/pcr/m/n/10 libcurl []\T1/ptm/m/n/10 in-st al-la-tion was seen di-vided into two li-braries, []\T1/pcr/m/n/10 libcurl []\T 1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 21732--21739 [][][]$\T1/pcr/m/n/10 https : / / curl . se / docs / sslcerts . html$[][] \T1/p tm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / curl . se / docs / [314] Underfull \hbox (badness 1112) in paragraph at lines 21805--21814 []\T1/ptm/m/n/10 At startup, the li-brary search path is ini-tial-ized from the en-vi-ron-ment vari-ables []\T1/pcr/m/n/10 R_LIBS[]\T1/ptm/m/n/10 , [315] Underfull \hbox (badness 2970) in paragraph at lines 21863--21866 []\T1/pcr/m/n/10 LOCALAPPDATA []\T1/ptm/m/n/10 (usu-ally []\T1/pcr/m/n/10 C:\Us ers\username\AppData\Local[]\T1/ptm/m/n/10 ) on Win-dows is a Underfull \hbox (badness 2951) in paragraph at lines 21863--21866 \T1/ptm/m/n/10 hid-den di-rec-tory and may not be viewed by some soft-ware. It may be opened by [316] [317] Underfull \hbox (badness 10000) in paragraph at lines 21976--21980 []\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use Underfull \hbox (badness 1454) in paragraph at lines 21976--21980 [][][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][][]\T1/ptm/m/n/10 : thi s will sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self Underfull \hbox (badness 1221) in paragraph at lines 21981--21988 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 library []\T1/ptm/m/n/10 is called with no []\T1/pcr/m/n/10 package []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 help []\T1/ptm/m /n/10 ar-gu-ment, it lists all avail-able pack- [318] [319] Underfull \hbox (badness 10000) in paragraph at lines 22110--22117 [][][]\T1/pcr/m/n/10 attach[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 detach [][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 search[][][][]\T1/ptm/m/n/10 , [] [][]\T1/pcr/m/n/10 objects[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 autoloa d[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 requireNamespace[][][][]\T1/ptm/ m/n/10 , [320] Underfull \hbox (badness 10000) in paragraph at lines 22231--22235 []\T1/ptm/m/n/10 Do not use [][][]\T1/pcr/m/n/10 dyn.unload[][][] []\T1/ptm/m/n /10 on a DLL loaded by []\T1/pcr/m/n/10 library.dynam[]\T1/ptm/m/n/10 : use [321] Underfull \hbox (badness 5161) in paragraph at lines 22301--22306 []\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di s-tributed un-der the Underfull \hbox (badness 6592) in paragraph at lines 22301--22306 \T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c opy of Underfull \hbox (badness 5133) in paragraph at lines 22301--22306 \T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L GPL-2.1\T1/ptm/m/n/10 ' and can be viewed Underfull \hbox (badness 10000) in paragraph at lines 22301--22306 \T1/ptm/m/n/10 by []\T1/pcr/m/n/10 RShowDoc("LGPL-2.1")[]\T1/ptm/m/n/10 . Ver-s ion 3 of the li-cense can be dis-played by [322] [323] [324] Overfull \hbox (6.78088pt too wide) in paragraph at lines 22469--22469 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 22473--22473 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] [325] Underfull \hbox (badness 3343) in paragraph at lines 22534--22538 [][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil e.access[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 files[][][] []\T1/ptm/ m/n/10 for many more file han-dling func-tions and [326] [327] Overfull \hbox (4.38043pt too wide) in paragraph at lines 22672--22672 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 22683--22683 [] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1, prob = 0.2))),[] [328] [329] Overfull \hbox (9.78043pt too wide) in paragraph at lines 22794--22794 []\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the same names ![] Overfull \hbox (74.58035pt too wide) in paragraph at lines 22797--22797 []\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w / same name in .GlobalEnv[] Underfull \hbox (badness 6380) in paragraph at lines 22844--22852 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- [330] [331] Underfull \hbox (badness 2564) in paragraph at lines 22947--22950 []\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/ ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of Overfull \hbox (4.38043pt too wide) in paragraph at lines 22988--22988 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other Unix-alikes[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 22992--22992 []\T1/pcr/m/n/9 c(m = months(then), wd = weekdays(then)) # in C_TIME locale \T S1/pcr/m/n/9 '\T1/pcr/m/n/9 cT\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 ; typically German [] Overfull \hbox (42.18039pt too wide) in paragraph at lines 22996--22996 []\T1/pcr/m/n/9 c(m = months(then), wd = weekdays(then)) # "standard" (still p latform specific ?)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 23003--23003 []\T1/pcr/m/n/9 ## Not run: Sys.setlocale("LC_COLLATE", "C") # turn off loca le-specific sorting,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 23005--23005 []\T1/pcr/m/n/9 Sys.setenv("LANGUAGE" = "es") # set the language for error/war ning messages[] [332] [333] [334] Underfull \hbox (badness 1400) in paragraph at lines 23179--23183 [][][]\T1/pcr/m/n/10 raw[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logical[] [][] []\T1/ptm/m/n/10 or `number-like' vec-tors (i.e., of types [][][]\T1/pcr/m /n/10 double[][][] []\T1/ptm/m/n/10 (class [335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] Overfull \hbox (52.98038pt too wide) in paragraph at lines 24021--24021 []\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary = r ), complex(real = r , imaginary = NA ),[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 24022--24022 [] \T1/pcr/m/n/9 complex(real = r , imaginary = NaN), complex(real = N aN, imaginary = r ))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 24025--24025 []\T1/pcr/m/n/9 zM ##--> many "NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s" (= 1) and th e four non-NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s (3 different ones, at 7,9,10)[] [347] [348] Overfull \hbox (20.58041pt too wide) in paragraph at lines 24122--24122 []\T1/pcr/m/n/9 match.arg(c("a", ""), c("", NA, "bb", "abc"), several.ok=TRUE ) # |--> "abc"[] Underfull \hbox (badness 1655) in paragraph at lines 24156--24160 []\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion (also known as a `clo-sure'): [349] [350] [351] [352] Underfull \hbox (badness 2277) in paragraph at lines 24407--24410 []\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross\T1/ptm/m/n/10 products, [][] []\T1/pcr/m/n/10 crossprod[][][]() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 tcross prod() []\T1/ptm/m/n/10 are typ-i-cally prefer-able. [353] [354] [355] [356] [357] [358] [359] [360] [361] Underfull \hbox (badness 1484) in paragraph at lines 25007--25015 []\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less the OS's de-fault has been Underfull \hbox (badness 1152) in paragraph at lines 25007--25015 \T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http s : / / docs . microsoft . com / en-[]gb / [362] Overfull \hbox (0.78088pt too wide) in paragraph at lines 25081--25081 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] [363] [364] [365] [366] [367] [368] [369] [370] Underfull \hbox (badness 1448) in paragraph at lines 25633--25641 []\T1/pcr/m/n/10 anyNA(recursive = FALSE) []\T1/ptm/m/n/10 works the same way a s []\T1/pcr/m/n/10 is.na[]\T1/ptm/m/n/10 ; []\T1/pcr/m/n/10 anyNA(recursive = [371] [372] Underfull \hbox (badness 3849) in paragraph at lines 25748--25753 []\T1/pcr/m/n/10 as.name []\T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter- nally to a char-ac-ter vec-tor (so meth-ods for [373] Underfull \hbox (badness 2165) in paragraph at lines 25825--25831 []\T1/ptm/m/n/10 For an [][][]\T1/pcr/m/n/10 environment[][][] env[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 names(env) []\T1/ptm/m/n/10 gives the names of the cor-r e-spond-ing list, Underfull \hbox (badness 1199) in paragraph at lines 25825--25831 \T1/ptm/m/n/10 i.e., []\T1/pcr/m/n/10 names(as.list(env, all.names = TRUE)) []\ T1/ptm/m/n/10 which are also given by [][][]\T1/pcr/m/n/10 ls[][][](env, Underfull \hbox (badness 3148) in paragraph at lines 25825--25831 \T1/pcr/m/n/10 all.names = TRUE, sorted = FALSE)[]\T1/ptm/m/n/10 . If the en-vi -ron-ment is used as a hash ta-ble, [374] [375] Underfull \hbox (badness 2237) in paragraph at lines 25988--25990 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of []\T1/pcr/m/n/1 0 c("bytes", "chars", [376] [377] [378] Underfull \hbox (badness 6188) in paragraph at lines 26215--26218 []\T1/ptm/m/n/10 optional [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 e ven-tu-ally to be passed to []\T1/pcr/m/n/10 print()[]\T1/ptm/m/n/10 , used by [379] [380] [381] Underfull \hbox (badness 1521) in paragraph at lines 26405--26419 \T1/ptm/m/n/10 tion []\T1/pcr/m/n/10 GetFinalPathNameByHandle []\T1/ptm/m/n/10 and in case of an er-ror (such as in-suf-fi-cient per- [382] [383] [384] [385] [386] Underfull \hbox (badness 2197) in paragraph at lines 26719--26723 []\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s tartup mes-sages given by Underfull \hbox (badness 4048) in paragraph at lines 26719--26723 []\T1/pcr/m/n/10 .onAttach[]\T1/ptm/m/n/10 . These mes-sages (and any es-sen-ti al ones from []\T1/pcr/m/n/10 .onLoad[]\T1/ptm/m/n/10 ) should use Underfull \hbox (badness 2846) in paragraph at lines 26733--26737 []\T1/ptm/m/n/10 Uses of []\T1/pcr/m/n/10 library []\T1/ptm/m/n/10 with ar-gu-m ent []\T1/pcr/m/n/10 help []\T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion ab out the pack- Underfull \hbox (badness 1990) in paragraph at lines 26733--26737 \T1/ptm/m/n/10 age should use []\T1/pcr/m/n/10 format []\T1/ptm/m/n/10 on the c om-puted pack-age in-for-ma-tion ob-ject and pass this to Overfull \hbox (12.78088pt too wide) in paragraph at lines 26775--26775 []\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ e.only) [387] Overfull \hbox (0.78088pt too wide) in paragraph at lines 26779--26779 [] \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk gs"))[] [388] Underfull \hbox (badness 10000) in paragraph at lines 26828--26834 []\T1/pcr/m/n/10 loadNamespace []\T1/ptm/m/n/10 does not at-tach the name space it loads to the search path. Underfull \hbox (badness 1168) in paragraph at lines 26828--26834 []\T1/pcr/m/n/10 attachNamespace []\T1/ptm/m/n/10 can be used to at-tach a fram e con-tain-ing the ex-ported val-ues of a Underfull \hbox (badness 10000) in paragraph at lines 26841--26843 []\T1/pcr/m/n/10 isNamespaceLoaded(pkg) []\T1/ptm/m/n/10 is equiv-a-lent to but more ef-fi-cient than []\T1/pcr/m/n/10 pkg %in% [389] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26908--26908 [] \T1/pcr/m/n/9 ## The string "foo" and the symbol \TS1/pcr/m/n/9 '\T1/pcr/m/ n/9 foo\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 can be used interchangably here:[] [390] [391] Underfull \hbox (badness 8189) in paragraph at lines 27103--27109 []\T1/ptm/m/n/10 The de-fault method for []\T1/pcr/m/n/10 is.numeric []\T1/ptm/ m/n/10 re-turns []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode[][][] [392] [393] [394] Underfull \hbox (badness 2591) in paragraph at lines 27329--27337 \T1/ptm/m/n/10 ject as ob-tained by [][][]\T1/pcr/m/n/10 R.version[][][][]\T1/p tm/m/n/10 . For []\T1/pcr/m/n/10 as.numeric_version []\T1/ptm/m/n/10 and [395] [396] [397] [398] [399] Underfull \hbox (badness 1603) in paragraph at lines 27611--27613 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [400] Underfull \hbox (badness 1210) in paragraph at lines 27738--27747 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini- [401] [402] [403] Underfull \hbox (badness 3271) in paragraph at lines 27960--27963 []\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men t vari-able [404] [405] [406] Underfull \hbox (badness 3138) in paragraph at lines 28273--28279 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][][]\T1/pcr/ m/n/10 setRepositories[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 28273--28279 \T1/ptm/m/n/10 e.g. the de-fault `[]\T1/pcr/m/n/10 "https://bioconductor.org"[] \T1/ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 2088) in paragraph at lines 28273--28279 \T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de "[]\T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 1194) in paragraph at lines 28286--28289 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][][]\T1/pcr/m/n/10 create.post[ ][][] []\T1/ptm/m/n/10 (and hence[][][]\T1/pcr/m/n/10 bug.report[][][] []\T1/pt m/m/n/10 and Underfull \hbox (badness 1389) in paragraph at lines 28312--28314 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see [407] Underfull \hbox (badness 10000) in paragraph at lines 28339--28345 []\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by Underfull \hbox (badness 3826) in paragraph at lines 28354--28359 []\T1/ptm/m/n/10 Used by [][][]\T1/pcr/m/n/10 install.packages[][][] []\T1/ptm/ m/n/10 (and in-di-rectly Underfull \hbox (badness 1009) in paragraph at lines 28372--28375 []\T1/ptm/m/n/10 default email-ing method used by [][][]\T1/pcr/m/n/10 create.p ost[][][] []\T1/ptm/m/n/10 and hence [][][]\T1/pcr/m/n/10 bug.report[][][] []\T 1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 28388--28391 []\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle d -- see Underfull \hbox (badness 10000) in paragraph at lines 28396--28402 []\T1/pcr/m/n/10 "source" []\T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma-cOS Underfull \hbox (badness 10000) in paragraph at lines 28396--28402 \T1/ptm/m/n/10 build), []\T1/pcr/m/n/10 "mac.binary" []\T1/ptm/m/n/10 and []\T1 /pcr/m/n/10 "both" []\T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS Underfull \hbox (badness 10000) in paragraph at lines 28396--28402 \T1/ptm/m/n/10 builds). ([]\T1/pcr/m/n/10 "mac.binary.el-capitan"[]\T1/ptm/m/n/ 10 , []\T1/pcr/m/n/10 "mac.binary.mavericks"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 5091) in paragraph at lines 28396--28402 []\T1/pcr/m/n/10 "mac.binary.leopard" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "ma c.binary.universal" []\T1/ptm/m/n/10 are no longer [408] [409] [410] [411] [412] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28777--28777 []\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec, 300X faster[] [413] Underfull \hbox (badness 10000) in paragraph at lines 28790--28794 []\T1/ptm/m/n/10 where el-e-ment []\T1/pcr/m/n/10 A[c(arrayindex.x, arrayindex. y)] = FUN(X[arrayindex.x], [414] [415] Underfull \hbox (badness 1210) in paragraph at lines 28937--28940 []\T1/pcr/m/n/10 str2expression(s) []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 str2la ng(s) []\T1/ptm/m/n/10 re-turn spe-cial ver-sions of []\T1/pcr/m/n/10 parse(tex t=s, [416] [417] Overfull \hbox (25.98041pt too wide) in paragraph at lines 29133--29133 []\T1/pcr/m/n/9 tryCatch(parse(text = txt, srcfile = sf), error = function(e) "Syntax error.")[] [418] Underfull \hbox (badness 1478) in paragraph at lines 29163--29168 \T1/ptm/m/n/10 zero-length [][][]\T1/pcr/m/n/10 character[][][](0)[]\T1/ptm/m/n /10 . Note that when []\T1/pcr/m/n/10 collapse []\T1/ptm/m/n/10 is a string, [419] Underfull \hbox (badness 7133) in paragraph at lines 29222--29228 [][][]\T1/pcr/m/n/10 toString[][][] []\T1/ptm/m/n/10 typ-i-cally calls []\T1/pc r/m/n/10 paste(*, collapse=", ")[]\T1/ptm/m/n/10 . String ma-nip-u-la-tion with Overfull \hbox (42.18039pt too wide) in paragraph at lines 29244--29244 []\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as the longest input.[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 29256--29256 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha t you wanted[] Overfull \hbox (17.87582pt too wide) in paragraph at lines 29269--29269 []\T1/pcr/m/n/9 ## zero length arguments recycled as \TS1/cmtt/m/n/9 `\T1/pcr/ m/n/9 ""\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 -- NB: \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 { }\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 <==> character(0) here[] [420] Overfull \hbox (15.18042pt too wide) in paragraph at lines 29272--29272 []\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 recycle0 = TRUE\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 allows standard vectorized behaviour, i.e., zero-length[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 29273--29273 []\T1/pcr/m/n/9 ## recycling resulting in zero-length result character(0):[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 29276--29276 []\T1/pcr/m/n/9 paste("The value is", val[valid], "-- not so good!") # -> ".. value is -- not .."[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 29277--29277 []\T1/pcr/m/n/9 paste("The value is", val[valid], "-- good: empty!", recycle0= TRUE) # -> character(0)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29280--29280 []\T1/pcr/m/n/9 paste("foo", {}, "bar", collapse = "|") # |-- > "foo bar"[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29282--29282 []\T1/pcr/m/n/9 ## If all arguments are empty (and collapse a string), "" r esults always[] [421] [422] [423] Overfull \hbox (25.98041pt too wide) in paragraph at lines 29471--29471 []\T1/pcr/m/n/9 mtcars |> subset(cyl == 4) |> nrow() # same as nrow(subset(mt cars, cyl == 4))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 29489--29489 []\T1/pcr/m/n/9 stop() |> (function(...) {})() # stop() is not used on RHS so is not evaluated[] [424] Underfull \hbox (badness 1360) in paragraph at lines 29544--29548 []\T1/ptm/m/n/10 All other []\T1/pcr/m/n/10 type[]\T1/ptm/m/n/10 s give a warn- ing or an er-ror; us-ing, e.g., []\T1/pcr/m/n/10 type = [425] [426] [427] [428] Underfull \hbox (badness 2277) in paragraph at lines 29856--29861 \T1/ptm/m/n/10 i.e., strictly in-clude the bounds of []\T1/pcr/m/n/10 x[]\T1/pt m/m/n/10 . New from \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0, al-low-ing [429] [430] Underfull \hbox (badness 1701) in paragraph at lines 29972--29976 []\T1/ptm/m/n/10 This func-tion is al-most never used: []\TS1/cmtt/m/n/10 `\T1/ pcr/m/n/10 name\TS1/cmtt/m/n/10 ` []\T1/ptm/m/n/10 or, more care-fully, [][][]\ T1/pcr/m/n/10 get[][][](name, envir = [431] Underfull \hbox (badness 1796) in paragraph at lines 30040--30043 []\T1/ptm/m/n/10 character string (or []\T1/pcr/m/n/10 NULL[]\T1/ptm/m/n/10 ) i n-di-cat-ing [][][]\T1/pcr/m/n/10 NA[][][] []\T1/ptm/m/n/10 val-ues in printed out-put, see [432] [433] [434] [435] Underfull \hbox (badness 10000) in paragraph at lines 30244--30247 []\T1/ptm/m/n/10 Option []\T1/pcr/m/n/10 width []\T1/ptm/m/n/10 con-trols the p rint-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion [436] [437] [438] [439] [440] [441] [442] [443] Underfull \hbox (badness 2961) in paragraph at lines 30790--30793 []\T1/ptm/m/n/10 LAPACK and LIN-PACK are from [][]$\T1/pcr/m/n/10 https : / / n etlib . org / lapack/$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / [444] [445] Overfull \hbox (25.98041pt too wide) in paragraph at lines 30939--30939 [] \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 = rep(c(0,0,1),2))[] [446] [447] [448] [449] Overfull \hbox (15.18042pt too wide) in paragraph at lines 31232--31232 []\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3 \u147b\u203c")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 31243--31243 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\ U147b\U203c"[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 31249--31249 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm l#Literal-constants[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 31255--31255 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow ed (parse errors)[] Underfull \vbox (badness 10000) has occurred while \output is active [450] [451] Underfull \hbox (badness 7415) in paragraph at lines 31352--31358 []\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use []\T1/pcr/m/n/10 R.v ersion$os []\T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use Overfull \hbox (42.18039pt too wide) in paragraph at lines 31376--31376 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu l bottom-right note[] [452] Overfull \hbox (6.78088pt too wide) in paragraph at lines 31422--31422 []\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind = NULL)[] [453] [454] Underfull \hbox (badness 3713) in paragraph at lines 31567--31578 []\T1/pcr/m/n/10 normal.kind []\T1/ptm/m/n/10 can be []\T1/pcr/m/n/10 "Kinderma n-Ramage"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Buggy Kinderman-Ramage" []\T1/ptm /m/n/10 (not [455] Underfull \hbox (badness 1248) in paragraph at lines 31719--31726 \T1/ptm/m/n/10 uni-form pseudo-random num-ber gen-er-a-tor, \T1/ptm/m/it/10 ACM Trans-ac-tions on Mod-el-ing and Com-puter Underfull \hbox (badness 10000) in paragraph at lines 31719--31726 \T1/ptm/m/n/10 Now see [][]$\T1/pcr/m/n/10 http : / / www . math . sci . hirosh ima-[]u . ac . jp / ~m-[]mat / MT / VERSIONS / [456] [457] Underfull \hbox (badness 1533) in paragraph at lines 31837--31840 []\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the [458] [459] Overfull \hbox (42.78088pt too wide) in paragraph at lines 31982--31982 [] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m ax", "min"))[] [460] Underfull \hbox (badness 1038) in paragraph at lines 32000--32011 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no []\T1/pcr/m/n/10 N A[]\T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [461] [462] Overfull \hbox (15.18042pt too wide) in paragraph at lines 32144--32144 []\T1/pcr/m/n/9 rapply(X, function(x) x, how = "replace") -> X.; stopifnot(ide ntical(X, X.))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 32146--32146 []\T1/pcr/m/n/9 rapply(X, deparse, control = "all") # passing extras. argument of deparse()[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 32147--32147 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h ow = "list")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 32148--32148 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h ow = "unlist")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 32149--32149 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", h ow = "unlist")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 32156--32156 []\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h ow = "unlist")[] [463] [464] [465] [466] [467] Overfull \hbox (25.98041pt too wide) in paragraph at lines 32464--32464 []\T1/pcr/m/n/9 ## Bit representation [ sign | exponent | mantissa ] of doubl e prec numbers :[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 32466--32466 []\T1/pcr/m/n/9 bitC <- function(x) noquote(vapply(as.double(x), function(x) { # split one double[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 32476--32476 []\T1/pcr/m/n/9 d2bI <- function(x) vapply(as.double(x), function(x) intToBits (numToInts(x)), raw(64L))[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 32477--32477 []\T1/pcr/m/n/9 d2b <- function(x) vapply(as.double(x), function(x) numToBits(x) , raw(64L))[] [468] Underfull \hbox (badness 4048) in paragraph at lines 32572--32577 []\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor to Underfull \hbox (badness 4582) in paragraph at lines 32572--32577 \T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the mode: Underfull \hbox (badness 1824) in paragraph at lines 32572--32577 \T1/ptm/m/n/10 one of []\T1/pcr/m/n/10 "numeric"[]\T1/ptm/m/n/10 , []\T1/pcr/m/ n/10 "double"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "integer"[]\T1/ptm/m/n/10 , [] \T1/pcr/m/n/10 "int"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/ 10 , [469] [470] [471] [472] [473] [474] [475] [476] Underfull \hbox (badness 2080) in paragraph at lines 33112--33122 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 infoRDS[]\T1/ptm/m/n/10 , an \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 list with el-e-ments []\T1/pcr/m/n/10 version []\T1/ptm/m/n /10 (ver-sion num-ber, cur-rently 2 or 3), [477] Overfull \hbox (4.38043pt too wide) in paragraph at lines 33146--33146 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene d as needed.[] [478] [479] [480] [481] [482] [483] [484] Underfull \hbox (badness 7558) in paragraph at lines 33666--33670 []\T1/pcr/m/n/10 regexpr []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 gregexpr []\T1/p tm/m/n/10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1968) in paragraph at lines 33676--33678 []\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P OSIX stan-dard, and the Underfull \hbox (badness 10000) in paragraph at lines 33687--33689 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / Underfull \hbox (badness 1975) in paragraph at lines 33690--33694 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 pcre2pattern []\T1/ptm/m/n/10 or []\T1/pc r/m/n/10 pcrepattern man []\T1/ptm/m/n/10 page (found as part of [][]$\T1/pcr/m /n/10 https : / / www . [485] [486] Underfull \vbox (badness 10000) has occurred while \output is active [487] [488] [489] [490] Overfull \hbox (4.38043pt too wide) in paragraph at lines 34061--34061 []\T1/pcr/m/n/9 rep(1:4, each = 2, times = 3) # length 24, 3 complete replications[] [491] Underfull \hbox (badness 10000) in paragraph at lines 34132--34136 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [492] [493] [494] Underfull \hbox (badness 2302) in paragraph at lines 34365--34370 []\T1/pcr/m/n/10 signif []\T1/ptm/m/n/10 rounds the val-ues in its first ar-gu- ment to the spec-i-fied num-ber of \T1/ptm/m/it/10 sig-nif-i-cant Underfull \hbox (badness 1824) in paragraph at lines 34365--34370 \T1/ptm/m/n/10 dig-its. Hence, for []\T1/pcr/m/n/10 numeric x[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 signif(x, dig) []\T1/ptm/m/n/10 is the same as []\T1/pcr/m/n/ 10 round(x, dig - [495] [496] Overfull \hbox (12.78088pt too wide) in paragraph at lines 34498--34498 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"))[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 34501--34501 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 34508--34508 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] [497] [498] [499] [500] [501] [502] [503] Overfull \hbox (66.78088pt too wide) in paragraph at lines 34956--34956 [] \T1/pcr/m/n/10 useHash = (n > 1e+07 && !replace && is.null(prob) && size <= n/2))[] [504] [505] [506] [507] [508] [509] Overfull \hbox (12.78088pt too wide) in paragraph at lines 35393--35393 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)[] [510] [511] Underfull \hbox (badness 1158) in paragraph at lines 35497--35502 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 strip.white []\T1/ptm/m/n/10 is of length 1, it ap-plies to all fields; oth-er-wise, if [512] [513] Overfull \hbox (15.18042pt too wide) in paragraph at lines 35683--35683 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data ", sep = "\n") [514] [515] [516] Underfull \hbox (badness 4752) in paragraph at lines 35942--35945 []\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence []\T1/pcr/ m/n/10 1, 2, ..., length(along.with)[]\T1/ptm/m/n/10 . Underfull \hbox (badness 5563) in paragraph at lines 35946--35952 []\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence []\T1/pcr/m/n/10 1, 2 , ..., length(from) []\T1/ptm/m/n/10 (as if ar-gu-ment [517] [518] [519] [520] [521] [522] [523] [524] [525] Underfull \hbox (badness 6094) in paragraph at lines 36532--36536 []\T1/pcr/m/n/10 getAllConnections []\T1/ptm/m/n/10 re-turns a se-quence of in- te-ger con-nec-tion de-scrip-tors for use Underfull \hbox (badness 6559) in paragraph at lines 36532--36536 \T1/ptm/m/n/10 with []\T1/pcr/m/n/10 getConnection[]\T1/ptm/m/n/10 , cor-re-spo nd-ing to the row names of the ta-ble re-turned by [526] [527] Underfull \hbox (badness 3826) in paragraph at lines 36623--36634 []\T1/ptm/m/n/10 In Win-dows, com-mand line in-ter-pre-ta-tion is done by the a p-pli-ca-tion as well as the Underfull \hbox (badness 3492) in paragraph at lines 36623--36634 \T1/ptm/m/n/10 shell. It may de-pend on the com-piler used: Mi-crosoft's rules for the C run-time Underfull \hbox (badness 10000) in paragraph at lines 36623--36634 \T1/ptm/m/n/10 are given at [][]$\T1/pcr/m/n/10 https : / / learn . microsoft . com / en-[]us / cpp / c-[]language / Underfull \hbox (badness 1635) in paragraph at lines 36623--36634 \T1/pcr/m/n/10 parsing-[]c-[]command-[]line-[]arguments ? view = msvc-[]160$[][ ]\T1/ptm/m/n/10 . It may de-pend on the [528] [529] [530] [531] [532] [533] [534] [535] Overfull \hbox (66.78088pt too wide) in paragraph at lines 37177--37177 [] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index .return = FALSE)[] [536] [537] [538] [539] Overfull \hbox (6.78088pt too wide) in paragraph at lines 37429--37429 [] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length = Inf,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 37431--37431 [] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes" , "keepNA"),[] Underfull \hbox (badness 4954) in paragraph at lines 37474--37480 [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 vec-tor, passed as []\T1/ pcr/m/n/10 control []\T1/ptm/m/n/10 to [][][]\T1/pcr/m/n/10 deparse[][][]()[]\T 1/ptm/m/n/10 , see also Underfull \hbox (badness 5050) in paragraph at lines 37474--37480 [][][]\T1/pcr/m/n/10 .deparseOpts[][][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \ T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to [540] [541] Overfull \hbox (20.58041pt too wide) in paragraph at lines 37585--37585 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments should print:)[] [542] [543] [544] [545] [546] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37928--37928 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m /n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37943--37943 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is being added[] [547] [548] [549] Underfull \hbox (badness 10000) in paragraph at lines 38168--38170 [][][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919 799 / functions / [550] [551] [552] Overfull \hbox (12.78088pt too wide) in paragraph at lines 38395--38395 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known") Overfull \hbox (12.78088pt too wide) in paragraph at lines 38396--38396 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile = FALSE)[] [553] [554] [555] [556] [557] Overfull \hbox (63.78036pt too wide) in paragraph at lines 38727--38727 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS E, nowadays often three [558] Underfull \hbox (badness 6110) in paragraph at lines 38823--38833 []\T1/ptm/m/n/10 A func-tion []\T1/pcr/m/n/10 .First []\T1/ptm/m/n/10 (and [][] []\T1/pcr/m/n/10 .Last[][][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-at e `\T1/pcr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or Underfull \hbox (badness 2635) in paragraph at lines 38823--38833 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have been saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want a dif-fer-ent Underfull \hbox (badness 1237) in paragraph at lines 38823--38833 \T1/ptm/m/n/10 set of pack-ages than the de-fault ones when you start, in-sert a call to [][][]\T1/pcr/m/n/10 options[][][] []\T1/ptm/m/n/10 in the Underfull \hbox (badness 1231) in paragraph at lines 38823--38833 \T1/pcr/m/n/10 = character()) []\T1/ptm/m/n/10 will at-tach no ex-tra pack-ages on startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (or Underfull \hbox (badness 1112) in paragraph at lines 38823--38833 \T1/ptm/m/n/10 set []\T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL []\T1/ptm/m/n/10 as an en-vi-ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/10 ). Us-ing [559] Underfull \hbox (badness 10000) in paragraph at lines 38879--38885 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 38879--38885 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1496) in paragraph at lines 38879--38885 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be Underfull \hbox (badness 1460) in paragraph at lines 38894--38901 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 38894--38901 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 38894--38901 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment [560] Overfull \hbox (4.38043pt too wide) in paragraph at lines 38956--38956 []\T1/pcr/m/n/9 # Variable expansion in double quotes, string literals with ba ckslashes in[] [561] [562] [563] Underfull \hbox (badness 1484) in paragraph at lines 39129--39133 []\T1/ptm/m/n/10 alternative to []\T1/pcr/m/n/10 exprs []\T1/ptm/m/n/10 or []\T 1/pcr/m/n/10 ...[]\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an Overfull \hbox (60.78088pt too wide) in paragraph at lines 39194--39194 [] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e xprs = exprs))) [564] Overfull \hbox (9.78043pt too wide) in paragraph at lines 39220--39220 []\T1/pcr/m/n/9 stopifnot(all.equal(pi, 3.141593), 2 < 2, (1:10 < 12), "a" < "b") |> try()[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 39236--39236 []\T1/pcr/m/n/9 stopifnot(all.equal(rep(list(pi),4), list(3.1, 3.14, 3.141, 3. 1415))) |> try()[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 39244--39244 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 {Yes, learn how to use do.c all(substitute, ...) in a powerful manner !!}[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 39246--39246 []\T1/pcr/m/n/9 bdy <- do.call(substitute, list(bdy, list(stopifnot = quote(warnifnot))))[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 39247--39247 []\T1/pcr/m/n/9 bdy[[N-1]] <- do.call(substitute, list(bdy[[N-1]], list(stop = quote(warning))))[] [565] Underfull \hbox (badness 1436) in paragraph at lines 39307--39311 []\T1/ptm/m/n/10 integer de-ter-min-ing the []\T1/pcr/m/n/10 format()[]\T1/ptm/ m/n/10 ing of sec-onds when needed. Note [566] [567] [568] [569] [570] Overfull \hbox (15.18042pt too wide) in paragraph at lines 39700--39700 []\T1/pcr/m/n/9 z3 # prints without fractional seconds by default, digits.sec = NULL ("= 0")[] [571] Overfull \hbox (9.78043pt too wide) in paragraph at lines 39728--39728 []\T1/pcr/m/n/9 format(s1 <- seq.Date(as.Date(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 19 78-01-01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ), by = \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 day \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , len = 7), "%a")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 39729--39729 []\T1/pcr/m/n/9 format(s2 <- seq.Date(as.Date(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 20 00-01-01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ), by = \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 mon th\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , len = 12), "%b")[] [572] [573] Overfull \hbox (0.78088pt too wide) in paragraph at lines 39841--39841 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [574] [575] [576] Overfull \hbox (6.78088pt too wide) in paragraph at lines 40104--40104 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] [577] Overfull \hbox (4.38043pt too wide) in paragraph at lines 40148--40148 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [578] [579] [580] [581] [582] [583] [584] Overfull \hbox (52.98038pt too wide) in paragraph at lines 40595--40595 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e verything gets added.[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 40598--40598 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also missing, ....[] [585] Underfull \hbox (badness 10000) in paragraph at lines 40649--40656 []\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][][]\T1/pcr/m/n/ 10 signif[][][]() []\T1/ptm/m/n/10 (for Underfull \hbox (badness 10000) in paragraph at lines 40649--40656 []\T1/pcr/m/n/10 summary.default[]\T1/ptm/m/n/10 ) or [][][]\T1/pcr/m/n/10 form at[][][]() []\T1/ptm/m/n/10 (for []\T1/pcr/m/n/10 summary.data.frame[]\T1/ptm/m /n/10 ). [586] Overfull \hbox (4.38043pt too wide) in paragraph at lines 40702--40702 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision [587] [588] [589] [590] Overfull \hbox (31.3804pt too wide) in paragraph at lines 41016--41016 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw ise: last"),"\n")[] [591] [592] [593] [594] Overfull \hbox (20.58041pt too wide) in paragraph at lines 41221--41221 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, macOS, FreeBSD:[] Underfull \hbox (badness 2293) in paragraph at lines 41251--41257 []\T1/ptm/m/n/10 This ex-pands tilde (see [][]tilde ex-pan-sion[][][]) and wild -cards in file paths. For pre-cise de- Underfull \hbox (badness 1237) in paragraph at lines 41251--41257 \T1/ptm/m/n/10 tails of wild-cards ex-pan-sion, see your sys-tem's doc-u-men-ta -tion on the []\T1/pcr/m/n/10 glob []\T1/ptm/m/n/10 sys-tem call. Underfull \hbox (badness 4792) in paragraph at lines 41270--41275 []\T1/ptm/m/n/10 If a file-name starts with []\T1/pcr/m/n/10 . []\T1/ptm/m/n/10 this may need to be matched ex-plic-itly: for ex-am-ple Underfull \hbox (badness 1107) in paragraph at lines 41270--41275 []\T1/pcr/m/n/10 Sys.glob("*.RData") []\T1/ptm/m/n/10 may or may not match `\T1 /pcr/m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match [595] [596] [597] [598] Underfull \hbox (badness 10000) in paragraph at lines 41558--41562 []\T1/pcr/m/n/10 sys.status() []\T1/ptm/m/n/10 re-turns a list with com-po-nent s []\T1/pcr/m/n/10 sys.calls[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sys.parents []\ T1/ptm/m/n/10 and Underfull \hbox (badness 1584) in paragraph at lines 41573--41576 []\T1/pcr/m/n/10 sys.call []\T1/ptm/m/n/10 re-turns a call, []\T1/pcr/m/n/10 sy s.function []\T1/ptm/m/n/10 a func-tion def-i-ni-tion, and []\T1/pcr/m/n/10 sys .frame []\T1/ptm/m/n/10 and [599] [600] [601] Overfull \hbox (25.98041pt too wide) in paragraph at lines 41711--41711 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths ), keepNA=TRUE))[] [602] Overfull \hbox (19.22812pt too wide) in paragraph at lines 41792--41792 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/cmtt /m/n/9 `\T1/pcr/m/n/9 A+C\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 could also be used [603] [604] Underfull \hbox (badness 1082) in paragraph at lines 41937--41940 []\T1/ptm/m/n/10 logical. If []\T1/pcr/m/n/10 TRUE[]\T1/ptm/m/n/10 , func-tions keep their source in-clud-ing com-ments, see Underfull \hbox (badness 10000) in paragraph at lines 41964--41966 [][][]\T1/pcr/m/n/10 source[][][][]\T1/ptm/m/n/10 , and [][][]\T1/pcr/m/n/10 lo adNamespace[][][] []\T1/ptm/m/n/10 which is called from [][][]\T1/pcr/m/n/10 li brary[][][](.) []\T1/ptm/m/n/10 and uses [605] [606] [607] Underfull \hbox (badness 1038) in paragraph at lines 42130--42133 []\T1/ptm/m/n/10 a log-i-cal (not []\T1/pcr/m/n/10 NA[]\T1/ptm/m/n/10 ) in-di-c at-ing whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or [608] [609] [610] [611] [612] Underfull \hbox (badness 1442) in paragraph at lines 42495--42499 \T1/ptm/m/n/10 con-sider it to be piped or redi-rected: []\T1/pcr/m/n/10 stdout = TRUE []\T1/ptm/m/n/10 uses a pipe whereas []\T1/pcr/m/n/10 stdout = [613] [614] [615] [616] Underfull \hbox (badness 4096) in paragraph at lines 42749--42752 []\T1/ptm/m/n/10 Use [][][]\T1/pcr/m/n/10 ftable[][][] []\T1/ptm/m/n/10 for pri nt-ing (and more) of mul-ti-di-men-sional ta-bles. [][][]\T1/pcr/m/n/10 margin. table[][][][]\T1/ptm/m/n/10 , [617] Underfull \hbox (badness 7888) in paragraph at lines 42863--42867 []\T1/ptm/m/n/10 On 64-bit plat-forms []\T1/pcr/m/n/10 bin []\T1/ptm/m/n/10 can have $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., []\T1/pcr/ m/n/10 length(bin) > [618] [619] [620] Overfull \hbox (63.78036pt too wide) in paragraph at lines 43025--43025 [] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1" , "2"), c("A", "B")))),[] Overfull \hbox (30.0281pt too wide) in paragraph at lines 43027--43027 [] \T1/pcr/m/n/9 array(list(\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 2\TS1/cm tt/m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), names = nq),[] Overfull \hbox (55.67578pt too wide) in paragraph at lines 43029--43029 [] \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 4\TS1/cmtt/m/n/9 ` \T1/pcr/m /n/9 = NULL, \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 5\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 = NULL), dim=4, dimnames=list(as.character(2:5)))))[] Underfull \hbox (badness 10000) in paragraph at lines 43042--43044 []\T1/pcr/m/n/10 removeTaskCallback []\T1/ptm/m/n/10 un-registers a func-tion t hat was reg-is-tered ear-lier via [621] Underfull \hbox (badness 10000) in paragraph at lines 43122--43125 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . [622] [623] Underfull \hbox (badness 3872) in paragraph at lines 43240--43243 []\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call -backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer . [624] Underfull \hbox (badness 5475) in paragraph at lines 43306--43310 [][][]\T1/pcr/m/n/10 addTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 removeTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 taskCallback Manager[][][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / [625] [626] [627] [628] [629] [630] Underfull \hbox (badness 1655) in paragraph at lines 43729--43736 \T1/ptm/m/n/10 may also be known as `[]\T1/pcr/m/n/10 GB[]\T1/ptm/m/n/10 ', `[] \T1/pcr/m/n/10 GB-Eire[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 Europe/Belfast[]\T1 /ptm/m/n/10 ', `[]\T1/pcr/m/n/10 Europe/Guernsey[]\T1/ptm/m/n/10 ', Underfull \hbox (badness 2253) in paragraph at lines 43737--43742 []\T1/pcr/m/n/10 OlsonNames []\T1/ptm/m/n/10 re-turns a char-ac-ter vec-tor, se e the ex-am-ples for typ-i-cal cases. It may Underfull \hbox (badness 1655) in paragraph at lines 43737--43742 \T1/ptm/m/n/10 have an at-tribute []\T1/pcr/m/n/10 "Version"[]\T1/ptm/m/n/10 , some-thing like `[]\T1/pcr/m/n/10 "2023a"[]\T1/ptm/m/n/10 '. (It does on sys-te ms us-ing [631] Underfull \hbox (badness 4467) in paragraph at lines 43787--43796 []\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 OlsonNames []\T1/ptm/m/n/10 re- turns the time-zone names known to the cur-rently se- Underfull \hbox (badness 3954) in paragraph at lines 43787--43796 \T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t he file sys-tem varies, [632] Underfull \hbox (badness 1337) in paragraph at lines 43890--43898 \T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 / usr/local/etc\T1/ptm/m/n/10 ' or Underfull \hbox (badness 10000) in paragraph at lines 43899--43902 []\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym -link tar-get name of [633] Underfull \hbox (badness 3460) in paragraph at lines 43955--43958 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / data . iana . org / Underfull \hbox (badness 4429) in paragraph at lines 43959--43961 [][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol- Overfull \hbox (31.3804pt too wide) in paragraph at lines 43968--43968 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET", "Eire", ..., but[] [634] [635] [636] [637] [638] Overfull \hbox (15.18042pt too wide) in paragraph at lines 44311--44311 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15 g)\n", ncp))),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 44313--44313 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp root finding:[] [639] [640] Overfull \hbox (84.78088pt too wide) in paragraph at lines 44413--44413 [] \T1/pcr/m/n/10 getOption("deparse .max.lines", -1L)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 44415--44415 [] \T1/pcr/m/n/10 getOption("deparse .max.lines", -1L)))[] [641] [642] [643] Underfull \hbox (badness 6542) in paragraph at lines 44689--44691 []\T1/pcr/m/n/10 cospi(x)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sinpi(x)[]\T1/ptm/ m/n/10 , and []\T1/pcr/m/n/10 tanpi(x)[]\T1/ptm/m/n/10 , com-pute []\T1/pcr/m/n /10 cos(pi*x)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sin(pi*x)[]\T1/ptm/m/n/10 , an d [644] [645] Overfull \hbox (30.78088pt too wide) in paragraph at lines 44808--44808 []\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[ \t\r\n]") [646] Underfull \hbox (badness 1708) in paragraph at lines 44876--44884 []\T1/pcr/m/n/10 try []\T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any er-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 3713) in paragraph at lines 44876--44884 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ][]\T1/pcr/m/n/10 stderr[][][] []\T1/ptm/m/n/10 con-nec-tion un-less [647] Underfull \hbox (badness 4859) in paragraph at lines 44916--44921 [][][]\T1/pcr/m/n/10 options[][][] []\T1/ptm/m/n/10 for set-ting er-ror han-dle rs and sup-press-ing the print-ing of er-ror mes-sages; [648] Underfull \hbox (badness 3895) in paragraph at lines 44978--44990 []\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the struc-ture []\T1/pcr/m/n/10 TypeTable []\T1/ptm/m/n/10 in Underfull \hbox (badness 1303) in paragraph at lines 44978--44990 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue s are the vec-tor types []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/ m/n/10 "integer"[]\T1/ptm/m/n/10 , [649] [650] [651] [652] [653] Overfull \hbox (9.78043pt too wide) in paragraph at lines 45326--45326 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp ression(1+x))[] [654] [655] Underfull \hbox (badness 1137) in paragraph at lines 45420--45427 []\T1/ptm/m/n/10 When a func-tion call-ing []\T1/pcr/m/n/10 UseMethod("fun") [] \T1/ptm/m/n/10 is ap-plied to an ob-ject with class vec-tor [656] [657] [658] [659] [660] Overfull \hbox (4.38043pt too wide) in paragraph at lines 45798--45798 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local es and fonts[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 45807--45807 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little- endian platforms[] [661] Underfull \hbox (badness 2057) in paragraph at lines 45873--45879 [][][]\T1/pcr/m/n/10 file[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.acc ess[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.append[][][][]\T1/ptm/m/n /10 , [][][]\T1/pcr/m/n/10 file.copy[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 file.create[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.exists[][][][] \T1/ptm/m/n/10 , Underfull \hbox (badness 3861) in paragraph at lines 45882--45887 [][][]\T1/pcr/m/n/10 dir.create[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 di r.exists[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 normalizePath[][][][]\T1/ ptm/m/n/10 , [][][]\T1/pcr/m/n/10 path.expand[][][][]\T1/ptm/m/n/10 , [][][]\T1 /pcr/m/n/10 pipe[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Sys.glob[][][][]\ T1/ptm/m/n/10 , [662] Overfull \hbox (36.7804pt too wide) in paragraph at lines 45975--45975 []\T1/pcr/m/n/9 try( substr(x, 1,1) ) # gives \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 in valid multibyte string\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 error in a UTF-8 locale[] [663] Underfull \hbox (badness 1803) in paragraph at lines 46038--46041 []\T1/ptm/m/n/10 The atomic modes are []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "integer"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "numeric" []\ T1/ptm/m/n/10 (syn-onym []\T1/pcr/m/n/10 "double"[]\T1/ptm/m/n/10 ), Underfull \hbox (badness 3471) in paragraph at lines 46042--46048 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 mode = "any"[]\T1/ptm/m/n/10 , []\T1/pcr/m /n/10 is.vector []\T1/ptm/m/n/10 may re-turn []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/ n/10 for the atomic modes, [][][]\T1/pcr/m/n/10 list[][][] []\T1/ptm/m/n/10 and [664] [665] [666] [667] Underfull \hbox (badness 1014) in paragraph at lines 46271--46274 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the warn-ing should be out-put im-me -di-ately, even if [668] Overfull \hbox (36.78088pt too wide) in paragraph at lines 46380--46380 [] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes sages:\n"),[] [669] Overfull \hbox (4.38043pt too wide) in paragraph at lines 46455--46455 []\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n /9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 46463--46463 []\T1/pcr/m/n/9 x <- 1:36; for(n in 1:13) for(m in 1:12) A <- matrix(x, n,m) # There were 105 warnings ...[] [670] Underfull \hbox (badness 1783) in paragraph at lines 46528--46530 []\T1/pcr/m/n/10 weekdays []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 months []\T1/pt m/m/n/10 re-turn a char-ac-ter vec-tor of names in the lo-cale in use, i.e., [671] Overfull \hbox (25.98041pt too wide) in paragraph at lines 46558--46558 []\T1/pcr/m/n/9 ## Show how easily you get month, day, year, day (of {month, w eek, yr}), ... :[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 46570--46570 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Even simpler: Date -> Matrix - dropping time info {sec,min,hour, isdst}[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 46573--46573 []\T1/pcr/m/n/9 d2mat(seq(as.Date("2000-02-02"), by=1, length.out=30)) # has R 1.0.0\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s release date[] [672] Underfull \hbox (badness 10000) in paragraph at lines 46635--46640 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 arr.ind == TRUE []\T1/ptm/m/n/10 and []\T1 /pcr/m/n/10 x []\T1/ptm/m/n/10 is an [][][]\T1/pcr/m/n/10 array[][][] []\T1/ptm /m/n/10 (has a [][][]\T1/pcr/m/n/10 dim[][][] []\T1/ptm/m/n/10 at-tribute), the re-sult is Underfull \hbox (badness 2564) in paragraph at lines 46635--46640 []\T1/pcr/m/n/10 arrayInd(which(x), dim(x), dimnames(x))[]\T1/ptm/m/n/10 , name ly a ma-trix whose rows each [673] Underfull \hbox (badness 2818) in paragraph at lines 46731--46737 []\T1/ptm/m/n/10 For a [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 vec- tor []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 with both []\T1/pcr/m/n/10 FALSE []\T1/ ptm/m/n/10 and []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 val-ues, []\T1/pcr/m/n/10 which.min(x) []\T1/ptm/m/n/10 and [674] Overfull \hbox (15.18042pt too wide) in paragraph at lines 46766--46766 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is at least one:[] [675] [676] [677] [678] [679] [680] Underfull \hbox (badness 2846) in paragraph at lines 47227--47231 []\T1/pcr/m/n/10 .packages() []\T1/ptm/m/n/10 re-turns the names of the cur-ren tly at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [681] Overfull \hbox (4.38043pt too wide) in paragraph at lines 47267--47267 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 47288--47292 []\T1/pcr/m/n/10 .standard_regexps []\T1/ptm/m/n/10 re-turns a list of `stan-da rd' reg-exps, in-clud-ing el-e-ments named [682]) (./compiler-pkg.tex Chapter 2. [683] Underfull \hbox (badness 2884) in paragraph at lines 106--120 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 options []\T1/ptm/m/n/10 ar-gu-ment can b e used to con-trol com-piler op-er-a-tion. There are cur- Underfull \hbox (badness 10000) in paragraph at lines 106--120 \T1/ptm/m/n/10 rently four op-tions: []\T1/pcr/m/n/10 optimize[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 suppressAll[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 suppressUndef ined[]\T1/ptm/m/n/10 , and [684] [685] [686]) (./datasets-pkg.tex Chapter 3. [687] [688] [689] [690] [691] Overfull \hbox (15.18042pt too wide) in paragraph at lines 301--301 [] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang e", cex = 1.2,[] [692] Overfull \hbox (4.38043pt too wide) in paragraph at lines 379--379 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi ven = FALSE)[] [693] [694] [695] [696] Overfull \hbox (4.38043pt too wide) in paragraph at lines 617--617 [] \T1/pcr/m/n/9 start = c(lrc = log(.35)), algorithm = "plinear", t race = TRUE)[] [697] Underfull \hbox (badness 4779) in paragraph at lines 704--707 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [698] [699] Underfull \hbox (badness 4779) in paragraph at lines 837--840 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [700] [701] [702] Underfull \hbox (badness 1097) in paragraph at lines 1037--1041 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [703] Underfull \hbox (badness 4779) in paragraph at lines 1152--1155 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [704] [705] [706] [707] [708] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1464--1464 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption time (sec)")[] [709] [710] Underfull \hbox (badness 10000) in paragraph at lines 1549--1552 []\T1/ptm/m/n/10 Finally, []\T1/pcr/m/n/10 freeny []\T1/ptm/m/n/10 is a data fr ame with vari-ables []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lag.q uarterly.revenue[]\T1/ptm/m/n/10 , Underfull \hbox (badness 2903) in paragraph at lines 1549--1552 []\T1/pcr/m/n/10 price.index[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 income.level[]\ T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 market.potential []\T1/ptm/m/n/10 ob-taine d from the above [711] [712] [713] Underfull \hbox (badness 4779) in paragraph at lines 1738--1741 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [714] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1832--1832 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil y = binomial())[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1840--1840 [] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum), data = infert)[] [715] [716] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1956--1956 [] \T1/pcr/m/n/9 sub(" W.",".Width", dn i3[[2]])))),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1957--1957 [] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d ni3[[3]]))))[] [717] [718] [719] [720] Underfull \hbox (badness 4779) in paragraph at lines 2160--2163 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [721] [722] [723] [724] [725] [726] [727] [728] Underfull \hbox (badness 4779) in paragraph at lines 2725--2728 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [729] [730] [731] [732] [733] [734] [735] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3154--3154 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 1.2, pch = ".")[] [736] [737] [738] [739] [740] [741] Overfull \hbox (47.58038pt too wide) in paragraph at lines 3505--3505 []\T1/pcr/m/n/9 ## Alaska and Hawaii are placed just off the West Coast (for c ompact map drawing):[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3507--3507 []\T1/pcr/m/n/9 ## state.center2 := version of state.center with "correct" coo rdinates for AK & HI:[] Overfull \hbox (85.38034pt too wide) in paragraph at lines 3508--3508 []\T1/pcr/m/n/9 ## From https://pubs.usgs.gov/gip/Elevations-Distances/elvadis t.html#Geographic%20Centers[] [742] [743] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3639--3639 [] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t he monthly one:[] [744] [745] Underfull \hbox (badness 4779) in paragraph at lines 3787--3790 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [746] [747] [748] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3996--3996 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] [749] Underfull \hbox (badness 10000) in paragraph at lines 4034--4036 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/pcr/m/n/10 h ttps : / / web . archive . org / web / Underfull \hbox (badness 10000) in paragraph at lines 4034--4036 \T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma n / sitephotos / [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762]) (./grDevices-pkg.tex Chapter 4. [763] [764] [765] [766] Underfull \hbox (badness 4752) in paragraph at lines 298--303 []\T1/ptm/m/n/10 Apart from that, [][][]\T1/pcr/m/n/10 axisTicks[][][]() []\T1/ ptm/m/n/10 just calls the C func-tion []\T1/pcr/m/n/10 CreateAtVector() []\T1/p tm/m/n/10 in [767] [768] [769] [770] Overfull \hbox (6.78088pt too wide) in paragraph at lines 519--519 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d .pdf",[] [771] [772] [773] [774] [775] [776] [777] [778] [779] [780] Underfull \hbox (badness 5175) in paragraph at lines 1193--1195 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [781] [782] [783] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1364--1364 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", scale.in = 255))[] [784] [785] [786] Underfull \hbox (badness 3302) in paragraph at lines 1625--1629 []\T1/ptm/m/n/10 character: Does the de-vice sup-port pat-tern fills? One or mo re of Underfull \hbox (badness 10000) in paragraph at lines 1625--1629 []\T1/pcr/m/n/10 c("LinearGradient", "RadialGradient", "TilingPattern") [787] [788] [789] [790] [791] Underfull \hbox (badness 1565) in paragraph at lines 1916--1921 []\T1/ptm/m/n/10 The de-fault for []\T1/pcr/m/n/10 dev.print []\T1/ptm/m/n/10 i s to pro-duce and print a postscript copy. This will not Underfull \hbox (badness 1354) in paragraph at lines 1916--1921 \T1/ptm/m/n/10 sys-tem: see [][][]\T1/pcr/m/n/10 postscript[][][] []\T1/ptm/m/n /10 for how to set this up. Win-dows users may pre-fer to use [792] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1999--1999 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] [793] Underfull \hbox (badness 1184) in paragraph at lines 2040--2050 []\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of []\T1/pcr /m/n/10 ghostscript[]\T1/ptm/m/n/10 , but are likely to in- Underfull \hbox (badness 2057) in paragraph at lines 2040--2050 []\T1/pcr/m/n/10 "tiffg4"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiffgray"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "tifflzw"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiffp ack"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiff12nc"[]\T1/ptm/m/n/10 , []\T1/pcr/ m/n/10 "tiff24nc"[]\T1/ptm/m/n/10 , [794] Underfull \hbox (badness 10000) in paragraph at lines 2152--2154 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [795] [796] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2288--2288 []\T1/pcr/m/n/10 embedGlyphs(file, glyphInfo, outfile = file, options = charac ter())[] [797] Underfull \hbox (badness 6758) in paragraph at lines 2338--2341 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [798] [799] Underfull \hbox (badness 2326) in paragraph at lines 2456--2466 []\T1/ptm/m/n/10 are given, then it uses those in a call to []\T1/pcr/m/n/10 se tGraphicsEventHandlers []\T1/ptm/m/n/10 to re-place Underfull \hbox (badness 2318) in paragraph at lines 2456--2466 \T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co m-pat-i-bil-ity with pre-2.12.0 Underfull \hbox (badness 2460) in paragraph at lines 2456--2466 \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e vent han-dlers is to set them us-ing Underfull \hbox (badness 1221) in paragraph at lines 2456--2466 []\T1/pcr/m/n/10 setGraphicsEventHandlers []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 setGraphicsEventEnv []\T1/ptm/m/n/10 on one or more graph-ics [800] [801] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2559--2559 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r" , yaxs = "r") {[] Underfull \vbox (badness 10000) has occurred while \output is active [802] [803] [804] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2815--2815 []\T1/pcr/m/n/10 gray.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re v = FALSE) Overfull \hbox (30.78088pt too wide) in paragraph at lines 2816--2816 []\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re v = FALSE)[] [805] [806] [807] [808] [809] Underfull \hbox (badness 10000) in paragraph at lines 3089--3090 [810] [811] [812] [813] [814] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3422--3422 []\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized = FALSE)[] [815] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3506--3506 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", scale.in = 255))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3507--3507 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale. out = NULL))[] [816] [817] [818] Underfull \hbox (badness 10000) in paragraph at lines 3665--3671 []\T1/pcr/m/n/10 nclass.FD []\T1/ptm/m/n/10 uses the Freedman-Diaconis choice b ased on the inter-quartile range [819] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3740--3740 []\T1/pcr/m/n/10 palette.colors(n = NULL, palette = "Okabe-Ito", alpha, recycl e = FALSE)[] [820] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3824--3824 []\T1/pcr/m/n/9 (palette(gray(seq(0,.9,length.out = 25)))) # gray scales; prin t old palette[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3844--3844 []\T1/pcr/m/n/9 ## Demonstrate the colors 1:8 in different palettes using a cu stom matplot()[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3851--3851 [] \T1/pcr/m/n/9 matplot(x, type = "l", lwd = 4, lty = 1, col = 1:8, ylab = "", main=main)[] [821] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3907--3907 []\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE, fixup = TRUE) [822] Underfull \hbox (badness 8170) in paragraph at lines 3936--3939 []\T1/ptm/m/n/10 the type of palettes to list: []\T1/pcr/m/n/10 "qualitative"[] \T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sequential"[]\T1/ptm/m/n/10 , [823] Underfull \hbox (badness 2189) in paragraph at lines 3997--4002 []\T1/ptm/m/n/10 For ex-am-ple, []\T1/pcr/m/n/10 "Dark 3" []\T1/ptm/m/n/10 work s well for shad-ing points or lines in up to five groups, Underfull \hbox (badness 10000) in paragraph at lines 4035--4039 \T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space & oldid = 883465135$[][]\T1/ptm/m/n/10 . [824] Underfull \vbox (badness 10000) has occurred while \output is active [825] Underfull \hbox (badness 5260) in paragraph at lines 4165--4168 []\T1/ptm/m/n/10 For use with []\T1/pcr/m/n/10 onefile = FALSE []\T1/ptm/m/n/10 give a C in-te-ger for-mat such as [826] [827] [828] [829] [830] Underfull \hbox (badness 5939) in paragraph at lines 4504--4509 []\T1/ptm/m/n/10 arguments []\T1/pcr/m/n/10 width[]\T1/ptm/m/n/10 , []\T1/pcr/m /n/10 height[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 onefile[]\T1/ptm/m/n/10 , []\T1 /pcr/m/n/10 family[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 title[]\T1/ptm/m/n/10 , [ ]\T1/pcr/m/n/10 fonts[]\T1/ptm/m/n/10 , [831] [832] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.symbol}) has been already used, duplicate ignored \relax l.4681 \aliasA{symbol}{plotmath}{symbol} [833] [834] [835] [836] [837] [838] Overfull \hbox (60.78088pt too wide) in paragraph at lines 5025--5025 [] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz w+p", "zip+p"),[] [839] [840] Underfull \hbox (badness 1348) in paragraph at lines 5236--5239 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, [][]$\T1/pcr/m/n/10 https : / / ww w . iso . org / standard / 34342 . html$[][]\T1/ptm/m/n/10 . See also [841] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5263--5263 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, height = 768)[] Underfull \hbox (badness 7522) in paragraph at lines 5304--5310 []\T1/ptm/m/n/10 For use with []\T1/pcr/m/n/10 onefile = FALSE []\T1/ptm/m/n/10 give a []\T1/pcr/m/n/10 printf []\T1/ptm/m/n/10 for-mat such as [842] Underfull \hbox (badness 1112) in paragraph at lines 5337--5341 []\T1/ptm/m/n/10 as `\T1/pcr/m/n/10 "CP1250.enc"\T1/ptm/m/n/10 ' (Cen-tral Eu-r o-pean), []\T1/pcr/m/n/10 "CP1251.enc" [843] [844] Underfull \hbox (badness 1755) in paragraph at lines 5481--5483 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [845] [846] Underfull \hbox (badness 7344) in paragraph at lines 5664--5666 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso Underfull \hbox (badness 7397) in paragraph at lines 5675--5679 [][][]\T1/pcr/m/n/10 postscriptFonts[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 Devices[][][][]\T1/ptm/m/n/10 , and [][][]\T1/pcr/m/n/10 check.options[][][] []\T1/ptm/m/n/10 which is called from both [847] [848] Underfull \hbox (badness 1552) in paragraph at lines 5802--5811 []\T1/pcr/m/n/10 "AvantGarde"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Bookman"[]\T1 /ptm/m/n/10 , []\T1/pcr/m/n/10 "Courier"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "He lvetica"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Helvetica-Narrow"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5802--5811 []\T1/pcr/m/n/10 "NewCenturySchoolbook"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Pal atino" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "Times"[]\T1/ptm/m/n/10 ; []\T1/pc r/m/n/10 "URWGothic"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5802--5811 []\T1/pcr/m/n/10 "URWBookman"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "NimbusMon"[]\ T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "NimbusSan" []\T1/ptm/m/n/10 (syn-onym []\T1/p cr/m/n/10 "URWHelvetica"[]\T1/ptm/m/n/10 ), Underfull \hbox (badness 2221) in paragraph at lines 5812--5814 []\T1/ptm/m/n/10 There are also map-pings for []\T1/pcr/m/n/10 "ComputerModern" []\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ComputerModernItalic" []\T1/ptm/m/n/10 and Underfull \hbox (badness 4686) in paragraph at lines 5844--5850 []\T1/pcr/m/n/10 "Japan1"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Japan1HeiMin"[]\T 1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Japan1GothicBBB"[]\T1/ptm/m/n/10 , and []\T1/p cr/m/n/10 "Japan1Ryumin" []\T1/ptm/m/n/10 for [849] Underfull \hbox (badness 5388) in paragraph at lines 5870--5872 []\T1/pcr/m/n/10 BousungEG-Light-GB []\T1/ptm/m/n/10 can be found at [][]$\T1/p cr/m/n/10 https : / / ftp . gnu . org / pub / non-[]gnu / [850] [851] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5974--5974 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r eg-tests-1c.R[] [852] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6086--6086 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100 , ...)[] [853] [854] Underfull \hbox (badness 10000) in paragraph at lines 6173--6175 []\T1/ptm/m/n/10 Calling []\T1/pcr/m/n/10 quartz() []\T1/ptm/m/n/10 sets [][][] \T1/pcr/m/n/10 .Device[][][] []\T1/ptm/m/n/10 to []\T1/pcr/m/n/10 "quartz" []\T 1/ptm/m/n/10 for on-screen de-vices and to [855] [856] [857] [858] [859] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6540--6540 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15, sep = "."))[] Underfull \hbox (badness 10000) in paragraph at lines 6554--6557 []\T1/pcr/m/n/10 rgb2hsv []\T1/ptm/m/n/10 trans-forms col-ors from RGB space (r ed/green/blue) into HSV space [860] [861] [862] [863] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6774--6774 []\T1/pcr/m/n/9 p <- persp(x, y, fxy <- outer(x,y), phi = 20, theta = 15, r = 3, ltheta = -75,[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6785--6785 []\T1/pcr/m/n/9 ## now some "horizontal rays" (going from center to very left or very right):[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 6787--6787 [] \T1/pcr/m/n/9 lines(trans3d(x=seq(x1, x2, by=0.5), y= -0.7, z = z, pmat = p, continuous = CNT),[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6789--6789 []\T1/pcr/m/n/9 doHor(-10, 0, z = -0.5, col = 2) # x in [-10, 0] -- to the v ery left : fine[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 6790--6790 []\T1/pcr/m/n/9 doHor(-.5, 2, z = -0.52,col = 4) # x in [-0.5, 2] only {to th e right} --> all fine[] Overfull \hbox (117.7803pt too wide) in paragraph at lines 6791--6791 []\T1/pcr/m/n/9 ## but now, x in [-0.5, 20] -- "too far" ==> "wrap around" pro blem (without \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 continuous=TRUE\TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 ):[] [864] [865] Overfull \hbox (0.78088pt too wide) in paragraph at lines 6923--6923 []\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp inch, Overfull \hbox (0.78088pt too wide) in paragraph at lines 6930--6930 []\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize = 12,[] [866] [867] [868] [869] Underfull \hbox (badness 10000) in paragraph at lines 7196--7201 []\T1/ptm/m/n/10 arguments []\T1/pcr/m/n/10 width[]\T1/ptm/m/n/10 , []\T1/pcr/m /n/10 height[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pointsize[]\T1/ptm/m/n/10 , []\ T1/pcr/m/n/10 record[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 rescale[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1803) in paragraph at lines 7196--7201 []\T1/pcr/m/n/10 xpinch[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 ypinch[]\T1/ptm/m/n/ 10 , []\T1/pcr/m/n/10 bg[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 canvas[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 gamma[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 xpos[]\T1/ptm/m /n/10 , []\T1/pcr/m/n/10 ypos[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 buffered[]\T1/ ptm/m/n/10 , Underfull \hbox (badness 2941) in paragraph at lines 7196--7201 []\T1/pcr/m/n/10 restoreConsole[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 clickToConfi rm[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 title[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 fillOddEven []\T1/ptm/m/n/10 and [870] [871] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7302--7302 []\T1/pcr/m/n/9 windows() # make sure we have the right device type (availabl e on Windows only)[] Underfull \hbox (badness 3590) in paragraph at lines 7341--7344 []\T1/ptm/m/n/10 The \T1/phv/m/n/10 R \T1/ptm/m/n/10 func-tion is a wrap-per fo r two de-vices, one based on Xlib ([][]$\T1/pcr/m/n/10 https : / / Underfull \hbox (badness 2393) in paragraph at lines 7341--7344 \T1/pcr/m/n/10 en . wikipedia . org / wiki / Xlib$[][]\T1/ptm/m/n/10 ) and one us-ing cairo-graph-ics ([][]$\T1/pcr/m/n/10 https : / / www . Overfull \hbox (12.78088pt too wide) in paragraph at lines 7352--7352 [] \T1/pcr/m/n/10 fonts, family, xpos, ypos, title, type, antialias, symbol family)[] [872] Underfull \hbox (badness 1189) in paragraph at lines 7417--7419 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [873] [874] Underfull \hbox (badness 10000) in paragraph at lines 7522--7524 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" []\T1/ptm/m/n/10 for CJ K lan-guages and Underfull \hbox (badness 10000) in paragraph at lines 7568--7575 []\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of [] \T1/pcr/m/n/10 quote(pi) []\T1/ptm/m/n/10 and Underfull \hbox (badness 2469) in paragraph at lines 7568--7575 []\T1/pcr/m/n/10 expression(10^degree)[]\T1/ptm/m/n/10 ) have been seen on Linu x sys-tems which have the Wine [875] Underfull \hbox (badness 5607) in paragraph at lines 7652--7656 []\T1/pcr/m/n/10 type = "Xlib" []\T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-d o-Color', `GrayScale', []\T1/pcr/m/n/10 StaticGray []\T1/ptm/m/n/10 and [876] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7704--7704 [] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height = 6, xpos = 0,[] [877] [878] Underfull \hbox (badness 5637) in paragraph at lines 7836--7842 []\T1/pcr/m/n/10 "Courier"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Helvetica" []\T1 /ptm/m/n/10 (the de-fault), []\T1/pcr/m/n/10 "Helvetica-Narrow"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1721) in paragraph at lines 7869--7872 []\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt p : / / www . schmidt-[]web-[]berlin . de / [879] [880] Overfull \hbox (63.78036pt too wide) in paragraph at lines 8004--8004 []\T1/pcr/m/n/9 op <- options(warn = 2)# ==> warnings would be errors, we supp ress the one "we know":[] [881] Underfull \hbox (badness 1231) in paragraph at lines 8043--8045 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., []\T1/pcr/m/n/10 number[i] []\T1/ptm/m/n/10 is the mul-ti-plic-ity of [882] [883] [884]) (./graphics-pkg.tex Chapter 5. Underfull \hbox (badness 4647) in paragraph at lines 16--18 []\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag es, use []\T1/pcr/m/n/10 library(help = [885] [886] [887] [888] [889] [890] [891] Overfull \hbox (6.05087pt too wide) in paragraph at lines 450--450 [] \T1/pcr/m/n/10 gap.axis <- if(perpendicular(side, las)) 0.25 else 1[] Underfull \hbox (badness 4048) in paragraph at lines 482--488 []\T1/ptm/m/n/10 When []\T1/pcr/m/n/10 at = NULL[]\T1/ptm/m/n/10 , pretty tick mark lo-ca-tions are com-puted in-ter-nally (the same way [892] [893] Overfull \hbox (47.58038pt too wide) in paragraph at lines 580--580 []\T1/pcr/m/n/9 ## now shrink the window (in x- and y-direction) and observe t he axis labels drawn[] [894] Overfull \hbox (15.18042pt too wide) in paragraph at lines 692--692 []\T1/pcr/m/n/9 axis.Date(3, at = as.integer(as.Date("2023-04-01")), col.axis = "darkgreen")[] [895] Overfull \hbox (15.18042pt too wide) in paragraph at lines 707--707 []\T1/pcr/m/n/9 axis.POSIXct(3, at = as.POSIXct("2022-10-01 00:01:30"), col.ax is = "orange")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 712--712 []\T1/pcr/m/n/9 axis.POSIXct(3, at = as.numeric(as.POSIXct("2022-10-01 00:00:3 0")) + 0.25,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 713--713 [] \T1/pcr/m/n/9 col.axis = "forestgreen", col = "darkgreen", m gp = c(3,2,0))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 719--719 []\T1/pcr/m/n/9 plot(data.frame(HST, y = 1), xaxt = "n", xlab = "Hawaii Standa rd Time (HST)")[] Underfull \hbox (badness 10000) in paragraph at lines 746--750 []\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][][]\T1/pcr /m/n/10 par[][][]("xaxp") []\T1/ptm/m/n/10 or Underfull \hbox (badness 3250) in paragraph at lines 746--750 [][][]\T1/pcr/m/n/10 par[][][]("yaxp") []\T1/ptm/m/n/10 de-pend-ing on the []\T 1/pcr/m/n/10 side []\T1/ptm/m/n/10 ar-gu-ment ([]\T1/pcr/m/n/10 par("xaxp") []\ T1/ptm/m/n/10 if [896] [897] Overfull \hbox (4.38043pt too wide) in paragraph at lines 833--833 [] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n intLog = 5))[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 870--870 [] \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend = NULL, ...)[] [898] [899] Underfull \hbox (badness 10000) in paragraph at lines 1017--1021 [][][]\T1/pcr/m/n/10 plot[][][](..., type = "h")[]\T1/ptm/m/n/10 , [][][]\T1/pc r/m/n/10 dotchart[][][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 hist[][][] []\T1 /ptm/m/n/10 for bars of a \T1/ptm/m/it/10 con-tin-u-ous \T1/ptm/m/n/10 vari-abl e. [900] Overfull \hbox (133.98029pt too wide) in paragraph at lines 1034--1034 [] \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = " # {passengers}", legend.text = TRUE)[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1036--1036 []\T1/pcr/m/n/9 (xt <- xtabs(Freq ~ Survived + Class + Sex, d.Titanic, subset = Age=="Adult"))[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 1038--1038 []\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur vived, *)", color=TRUE)[] Underfull \vbox (badness 10000) has occurred while \output is active [901] [902] [903] [904] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1322--1322 []\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches .. outside hinges"):[] [905] [906] [907] Underfull \hbox (badness 2503) in paragraph at lines 1484--1493 \T1/ptm/m/n/10 when []\T1/pcr/m/n/10 horizontal []\T1/ptm/m/n/10 is false, and []\T1/pcr/m/n/10 xlim []\T1/ptm/m/n/10 hor-i-zon-tally. []\T1/pcr/m/n/10 xaxt[] \T1/ptm/m/n/10 , []\T1/pcr/m/n/10 yaxt[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3375) in paragraph at lines 1519--1521 []\T1/ptm/m/n/10 whisker line type (de-fault: []\T1/pcr/m/n/10 "dashed"[]\T1/pt m/m/n/10 ), [908] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1593--1593 []\T1/pcr/m/n/9 boxplot(z, col.axis = "skyblue3", main = "boxplot(*, col.axi s=..,main=..)")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1594--1594 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main = "plot(*, col.axi s=..,main=..)")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1600--1600 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill = "grey40",[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1601--1601 [] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl ty = 1, outpch = NA)[] [909] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1634--1634 [] \T1/pcr/m/n/10 yaxlabels = NULL, xlim = NULL, ylim = c(0, 1), weights = NU LL, ...)[] [910] [911] [912] [913] Underfull \hbox (badness 10000) in paragraph at lines 1907--1913 [][][]\T1/pcr/m/n/10 contourLines[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 filled.contour[][][] []\T1/ptm/m/n/10 for color-filled con-tours, [][][]\T1/pcr /m/n/10 contourplot[][][] []\T1/ptm/m/n/10 (and [914] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1927--1927 []\T1/pcr/m/n/9 contour(x, x, z, ylim = c(-6, 6), nlevels = 20, lty = 2, metho d = "simple",[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 1939--1939 []\T1/pcr/m/n/9 contour(z, levels=levs[-c(1,length(levs))], col = 1:5, lwd = 1 :3 *1.5, lty = 1:3)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1955--1955 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1964--1964 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [915] [916] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2049--2049 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [917] [918] Overfull \hbox (31.3804pt too wide) in paragraph at lines 2178--2178 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.values = given .depth, rows = 1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2183--2183 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c( TRUE, FALSE))[] [919] [920] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2357--2357 []\T1/pcr/m/n/10 dotchart(x, labels = NULL, groups = NULL, gdata = NULL, offse t = 1/8, Overfull \hbox (54.78088pt too wide) in paragraph at lines 2358--2358 [] \T1/pcr/m/n/10 ann = par("ann"), xaxt = par("xaxt"), frame.plot = T RUE, log = "",[] [921] Underfull \hbox (badness 1430) in paragraph at lines 2388--2390 []\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use []\T1/pcr/m/n/10 "n" []\T1/ptm/m/n/10 to sup-press and see also [922] Overfull \hbox (78.78088pt too wide) in paragraph at lines 2469--2469 [] \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO rRd", rev = TRUE),[] Underfull \hbox (badness 1009) in paragraph at lines 2481--2488 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [923] Underfull \hbox (badness 7273) in paragraph at lines 2563--2567 [][][]\T1/pcr/m/n/10 contour[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 image [][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 hcl.colors[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gray.colors[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 palette[][][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 contourplot[][][] []\T1/p tm/m/n/10 and [924] [925] [926] [927] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2811--2811 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [928] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2848--2848 [] \T1/pcr/m/n/10 density = NULL, angle = 45, col = "lightgray", border = NULL,[] [929] [930] Underfull \hbox (badness 1226) in paragraph at lines 2975--2979 \T1/pcr/m/n/10 1)[]\T1/ptm/m/n/10 , they are the rel-a-tive fre-quen-cies []\T1 /pcr/m/n/10 counts/n []\T1/ptm/m/n/10 and in gen-eral sat-isfy [931] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3028--3028 []\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3032--3032 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a suggestion only"[] [932] Underfull \hbox (badness 10000) in paragraph at lines 3094--3097 [][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][][]\T1 /pcr/m/n/10 hist.default[][][] []\T1/ptm/m/n/10 such as Overfull \hbox (15.18042pt too wide) in paragraph at lines 3145--3145 []\T1/pcr/m/n/9 ## The default fuzz in hist.default() "kills" this, with a "w rong" message:[] [933] [934] [935] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3309--3309 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL SE, pch = 19, ...)[] Overfull \hbox (79.98035pt too wide) in paragraph at lines 3314--3314 [] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel) , n = 1, plot = plot, ...)[] [936] [937] Underfull \hbox (badness 10000) in paragraph at lines 3456--3461 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 useRaster []\T1/ptm/m/n/10 is not spec-i-f ied, raster im-ages are used when the Underfull \hbox (badness 10000) in paragraph at lines 3456--3461 [][][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") []\T1/ptm/m/n/10 is true, the grid is reg-u-lar and ei-ther Underfull \hbox (badness 10000) in paragraph at lines 3456--3461 [][][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage []\T1/pt m/m/n/10 is []\T1/pcr/m/n/10 "yes" []\T1/ptm/m/n/10 or it is Overfull \hbox (31.3804pt too wide) in paragraph at lines 3491--3491 []\T1/pcr/m/n/9 # Visualize as matrix. Need to transpose matrix and then flip it horizontally:[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 3493--3493 []\T1/pcr/m/n/9 imageM <- function(m, grid = max(dim(m)) <= 25, asp = (nrow(m) -1)/(ncol(m)-1), ...) {[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3496--3496 [] \T1/pcr/m/n/9 axis(side, at=at, labels=as.character(j+1L), col="gray ", col.axis=1, ...)[] [938] [939] [940] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3653--3653 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 0, horiz = TRUE)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3672--3672 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3676--3676 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [941] [942] [943] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3861--3861 [] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c ex = 0.8, adj = 0)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3862--3862 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3866--3866 [] \T1/pcr/m/n/9 cex = 1+(-1:2)/8, trace = TRUE)# trace: show computed l engths & coords[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3876--3876 [] \T1/pcr/m/n/9 title("legend(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 top\TS1/pcr/m/n/ 9 '\T1/pcr/m/n/9 , lty = c(2, -1, 1), pch = c(NA, 3, 4), merge = TRUE)",[] [944] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3907--3907 [] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj = c(0, 0.3))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3933--3933 []\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Filled\TS1/pcr/m/n/9 ' \T1/pc r/m/n/9 boxes -- see also example(barplot) which may call legend(*, fill=)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3935--3935 []\T1/pcr/m/n/9 legend("topright", rownames(VADeaths), fill = gray.colors(nrow (VADeaths)))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3946--3946 []\T1/pcr/m/n/9 legend("bottomright", paste("sin(", 1:7, "pi * x)"), col = 1:7 , lty = 1:7,[] Underfull \vbox (badness 10000) has occurred while \output is active [945] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3961--3961 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c ol = "blue")[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3969--3969 []\T1/pcr/m/n/9 legend("topleft", "(x,y)", pch=1, title= "topleft, inset = .05", inset = .05)[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3971--3971 []\T1/pcr/m/n/9 legend("topright", "(x,y)", pch=1, title= "topright, inset = .02",inset = .02)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3979--3979 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3989--3989 []\T1/pcr/m/n/9 legend("bottomleft", c("This legend", "has", "optimally sized" , "columns."),[] [946] Underfull \hbox (badness 10000) in paragraph at lines 4051--4055 [][][]\T1/pcr/m/n/10 lines.formula[][][] []\T1/ptm/m/n/10 for the for-mula meth od; [][][]\T1/pcr/m/n/10 points[][][][]\T1/ptm/m/n/10 , par-tic-u-larly for []\ T1/pcr/m/n/10 type %in% [947] [948] Overfull \hbox (6.78088pt too wide) in paragraph at lines 4163--4163 [] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb ose"))[] [949] [950] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4317--4317 []\T1/pcr/m/n/9 nd <- length(dv <- seq(as.Date("1959-02-21"), by = "weeks", le ngth.out = 100))[] [951] Underfull \hbox (badness 3930) in paragraph at lines 4396--4398 []\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a mul-ti-ple of [952] [953] [954] [955] [956] Underfull \hbox (badness 1286) in paragraph at lines 4707--4710 []\T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify []\T1/pcr/m/n /10 oma []\T1/ptm/m/n/10 when chang-ing Underfull \hbox (badness 3229) in paragraph at lines 4715--4720 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used, see [957] [958] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4811--4811 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel = panel.cor,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4816--4816 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] [959] Underfull \hbox (badness 1264) in paragraph at lines 5007--5020 \T1/ptm/m/n/10 func-tions such as [][][]\T1/pcr/m/n/10 plot.default[][][][]\T1/ ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.window[][][][]\T1/ptm/m/n/10 , [][][]\T1 /pcr/m/n/10 points[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lines[][][][]\T 1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 abline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc r/m/n/10 axis[][][][]\T1/ptm/m/n/10 , [960] [961] [962] [963] Underfull \hbox (badness 10000) in paragraph at lines 5273--5276 [964 ] Underfull \hbox (badness 10000) in paragraph at lines 5334--5336 [965 ] [966] [967] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5580--5580 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, physicians = 9,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5581--5581 [] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t eachers = 4,[] Underfull \vbox (badness 10000) has occurred while \output is active [968] [969] [970] [971] [972] [973] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5945--5945 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p yramid" = 5),[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 5946--5946 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] [974] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot}) ha s been already used, duplicate ignored \relax l.6005 \aliasA{plot}{plot.default}{plot} [975] [976] [977] [978] [979] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6337--6337 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6343--6343 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [980] [981] Overfull \hbox (66.78088pt too wide) in paragraph at lines 6467--6467 [] \T1/pcr/m/n/10 main = paste("Histogram of", paste(x$xname, co llapse = "\n")),[] [982] [983] [984] [985] Underfull \hbox (badness 10000) in paragraph at lines 6772--6774 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [986] [987] Underfull \hbox (badness 1028) in paragraph at lines 6866--6868 []\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th is works as a mul-ti-ple of Overfull \hbox (31.57222pt too wide) in paragraph at lines 6909--6910 [][] [988 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7003--7003 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [989] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7034--7034 [] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab = "", main = main)[] Underfull \vbox (badness 10000) has occurred while \output is active [990] [991] Underfull \hbox (badness 10000) in paragraph at lines 7156--7158 []\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev in Buhr Overfull \hbox (15.18042pt too wide) in paragraph at lines 7183--7183 [] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b order = "red")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7189--7189 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [992] Underfull \hbox (badness 2600) in paragraph at lines 7246--7248 []\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther []\T 1/pcr/m/n/10 "winding" []\T1/ptm/m/n/10 or [993] [994] [995] [996] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7478--7478 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7 , end = 0.1))[] [997] [998] [999] [1000] [1001] [1002] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7865--7865 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp ace = "Lab")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7869--7869 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [1003] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7881--7881 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 7908--7908 [] \T1/pcr/m/n/10 xlim = NULL, ylim = c(0, 1), axes = TRUE, weights = NULL, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 7917--7917 [] \T1/pcr/m/n/10 subset = NULL, weights = NULL, drop.unused.levels = FALSE)[] [1004] [1005] [1006] [1007] [1008] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8234--8234 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8237--8237 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] [1009] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8241--8241 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [1010] [1011] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8412--8412 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...) Overfull \hbox (36.78088pt too wide) in paragraph at lines 8413--8413 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [1012] [1013] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8517--8517 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] [1014] Underfull \hbox (badness 1112) in paragraph at lines 8576--8580 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 number[i] == 1[]\T1/ptm/m/n/10 , a (sligh tly en-larged) usual plot-ting sym-bol ([]\T1/pcr/m/n/10 pch[]\T1/ptm/m/n/10 ) is drawn. For [1015] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8636--8636 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035 , seg.lwd = .8)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8651--8651 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [1016] [1017] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8788--8788 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [1018] [1019] [1020] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8973--8973 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est facile: Règles, Liberté, Egalité, Fraternité...")[] Underfull \hbox (badness 1215) in paragraph at lines 9001--9003 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color []\T1/pcr/m /n/10 par(c("font.sub", Underfull \hbox (badness 1584) in paragraph at lines 9035--9041 []\T1/ptm/m/n/10 The po-si-tions of []\T1/pcr/m/n/10 xlab[]\T1/ptm/m/n/10 , []\ T1/pcr/m/n/10 ylab []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 sub []\T1/ptm/m/n/10 a re []\T1/pcr/m/n/10 line []\T1/ptm/m/n/10 (de-fault for []\T1/pcr/m/n/10 xlab [ ]\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 ylab []\T1/ptm/m/n/10 be-ing [1021] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.units}) h as been already used, duplicate ignored \relax l.9083 \HeaderA{units}{Graphical Units}{units} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.units.1}) has been already used, duplicate ignored \relax l.9083 \HeaderA{units}{Graphical Units}{units} [1022] Underfull \hbox (badness 1205) in paragraph at lines 9148--9150 []\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th e poly-gon. See [1023] [1024] Overfull \hbox (25.98041pt too wide) in paragraph at lines 9267--9267 []\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code = 2, length = 0.1)[] [1025]) (./grid-pkg.tex [1026] Chapter 6. [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] Underfull \hbox (badness 4859) in paragraph at lines 634--637 []\T1/ptm/m/n/10 Modification of the view-port (should all be valid ar-gu-ments to the [1037] [1038] [1039] [1040] [1041] [1042] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1028--1028 [] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un it(1, "inches")))[] [1043] [1044] [1045] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1239--1239 [] \T1/pcr/m/n/9 vpList(vpStack(viewport(x=0.1, y=0.1, width=0.5 , height=0.5,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1240--1240 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1241--1241 [] \T1/pcr/m/n/9 viewport(x=0.1, y=0.1, width=0.5 , height=0.5,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1242--1242 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1243--1243 [] \T1/pcr/m/n/9 viewport(x=0.1, y=0.1, width=0.5 , height=0.5,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1244--1244 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] [1046] [1047] [1048] [1049] Underfull \hbox (badness 3219) in paragraph at lines 1503--1506 []\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject de-scrib-ing a cir-cle), but only [1050] [1051] [1052] [1053] [1054] [1055] [1056] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1891--1891 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [1057] [1058] [1059] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2105--2105 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla ck"), name="r1")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2106--2106 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey" ), name="r2")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2107--2107 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [1060] Underfull \hbox (badness 2961) in paragraph at lines 2142--2147 []\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio ns []\T1/pcr/m/n/10 preDrawDetails[]\T1/ptm/m/n/10 , [1061] Underfull \hbox (badness 4479) in paragraph at lines 2230--2233 []\T1/ptm/m/n/10 Both func-tions call []\T1/pcr/m/n/10 editDetails []\T1/ptm/m/ n/10 to al-low a grob to per-form cus-tom ac-tions and [1062] [1063] [1064] Underfull \hbox (badness 2894) in paragraph at lines 2437--2444 []\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de -scrib-ing a frame), but only [1065] [1066] [1067] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2593--2593 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] [1068] Underfull \hbox (badness 1014) in paragraph at lines 2679--2684 []\T1/ptm/m/n/10 The jus-ti-fi-ca-tion of the glyphs rel-a-tive to the ([]\T1/p cr/m/n/10 x[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 ) lo-ca-tion. Can be [1069] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2725--2725 []\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs = FALSE,[] [1070] [1071] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2887--2887 [] \T1/pcr/m/n/9 children=gList(grob(name="child", vp ="vp1::vp2")),[] [1072] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2919--2919 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [1073] [1074] Underfull \hbox (badness 10000) in paragraph at lines 3102--3104 []\T1/ptm/m/n/10 A func-tion that re-turns an affine trans-for-ma-tion ma-trix; see [1075] Underfull \hbox (badness 1077) in paragraph at lines 3119--3138 []\T1/ptm/m/n/10 Another pos-si-ble use of []\T1/pcr/m/n/10 grid.group() []\T1/ ptm/m/n/10 is to spec-ify both []\T1/pcr/m/n/10 src []\T1/ptm/m/n/10 and []\T1/ pcr/m/n/10 dst []\T1/ptm/m/n/10 and com-bine Underfull \hbox (badness 1622) in paragraph at lines 3119--3138 []\T1/ptm/m/n/10 is only drawn where it is NOT over-lapped by []\T1/pcr/m/n/10 src[]\T1/ptm/m/n/10 . The fol-low-ing (ex-tended) Porter- Underfull \hbox (badness 2057) in paragraph at lines 3119--3138 []\T1/pcr/m/n/10 "multiply"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "screen"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "overlay"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "darke n"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lighten"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n /10 "color.dodge"[]\T1/ptm/m/n/10 , [1076] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3191--3191 [] \T1/pcr/m/n/9 mask <- as.mask(rectGrob(gp=gpar(col=NA, fill="grey50")), ty pe="luminance")[] [1077] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3307--3307 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [1078] [1079] [1080] [1081] [1082] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3622--3622 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [1083] [1084] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3718--3718 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, width=0.25, height=0.25, just= c("left", "bottom")))[] Underfull \hbox (badness 2799) in paragraph at lines 3755--3761 []\T1/ptm/m/n/10 There are two hooks called []\T1/pcr/m/n/10 "before.grid.newpa ge" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "grid.newpage" []\T1/ptm/m/n/10 (see [1085] [1086] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3847--3847 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3854--3854 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [1087] [1088] [1089] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4055--4055 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] [1090] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4070--4070 [] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other anti-clockwise")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4091--4091 []\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s ame path, thus[] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] Underfull \hbox (badness 1067) in paragraph at lines 4840--4843 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1103] [1104] [1105] [1106] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5056--5056 [] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un it(1, "inches")))[] [1107] [1108] Underfull \hbox (badness 7256) in paragraph at lines 5191--5193 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1109] Overfull \hbox (69.18036pt too wide) in paragraph at lines 5258--5258 []\T1/pcr/m/n/9 grid.text(quote(frac(e^{-x^2/2}, sqrt(2*pi))), x=x, y=y, rot=s tats::runif(20, -45,45),[] [1110] [1111] [1112] [1113] [1114] [1115] Underfull \hbox (badness 2726) in paragraph at lines 5645--5649 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 gridCoords []\T1/ptm/m/n/10 a nu-meric ve c-tor. For []\T1/pcr/m/n/10 gridGrobCoords []\T1/ptm/m/n/10 a list Underfull \hbox (badness 1231) in paragraph at lines 5645--5649 \T1/ptm/m/n/10 of []\T1/pcr/m/n/10 "GridCoords" []\T1/ptm/m/n/10 ob-jects. For []\T1/pcr/m/n/10 gridGTreeCoords []\T1/ptm/m/n/10 a list of ei-ther [1116] Underfull \hbox (badness 2080) in paragraph at lines 5727--5732 []\T1/ptm/m/n/10 Either a []\T1/pcr/m/n/10 "GridGrobCoords" []\T1/ptm/m/n/10 ob -ject (a list of lists with com-po-nents []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 an d []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 ) or a [1117] [1118] [1119] Underfull \hbox (badness 10000) in paragraph at lines 5907--5909 []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 grid.legend()[]\T1/ptm/m/n/10 : all the a r-gu-ments above are passed to [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7002--7002 []\T1/pcr/m/n/9 unitType(min(unit(1, "in"), unit(1, "npc") + unit(1, "mm")), r ecurse=TRUE)[] [1137] [1138] Overfull \hbox (54.78088pt too wide) in paragraph at lines 7122--7122 []\T1/pcr/m/n/10 viewportTransform(group, shear=groupShear(), flip=groupFlip() , device=TRUE) [1139] Underfull \hbox (badness 1867) in paragraph at lines 7224--7226 []\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for use in []\T1/pcr/m/n/10 downViewport []\T1/ptm/m/n/10 or [1140] Underfull \hbox (badness 10000) in paragraph at lines 7261--7267 [][][]\T1/pcr/m/n/10 viewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 push Viewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 popViewport[][][][]\T1/pt m/m/n/10 , [][][]\T1/pcr/m/n/10 downViewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 seekViewport[][][][]\T1/ptm/m/n/10 , [1141] [1142] [1143] Underfull \vbox (badness 10000) has occurred while \output is active [1144] [1145] [1146] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7597--7597 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp ar(col="red"))))[] [1147]) (./methods-pkg.tex [1148] Chapter 7. [1149] [1150] Underfull \hbox (badness 1688) in paragraph at lines 166--171 []\T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how co-erce meth-ods work. Use [1151] [1152] [1153] Underfull \hbox (badness 1348) in paragraph at lines 392--395 [][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] []\T1/ptm/m/n/10 for other in- for-ma-tion about group generic func-tions; [][]Meth- [1154] [1155] Overfull \hbox (15.18042pt too wide) in paragraph at lines 558--558 []\T1/pcr/m/n/9 ## vector. The next method will always be the default, usuall y a primitive.[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w ith no arguments[] [1156] Overfull \hbox (4.38043pt too wide) in paragraph at lines 619--619 []\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho ut arguments[] Underfull \vbox (badness 10000) has occurred while \output is active [1157] Overfull \hbox (25.98041pt too wide) in paragraph at lines 637--637 []\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th e default method[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 640--640 []\T1/pcr/m/n/9 ## call f() with 1 argument: the default "B0" is not passed b y callNextMethod[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 657--657 []\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the "B0" method[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 672--672 []\T1/pcr/m/n/9 ## Although the argument here is numeric, it\TS1/pcr/m/n/9 '\T 1/pcr/m/n/9 s still the "B0" method that\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s called[ ] Underfull \vbox (badness 10000) has occurred while \output is active [1158] [1159] [1160] [1161] [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1794--1794 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N umber" method[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1796--1796 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE)) ) # the default[] [1173] [1174] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to []\T1/pcr/m/n/10 insertSource []\T1/ptm/m/n/ 10 can be an ob-ject of class [1175] [1176] [1177] Underfull \hbox (badness 1478) in paragraph at lines 2213--2218 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use []\T1/pcr/m/n/10 where = [1178] [1179] Underfull \hbox (badness 10000) in paragraph at lines 2327--2331 []\T1/ptm/m/n/10 To see the ac-tual ta-ble (an [][][]\T1/pcr/m/n/10 environment [][][][]\T1/ptm/m/n/10 ) used for meth-ods dis-patch, call [1180] [1181] [1182] Underfull \hbox (badness 3792) in paragraph at lines 2573--2576 []\T1/ptm/m/n/10 As you might ex-pect [][][]\T1/pcr/m/n/10 setGeneric[][][] []\ T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 setGroupGeneric[][][] []\T1/ptm/m/n/10 c re-ate ob-jects of class Underfull \hbox (badness 1194) in paragraph at lines 2604--2608 []\T1/ptm/m/n/10 Object of class []\T1/pcr/m/n/10 "optionalMethod" []\T1/ptm/m/ n/10 (a union of classes []\T1/pcr/m/n/10 "function" []\T1/ptm/m/n/10 and [1183] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2660--2660 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin g(where))[] [1184] [1185] [1186] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2879--2879 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers ions visible:[] [1187] [1188] [1189] [1190] [1191] [1192] [1193] Underfull \hbox (badness 10000) in paragraph at lines 3402--3407 []\T1/ptm/m/n/10 Function []\T1/pcr/m/n/10 implicitGeneric() []\T1/ptm/m/n/10 r e-turns the im-plicit generic ver-sion, Underfull \hbox (badness 6268) in paragraph at lines 3402--3407 []\T1/pcr/m/n/10 setGenericImplicit() []\T1/ptm/m/n/10 turns a generic im-plici t, []\T1/pcr/m/n/10 prohibitGeneric() []\T1/ptm/m/n/10 pre-vents [1194] [1195] Underfull \hbox (badness 10000) in paragraph at lines 3530--3534 []\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][][]\T1/pcr/m/n/10 getClass[][][] []\T1/ptm/m/n/10 and the de-scrip-tion of class [1196] Overfull \hbox (14.78088pt too wide) in paragraph at lines 3641--3650 [] [1197] [1198] Underfull \hbox (badness 10000) in paragraph at lines 3761--3762 [] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longit ude = Underfull \hbox (badness 10000) in paragraph at lines 3808--3809 []\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) { [1199] Underfull \hbox (badness 10000) in paragraph at lines 3845--3846 []\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , Underfull \hbox (badness 6157) in paragraph at lines 3907--3911 []\T1/ptm/m/n/10 A call to [][][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) [] \T1/ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to [1200] [1201] [1202] [1203] [1204] [1205] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4312--4312 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char acter(), Overfull \hbox (0.78088pt too wide) in paragraph at lines 4313--4313 [] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac cess,[] [1206] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4370--4370 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w here) [1207] [1208] [1209] Underfull \hbox (badness 2126) in paragraph at lines 4578--4586 []\T1/ptm/m/n/10 For ad-di-tional in-for-ma-tion see doc-u-men-ta-tion for the im-por-tant steps: ([][][]\T1/pcr/m/n/10 setMethod[][][]()[]\T1/ptm/m/n/10 , [1210] [1211] [1212] Underfull \hbox (badness 10000) in paragraph at lines 4815--4824 []\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha t eval-u-ates a call to [1213] [1214] [1215] [1216] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5203--5203 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate inheritance[] [1217] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5231--5231 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli er fails here)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5245--5245 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho d for classB[] Underfull \vbox (badness 10000) has occurred while \output is active [1218] [1219] Underfull \hbox (badness 10000) in paragraph at lines 5363--5364 []\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1220] [1221] Underfull \hbox (badness 3803) in paragraph at lines 5520--5522 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1222] [1223] [1224] Underfull \hbox (badness 1087) in paragraph at lines 5752--5757 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1225] [1226] [1227] [1228] [1229] [1230] Underfull \hbox (badness 10000) in paragraph at lines 6218--6234 []\T1/ptm/m/n/10 The de-fault method for []\T1/pcr/m/n/10 $initialize() []\T1/p tm/m/n/10 is equiv-a-lent to in-vok-ing the method [1231] [1232] Underfull \hbox (badness 1248) in paragraph at lines 6351--6355 []\T1/ptm/m/n/10 Typically, a spe-cial-ized []\T1/pcr/m/n/10 $initialize() []\T 1/ptm/m/n/10 method car-ries out its own com-pu-ta-tions, Underfull \hbox (badness 1960) in paragraph at lines 6351--6355 \T1/ptm/m/n/10 then in-vokes []\T1/pcr/m/n/10 $initFields() []\T1/ptm/m/n/10 to per-form stan-dard ini-tial-iza-tion, as shown in the [1233] Underfull \hbox (badness 4647) in paragraph at lines 6506--6508 []\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func- tion re-turned by [1234] [1235] Underfull \hbox (badness 2875) in paragraph at lines 6655--6664 []\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen se as any S4 class (see Underfull \hbox (badness 1436) in paragraph at lines 6655--6664 [][][]\T1/pcr/m/n/10 setValidity[][][][]\T1/ptm/m/n/10 ). Such meth-ods are of- ten a good idea; they will be called by call-ing [1236] Underfull \vbox (badness 10000) has occurred while \output is active [1237] [1238] [1239] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6981 \aliasA{S4}{S3Part}{S4} [1240] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7017--7017 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement version of as().[] [1241] [1242] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7208--7208 []\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data = datasets::iris)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7212--7212 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con tains = "mlm")[] [1243] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Complex}) has been already used, duplicate ignored \relax l.7237 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Logic}) h as been already used, duplicate ignored \relax l.7239 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) ha s been already used, duplicate ignored \relax l.7240 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7242 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignored \relax l.7243 \aliasA{Summary}{S4groupGeneric}{Summary} Underfull \hbox (badness 2050) in paragraph at lines 7304--7308 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1244] Underfull \hbox (badness 6708) in paragraph at lines 7317--7329 []\T1/pcr/m/n/10 "abs"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sign"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "sqrt"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ceiling"[]\T1/p tm/m/n/10 , []\T1/pcr/m/n/10 "floor"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "trunc" []\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cummax"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 2012) in paragraph at lines 7317--7329 []\T1/pcr/m/n/10 "acosh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "asin"[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 "asinh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "atan"[]\T1/p tm/m/n/10 , []\T1/pcr/m/n/10 "atanh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "exp"[] \T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "expm1"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "c os"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3209) in paragraph at lines 7317--7329 []\T1/pcr/m/n/10 "cosh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cospi"[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 "sin"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sinh"[]\T1/ptm /m/n/10 , []\T1/pcr/m/n/10 "sinpi"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tan"[]\T 1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tanh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tanp i"[]\T1/ptm/m/n/10 , [1245] [1246] Underfull \hbox (badness 1694) in paragraph at lines 7480--7482 []\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t ion ob-ject (see Underfull \hbox (badness 10000) in paragraph at lines 7504--7507 []\T1/ptm/m/n/10 The typ-i-cal user level func-tion is []\T1/pcr/m/n/10 selectS uperClasses() []\T1/ptm/m/n/10 which calls [1247] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7525--7525 []\T1/pcr/m/n/9 selectSuperClasses("C", dropVirtual=TRUE, directOnly=FALSE)# d itto w/o "Root"[] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8630--8630 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact er(), [1261] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8705--8705 [] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class Def =,[] [1262] [1263] [1264] [1265] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8967--8967 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col umn matrices[] [1266] [1267] [1268] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9175--9175 [] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns), "setCount")[] [1269] [1270] [1271] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9437--9437 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo rmal arguments[] [1272] [1273] [1274] [1275] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9745--9745 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre es of freedom[] [1276] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9855--9855 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9866--9866 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] Underfull \hbox (badness 10000) in paragraph at lines 10564--10566 []\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., []\T1/pcr/m/n/10 "functi on" []\T1/ptm/m/n/10 for class Underfull \hbox (badness 1852) in paragraph at lines 10572--10576 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., Underfull \hbox (badness 1681) in paragraph at lines 10572--10576 []\T1/pcr/m/n/10 "functionWithTrace" []\T1/ptm/m/n/10 ex-tends []\T1/pcr/m/n/10 "function"[]\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends [1287] [1288] [1289]) (./parallel-pkg.tex [1290] Chapter 8. Underfull \hbox (badness 2418) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `[]\T1/p cr/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"[]\T1/ptm/m/n/10 ' [][] RNG[][][]: see [1291] Underfull \hbox (badness 4242) in paragraph at lines 97--99 []\T1/ptm/m/n/10 a vec-tor for []\T1/pcr/m/n/10 clusterApply []\T1/ptm/m/n/10 a nd []\T1/pcr/m/n/10 clusterApplyLB[]\T1/ptm/m/n/10 , a ma-trix for [1292] [1293] Underfull \hbox (badness 1024) in paragraph at lines 214--217 []\T1/ptm/m/n/10 Two ex-cep-tions: []\T1/pcr/m/n/10 parLapply []\T1/ptm/m/n/10 has ar-gu-ment []\T1/pcr/m/n/10 X []\T1/ptm/m/n/10 not []\T1/pcr/m/n/10 x []\T1 /ptm/m/n/10 for con-sis-tency with [][][]\T1/pcr/m/n/10 lapply[][][][]\T1/ptm/m /n/10 , and [1294] Underfull \hbox (badness 1320) in paragraph at lines 301--304 []\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD, So-laris and Win-dows. [1295] [1296] Underfull \hbox (badness 10000) in paragraph at lines 437--439 []\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for []\T1/pcr/m/ n/10 Rscript []\T1/ptm/m/n/10 such as [1297] [1298] [1299] [1300] [1301] Underfull \hbox (badness 1917) in paragraph at lines 771--780 []\T1/pcr/m/n/10 mcfork []\T1/ptm/m/n/10 re-turns an ob-ject of the class []\T1 /pcr/m/n/10 "childProcess" []\T1/ptm/m/n/10 to the mas-ter and of class Underfull \hbox (badness 1178) in paragraph at lines 771--780 []\T1/pcr/m/n/10 "masterProcess" []\T1/ptm/m/n/10 to the child: both the classe s in-herit from class []\T1/pcr/m/n/10 "process"[]\T1/ptm/m/n/10 . If [1302] Overfull \hbox (60.78088pt too wide) in paragraph at lines 864--864 [] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini ty.list = NULL)[] [1303] [1304] [1305] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1055--1055 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit y.list = affL)[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 1059--1059 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch eduled to suitable CPUs[] [1306] [1307] Underfull \hbox (badness 5388) in paragraph at lines 1174--1179 []\T1/pcr/m/n/10 mcparallel []\T1/ptm/m/n/10 re-turns an ob-ject of the class [ ]\T1/pcr/m/n/10 "parallelJob" []\T1/ptm/m/n/10 which in-her-its from Underfull \hbox (badness 10000) in paragraph at lines 1198--1206 []\T1/ptm/m/n/10 The be-haviour with []\T1/pcr/m/n/10 mc.set.seed = TRUE []\T1/ ptm/m/n/10 is dif-fer-ent only if [1308] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1235--1235 []\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[] [1309] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1351--1351 [] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif (N, 1, 28)))[] [1310] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1365--1365 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format = "%Y-%m-%d")))[] Underfull \hbox (badness 1577) in paragraph at lines 1394--1397 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by []\T1/pcr/m/n/10 .Random.seed []\T1/ptm/m/n/10 when the [1311] Underfull \hbox (badness 3375) in paragraph at lines 1441--1443 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 nextRNGStream []\T1/ptm/m/n/10 and []\T1/ pcr/m/n/10 nextRNGSubStream[]\T1/ptm/m/n/10 , a value which can be as-signed to [1312] [1313]) (./splines-pkg.tex [1314] Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1315] [1316] [1317] [1318] [1319] [1320] [1321] [1322] Overfull \hbox (4.38043pt too wide) in paragraph at lines 499--499 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl ine = TRUE))[] [1323] Underfull \hbox (badness 1043) in paragraph at lines 600--602 []\T1/ptm/m/n/10 An in-te-ger be-tween 0 and []\T1/pcr/m/n/10 splineOrder(objec t) - 1 []\T1/ptm/m/n/10 spec-i-fy-ing the [1324] [1325] Overfull \hbox (25.98041pt too wide) in paragraph at lines 715--715 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, sparse = TRUE)))[] [1326] [1327] [1328]) (./stats-pkg.tex Chapter 10. [1329] Underfull \hbox (badness 1077) in paragraph at lines 71--74 []\T1/pcr/m/n/10 .MFclass() []\T1/ptm/m/n/10 re-turns a char-ac-ter string, one of []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ordered"[]\T 1/ptm/m/n/10 , []\T1/pcr/m/n/10 "factor"[]\T1/ptm/m/n/10 , Overfull \hbox (69.18036pt too wide) in paragraph at lines 91--91 []\T1/pcr/m/n/9 (xl <- .getXlevels(terms(mf), mf)) # a list with one entry " $ Species" with 3 levels:[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 94--94 [] \T1/pcr/m/n/9 identical(.getXlevels(terms(mc), mc), xl[0]) # a empty named list, as no factors[] [1330] [1331] [1332] [1333] [1334] Overfull \hbox (20.58041pt too wide) in paragraph at lines 445--445 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea rson Chi-square[] [1335] Overfull \hbox (6.78088pt too wide) in paragraph at lines 468--468 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = FALSE) [1336] [1337] [1338] [1339] [1340] [1341] Underfull \hbox (badness 1024) in paragraph at lines 901--903 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from []\T1/pcr/m/n/10 l m []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 aov[]\T1/ptm/m/n/10 , or a for-mula for [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1640--1640 [] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm = TRUE)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1643--1643 [] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm = TRUE)[] [1354] [1355] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1790--1790 [] \T1/pcr/m/n/9 approx(xn, yn, xout=xout, method=M, rule=R, n a.rm=na.)$y),[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1802--1802 []\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$y) # warning, can be avoided by specifying \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ties=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[ ] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2820--2820 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F ALSE) [1371] [1372] [1373] [1374] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3068--3068 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co l = "green")[] [1375] [1376] [1377] Underfull \hbox (badness 10000) in paragraph at lines 3279--3281 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Bartlett test of homo geneity of [1378] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3328--3328 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3329--3329 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1379] [1380] [1381] [1382] Package amsmath Warning: Foreign command \atopwithdelims; (amsmath) \frac or \genfrac should be used instead (amsmath) on input line 3658. [1383] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3724--3724 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = " log density",[] [1384] [1385] [1386] [1387] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4003--4003 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0) [1388] [1389] [1390] [1391] [1392] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4292--4292 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4293--4293 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1393] [1394] [1395] [1396] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4534--4534 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1397] [1398] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4709--4709 [] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df = df, ncp = L)),[] [1399] [1400] Underfull \hbox (badness 3989) in paragraph at lines 4803--4810 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1401] [1402] [1403] [1404] [1405] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5192--5192 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1)) , ci = c(-1,-1))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5194--5194 []\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci = c(-0.9,0.1))[] [1406] [1407] [1408] [1409] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5416--5416 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works with these :[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5434--5434 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter")) [1410] [1411] [1412] Underfull \hbox (badness 1436) in paragraph at lines 5644--5649 []\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i ng co-vari-ances Underfull \hbox (badness 1377) in paragraph at lines 5644--5649 \T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi -a-tion of) Underfull \hbox (badness 1448) in paragraph at lines 5644--5649 \T1/ptm/m/n/10 one of the strings []\T1/pcr/m/n/10 "everything"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "all.obs"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "complete.obs" []\T1/ptm/m/n/10 , [1413] [1414] Underfull \vbox (badness 10000) has occurred while \output is active [1415] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5847--5847 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1416] [1417] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6014--6014 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE, [1418] [1419] [1420] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6199--6199 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL) [1421] [1422] Overfull \hbox (84.78088pt too wide) in paragraph at lines 6307--6307 []\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en v = parent.frame())[] [1423] [1424] [1425] [1426] Underfull \hbox (badness 5954) in paragraph at lines 6570--6572 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1427] Underfull \hbox (badness 2503) in paragraph at lines 6652--6655 []\T1/ptm/m/n/10 Objects of class []\T1/pcr/m/n/10 "hclust" []\T1/ptm/m/n/10 ca n be con-verted to class []\T1/pcr/m/n/10 "dendrogram" []\T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 5563) in paragraph at lines 6656--6658 []\T1/pcr/m/n/10 rev.dendrogram []\T1/ptm/m/n/10 sim-ply re-turns the den-dro-g ram []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 with re-versed nodes, see also Underfull \hbox (badness 1655) in paragraph at lines 6659--6664 \T1/ptm/m/n/10 has []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 y [ ]\T1/ptm/m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be- fore \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.1.2, [1428] Underfull \hbox (badness 7238) in paragraph at lines 6695--6698 [][][]\T1/pcr/m/n/10 dendrapply[][][] []\T1/ptm/m/n/10 for ap-ply-ing a func-ti on to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][][]\T1/pcr/m/n/10 order.dend rogram[][][] []\T1/ptm/m/n/10 and Overfull \hbox (4.38043pt too wide) in paragraph at lines 6707--6707 []\T1/pcr/m/n/9 str(dend1, max.level = 2, last.str = "\TS1/pcr/m/n/9 '\T1/pcr /m/n/9 ") # only the first two sub-levels[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6730--6730 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, type = "tr")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6745--6745 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] [1429] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6760--6760 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h oriz = TRUE)[] [1430] [1431] [1432] Underfull \vbox (badness 10000) has occurred while \output is active [1433] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7028--7028 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] [1434] [1435] Underfull \vbox (badness 10000) has occurred while \output is active [1436] [1437] [1438] [1439] Underfull \hbox (badness 10000) in paragraph at lines 7428--7432 []\T1/pcr/m/n/10 "maximum"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "manhattan"[]\T1/ ptm/m/n/10 , []\T1/pcr/m/n/10 "canberra"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "bi nary" []\T1/ptm/m/n/10 or [1440] Underfull \hbox (badness 6493) in paragraph at lines 7531--7534 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][][] \T1/pcr/m/n/10 dist[][][]()[]\T1/ptm/m/n/10 , the [1441] [1442] Underfull \hbox (badness 10000) in paragraph at lines 7668--7671 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht tps : / / CRAN . R-[]project . org / view = [1443] [1444] [1445] [1446] [1447] [1448] Underfull \hbox (badness 10000) in paragraph at lines 8080--8085 []\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences [] \T1/pcr/m/n/10 x[t][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 x[t-1][]\T1/ptm/m/n/10 , ..., [1449] [1450] [1451] [1452] [1453] [1454] Underfull \hbox (badness 1210) in paragraph at lines 8435--8437 []\T1/ptm/m/n/10 Components of []\T1/pcr/m/n/10 control []\T1/ptm/m/n/10 can al so be sup-plied as named ar-gu-ments to [1455] [1456] [1457] [1458] [1459] [1460] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8901--8901 []\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q uasipoisson())[] [1461] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8946--8946 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link = "log")) # fails[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 8949--8949 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit "), start = c(0,1))[] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9529--9529 [] \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4 0k", "> 40k"),[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 9530--9530 [] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod erateS", "VeryS")))[] [1470] [1471] [1472] Underfull \hbox (badness 7291) in paragraph at lines 9709--9711 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Fligner-Killeen test of homogeneity of [1473] [1474] [1475] [1476] [1477] [1478] [1479] Underfull \hbox (badness 6944) in paragraph at lines 10201--10207 [][][]\T1/pcr/m/n/10 ftable.formula[][][] []\T1/ptm/m/n/10 for the for-mula in- ter-face (which al-lows a []\T1/pcr/m/n/10 data = . []\T1/ptm/m/n/10 ar-gu-ment ); [1480] [1481] [1482] Underfull \hbox (badness 3758) in paragraph at lines 10415--10418 []\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or [1483] [1484] [1485] [1486] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10659--10659 [] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL , ...)[] Underfull \hbox (badness 4518) in paragraph at lines 10685--10690 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1487] Underfull \hbox (badness 4132) in paragraph at lines 10724--10728 []\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth od Underfull \hbox (badness 1112) in paragraph at lines 10778--10784 []\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form []\T1/pcr/m/n/10 first:second []\T1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak- [1488] Underfull \hbox (badness 10000) in paragraph at lines 10829--10832 []\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][][]\T1/pcr/m/n/10 coeffic ients[][][][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 effects[]\T1/ptm/m/n/10 , []\T1/ pcr/m/n/10 fitted.values []\T1/ptm/m/n/10 and [1489] [1490] [1491] Underfull \hbox (badness 2142) in paragraph at lines 11046--11049 []\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1 0 dev \OMS/cmsy/m/n/10 ^^@ [1492] Underfull \hbox (badness 1708) in paragraph at lines 11127--11131 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1493] Underfull \hbox (badness 10000) in paragraph at lines 11169--11175 [][][]\T1/pcr/m/n/10 glm[][][] []\T1/ptm/m/n/10 for com-put-ing []\T1/pcr/m/n/1 0 glm.obj[]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 anova.glm[][][][]\T1/ptm/m/n/1 0 ; the cor-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions, Underfull \hbox (badness 1418) in paragraph at lines 11207--11212 []\T1/pcr/m/n/10 "average" []\T1/ptm/m/n/10 (= UP-GMA), []\T1/pcr/m/n/10 "mcqui tty" []\T1/ptm/m/n/10 (= WPGMA), []\T1/pcr/m/n/10 "median" []\T1/ptm/m/n/10 (= [1494] [1495] Underfull \hbox (badness 2635) in paragraph at lines 11340--11343 \T1/ptm/m/n/10 There are [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/n/10 , [][ ][]\T1/pcr/m/n/10 plot[][][] []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 identify []\ T1/ptm/m/n/10 (see [][][]\T1/pcr/m/n/10 identify.hclust[][][][]\T1/ptm/m/n/10 ) meth-ods and the [1496] [1497] [1498] Underfull \hbox (badness 1694) in paragraph at lines 11523--11526 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1499] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11621--11621 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col SideColors = cc,[] [1500] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11654--11654 [] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 0.1),[] Underfull \hbox (badness 10000) in paragraph at lines 11667--11671 []\T1/ptm/m/n/10 Character string to se-lect an []\T1/pcr/m/n/10 "additive" []\ T1/ptm/m/n/10 (the de-fault) or [1501] [1502] [1503] [1504] [1505] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11989--11989 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] [1506] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.12004 \aliasA{hat}{influence.measures}{hat} Overfull \hbox (0.78088pt too wide) in paragraph at lines 12064--12064 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] [1507] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12076--12076 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] Underfull \hbox (badness 1062) in paragraph at lines 12129--12134 []\T1/ptm/m/n/10 The op-tional []\T1/pcr/m/n/10 infl[]\T1/ptm/m/n/10 , []\T1/pc r/m/n/10 res []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 sd []\T1/ptm/m/n/10 ar-gu-me nts are there to en-cour-age the use of these di- Underfull \hbox (badness 1052) in paragraph at lines 12146--12148 []\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 hat() []\T1/ptm/m/n/10 ex-ists mainly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1508] [1509] [1510] [1511] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12401--12401 [] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = TRUE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12402--12402 [] \T1/pcr/m/n/10 trace.label = deparse1(substitute(trace.fact or)),[] [1512] [1513] [1514] [1515] [1516] [1517] Underfull \hbox (badness 10000) in paragraph at lines 12749--12751 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][][]\T1/pcr/m/n/10 solve.de fault[][][] []\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 SSinit = Underfull \hbox (badness 4739) in paragraph at lines 12772--12774 []\T1/ptm/m/n/10 the es-ti-mate at time $\OML/cmm/m/it/10 t \OMS/cmsy/m/n/10 ^^ @ \OT1/cmr/m/n/10 1$ \T1/ptm/m/n/10 of the state un-cer-tainty ma-trix $\OML/cm m/m/it/10 Q$ \T1/ptm/m/n/10 (not up-dated by [1518] [1519] [1520] [1521] [1522] Underfull \hbox (badness 3417) in paragraph at lines 13079--13081 []\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class []\T1/pcr/ m/n/10 "kmeans"[]\T1/ptm/m/n/10 , typ-i-cally the re-sult []\T1/pcr/m/n/10 ob [ ]\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 ob <- Underfull \hbox (badness 2894) in paragraph at lines 13085--13089 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method Underfull \hbox (badness 1038) in paragraph at lines 13085--13089 \T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 "Hartigan-Wong"[]\T1/ptm/m/n/10 ): if pos-i-ti ve (or true), trac-ing in-for-ma-tion on the [1523] [1524] [1525] [1526] [1527] [1528] Underfull \hbox (badness 1496) in paragraph at lines 13508--13514 []\T1/ptm/m/n/10 Gunar Schröer and Di-et-rich Tren-kler (1995). Ex-act and Ran- dom-iza-tion Dis-tri-bu-tions of [1529] [1530] [1531] [1532] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13757--13757 []\T1/pcr/m/n/9 lag.plot(sqrt(sunspots), set.lags = c(1:4, 9:12), pch = ".", c ol = "gold")[] [1533] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13858--13858 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep t", "slope"))[] [1534] Underfull \hbox (badness 4518) in paragraph at lines 13906--13911 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1535] [1536] [1537] Underfull \hbox (badness 10000) in paragraph at lines 14107--14111 []\T1/ptm/m/n/10 More []\T1/pcr/m/n/10 lm() []\T1/ptm/m/n/10 ex-am-ples are ava il-able e.g., in [][][]\T1/pcr/m/n/10 anscombe[][][][]\T1/ptm/m/n/10 , [][][]\T 1/pcr/m/n/10 attitude[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 freeny[][][] []\T1/ptm/m/n/10 , [1538] [1539] [1540] [1541] [1542] Underfull \hbox (badness 1163) in paragraph at lines 14446--14454 \T1/ptm/m/n/10 els, [][][]\T1/pcr/m/n/10 influence[][][] []\T1/ptm/m/n/10 (etc on that page) for re-gres-sion di-ag-nos-tics, [][][]\T1/pcr/m/n/10 weighted.re siduals[][][][]\T1/ptm/m/n/10 , [1543] [1544] Underfull \hbox (badness 4518) in paragraph at lines 14566--14571 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1545] [1546] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14754--14754 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14755--14755 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1547] [1548] [1549] [1550] [1551] Overfull \hbox (6.78088pt too wide) in paragraph at lines 15098--15098 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 15099--15099 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1552] [1553] Overfull \hbox (18.78088pt too wide) in paragraph at lines 15192--15192 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra nge(x))) [1554] [1555] [1556] [1557] [1558] [1559] Underfull \hbox (badness 2726) in paragraph at lines 15601--15604 []\T1/ptm/m/n/10 character; one of []\T1/pcr/m/n/10 "logit"[]\T1/ptm/m/n/10 , [ ]\T1/pcr/m/n/10 "probit"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cauchit"[]\T1/ptm/ m/n/10 , []\T1/pcr/m/n/10 "cloglog"[]\T1/ptm/m/n/10 , [1560] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15695--15695 []\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i n R <= 3.5.0[] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] Overfull \hbox (31.3804pt too wide) in paragraph at lines 16324--16324 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc gp, data = esoph) [1571] [1572] Underfull \hbox (badness 1490) in paragraph at lines 16471--16476 \T1/ptm/m/n/10 those spec-i-fied in []\T1/pcr/m/n/10 ... []\T1/ptm/m/n/10 which are re-cy-cled to the num-ber of data frame rows. Un-like [1573] Underfull \hbox (badness 1648) in paragraph at lines 16539--16541 []\T1/ptm/m/n/10 a data frame cre-ated with [][][]\T1/pcr/m/n/10 model.frame[][ ][][]\T1/ptm/m/n/10 . If an-other sort of ob-ject, [1574] Overfull \hbox (36.7804pt too wide) in paragraph at lines 16624--16624 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts.arg = list(a = "contr.sum" , b = contr.poly))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16625--16625 []\T1/pcr/m/n/9 m.orth <- model.matrix(~a+b, dd, contrasts.arg = list(a = "con tr.helmert"))[] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17182--17182 []\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3)) # does not affect objects with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[] [1584] [1585] [1586] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17414--17414 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, s, prob = 0.4)),[] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] Underfull \vbox (badness 10000) has occurred while \output is active [1597] Overfull \hbox (42.18039pt too wide) in paragraph at lines 18136--18136 []\T1/pcr/m/n/9 ## adjusting the convergence test by adding \TS1/pcr/m/n/9 '\T 1/pcr/m/n/9 scaleOffset\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 to its denominator RSS:[] Underfull \vbox (badness 10000) has occurred while \output is active [1598] Overfull \hbox (74.58035pt too wide) in paragraph at lines 18154--18154 []\T1/pcr/m/n/9 ## Here, requiring close convergence, must use more accurate n umerical differentiation,[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 18155--18155 []\T1/pcr/m/n/9 ## as this typically gives Error: "step factor .. reduced belo w \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 minFactor\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 .."[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 18159--18159 []\T1/pcr/m/n/9 ## central differencing works here typically (PR#18165: not co nverging on *some*):[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18160--18160 []\T1/pcr/m/n/9 ctr2 <- nls.control(nDcentral=TRUE, tol = 8e-8, # <- even smal ler than above[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 18163--18163 [] \T1/pcr/m/n/9 (grepl("^aarch64.*linux", R.version$platform) && grepl ("^NixOS", osVersion)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18195--18195 [] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21 ), th = b[1]))[] [1599] [1600] [1601] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18371--18371 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi ty), DNase.2)[] [1602] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18418--18418 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18465--18465 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1603] [1604] [1605] [1606] Overfull \hbox (102.78088pt too wide) in paragraph at lines 18678--18678 [] \T1/pcr/m/n/10 eps = .Machine$double.eps ^ (1/if(central) 3 els e 2), central = FALSE)[] [1607] [1608] [1609] [1610] [1611] Underfull \hbox (badness 1248) in paragraph at lines 18993--18996 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 1661) in paragraph at lines 19006--19010 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 1478) in paragraph at lines 19014--19018 \T1/ptm/m/n/10 if []\T1/pcr/m/n/10 control$trace []\T1/ptm/m/n/10 is pos-i-tive . De-faults to ev-ery 10 it-er-a-tions for []\T1/pcr/m/n/10 "BFGS" []\T1/ptm/m/ n/10 and [1612] Underfull \hbox (badness 2042) in paragraph at lines 19072--19074 []\T1/ptm/m/n/10 indicates an er-ror from the []\T1/pcr/m/n/10 "L-BFGS-B" []\T1 /ptm/m/n/10 method; see com-po-nent [1613] Overfull \hbox (15.18042pt too wide) in paragraph at lines 19178--19178 [] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no t* at boundary[] [1614] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19221--19221 [] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", axes = FALSE)[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 19239--19239 []\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 19242--19242 []\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 19262--19262 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max (interval), [1615] Overfull \hbox (36.78088pt too wide) in paragraph at lines 19265--19265 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max (interval),[] Underfull \hbox (badness 2564) in paragraph at lines 19300--19311 []\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 f []\T1/ptm/m/n/10 is never eva l-u-ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m /n/10 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/ 10 tol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 , Underfull \hbox (badness 1082) in paragraph at lines 19300--19311 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately []\T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) []\T1/ptm/m/n/10 and $\OML /cmm/m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa [1616] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19363--19363 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1617] [1618] [1619] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19590--19590 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 1, lty = 1:6,[] [1620] [1621] Underfull \hbox (badness 1337) in paragraph at lines 19701--19704 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1622] [1623] [1624] [1625] [1626] Overfull \hbox (0.78088pt too wide) in paragraph at lines 20020--20020 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1627] [1628] Overfull \hbox (24.78088pt too wide) in paragraph at lines 20108--20108 [] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist vs Leverage* " * h[ii] / (1 - h[ii]))),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 20110--20110 [] \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else points,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20112--20112 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1629] Underfull \hbox (badness 10000) in paragraph at lines 20172--20178 \T1/pcr/m/n/10 "bottomleft", legend = "Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s di stance", lty = cook.lty, Underfull \hbox (badness 10000) in paragraph at lines 20172--20178 \T1/pcr/m/n/10 col = cook.col, text.col = cook.col, bty = "n", x.intersp Underfull \hbox (badness 10000) in paragraph at lines 20180--20186 []\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment []\T 1/pcr/m/n/10 iter []\T1/ptm/m/n/10 in Underfull \hbox (badness 10000) in paragraph at lines 20191--20194 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 1 or 2, to be used in []\T1/pcr/m /n/10 ylim <- [1630] [1631] [1632] [1633] [1634] Overfull \hbox (0.78088pt too wide) in paragraph at lines 20500--20500 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] Underfull \hbox (badness 1194) in paragraph at lines 20510--20513 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1635] Underfull \hbox (badness 1107) in paragraph at lines 20568--20570 []\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate [] \T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . De-faults to [1636] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20623--20623 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange ") # all colors[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 20630--20630 []\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 1, y.intersp = 1)[] [1637] [1638] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20724--20724 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1639] [1640] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20853--20853 [] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no cancellation[] [1641] Underfull \hbox (badness 7740) in paragraph at lines 20916--20918 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Exact Poisson test" [ ]\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 "Comparison of Overfull \hbox (6.78088pt too wide) in paragraph at lines 20964--20964 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) [1642] Underfull \hbox (badness 10000) in paragraph at lines 21020--21022 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 poly(*, simple=TRUE)[]\T1/ptm/m/n/10 , [] \T1/pcr/m/n/10 polym(*, coefs=)[]\T1/ptm/m/n/10 , and [1643] Overfull \hbox (4.38043pt too wide) in paragraph at lines 21057--21057 [] \T1/pcr/m/n/9 zm <- zapsmall(polym ( 1:4, c(1, 4:6), degree = 3)) # or just poly():[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 21062--21062 []\T1/pcr/m/n/9 ## poly(, df) --- used to fail till July 14 (vive la F rance!), 2017:[] [1644] [1645] [1646] [1647] [1648] [1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656] Overfull \hbox (58.38037pt too wide) in paragraph at lines 21917--21917 [] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tolerance = 1e-15)) # e xactly equal typically[] [1657] Underfull \hbox (badness 6859) in paragraph at lines 21984--21991 [][][]\T1/pcr/m/n/10 predict.glm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 p redict.lm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.loess[][][][]\T1 /ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.nls[][][][]\T1/ptm/m/n/10 , [][][]\T 1/pcr/m/n/10 predict.poly[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 21995--22001 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][][]\T1/pcr/m/n/10 predict.ar[ ][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.Arima[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/pcr/m/n/10 predict.arima0[][][][]\T1/ptm/m/n/10 , [1658] [1659] [1660] [1661] [1662] Overfull \hbox (54.78088pt too wide) in paragraph at lines 22283--22283 [] \T1/pcr/m/n/10 rankdeficient = c("warnif", "simple", "non-estim", "N A", "NAwarn"),[] Underfull \hbox (badness 10000) in paragraph at lines 22309--22312 []\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string spec-i-fy-ing what should hap-pen in the Underfull \hbox (badness 10000) in paragraph at lines 22309--22312 \T1/ptm/m/n/10 case of a rank de-fi-cient model, i.e., when []\T1/pcr/m/n/10 ob ject$rank < [1663] Underfull \hbox (badness 5832) in paragraph at lines 22314--22319 \T1/ptm/m/n/10 cases, i.e., vec-tors not in the same pre-dic-tor sub-space as t he Underfull \hbox (badness 8151) in paragraph at lines 22314--22319 \T1/ptm/m/n/10 orig-i-nal data (with tol-er-ance []\T1/pcr/m/n/10 tol[]\T1/ptm/ m/n/10 ). In that case, the non- Underfull \hbox (badness 1184) in paragraph at lines 22314--22319 \T1/ptm/m/n/10 estimable in-dices are also re-turned as at-tribute []\T1/pcr/m/ n/10 "non-estim" []\T1/ptm/m/n/10 (see [1664] [1665] [1666] [1667] [1668] [1669] [1670] Overfull \hbox (48.78088pt too wide) in paragraph at lines 22782--22782 [] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign = TRUE, ...)[] [1671] [1672] [1673] [1674] Overfull \hbox (0.78088pt too wide) in paragraph at lines 23066--23066 [] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x )) &&[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 23067--23067 [] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr(" , "p-v"),[] [1675] [1676] [1677] [1678] [1679] Underfull \hbox (badness 1337) in paragraph at lines 23393--23399 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1680] [1681] [1682] [1683] [1684] Overfull \hbox (15.18042pt too wide) in paragraph at lines 23705--23705 []\T1/pcr/m/n/9 with(d, qqplot(Female, Male, pch = 19, xlim = c(-31, 31), ylim = c(-31, 31),[] [1685] [1686] [1687] [1688] Underfull \hbox (badness 10000) in paragraph at lines 24017--24019 []\T1/ptm/m/n/10 Wicklin, R. (2017) Sam-ple quan-tiles: A com-par-i-son of 9 de f-i-ni-tions; Underfull \hbox (badness 10000) in paragraph at lines 24017--24019 \T1/ptm/m/n/10 SAS Blog. [][]$\T1/pcr/m/n/10 https : / / blogs . sas . com / co ntent / iml / 2017 / 05 / 24 / [1689] Underfull \hbox (badness 10000) in paragraph at lines 24024--24025 []\T1/ptm/m/n/10 Wikipedia: [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . or g / wiki / Quantile # Estimating _ [1690] Overfull \hbox (48.78088pt too wide) in paragraph at lines 24135--24135 [] \T1/pcr/m/n/10 method = c("non.compact", "row.compact", "col.compact" , "compact"),[] [1691] Underfull \hbox (badness 1028) in paragraph at lines 24193--24196 []\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for []\T 1/pcr/m/n/10 write() []\T1/ptm/m/n/10 and [1692] [1693] Underfull \hbox (badness 10000) in paragraph at lines 24308--24311 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1694] Underfull \hbox (badness 7099) in paragraph at lines 24363--24365 []\T1/ptm/m/n/10 This, as [][][]\T1/pcr/m/n/10 reorder[][][]()[]\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [][][]\T1/pcr/m/n/10 factor[][][](x, l evels = [1695] Underfull \hbox (badness 7099) in paragraph at lines 24427--24429 []\T1/ptm/m/n/10 This, as [][][]\T1/pcr/m/n/10 relevel[][][]()[]\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [][][]\T1/pcr/m/n/10 factor[][][](x, l evels = Overfull \hbox (31.3804pt too wide) in paragraph at lines 24462--24462 []\T1/pcr/m/n/9 bymedianR <- with(InsectSprays, reorder(spray, count, median, decreasing=TRUE))[] [1696] [1697] Overfull \hbox (9.78043pt too wide) in paragraph at lines 24538--24538 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")[] [1698] [1699] Overfull \hbox (0.78088pt too wide) in paragraph at lines 24655--24655 []\T1/pcr/m/n/10 # varying = ___, # list / matrix / vector (use with care)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 24656--24656 []\T1/pcr/m/n/10 # v.names = ___, # vector of variable names in long format[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 24657--24657 []\T1/pcr/m/n/10 # timevar, times, # name / values of constructed time variable[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 24658--24658 []\T1/pcr/m/n/10 # idvar, ids) # name / values of constructed id v ariable[] [1700] [1701] Underfull \hbox (badness 10000) in paragraph at lines 24818--24823 [][][]\T1/pcr/m/n/10 stack[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 aperm[] [][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 relist[][][] []\T1/ptm/m/n/10 for r e-shap-ing the re-sult of [][][]\T1/pcr/m/n/10 unlist[][][][]\T1/ptm/m/n/10 . [ ][][]\T1/pcr/m/n/10 xtabs[][][] []\T1/ptm/m/n/10 and Underfull \hbox (badness 2495) in paragraph at lines 24818--24823 [][][]\T1/pcr/m/n/10 as.data.frame.table[][][] []\T1/ptm/m/n/10 for cre-at-ing con-tin-gency ta-bles and con-vert-ing them back to Overfull \hbox (15.18042pt too wide) in paragraph at lines 24829--24829 []\T1/pcr/m/n/9 ## long to wide (direction = "wide") requires idvar and timeva r at a minimum[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 24830--24830 []\T1/pcr/m/n/9 reshape(Indometh, direction = "wide", idvar = "Subject", timev ar = "time")[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 24849--24849 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide ", v.names = "x")[] [1702] [1703] Overfull \hbox (60.78088pt too wide) in paragraph at lines 24953--24953 [] \T1/pcr/m/n/10 na.action = c("+Big_alternate", "-Big_alternate", "na. omit", "fail"),[] Underfull \hbox (badness 1033) in paragraph at lines 24996--25002 \T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/ m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where [1704] Underfull \hbox (badness 10000) in paragraph at lines 25017--25020 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult []\T1/pcr/m/n/10 y = r unmed(x, k) []\T1/ptm/m/n/10 sim-ply has []\T1/pcr/m/n/10 y[j] = [1705] Overfull \hbox (9.78043pt too wide) in paragraph at lines 25099--25099 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi ans Example")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 25128--25128 []\T1/pcr/m/n/9 ## An example with initial NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s - used to fail badly (notably for "Turlach"):[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 25140--25140 []\T1/pcr/m/n/9 matplot(y = cbind(x15, rT15), type = "b", ylim = c(1,9), pch=1 :5, xlab = NA,[] [1706] [1707] [1708] [1709] [1710] [1711] Underfull \vbox (badness 10000) has occurred while \output is active [1712] [1713] Underfull \hbox (badness 6268) in paragraph at lines 25599--25604 [][][]\T1/pcr/m/n/10 SSasympOrig[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 S Sbiexp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSfol[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSfpl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSgo mpertz[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSlogis[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 SSmicmen[][][][]\T1/ptm/m/n/10 , [1714] [1715] [1716] Underfull \hbox (badness 1867) in paragraph at lines 25809--25811 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 25825--25829 []\T1/ptm/m/n/10 where []\T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallba ck = use.fallback) []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 PP Underfull \hbox (badness 10000) in paragraph at lines 25825--25829 \T1/pcr/m/n/10 <- sum(!is.na([][]coef[][][](object))) []\T1/ptm/m/n/10 -- where in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was [1717] Overfull \hbox (20.58041pt too wide) in paragraph at lines 25867--25867 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr om summary(lm1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 25874--25874 []\T1/pcr/m/n/9 stopifnot(all.equal(sigma(fm.DN1), summary(fm.DN1)$sigma, tole rance=1e-15))[] [1718] [1719] [1720] Underfull \hbox (badness 2495) in paragraph at lines 26057--26066 []\T1/ptm/m/n/10 For an in-verse gaus-sian GLM the model as-sumed is $\OML/cmm/ m/it/10 IG\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^V[]; ^^Uw[]\OT1/cmr/m/n/10 )$ \T1 /ptm/m/n/10 (see [][]$\T1/pcr/m/n/10 https : / / en . [1721] [1722] Underfull \hbox (badness 2197) in paragraph at lines 26199--26202 []\T1/pcr/m/n/10 psmirnov []\T1/ptm/m/n/10 gives the dis-tri-bu-tion func-tion, []\T1/pcr/m/n/10 qsmirnov []\T1/ptm/m/n/10 gives the quan-tile func-tion, and Overfull \hbox (24.78088pt too wide) in paragraph at lines 26219--26219 [] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)[] Underfull \hbox (badness 1412) in paragraph at lines 26226--26228 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1723] Overfull \hbox (25.98041pt too wide) in paragraph at lines 26313--26313 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS S"), smooth(x)))[] [1724] Overfull \hbox (84.78088pt too wide) in paragraph at lines 26338--26338 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda = NULL, cv = FALSE, Overfull \hbox (66.78088pt too wide) in paragraph at lines 26341--26341 [] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee p.stuff = FALSE)[] [1725] [1726] [1727] Overfull \hbox (6.78088pt too wide) in paragraph at lines 26576--26576 [] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / t ol) ))[] Underfull \hbox (badness 2547) in paragraph at lines 26580--26586 []\T1/ptm/m/n/10 The de-fault []\T1/pcr/m/n/10 all.knots = FALSE []\T1/ptm/m/n/ 10 and []\T1/pcr/m/n/10 nknots = .nknots.smspl[]\T1/ptm/m/n/10 , en-tails us-in g only [1728] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26627--26627 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi ng splines")[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 26648--26648 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # = = unique(cars$speed)[] Underfull \vbox (badness 10000) has occurred while \output is active [1729] [1730] [1731] Overfull \hbox (0.78088pt too wide) in paragraph at lines 26840--26840 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail, [1732] [1733] [1734] [1735] [1736] [1737] Overfull \hbox (36.78088pt too wide) in paragraph at lines 27220--27220 [] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC" , "hyman"),[] [1738] [1739] Overfull \hbox (69.18036pt too wide) in paragraph at lines 27401--27401 []\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi * x) + rnorm(30)/10, 3)[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 27407--27407 []\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean)) for when x has ties")[] Underfull \vbox (badness 10000) has occurred while \output is active [1740] Overfull \hbox (31.3804pt too wide) in paragraph at lines 27416--27416 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c ol = 3, n = 1001)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 27417--27417 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c ol = 4, n = 1001)[] [1741] Underfull \hbox (badness 2922) in paragraph at lines 27486--27491 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (9.78043pt too wide) in paragraph at lines 27523--27523 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim = c(-.3, 5),[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 27526--27526 [] \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^ {-e^{phi[3]}*~x}}))[] [1742] Overfull \hbox (20.58041pt too wide) in paragraph at lines 27535--27535 [] \T1/pcr/m/n/9 c(0 , 1 ), 1, length = 0.08, angle = 25); text(0. 5, 1, quote(1))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27536--27536 [] \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3 # (Asym + R0)/2[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 27540--27540 [] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi [1]+phi[2],2), phi[1]),[] Underfull \hbox (badness 3240) in paragraph at lines 27594--27597 [][][]\T1/pcr/m/n/10 nls[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 selfStart [][][][]\T1/ptm/m/n/10 ; []\T1/pcr/m/n/10 example(SSasympOff) []\T1/ptm/m/n/10 gives graph show-ing the []\T1/pcr/m/n/10 SSasympOff [1743] Overfull \hbox (36.7804pt too wide) in paragraph at lines 27615--27615 [] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log( 0.4), c0 = 3/4)) )[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27618--27618 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim = c(-1, 8),[] [1744] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27701--27701 [] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log (log(2)))) )[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27705--27705 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim = c(-1/4, 5),[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 27715--27715 [] \T1/pcr/m/n/9 axis(2, at = 5*c(1/2,1), labels= expression(frac(phi[1],2), phi[1]), pos=0, las=1)[] [1745] Overfull \hbox (106.98032pt too wide) in paragraph at lines 27720--27720 [] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] Underfull \hbox (badness 2922) in paragraph at lines 27756--27762 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 27778--27778 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat a = Indo.1),[] [1746] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27794--27794 [] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 1.5 * exp(-x)"),[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 27808--27808 []\T1/pcr/m/n/9 ## Fails by default (scaleOffset=0) on most platforms {also af ter increasing maxiter !}[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27810--27810 [] \T1/pcr/m/n/9 nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d atN, trace=TRUE)[] Overfull \hbox (128.58029pt too wide) in paragraph at lines 27813--27813 []\T1/pcr/m/n/9 fmX1 <- nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d atN, control = list(scaleOffset=1))[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 27815--27815 [] \T1/pcr/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol=1 e-11, nDcentral=TRUE), trace=TRUE)[] [1747] [1748] Overfull \hbox (30.78088pt too wide) in paragraph at lines 27927--27927 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK a)*input)) [1749] Underfull \hbox (badness 2922) in paragraph at lines 27989--27994 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1750] Overfull \hbox (69.18036pt too wide) in paragraph at lines 28027--28027 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm id", phi[4] == "scal")))[] Underfull \hbox (badness 2922) in paragraph at lines 28076--28081 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1751] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28107--28107 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = " red", lwd=2)[] Underfull \hbox (badness 2922) in paragraph at lines 28141--28146 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1752] Overfull \hbox (25.98041pt too wide) in paragraph at lines 28166--28166 []\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number of iter...: 0" :[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 28170--28170 []\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR UE), trace = TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28190--28190 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] == "scal")))[] [1753] Overfull \hbox (20.58041pt too wide) in paragraph at lines 28200--28200 [] \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0, 2.5,3.5), # NB. SSlogis(x = xmid = 2) = 2.5[] Underfull \hbox (badness 2922) in paragraph at lines 28235--28240 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 28257--28257 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt), digits = 3)[] [1754] Overfull \hbox (15.18042pt too wide) in paragraph at lines 28275--28275 [] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS micmen model")[] [1755] Underfull \hbox (badness 6493) in paragraph at lines 28327--28332 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 x[]\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 28355--28355 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28358--28358 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 28361--28361 []\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul l() fit to Chick.6")[] Overfull \hbox (69.18036pt too wide) in paragraph at lines 28364--28364 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f m1)[["Drop"]]), lty = 3)[] [1756] [1757] [1758] [1759] [1760] [1761] [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] Underfull \hbox (badness 3396) in paragraph at lines 29248--29250 []\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.glm"[]\T1/ptm/m/ n/10 , usu-ally, a re-sult of a call to [1770] [1771] [1772] Underfull \hbox (badness 2237) in paragraph at lines 29427--29429 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /pcr/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1773] [1774] Underfull \hbox (badness 2591) in paragraph at lines 29591--29593 []\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.nls"[]\T1/ptm/m/ n/10 , usu-ally the re-sult of a call to [1775] Underfull \hbox (badness 2237) in paragraph at lines 29637--29640 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /pcr/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1776] Overfull \hbox (48.78088pt too wide) in paragraph at lines 29710--29710 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t race = FALSE) [1777] [1778] Underfull \hbox (badness 3407) in paragraph at lines 29819--29823 []\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m ented\T1/ptm/m/n/10 , see []\T1/pcr/m/n/10 corr []\T1/ptm/m/n/10 be-low) [1779] Overfull \hbox (47.58038pt too wide) in paragraph at lines 29889--29889 []\T1/pcr/m/n/9 symnum(ii, cutpoints = 2*(0:4), symbols = c(".", "-", "+", "$ "), show.max = TRUE)[] [1780] Underfull \hbox (badness 1337) in paragraph at lines 29952--29956 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1781] [1782] [1783] [1784] Overfull \hbox (9.78043pt too wide) in paragraph at lines 30219--30219 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, main = t.tit,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30262--30262 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] [1785] Underfull \hbox (badness 1616) in paragraph at lines 30288--30291 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1786] Overfull \hbox (20.58041pt too wide) in paragraph at lines 30367--30367 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1787] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30445--30445 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1788] [1789] Underfull \hbox (badness 2205) in paragraph at lines 30540--30545 []\T1/ptm/m/n/10 If a []\T1/pcr/m/n/10 specials []\T1/ptm/m/n/10 ar-gu-ment was given to [][][]\T1/pcr/m/n/10 terms.formula[][][] []\T1/ptm/m/n/10 there is a [1790] [1791] Overfull \hbox (12.78088pt too wide) in paragraph at lines 30681--30681 []\T1/pcr/m/n/10 toeplitz2(x, nrow = length(x) +1 - ncol, ncol = length(x) +1 - nrow)[] Underfull \hbox (badness 2913) in paragraph at lines 30687--30691 []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 toeplitz(x, *)[]\T1/ptm/m/n/10 : the firs t col-umn of the Toeplitz ma-trix; for [1792] Overfull \hbox (36.7804pt too wide) in paragraph at lines 30724--30724 []\T1/pcr/m/n/9 # Matrix of character (could also have logical, raw, complex . .) {also warning}:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 30737--30737 [] \T1/pcr/m/n/9 colnames(W) <- paste0(",", if(n <= 9) 1:n else c(1:9, lette rs[seq_len(n-9)]))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 30748--30748 []\T1/pcr/m/n/9 y.hat <- W. %*% y # y.hat := smoothed(y) ("mass preserving" -> longer than y)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 30750--30750 []\T1/pcr/m/n/9 plot(x,y, type="b", xlim=c(1,m)); curve(f(x), 1,n, col="gray", lty=2, add=TRUE)[] [1793] Overfull \hbox (30.78088pt too wide) in paragraph at lines 30780--30780 [] \T1/pcr/m/n/10 class = if(nseries > 1) c("mts", "ts", "matrix", "array") else "ts",[] [1794] Underfull \hbox (badness 1655) in paragraph at lines 30858--30861 []\T1/pcr/m/n/10 is.mts(x) []\T1/ptm/m/n/10 tests if an ob-ject []\T1/pcr/m/n/1 0 x []\T1/ptm/m/n/10 is a mul-ti-vari-ate time se-ries, i.e., ful-fills []\T1/p cr/m/n/10 is.ts(x)[]\T1/ptm/m/n/10 , [1795] [1796] [1797] [1798] [1799] Overfull \hbox (12.78088pt too wide) in paragraph at lines 31222--31222 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE) Overfull \hbox (12.78088pt too wide) in paragraph at lines 31223--31223 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1800] [1801] [1802] [1803] [1804] Overfull \hbox (30.78088pt too wide) in paragraph at lines 31523--31523 [] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con v = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 31524--31524 [] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace = 0)[] [1805] [1806] Overfull \hbox (31.3804pt too wide) in paragraph at lines 31653--31653 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 31662--31662 []\T1/pcr/m/n/9 ## where as \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 simply first enlarges the search interval:[] Underfull \vbox (badness 10000) has occurred while \output is active [1807] [1808] [1809] Underfull \hbox (badness 1337) in paragraph at lines 31879--31883 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1810] [1811] [1812] [1813] [1814] [1815] [1816] [1817] Underfull \hbox (badness 1337) in paragraph at lines 32408--32412 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1818] [1819] [1820] Overfull \hbox (117.7803pt too wide) in paragraph at lines 32616--32616 []\T1/pcr/m/n/9 wilcox.test( 4:2, 3:1, paired=TRUE) # Warning: canno t compute exact p-value with ties[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 32618--32618 []\T1/pcr/m/n/9 wilcox.test((4:2)/10, (3:1)/10, paired=TRUE, digits.rank = 9) # same ties as (4:2, 3:1)[] [1821] [1822] [1823] Overfull \hbox (138.78088pt too wide) in paragraph at lines 32777--32777 [] \T1/pcr/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps = getOption("ts.eps"), ...)[] [1824] Overfull \hbox (0.78088pt too wide) in paragraph at lines 32862--32862 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, [1825] [1826] Overfull \hbox (47.58038pt too wide) in paragraph at lines 32995--32995 []\T1/pcr/m/n/9 ## The Female:Rejected combination has NA \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 Freq\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 (and NA prints \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 invisibly\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 as "")[] [1827]) (./stats4-pkg.tex [1828] Chapter 11. [1829] [1830] [1831] Overfull \hbox (15.18042pt too wide) in paragraph at lines 224--224 [] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf)) , log = TRUE))[] Underfull \vbox (badness 10000) has occurred while \output is active [1832] Overfull \hbox (9.78043pt too wide) in paragraph at lines 278--278 []\T1/pcr/m/n/9 ## Boundary case: This works, but fails if limits are set clos er to 0 and 1[] [1833] [1834] [1835] [1836] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdas h.methods}) has been already used, duplicate ignored \relax l.503 ...Package \pkg{stats4}}{show.Rdash.methods} [1837] [1838] [1839]) (./tcltk-pkg.tex [1840] Chapter 12. [1841] [1842] [1843] [1844] [1845] Overfull \hbox (36.7804pt too wide) in paragraph at lines 360--360 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all.names = TRUE) # .Tcl.args put a ca llback ref in here[] [1846] [1847] Underfull \vbox (badness 10000) has occurred while \output is active [1848] Underfull \hbox (badness 1292) in paragraph at lines 671--678 []\T1/pcr/m/n/10 tcl []\T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-i ng any Tk or Tcl com-mand by sim-ply run-ning Underfull \vbox (badness 1603) has occurred while \output is active [1849] [1850] [1851] [1852] [1853] Underfull \vbox (badness 10000) has occurred while \output is active [1854] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1084--1084 []\T1/pcr/m/n/9 eval.txt <- function() eval(str2lang(tclvalue(tkget(txt.w, "0. 0", "end"))))[] [1855] [1856] [1857] [1858] [1859] Underfull \hbox (badness 1189) in paragraph at lines 1412--1415 [][][]\T1/pcr/m/n/10 select.list[][][] []\T1/ptm/m/n/10 (a text ver-sion ex-cep t on Win-dows and the ma-cOS GUI), [][][]\T1/pcr/m/n/10 menu[][][] []\T1/ptm/m/ n/10 (whose [1860]) (./tools-pkg.tex Chapter 13. [1861] Overfull \hbox (9.78043pt too wide) in paragraph at lines 69--69 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for new methods.[] [1862] Underfull \hbox (badness 1253) in paragraph at lines 167--170 []\T1/pcr/m/n/10 assertWarning() []\T1/ptm/m/n/10 as-serts that a warn-ing will be sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1863] Overfull \hbox (4.38043pt too wide) in paragraph at lines 218--218 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch ing warning)[] [1864] Underfull \hbox (badness 5147) in paragraph at lines 288--301 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 Underfull \hbox (badness 4792) in paragraph at lines 288--301 \T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][][]\T1/pcr/m/n /10 bibentry[][][] []\T1/ptm/m/n/10 as well as sev-eral other rou- Underfull \hbox (badness 2237) in paragraph at lines 288--301 \T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named []\T1/pcr/m/n /10 formatArticle[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 formatBook[]\T1/ptm/m/n/10 , [1865] Overfull \hbox (42.78088pt too wide) in paragraph at lines 373--373 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta ngle = TRUE, Underfull \hbox (badness 2460) in paragraph at lines 392--394 []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gin e to use. Over-rides any [1866] [1867] Underfull \hbox (badness 1142) in paragraph at lines 464--468 \T1/ptm/m/n/10 If given, vi-gnette source files are by de-fault looked for in s ub-di-rec-tory [1868] [1869] [1870] [1871] [1872] [1873] [1874] Overfull \hbox (0.78088pt too wide) in paragraph at lines 921--921 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", " xz"),[] [1875] Overfull \hbox (31.3804pt too wide) in paragraph at lines 976--976 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co mpress == "none")[] [1876] [1877] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1145--1145 [] \T1/pcr/m/n/10 outputs = FALSE, sources = FALS E, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1146--1146 []\T1/pcr/m/n/10 check_packages_in_dir_details(dir, logs = NULL, drop_ok = TRU E, ...)[] [1878] Underfull \hbox (badness 1014) in paragraph at lines 1188--1190 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1194--1196 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous [1879] Underfull \hbox (badness 10000) in paragraph at lines 1231--1234 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us- Underfull \hbox (badness 10000) in paragraph at lines 1231--1234 \T1/ptm/m/n/10 ing []\T1/pcr/m/n/10 summarize_check_packages_in_dir_results []\ T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 1239--1242 []\T1/pcr/m/n/10 check_packages_in_dir []\T1/ptm/m/n/10 re-turns an ob-ject in- her-it-ing from class [1880] [1881] Underfull \hbox (badness 10000) in paragraph at lines 1386--1389 []\T1/pcr/m/n/10 codocClasses []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 codocData [ ]\T1/ptm/m/n/10 re-turn ob-jects of class []\T1/pcr/m/n/10 "codocClasses" []\T1 /ptm/m/n/10 and [1882] [1883] Underfull \hbox (badness 4647) in paragraph at lines 1557--1562 []\T1/pcr/m/n/10 CRAN_package_db() []\T1/ptm/m/n/10 re-turns a data frame with char-ac-ter columns con-tain-ing most Underfull \hbox (badness 7869) in paragraph at lines 1557--1562 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' meta-data for the cu r-rent pack-ages in the CRAN pack-age repos-i- Underfull \hbox (badness 1681) in paragraph at lines 1557--1562 \T1/ptm/m/n/10 tory, in-clud-ing in par-tic-u-lar the De-scrip-tion and Main-ta iner in-for-ma-tion not pro-vided by [1884] Underfull \hbox (badness 2762) in paragraph at lines 1606--1609 []\T1/ptm/m/n/10 Internal func-tions []\T1/pcr/m/n/10 CRAN_aliases_db[]\T1/ptm/ m/n/10 , []\T1/pcr/m/n/10 CRAN_archive_db[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 CR AN_current_db []\T1/ptm/m/n/10 and [1885] [1886] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1718--1718 [] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En hances"))[] Underfull \hbox (badness 7981) in paragraph at lines 1725--1733 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 1725--1733 []\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", Underfull \hbox (badness 1558) in paragraph at lines 1725--1733 \T1/pcr/m/n/10 "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string []\T1/pcr/m/n/1 0 "all" []\T1/ptm/m/n/10 is short-hand for that vec-tor, [1887] [1888] [1889] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.GSC}) has been already used, duplicate ignored \relax l.1937 \aliasA{GSC}{find\_gs\_cmd}{GSC} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSC MD}) has been already used, duplicate ignored \relax l.1938 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1890] [1891] [1892] [1893] Underfull \hbox (badness 1142) in paragraph at lines 2207--2213 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 loadPkgRdMacros []\T1/ptm/m/n/10 func-tio n first looks for an []\T1/pcr/m/n/10 "RdMacros" []\T1/ptm/m/n/10 en-try in the pack-age [1894] Underfull \hbox (badness 2359) in paragraph at lines 2271--2278 []\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user and site spe-cific com-pi-la- Underfull \hbox (badness 1102) in paragraph at lines 2271--2278 \T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1 0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com- Underfull \hbox (badness 4168) in paragraph at lines 2271--2278 \T1/ptm/m/n/10 pi-la-tions in sub-di-rec-to-ries of `\T1/pcr/m/n/10 src\T1/ptm/ m/n/10 '), e.g., by adding con-fig-ure code call-ing \T1/phv/m/n/10 R \T1/ptm/m /n/10 with [1895] Underfull \hbox (badness 1342) in paragraph at lines 2323--2329 \T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in Underfull \hbox (badness 10000) in paragraph at lines 2348--2355 []\T1/pcr/m/n/10 matchConcordance []\T1/ptm/m/n/10 con-verts from out-put lo-ca -tions to source lo-ca-tions. 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[1897] [1898] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2537--2537 []\T1/pcr/m/n/10 package_dependencies(packages = NULL, db = NULL, which = "str ong", Underfull \hbox (badness 7981) in paragraph at lines 2552--2560 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 2552--2560 []\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", Underfull \hbox (badness 1558) in paragraph at lines 2552--2560 \T1/pcr/m/n/10 "Enhances")[]\T1/ptm/m/n/10 . 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Rd"),[] [1904] Underfull \hbox (badness 2486) in paragraph at lines 2950--2958 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion 3.2.0, User-d efined macros may be given in a sep-a-rate file us-ing [1905] [1906] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3162--3162 []\T1/pcr/m/n/10 checkDocFiles (package, dir, lib.loc = NULL, chkInternal = FALSE) [1907] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3166--3166 []\T1/pcr/m/n/10 checkRdContents (package, dir, lib.loc = NULL, chkInternal = FALSE)[] [1908] [1909] [1910] Underfull \hbox (badness 1072) in paragraph at lines 3358--3360 []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec- tor of links, as re-turned by [1911] [1912] [1913] [1914] [1915] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3706--3706 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro s", "system.Rd"))[] Underfull \hbox (badness 5417) in paragraph at lines 3744--3754 []\T1/ptm/m/n/10 By de-fault, the tags \T1/pcr/m/n/10 \S3method\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \S4method\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \command\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \docType\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \email\T1/ptm/m/n/10 , [1916] [1917] [1918] Underfull \hbox (badness 4108) in paragraph at lines 3960--3967 []\T1/ptm/m/n/10 This func-tion starts the in-ter-nal HTTP server, which runs o n the loop-back in-ter-face [1919] [1920] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4060--4060 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 4063--4063 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 4080--4082 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [1921] Underfull \hbox (badness 2932) in paragraph at lines 4097--4103 []\T1/pcr/m/n/10 testInstalledBasic []\T1/ptm/m/n/10 runs the ba-sic tests, if in-stalled. This should be run with [1922] Underfull \hbox (badness 7832) in paragraph at lines 4219--4222 []\T1/ptm/m/n/10 Where sup-ported ([]\T1/pcr/m/n/10 texi2dvi []\T1/ptm/m/n/10 5 .0 and later; []\T1/pcr/m/n/10 texify.exe []\T1/ptm/m/n/10 from MiK-TeX), op-ti on [1923] [1924] [1925] [1926] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4454--4454 [] \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry run),[] [1927] [1928] Overfull \hbox (96.78088pt too wide) in paragraph at lines 4616--4616 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, mergeOpts = "", copyright, bugs) Underfull \hbox (badness 3118) in paragraph at lines 4627--4631 []\T1/ptm/m/n/10 a string, by de-fault empty, of op-tions to []\T1/pcr/m/n/10 m sgmerge []\T1/ptm/m/n/10 in ad-di-tion to Underfull \hbox (badness 10000) in paragraph at lines 4631--4634 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `[]\T1/pcr/m/n/10 Copyrig ht[]\T1/ptm/m/n/10 ' and [1929] Underfull \hbox (badness 6859) in paragraph at lines 4647--4652 []\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory []\T1/pcr/m/n/10 po []\T1/ ptm/m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\ T1/ptm/m/n/10 ' are up-dated from Underfull \hbox (badness 1184) in paragraph at lines 4655--4661 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po /\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T he Underfull \hbox (badness 2941) in paragraph at lines 4655--4661 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t he pack-age are ex-am-ined to cre-ate a file [1930] [1931] [1932] Underfull \hbox (badness 10000) in paragraph at lines 4889--4891 []\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 vignetteEngine[][][][]\T1/ptm/m/n/10 , such as []\T1/pcr/m/n/10 "utils::Sweave" []\T1/ptm/m/n/10 or [1933] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4918--4918 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4919--4919 [] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr ess = "xz",[] Underfull \hbox (badness 3240) in paragraph at lines 4932--4935 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T 1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ', Underfull \hbox (badness 1742) in paragraph at lines 4936--4946 []\T1/pcr/m/n/10 "Package"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Version"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "Priority"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Depe nds"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Imports"[]\T1/ptm/m/n/10 , [1934] Underfull \hbox (badness 1127) in paragraph at lines 4974--4980 []\T1/pcr/m/n/10 write_PACKAGES []\T1/ptm/m/n/10 scans the named di-rec-tory fo r R pack-ages, ex-tracts in-for-ma-tion from Underfull \hbox (badness 1635) in paragraph at lines 4974--4980 \T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file , and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1 0 ', Underfull \hbox (badness 1571) in paragraph at lines 5002--5006 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by Underfull \hbox (badness 2772) in paragraph at lines 5028--5033 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 PACKAGES.gz\T1/ptm/m/n/10 ' files. See [][][ ]\T1/pcr/m/n/10 update_PACKAGES[][][] []\T1/ptm/m/n/10 for ef-fi-ciently up-dat -ing ex-ist-ing [1935] [1936] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5170--5170 []\T1/pcr/m/n/9 xgettext(tmpPkg, asCall=TRUE )[[1]] # default; shows \TS1/pcr /m/n/9 ' \T1/pcr/m/n/9 sqrt(as.complex(x)) \TS1/pcr/m/n/9 '[] [1937]) (./utils-pkg.tex [1938] Chapter 14. Underfull \hbox (badness 1072) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[] \T1/pcr/m/n/10 insertions[]\T1/ptm/m/n/10 ', [1939] [1940] [1941] [1942] Overfull \hbox (4.38043pt too wide) in paragraph at lines 261--261 []\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with these names[] [1943] [1944] Underfull \hbox (badness 10000) in paragraph at lines 381--386 \T1/ptm/m/n/10 are []\T1/pcr/m/n/10 c("vertical", "horizontal", "cascade", "min imize", Underfull \hbox (badness 10000) in paragraph at lines 387--389 []\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 list[][][] []\T1/ptm/m/n/10 of win-dow han-dles, by de-fault pro-duced by [1945] Overfull \hbox (9.78043pt too wide) in paragraph at lines 453--453 []\T1/pcr/m/n/9 # This default is useful only in SDI mode: it will tile any F irefox window[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 455--455 []\T1/pcr/m/n/9 .arrangeWindowsDefaults <- list(c("R", "all"), pattern = c("", "Firefox"))[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 472--472 [] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No ", "Cancel"))),[] [1946] [1947] [1948] Overfull \hbox (0.78088pt too wide) in paragraph at lines 686--686 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc es"), Overfull \hbox (6.78088pt too wide) in paragraph at lines 692--692 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 693--693 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 694--694 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 695--695 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] [1949] Underfull \hbox (badness 10000) in paragraph at lines 729--735 []\T1/ptm/m/n/10 Functions []\T1/pcr/m/n/10 aspell_package_Rd_files[]\T1/ptm/m/ n/10 , []\T1/pcr/m/n/10 aspell_package_vignettes[]\T1/ptm/m/n/10 , Underfull \hbox (badness 4416) in paragraph at lines 729--735 []\T1/pcr/m/n/10 aspell_package_R_files []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 a spell_package_C_files []\T1/ptm/m/n/10 per-form spell check- [1950] [1951] [1952] [1953] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1053--1053 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL, [1954] Underfull \hbox (badness 7649) in paragraph at lines 1127--1133 [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 in-di-cat-ing if Bib-TeX co de should be given ad-di-tion-ally; Underfull \hbox (badness 5533) in paragraph at lines 1127--1133 \T1/ptm/m/n/10 cur-rently ap-plies only to []\T1/pcr/m/n/10 style = "citation"[ ]\T1/ptm/m/n/10 . The de-fault for Underfull \hbox (badness 4739) in paragraph at lines 1127--1133 \T1/ptm/m/n/10 the []\T1/pcr/m/n/10 print() []\T1/ptm/m/n/10 method de-pends on the num-ber of (bib) en-tries and Underfull \hbox (badness 1817) in paragraph at lines 1127--1133 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 1136--1138 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1955] [1956] Underfull \hbox (badness 10000) in paragraph at lines 1255--1258 []\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Digital _ Object _ [1957] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1338--1338 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] Underfull \vbox (badness 10000) has occurred while \output is active [1958] [1959] [1960] [1961] [1962] [1963] Underfull \hbox (badness 1859) in paragraph at lines 1747--1756 []\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b e quite large the com- Underfull \hbox (badness 2042) in paragraph at lines 1747--1756 \T1/ptm/m/n/10 mand []\T1/pcr/m/n/10 data.frame(x, y, z, monday, tuesday) []\T1 /ptm/m/n/10 never re-turns. Do not re-port that [1964] [1965] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1852--1852 [] \T1/pcr/m/n/9 data = infert, family = b inomial())))[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 1887--1887 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b efore$timestamp,[] [1966] [1967] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2033--2033 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp" ), md5sum=TRUE)[] [1968] Underfull \hbox (badness 2277) in paragraph at lines 2102--2107 []\T1/pcr/m/n/10 charClass []\T1/ptm/m/n/10 was added in \T1/phv/m/n/10 R \T1/p tm/m/n/10 4.1.0. A less di-rect way to ex-am-ine char-ac-ter classes [1969] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2134--2134 []\T1/pcr/m/n/9 cl <- c("alnum", "alpha", "blank", "digit", "graph", "punct", "upper", "xdigit")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2136--2136 []\T1/pcr/m/n/9 X <- as.data.frame(X); row.names(X) <- sQuote(intToUtf8(x, mul tiple = TRUE))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2144--2144 []\T1/pcr/m/n/9 ## How many printable characters are there? (Around 280,000 in Unicode 13.)[] [1970] [1971] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2292--2292 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind = NULL, [1972] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2344--2344 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind = NULL, [1973] Underfull \hbox (badness 1117) in paragraph at lines 2459--2466 []\T1/ptm/m/n/10 If the ob-ject re-turned by []\T1/pcr/m/n/10 citation() []\T1/ ptm/m/n/10 con-tains only one ref-er-ence, the as-so-ci-ated print Underfull \hbox (badness 1400) in paragraph at lines 2459--2466 \T1/ptm/m/n/10 method shows both a text ver-sion and a Bib-TeX en-try for it. I f a pack-age has more [1974] [1975] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2542--2542 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after = NULL,[] [1976] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2662--2662 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1977] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2702--2702 []\T1/pcr/m/n/10 citEntry(entry, textVersion = NULL, header = NULL, footer = N ULL, ...) Underfull \hbox (badness 1082) in paragraph at lines 2731--2735 [][][]\T1/pcr/m/n/10 citation[][][] []\T1/ptm/m/n/10 for more in-for-ma-tion ab out cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file s; [1978] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard }) has been already used, duplicate ignored \relax l.2736 ... the Clipboard in MS Windows}{clipboard} Underfull \hbox (badness 1163) in paragraph at lines 2767--2769 []\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats: see e.g. [][]$\T1/pcr/m/n/10 https : / / docs . [1979] [1980] Underfull \hbox (badness 10000) in paragraph at lines 2860--2862 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [1981] [1982] [1983] Underfull \hbox (badness 10000) in paragraph at lines 3078--3080 []\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see [1984] [1985] [1986] [1987] Underfull \hbox (badness 1762) in paragraph at lines 3371--3374 []\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re c-tory of the cur-rent work-ing di-rec-tory, set []\T1/pcr/m/n/10 package = [1988] Overfull \hbox (63.78036pt too wide) in paragraph at lines 3463--3463 []\T1/pcr/m/n/9 try(data(package = "rpart"), silent = TRUE) # list the data se ts in the rpart package[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3464--3464 []\T1/pcr/m/n/9 data(USArrests, "VADeaths") # load the data sets \TS1/pcr/m /n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] [1989] Underfull \hbox (badness 2452) in paragraph at lines 3538--3541 []\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class []\ T1/pcr/m/n/10 R_dataentry[]\T1/ptm/m/n/10 . Re-sources [1990] [1991] [1992] [1993] [1994] [1995] Overfull \hbox (74.58035pt too wide) in paragraph at lines 3967--3967 [] \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf orm$r_arch, "stats.dll"))[] [1996] Underfull \hbox (badness 4779) in paragraph at lines 4046--4051 []\T1/ptm/m/n/10 Support for method []\T1/pcr/m/n/10 "libcurl" []\T1/ptm/m/n/10 was op-tional on Win-dows prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0: use [1997] Underfull \hbox (badness 1072) in paragraph at lines 4109--4113 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the []\T1/pcr/m/n/10 quiet []\T1/ptm/m/n/10 ar-gu-ment and the [1998] Underfull \hbox (badness 7238) in paragraph at lines 4165--4170 []\T1/ptm/m/n/10 For the []\T1/pcr/m/n/10 "libcurl" []\T1/ptm/m/n/10 and []\T1/ pcr/m/n/10 "curl" []\T1/ptm/m/n/10 meth-ods, prox-ies can be set \T1/ptm/m/it/1 0 via \T1/ptm/m/n/10 the en-vi-ron- Underfull \hbox (badness 1337) in paragraph at lines 4165--4170 \T1/ptm/m/n/10 ment vari-ables []\T1/pcr/m/n/10 http_proxy []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 ftp_proxy[]\T1/ptm/m/n/10 . See [][]$\T1/pcr/m/n/10 https : / / curl . se / libcurl / c / Underfull \hbox (badness 1184) in paragraph at lines 4180--4196 \T1/ptm/m/n/10 string con-tain-ing `[]\T1/pcr/m/n/10 "Schannel"[]\T1/ptm/m/n/10 '. If it does not, for ver-i-fi-ca-tion to be on the en-vi-ron- [1999] [2000] Underfull \hbox (badness 4660) in paragraph at lines 4306--4309 \T1/ptm/m/n/10 able at the repos-i-to-ries, or []\T1/pcr/m/n/10 NULL []\T1/ptm/ m/n/10 which makes an in-ter-nal call to Underfull \hbox (badness 10000) in paragraph at lines 4330--4332 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][][]\T1/pcr/m/n/10 do wnload.file[][][] []\T1/ptm/m/n/10 and [2001] [2002] [2003] Underfull \hbox (badness 1565) in paragraph at lines 4517--4521 []\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of [2004] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4600--4600 [] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F ALSE,[] [2005] Underfull \hbox (badness 1910) in paragraph at lines 4634--4641 \T1/ptm/m/n/10 is saved, then ini-tial-ized to a spec-i-fied state, the ex-am-p le is run and Underfull \hbox (badness 1655) in paragraph at lines 4634--4641 \T1/ptm/m/n/10 the (saved) state is re-stored. []\T1/pcr/m/n/10 setRNG = TRUE [ ]\T1/ptm/m/n/10 sets the same state as Underfull \hbox (badness 2846) in paragraph at lines 4634--4641 []\T1/pcr/m/n/10 R CMD [][]check[][][] []\T1/ptm/m/n/10 does for run-ning a pac k-age's ex-am-ples. This is cur- Underfull \hbox (badness 3460) in paragraph at lines 4634--4641 \T1/ptm/m/n/10 rently equiv-a-lent to []\T1/pcr/m/n/10 setRNG = {RNGkind("defau lt", "default", Underfull \hbox (badness 1931) in paragraph at lines 4641--4648 []\T1/ptm/m/n/10 logical (or []\T1/pcr/m/n/10 "default"[]\T1/ptm/m/n/10 ) in-di -cat-ing if [][][]\T1/pcr/m/n/10 devAskNewPage[][][](ask = TRUE) [2006] [2007] [2008] Underfull \hbox (badness 5939) in paragraph at lines 4887--4889 []\T1/ptm/m/n/10 An en-try in []\T1/pcr/m/n/10 getOption("repos") []\T1/ptm/m/n /10 named `[]\T1/pcr/m/n/10 CRAN[]\T1/ptm/m/n/10 ' which is not the de-fault [2009] [2010] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5030--5030 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [2011] [2012] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.5101 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format.1} ) has been already used, duplicate ignored \relax l.5101 ...mat Unordered and Ordered Lists}{format} [2013] [2014] [2015] [2016] [2017] [2018] [2019] [2020] Underfull \hbox (badness 1622) in paragraph at lines 5624--5628 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [2021] [2022] [2023] [2024] [2025] Underfull \hbox (badness 1448) in paragraph at lines 6003--6008 []\T1/ptm/m/n/10 External pointer ob-jects are com-pared as ref-er-ence ob-ject s, cor-re-spond-ing to call-ing [2026] [2027] Overfull \hbox (96.78088pt too wide) in paragraph at lines 6153--6153 []\T1/pcr/m/n/10 ## NB: The methods for \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 data.f rame\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 and \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 array\ TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 are identical to the \TS1/pcr/m/n/10 '\T1/pcr/ m/n/10 matrix\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 one[] [2028] Overfull \hbox (66.78088pt too wide) in paragraph at lines 6165--6165 []\T1/pcr/m/n/10 tail(x, n = 6L, keepnums = TRUE, addrownums, ...) # exported as tail.matrix()[] [2029] [2030] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6299--6299 [] \T1/pcr/m/n/9 ## BUT if I use "useAttrib(.)", this is *not* ok, when n i s of length 2:[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 6300--6300 [] \T1/pcr/m/n/9 ## --- because [i,j]-indexing of data frames *also* drops "other" attributes ..[] [2031] [2032] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6510--6510 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h elp(dgamma):[] [2033] Underfull \hbox (badness 10000) in paragraph at lines 6594--6596 []\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 https : / / www . r-[] project . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also [2034] Underfull \hbox (badness 1502) in paragraph at lines 6643--6648 []\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words '. `Key- Underfull \hbox (badness 2103) in paragraph at lines 6643--6648 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2035] [2036] [2037] Underfull \hbox (badness 10000) in paragraph at lines 6816--6825 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, Underfull \hbox (badness 10000) in paragraph at lines 6816--6825 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10 ', which can be re-made by [2038] Underfull \hbox (badness 2150) in paragraph at lines 6880--6883 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See Underfull \hbox (badness 5175) in paragraph at lines 6896--6899 []\T1/pcr/m/n/10 hsearch_db() []\T1/ptm/m/n/10 builds and caches the help searc h database for sub-se-quent use by [2039] [2040] Underfull \hbox (badness 3118) in paragraph at lines 7019--7021 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for [2041] [2042] Underfull \hbox (badness 5091) in paragraph at lines 7194--7196 []\T1/ptm/m/n/10 download method, see [][][]\T1/pcr/m/n/10 download.file[][][][ ]\T1/ptm/m/n/10 . Un-used if a non-[]\T1/pcr/m/n/10 NULL Underfull \hbox (badness 10000) in paragraph at lines 7224--7231 []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 means to use []\T1/pcr/m/n/10 c("Depends ", "Imports", "LinkingTo", Underfull \hbox (badness 10000) in paragraph at lines 7224--7231 \T1/pcr/m/n/10 "Suggests") []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pkgs []\T1/ptm /m/n/10 and []\T1/pcr/m/n/10 c("Depends", "Imports", Underfull \hbox (badness 1270) in paragraph at lines 7224--7231 \T1/pcr/m/n/10 "LinkingTo") []\T1/ptm/m/n/10 for added de-pen-den-cies: this in -stalls all the pack-ages [2043] Underfull \hbox (badness 1270) in paragraph at lines 7239--7249 \T1/ptm/m/n/10 for the `[]\T1/pcr/m/n/10 --configure-args[]\T1/ptm/m/n/10 ' fla g in the call to []\T1/pcr/m/n/10 R CMD INSTALL[]\T1/ptm/m/n/10 . If Underfull \hbox (badness 4441) in paragraph at lines 7282--7285 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed to Underfull \hbox (badness 2837) in paragraph at lines 7282--7285 []\T1/pcr/m/n/10 R CMD INSTALL []\T1/ptm/m/n/10 for a source pack-age in-stall. E.g., []\T1/pcr/m/n/10 c("--html", Underfull \hbox (badness 1424) in paragraph at lines 7290--7293 []\T1/ptm/m/n/10 logical: if true, re-duce the amount of out-put. This is \T1/p tm/m/it/10 not \T1/ptm/m/n/10 passed to [2044] Underfull \hbox (badness 2376) in paragraph at lines 7361--7368 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is []\T1/pcr/m/n /10 "both" []\T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 7361--7368 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 7361--7368 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1087) in paragraph at lines 7369--7372 []\T1/ptm/m/n/10 Using pack-ages with []\T1/pcr/m/n/10 type = "source" []\T1/pt m/m/n/10 al-ways works pro-vided the pack-age con-tains no [2045] Underfull \hbox (badness 1314) in paragraph at lines 7449--7456 []\T1/pcr/m/n/10 install.packages []\T1/ptm/m/n/10 needs to be able to com-pute all the de-pen-den-cies of []\T1/pcr/m/n/10 pkgs []\T1/ptm/m/n/10 from [2046] Underfull \hbox (badness 10000) in paragraph at lines 7532--7537 [][][]\T1/pcr/m/n/10 update.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 download.pac kages[][][][]\T1/ptm/m/n/10 , Overfull \hbox (25.98041pt too wide) in paragraph at lines 7555--7555 [] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc lude/udunits2"))[] [2047] Underfull \hbox (badness 5133) in paragraph at lines 7591--7595 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each pack-age's Underfull \hbox (badness 1983) in paragraph at lines 7605--7608 []\T1/pcr/m/n/10 installed.packages []\T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along [2048] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7652--7652 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields = "License")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7657--7657 []\T1/pcr/m/n/9 ## Keep packages that come with R (priority="high") and all ot hers separate![] [2049] [2050] Underfull \hbox (badness 4132) in paragraph at lines 7783--7785 []\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion of []\T1/pcr/m/n/10 libtool []\T1/ptm/m/n/10 in-stalled at [2051] [2052] [2053] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7950--7950 []\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h ave defined?[] [2054] [2055] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8093--8093 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE) [2056] Underfull \hbox (badness 10000) in paragraph at lines 8133--8135 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [2057] Underfull \hbox (badness 10000) in paragraph at lines 8240--8242 []\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if Underfull \hbox (badness 10000) in paragraph at lines 8252--8254 []\T1/ptm/m/n/10 typically the re-sult of []\T1/pcr/m/n/10 methods(..)[]\T1/ptm /m/n/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of S3 class [2058] [2059] [2060] [2061] Underfull \hbox (badness 1859) in paragraph at lines 8482--8485 []\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br owser (by Underfull \hbox (badness 1052) in paragraph at lines 8501--8511 \T1/ptm/m/n/10 ac-cord-ing to ver-sion us-ing \T1/pcr/m/n/10 section \T1/ptm/m/ n/10 el-e-ments with names start-ing with a suit-able pre-fix [2062] Underfull \hbox (badness 1655) in paragraph at lines 8576--8579 []\T1/ptm/m/n/10 A data frame in-her-it-ing from class []\T1/pcr/m/n/10 "news_d b"[]\T1/ptm/m/n/10 , with [][][]\T1/pcr/m/n/10 attributes[][][] "package" []\T1 /ptm/m/n/10 (and Overfull \hbox (25.98041pt too wide) in paragraph at lines 8587--8587 []\T1/pcr/m/n/9 db4 <- news(Version == "4.0.0" & grepl("^BUG", Category) & gre pl("PR#", Text),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8595--8595 []\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[] [2063] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8603--8603 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st andardize a bit more[] [2064] Underfull \hbox (badness 1917) in paragraph at lines 8690--8692 []\T1/pcr/m/n/10 "B"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "KiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "MiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "GiB"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "TiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "PiB"[]\T1/ptm/m/ n/10 , [2065] [2066] [2067] [2068] Overfull \hbox (66.78088pt too wide) in paragraph at lines 8964--8964 [] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica tion", "Built"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8965--8965 [] \T1/pcr/m/n/10 tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%D", "%m/ %d/%y"),[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 8966--8966 [] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f ields=date.fields))[] [2069] Underfull \hbox (badness 10000) in paragraph at lines 8994--8996 []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 asDateBuilt()[]\T1/ptm/m/n/10 , a [][][]\ T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string as from Underfull \hbox (badness 10000) in paragraph at lines 9008--9010 []\T1/pcr/m/n/10 packageVersion() []\T1/ptm/m/n/10 is a con-ve-nience short-cut , al-low-ing things like []\T1/pcr/m/n/10 if Underfull \hbox (badness 1259) in paragraph at lines 9016--9021 []\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2070] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9060--9060 [] \T1/pcr/m/n/9 identical(pu, packageDate("stats"))) # as "utils" an d "stats" are[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9061--9061 [] \T1/pcr/m/n/9 # both \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 base R\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and "Built" at same time[] [2071] [2072] Underfull \hbox (badness 10000) in paragraph at lines 9189--9194 []\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 "Status"[]\T1/ptm/m/n/10 , a fac-tor wit h lev-els []\T1/pcr/m/n/10 c("ok", "upgrade", Underfull \hbox (badness 10000) in paragraph at lines 9196--9199 []\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 "Status"[]\T1/ptm/m/n/10 , a fac-tor wit h lev-els []\T1/pcr/m/n/10 c("installed", "not [2073] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9311--9311 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9312--9312 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [2074] [2075] [2076] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9492--9492 [] \T1/pcr/m/n/9 "S original, "),[] [2077] [2078] Underfull \hbox (badness 1789) in paragraph at lines 9662--9664 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [2079] [2080] [2081] [2082] Underfull \hbox (badness 2600) in paragraph at lines 9886--9889 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the name of the help topic; de-faults to [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] Overfull \hbox (30.78088pt too wide) in paragraph at lines 10499--10499 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", " no.loss"),[] [2091] [2092] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10660--10660 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr anspose = TRUE)[] [2093] [2094] [2095] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10841--10841 []\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23 456 98 76 54[] [2096] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10927--10927 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"),[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 10928--10928 [] \T1/pcr/m/n/10 row.names, col.names, as.is = !stringsAsFactors, t ryLogical = TRUE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10930--10930 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 10935--10935 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski pNul = FALSE)[] [2097] Underfull \hbox (badness 2027) in paragraph at lines 11007--11010 []\T1/ptm/m/n/10 Using []\T1/pcr/m/n/10 row.names = NULL []\T1/ptm/m/n/10 force s row num-ber-ing. Miss-ing or []\T1/pcr/m/n/10 NULL [2098] Underfull \hbox (badness 2435) in paragraph at lines 11030--11034 []\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 de-ter-m in-ing if columns con-sist-ing en-tirely of []\T1/pcr/m/n/10 "F"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1824) in paragraph at lines 11030--11034 []\T1/pcr/m/n/10 "FALSE"[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 "TRUE" []\T1/pt m/m/n/10 should be con-verted to [][][]\T1/pcr/m/n/10 logical[][][][]\T1/ptm/m/ n/10 ; passed to [2099] [2100] [2101] Overfull \hbox (12.78088pt too wide) in paragraph at lines 11291--11291 []\T1/pcr/m/n/10 readRegistry(key, hive = c("HLM", "HCR", "HCU", "HU", "HCC", "HPD"), Overfull \hbox (6.78088pt too wide) in paragraph at lines 11292--11292 [] \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64- bit"))[] Underfull \hbox (badness 10000) in paragraph at lines 11299--11304 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are Underfull \hbox (badness 10000) in paragraph at lines 11299--11304 \T1/ptm/m/n/10 for []\T1/pcr/m/n/10 HKEY_LOCAL_MACHINE[]\T1/ptm/m/n/10 , []\T1/ pcr/m/n/10 HKEY_CLASSES_ROOT[]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 11299--11304 []\T1/pcr/m/n/10 HKEY_CURRENT_USER[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 HKEY_USER S[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 HKEY_CURRENT_CONFIG [2102] [2103] [2104] [2105] Overfull \hbox (18.78088pt too wide) in paragraph at lines 11531--11531 [] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c (1, 0))) [2106] [2107] [2108] [2109] Underfull \hbox (badness 10000) in paragraph at lines 11797--11801 \T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral s & oldid = 78252134$[][]\T1/ptm/m/n/10 . Overfull \hbox (20.58041pt too wide) in paragraph at lines 11815--11815 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni ng for "IIIIII"[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11820--11820 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [2110] [2111] Overfull \hbox (18.78088pt too wide) in paragraph at lines 11956--11956 []\T1/pcr/m/n/10 4. | \-base:::tryCatchOne(expr, names, parentenv, handler s[[1L]])[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 11957--11957 []\T1/pcr/m/n/10 5. | \-base:::doTryCatch(return(expr), name, parentenv, handler)[] [2112] [2113] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12092--12092 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [2114] [2115] Underfull \hbox (badness 1917) in paragraph at lines 12224--12227 []\T1/ptm/m/n/10 If `[]\T1/pcr/m/n/10 --default-packages[]\T1/ptm/m/n/10 ' is n ot used, then []\T1/pcr/m/n/10 Rscript []\T1/ptm/m/n/10 checks the en-vi-ron-me nt vari- Underfull \hbox (badness 4328) in paragraph at lines 12224--12227 \T1/ptm/m/n/10 able []\T1/pcr/m/n/10 R_SCRIPT_DEFAULT_PACKAGES[]\T1/ptm/m/n/10 . If this is set, then it takes prece-dence over Overfull \hbox (106.98032pt too wide) in paragraph at lines 12247--12247 []\T1/pcr/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 sessionInfo()\TS1/pcr/m/n/9 '[] [2116] [2117] Overfull \hbox (54.78088pt too wide) in paragraph at lines 12339--12339 [] \T1/pcr/m/n/10 restrict = c("functions", "descriptions", "news", "Rfunctions",[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 12340--12340 [] \T1/pcr/m/n/10 "Rmanuals", "READMEs", "views", "vig nettes"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 12342--12342 [] \T1/pcr/m/n/10 sortby = c("score", "date:late", "date:early", "s ubject",[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 12343--12343 [] \T1/pcr/m/n/10 "subject:descending", "size", "size:de scending"),[] Underfull \hbox (badness 6725) in paragraph at lines 12366--12374 \T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 score[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 date: late []\T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first, Underfull \hbox (badness 2662) in paragraph at lines 12366--12374 \T1/ptm/m/n/10 der, []\T1/pcr/m/n/10 subject:descending []\T1/ptm/m/n/10 for re -verse al-pha-bet-i-cal or-der, []\T1/pcr/m/n/10 size []\T1/ptm/m/n/10 or [2118] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12411--12411 []\T1/pcr/m/n/9 fullquery <- RSiteSearch("lattice", restrict = c("vignettes"," Rfunctions"))[] [2119] Underfull \hbox (badness 1377) in paragraph at lines 12467--12470 []\T1/ptm/m/n/10 Character string spec-i-fy-ing whether emacs style ([]\T1/pcr/ m/n/10 "etags"[]\T1/ptm/m/n/10 ) or vi style Underfull \hbox (badness 3646) in paragraph at lines 12502--12504 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software / [2120] Overfull \hbox (30.78088pt too wide) in paragraph at lines 12540--12540 [] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F ALSE, ...)[] [2121] [2122] Underfull \hbox (badness 10000) in paragraph at lines 12722--12726 []\T1/ptm/m/n/10 The de-fault for []\T1/pcr/m/n/10 stylepath []\T1/ptm/m/n/10 i s now taken from the en-vi-ron-ment vari-able [2123] Underfull \hbox (badness 10000) in paragraph at lines 12755--12761 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a Underfull \hbox (badness 2027) in paragraph at lines 12770--12776 []\T1/ptm/m/n/10 The use of fancy quotes (see [][][]\T1/pcr/m/n/10 sQuote[][][] []\T1/ptm/m/n/10 ) can cause prob-lems when set-ting \T1/phv/m/n/10 R \T1/ptm/m /n/10 out-put in [2124] [2125] Overfull \hbox (6.78088pt too wide) in paragraph at lines 12927--12927 [] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa rent")[] Underfull \hbox (badness 1009) in paragraph at lines 12945--12957 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If [2126] Underfull \hbox (badness 2600) in paragraph at lines 12985--12987 []\T1/ptm/m/n/10 The file `\T1/pcr/m/n/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ures the R GUI ([]\T1/pcr/m/n/10 Rgui[]\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows and Underfull \hbox (badness 1043) in paragraph at lines 13028--13033 []\T1/ptm/m/n/10 At the time of writ-ing `\T1/pcr/m/n/10 Rdevga\T1/ptm/m/n/10 ' con-fig-ured the map-ping of font num-bers to fonts, and [2127] [2128] [2129] [2130] [2131] Underfull \hbox (badness 1888) in paragraph at lines 13330--13333 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form \T1/phv/m/n/10 R \T1/ptm/m/n/10 was built un-der. Where Underfull \hbox (badness 10000) in paragraph at lines 13347--13350 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g Underfull \hbox (badness 10000) in paragraph at lines 13350--13353 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g [2132] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13396--13396 []\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at end of report[] [2133] Underfull \hbox (badness 2158) in paragraph at lines 13455--13458 []\T1/ptm/m/n/10 Repository `[]\T1/pcr/m/n/10 CRAN[]\T1/ptm/m/n/10 ' is treated spe-cially: the value is taken from the cur-rent set-ting of Overfull \hbox (0.78088pt too wide) in paragraph at lines 13503--13503 []\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf fix)) [2134] [2135] [2136] Underfull \hbox (badness 2302) in paragraph at lines 13660--13662 []\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t o the Win-dows API call [2137] Underfull \hbox (badness 3333) in paragraph at lines 13768--13770 []\T1/pcr/m/n/10 getSrcFilename []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 getSrcDir ectory []\T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file- [2138] [2139] [2140] Overfull \hbox (42.78088pt too wide) in paragraph at lines 13935--13935 [] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing = TRUE, ...))[] Underfull \hbox (badness 2012) in paragraph at lines 13959--13964 []\T1/ptm/m/n/10 logical; if []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 (de-fault), [][][]\T1/pcr/m/n/10 deparse[][][](control = ) []\T1/ptm/m/n/10 will not ha ve Underfull \hbox (badness 5970) in paragraph at lines 13968--13971 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive Underfull \hbox (badness 2600) in paragraph at lines 13968--13971 [][][]\T1/pcr/m/n/10 options[][][]("width")[]\T1/ptm/m/n/10 ; note that this ha s only a weak ef-fect, un-less Underfull \hbox (badness 1052) in paragraph at lines 13979--13988 []\T1/ptm/m/n/10 (see [][][]\T1/pcr/m/n/10 options[][][][]\T1/ptm/m/n/10 ) whic h de-faults to []\T1/pcr/m/n/10 "no" []\T1/ptm/m/n/10 for back com-pat-i-bil-it y rea-sons; [2141] Underfull \hbox (badness 1442) in paragraph at lines 13995--13999 []\T1/ptm/m/n/10 numeric or []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 as by de-fau lt, de-ter-min-ing the []\T1/pcr/m/n/10 nlines []\T1/ptm/m/n/10 ar-gu-ment to Overfull \hbox (36.7804pt too wide) in paragraph at lines 14041--14041 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification of binary numbers[] [2142] Overfull \hbox (15.18042pt too wide) in paragraph at lines 14068--14068 []\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo ng" non-ASCII:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 14075--14075 []\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of 2 in order to se e 1 (in UTF-8!):[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 14077--14077 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) # "1 is 1" here[] [2143] [2144] [2145] Underfull \hbox (badness 10000) in paragraph at lines 14243--14245 []\T1/ptm/m/n/10 Options other than []\T1/pcr/m/n/10 memory = "none" []\T1/ptm/ m/n/10 ap-ply only to files pro-duced by [2146] Underfull \hbox (badness 10000) in paragraph at lines 14353--14356 []\T1/ptm/m/n/10 further ar-gu-ments passed to the driver's setup func-tion. Se e Underfull \hbox (badness 1389) in paragraph at lines 14353--14356 [][][]\T1/pcr/m/n/10 RweaveLatexSetup[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/ m/n/10 RtangleSetup[][][][]\T1/ptm/m/n/10 , re-spec-tively, for the ar-gu- [2147] Underfull \hbox (badness 6300) in paragraph at lines 14401--14408 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 syntax = NULL []\T1/ptm/m/n/10 (the de-fau lt) then the avail-able syn-tax ob-jects are con-sulted in Underfull \hbox (badness 6252) in paragraph at lines 14401--14408 \T1/ptm/m/n/10 turn, and se-lected if their []\T1/pcr/m/n/10 extension []\T1/pt m/m/n/10 com-po-nent matches (as a reg-exp) the file Underfull \hbox (badness 4556) in paragraph at lines 14401--14408 \T1/ptm/m/n/10 name. Ob-jects []\T1/pcr/m/n/10 SweaveSyntaxNoweb []\T1/ptm/m/n/ 10 (with []\T1/pcr/m/n/10 extension = "[.][rsRS]nw$"[]\T1/ptm/m/n/10 ) and [2148] [2149] Underfull \hbox (badness 2020) in paragraph at lines 14565--14573 \T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `[]\T1/pcr/m/n/10 -h[]\T1/ptm/m/ n/10 ' (fol-low sym-bolic links, also `[]\T1/pcr/m/n/10 -L[]\T1/ptm/m/n/10 ' on some plat-forms), Underfull \hbox (badness 1194) in paragraph at lines 14565--14573 \T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 --acls[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 -- exclude-backups[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 --exclude-vcs[]\T1/ptm/m/n /10 ' (and sim-i-lar) and on Win-dows [2150] Underfull \hbox (badness 1622) in paragraph at lines 14574--14581 []\T1/ptm/m/n/10 A con-ve-nient and ro-bust way to set op-tions for GNU []\T1/p cr/m/n/10 tar []\T1/ptm/m/n/10 is via en-vi-ron-ment vari-able [2151] Underfull \hbox (badness 5022) in paragraph at lines 14714--14718 []\T1/ptm/m/n/10 When ar-gu-ment []\T1/pcr/m/n/10 tar []\T1/ptm/m/n/10 is set t o the com-mand []\T1/pcr/m/n/10 tar []\T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 14721--14724 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / pubs . Underfull \hbox (badness 10000) in paragraph at lines 14721--14724 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht ml # tag _ 20 _ 92 _ [2152] [2153] [2154] [2155] [2156] [2157] [2158] [2159] [2160] Overfull \hbox (6.78088pt too wide) in paragraph at lines 15339--15339 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 15345--15345 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] [2161] Underfull \hbox (badness 4467) in paragraph at lines 15366--15368 []\T1/ptm/m/n/10 Download method, see [][][]\T1/pcr/m/n/10 download.file[][][][ ]\T1/ptm/m/n/10 . Un-used if a non-[]\T1/pcr/m/n/10 NULL Underfull \hbox (badness 4660) in paragraph at lines 15381--15385 \T1/ptm/m/n/10 able at the repos-i-to-ries, or []\T1/pcr/m/n/10 NULL []\T1/ptm/ m/n/10 which makes an in-ter-nal call to Underfull \hbox (badness 1694) in paragraph at lines 15395--15399 []\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][][]\T1/pcr/m/n/10 ins talled.packages[][][](lib.loc = Underfull \hbox (badness 10000) in paragraph at lines 15401--15406 []\T1/ptm/m/n/10 Arguments such as []\T1/pcr/m/n/10 destdir []\T1/ptm/m/n/10 an d []\T1/pcr/m/n/10 dependencies []\T1/ptm/m/n/10 to be Underfull \hbox (badness 10000) in paragraph at lines 15401--15406 \T1/ptm/m/n/10 passed to [][][]\T1/pcr/m/n/10 install.packages[][][] []\T1/ptm/ m/n/10 and []\T1/pcr/m/n/10 ignore_repo_cache[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 15401--15406 []\T1/pcr/m/n/10 max_repo_cache_age []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 noCac he []\T1/ptm/m/n/10 to [][][]\T1/pcr/m/n/10 available.packages[][][] Underfull \hbox (badness 1052) in paragraph at lines 15407--15409 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See [2162] Underfull \hbox (badness 10000) in paragraph at lines 15437--15442 []\T1/pcr/m/n/10 available = NULL []\T1/ptm/m/n/10 make a call to []\T1/pcr/m/n /10 available.packages(contriburl = Underfull \hbox (badness 1226) in paragraph at lines 15437--15442 \T1/pcr/m/n/10 contriburl, method = method) []\T1/ptm/m/n/10 and hence by de-fa ult fil-ters on \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion, OS type Underfull \hbox (badness 10000) in paragraph at lines 15458--15463 []\T1/ptm/m/n/10 Take care when us-ing []\T1/pcr/m/n/10 dependencies []\T1/ptm/ m/n/10 (passed to [][][]\T1/pcr/m/n/10 install.packages[][][][]\T1/ptm/m/n/10 ) with Underfull \hbox (badness 10000) in paragraph at lines 15466--15469 [][][]\T1/pcr/m/n/10 install.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n /10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 download.pa ckages[][][][]\T1/ptm/m/n/10 , [2163] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15543--15543 []\T1/pcr/m/n/9 ## Not run: url.show("https://www.stats.ox.ac.uk/pub/datasets/ csb/ch3a.txt") [2164] [2165] [2166] Underfull \hbox (badness 2293) in paragraph at lines 15750--15753 [][][]\T1/pcr/m/n/10 browseVignettes[][][] []\T1/ptm/m/n/10 for an HTML-based v i-gnette browser; [][][]\T1/pcr/m/n/10 RShowDoc[][][](, [2167] Overfull \hbox (42.18039pt too wide) in paragraph at lines 15766--15766 []\T1/pcr/m/n/9 ## Note that \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 package = *\TS1/pcr /m/n/9 ' \T1/pcr/m/n/9 is much faster in the case of many installed packages:[] [2168] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15833--15833 [] \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d ata = DAT)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 15855--15855 [] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal), data = DD)))[] [2169] [2170] Underfull \hbox (badness 1297) in paragraph at lines 15987--15989 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i s se-lected, or [2171] Underfull \hbox (badness 4036) in paragraph at lines 16034--16036 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 winMenuDel []\T1/ptm/m/n/10 func-tion wil l delete a menu and all of its items and sub-menus. [2172] [2173] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16154--16154 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", [2174] Underfull \hbox (badness 1715) in paragraph at lines 16206--16209 []\T1/ptm/m/n/10 arguments to []\T1/pcr/m/n/10 write.table[]\T1/ptm/m/n/10 : [] \T1/pcr/m/n/10 append[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 col.names[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 sep[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 dec []\T1/ptm/m/n /10 and Underfull \hbox (badness 10000) in paragraph at lines 16251--16253 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion e.g. []\T1/pcr/m/n/10 file = [2175] [2176] [2177]) [2178] [2179] [2180] (./KernSmooth-pkg.tex Chapter 15. [2181] Overfull \hbox (24.78088pt too wide) in paragraph at lines 123--123 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat e = TRUE) [2182] [2183] [2184] [2185] [2186] Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun = 0.05, [2187] [2188] [2189] [2190]) (./MASS-pkg.tex Chapter 16. [2191] [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] [2200] [2201] Overfull \hbox (20.58041pt too wide) in paragraph at lines 776--776 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b eav2$hours/24))[] [2202] [2203] [2204] [2205] [2206] [2207] [2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218] [2219] [2220] [2221] [2222] [2223] [2224] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2422--2422 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2426--2426 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] [2225] [2226] [2227] [2228] Underfull \hbox (badness 6559) in paragraph at lines 2707--2710 []\T1/ptm/m/n/10 further ar-gu-ments for []\T1/pcr/m/n/10 plot []\T1/ptm/m/n/10 and graph-i-cal pa-ram-e-ters. Note that [2229] [2230] [2231] Underfull \hbox (badness 10000) in paragraph at lines 2877--2882 []\T1/pcr/m/n/10 "gamma"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "geometric"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "log-normal"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lo gnormal"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2877--2882 []\T1/pcr/m/n/10 "logistic"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "negative binomi al"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "normal"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n /10 "Poisson"[]\T1/ptm/m/n/10 , [2232] [2233] Underfull \hbox (badness 4686) in paragraph at lines 3049--3051 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [2234] [2235] [2236] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3249--3249 [] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL SE, ...)[] [2237] [2238] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3381--3381 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist = "exponential")[] [2239] [2240] [2241] [2242] [2243] [2244] [2245] [2246] [2247] [2248] [2249] Underfull \hbox (badness 1845) in paragraph at lines 4183--4185 []\T1/ptm/m/n/10 The va-ri-ety of bar-ley ([]\T1/pcr/m/n/10 "manchuria"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "svansota"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "velv et"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "trebi" []\T1/ptm/m/n/10 and [2250] [2251] [2252] [2253] [2254] [2255] [2256] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4677--4677 [] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n", ...)[] [2257] [2258] [2259] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4899--4899 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model = FALSE, [2260] [2261] [2262] [2263] [2264] [2265] [2266] [2267] [2268] [2269] [2270] [2271] [2272] [2273] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5954--5954 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP ACK = FALSE) [2274] Overfull \hbox (48.78088pt too wide) in paragraph at lines 6015--6015 []\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/ 10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log") [2275] [2276] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.npk}) has been already used, duplicate ignored \relax l.6175 ...sical N, P, K Factorial Experiment}{npk} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.npk.1}) h as been already used, duplicate ignored \relax l.6175 ...sical N, P, K Factorial Experiment}{npk} [2277] [2278] [2279] [2280] [2281] [2282] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6595--6595 [] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb ose = TRUE)))[] [2283] Overfull \hbox (18.78088pt too wide) in paragraph at lines 6683--6683 [] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr ellis"))[] [2284] [2285] [2286] [2287] [2288] [2289] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7122--7122 []\T1/pcr/m/n/9 nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100 , A=10, B=1))[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7139--7139 [] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c auchit"))[] [2290] Underfull \hbox (badness 3138) in paragraph at lines 7217--7223 []\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c mr/m/n/10 ) = [2291] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7287--7287 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da ta = housing)[] [2292] [2293] Underfull \hbox (badness 1389) in paragraph at lines 7396--7399 []\T1/ptm/m/n/10 the di-men-sion of the space to be used. If this is less than []\T1/pcr/m/n/10 min(p, [2294] [2295] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7526--7526 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam p = "exact")[] [2296] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7591--7591 [] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC V"), ...)[] [2297] [2298] [2299] [2300] [2301] [2302] Underfull \hbox (badness 4686) in paragraph at lines 8029--8031 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [2303] [2304] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8148--8148 [] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control = NULL)[] Underfull \hbox (badness 1590) in paragraph at lines 8172--8176 []\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if []\T1/pcr/m /n/10 NA[]\T1/ptm/m/n/10 s are found. The [2305] [2306] [2307] [2308] [2309] [2310] [2311] [2312] [2313] [2314] [2315] [2316] [2317] [2318] [2319] [2320] [2321] [2322] [2323] [2324] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9554--9554 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS E, ...)[] [2325] Underfull \hbox (badness 2035) in paragraph at lines 9666--9668 []\T1/ptm/m/n/10 ``Fold your arms! Which is on top'' (Fac-tor, with lev-els []\ T1/pcr/m/n/10 "R on L"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "L on R"[]\T1/ptm/m/n /10 , Underfull \hbox (badness 1158) in paragraph at lines 9681--9684 []\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els []\T1/pcr/m/n/ 10 "Heavy"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Regul" []\T1/ptm/m/n/10 (reg-u-l arly), [2326] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9763--9763 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub le.eps^0.25) Overfull \hbox (30.78088pt too wide) in paragraph at lines 9765--9765 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double .eps^0.25,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9768--9768 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub le.eps^0.25)[] [2327] [2328] [2329] [2330] [2331] [2332] [2333] [2334] [2335] [2336] [2337] [2338] [2339]) (./Matrix-pkg.tex [2340] Chapter 17. Underfull \hbox (badness 10000) in paragraph at lines 35--38 []\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec t to change, and if you Underfull \hbox (badness 10000) in paragraph at lines 35--38 \T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack- age main-tain-ers [2341] Underfull \hbox (badness 1769) in paragraph at lines 89--92 []\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o wn code. Please con-tact us [2342] Underfull \hbox (badness 2229) in paragraph at lines 154--157 []\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm /m/n/10 ob-jects; here, when the first is Underfull \hbox (badness 1147) in paragraph at lines 154--157 \T1/ptm/m/n/10 an []\T1/pcr/m/n/10 "[][]abIndex[][][]" []\T1/ptm/m/n/10 vec-tor , these ar-gu-ments will be con-cate-nated to a new pdfTeX warning (ext4): destination with the same identifier (name{Rfn.all.equal }) has been already used, duplicate ignored \relax l.184 ...{all.equal}{all.equal-methods}{all.equal} Underfull \hbox (badness 10000) in paragraph at lines 211--214 []\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing Underfull \hbox (badness 10000) in paragraph at lines 217--219 []\T1/ptm/m/n/10 There are more meth-ods, no-tably also for []\T1/pcr/m/n/10 "[ ][]sparseVector[][][]"[]\T1/ptm/m/n/10 's, see [2343] Underfull \hbox (badness 3098) in paragraph at lines 266--268 []\T1/ptm/m/n/10 optional ar-gu-ments passed to the de-fault method for generic func-tion [2344] [2345] [2346] Overfull \hbox (15.18042pt too wide) in paragraph at lines 500--500 [] \T1/pcr/m/n/9 band(sm5, -1, 1)# "dsyMatrix": symmetric band preserves sym metry property[] [2347] Underfull \hbox (badness 5119) in paragraph at lines 543--547 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class Underfull \hbox (badness 1668) in paragraph at lines 547--552 [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/ m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse Overfull \hbox (4.38043pt too wide) in paragraph at lines 578--578 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 580--580 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] [2348] Overfull \hbox (36.7804pt too wide) in paragraph at lines 589--589 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20, 1), rpois(20, 3))[ c(1:3, 2:3, 3:2)],[] [2349] Overfull \hbox (52.98038pt too wide) in paragraph at lines 705--705 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd iag() -- for the case of *many* (k x k) matrices:[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 706--706 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(, , ....., ) where each mat_j is a k x k \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 matrix\TS1/pcr/m/n/9 '[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 707--707 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @return a sparse (N*k x N*k) matrix of class \code{"\linkS4class{dgCMatrix}"}.[] [2350] Overfull \hbox (31.3804pt too wide) in paragraph at lines 720--720 [] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \ T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri x indexing), but elegant?[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 721--721 [] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len( N), each=k)]),[] [2351] Overfull \hbox (9.78043pt too wide) in paragraph at lines 888--888 []\T1/pcr/m/n/9 L. <- L; L.[1:2,1] <- TRUE; L.@x[1:2] <- FALSE; L. # has "zero s" to drop0()[] [2352] Underfull \hbox (badness 1635) in paragraph at lines 970--975 []\T1/pcr/m/n/10 new("pBunchKaufman", ...)[]\T1/ptm/m/n/10 , but they are more typ-i-cally ob-tained as the value of Underfull \hbox (badness 10000) in paragraph at lines 980--983 []\T1/pcr/m/n/10 signature(from = "BunchKaufman", to = "dtrMatrix")[]\T1/ptm/m/ n/10 : re-turns a Underfull \hbox (badness 10000) in paragraph at lines 983--986 []\T1/pcr/m/n/10 signature(from = "pBunchKaufman", to = "dtpMatrix")[]\T1/ptm/m /n/10 : re-turns a Underfull \hbox (badness 10000) in paragraph at lines 986--989 []\T1/pcr/m/n/10 signature(from = "p?BunchKaufman", logarithm = [2353] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1059--1059 []\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m atrix"), ...)[] [2354] Underfull \hbox (badness 10000) in paragraph at lines 1132--1137 []\T1/ptm/m/n/10 An ob-ject rep-re-sent-ing the fac-tor-iza-tion, in-her-it-ing from vir-tual class [2355] Overfull \hbox (3.02814pt too wide) in paragraph at lines 1188--1188 []\T1/pcr/m/n/9 stopifnot(all.equal(as(A, "matrix"), as(Reduce(\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 %*%\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 , e.bk.A), "matrix")))[] [2356] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cbind2.Rd ash.methods}) has been already used, duplicate ignored \relax l.1236 ... on cbind2/rbind2}{cbind2.Rdash.methods} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cbind2}) has been already used, duplicate ignored \relax l.1237 \aliasA{cbind2}{cbind2-methods}{cbind2} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rbind2}) has been already used, duplicate ignored \relax l.1246 \aliasA{rbind2}{cbind2-methods}{rbind2} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rbind2.Rd ash.methods}) has been already used, duplicate ignored \relax l.1255 ...s}{cbind2-methods}{rbind2.Rdash.methods} [2357] Underfull \hbox (badness 10000) in paragraph at lines 1318--1323 []\T1/ptm/m/n/10 Our class def-i-ni-tion help pages men-tion-ing []\T1/pcr/m/n/ 10 cbind2() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 rbind2() []\T1/ptm/m/n/10 met h-ods: Underfull \hbox (badness 10000) in paragraph at lines 1373--1380 []\T1/ptm/m/n/10 The im-ple-men-ta-tion of class []\T1/pcr/m/n/10 CHMfactor []\ T1/ptm/m/n/10 is based on CHOLMOD's C-level [2358] [2359] Underfull \hbox (badness 5008) in paragraph at lines 1535--1550 []\T1/pcr/m/n/10 signature(from = "CHMfactor", logarithm = "logical")[]\T1/ptm/ m/n/10 : be- Underfull \hbox (badness 10000) in paragraph at lines 1585--1587 []\T1/pcr/m/n/10 signature(update = ., C = ., object = "CHMfactor")[]\T1/ptm/m/ n/10 : see [2360] Underfull \hbox (badness 1917) in paragraph at lines 1593--1597 []\T1/ptm/m/n/10 The CHOLMOD source code; see [][]$\T1/pcr/m/n/10 https : / / g ithub . com / DrTimothyAldenDavis / Underfull \hbox (badness 8132) in paragraph at lines 1593--1597 \T1/pcr/m/n/10 SuiteSparse$[][]\T1/ptm/m/n/10 , no-tably the header file `\T1/p cr/m/n/10 CHOLMOD/Include/cholmod.h\T1/ptm/m/n/10 ' defin-ing Overfull \hbox (9.78043pt too wide) in paragraph at lines 1643--1643 []\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m atrix"), ...)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1651--1651 [] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(list( NULL), dn[2L]),[] [2361] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1660--1660 [] \T1/pcr/m/n/9 ae2(A[ch.A@perm + 1L, ch.A@perm + 1L], with(e.ch.A, L1 %*% D %*% L1.))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1661--1661 [] \T1/pcr/m/n/9 ae2(A[ch.A@perm + 1L, ch.A@perm + 1L], with(E.ch.A, L %*% L. ))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1671--1671 []\T1/pcr/m/n/9 u2 <- update(ch.A, t(M), mult = sqrt(2)) # updating with cross prod(M), not M[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol}) ha s been already used, duplicate ignored \relax l.1676 \aliasA{chol}{chol-methods}{chol} [2362] Underfull \hbox (badness 10000) in paragraph at lines 1781--1785 \T1/pcr/m/n/10 double / dpstrf . f$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 htt ps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and Underfull \hbox (badness 1917) in paragraph at lines 1786--1790 []\T1/ptm/m/n/10 The CHOLMOD source code; see [][]$\T1/pcr/m/n/10 https : / / g ithub . com / DrTimothyAldenDavis / Underfull \hbox (badness 8132) in paragraph at lines 1786--1790 \T1/pcr/m/n/10 SuiteSparse$[][]\T1/ptm/m/n/10 , no-tably the header file `\T1/p cr/m/n/10 CHOLMOD/Include/cholmod.h\T1/ptm/m/n/10 ' defin-ing [2363] [2364] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol2inv} ) has been already used, duplicate ignored \relax l.1905 ...sA{chol2inv}{chol2inv-methods}{chol2inv} [2365] [2366] Underfull \hbox (badness 1931) in paragraph at lines 2041--2046 []\T1/ptm/m/n/10 a nu-meric vec-tor of length []\T1/pcr/m/n/10 n*n []\T1/ptm/m/ n/10 ([]\T1/pcr/m/n/10 Cholesky[]\T1/ptm/m/n/10 ) or []\T1/pcr/m/n/10 n*(n+1)/2 []\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 pCholesky[]\T1/ptm/m/n/10 ), where Underfull \hbox (badness 1226) in paragraph at lines 2056--2059 []\T1/ptm/m/n/10 Class [][][]\T1/pcr/m/n/10 CholeskyFactorization[][][][]\T1/pt m/m/n/10 , di-rectly. Class [][][]\T1/pcr/m/n/10 MatrixFactorization[][][][]\T1 /ptm/m/n/10 , by class Underfull \hbox (badness 3000) in paragraph at lines 2062--2070 []\T1/ptm/m/n/10 Objects can be gen-er-ated di-rectly by calls of the form []\T 1/pcr/m/n/10 new("Cholesky", ...) []\T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 2079--2083 []\T1/pcr/m/n/10 signature(from = "pCholesky", to = "dtpMatrix")[]\T1/ptm/m/n/1 0 : re-turns a Underfull \hbox (badness 10000) in paragraph at lines 2083--2086 []\T1/pcr/m/n/10 signature(from = "p?Cholesky", logarithm = "logical")[]\T1/ptm /m/n/10 : Underfull \hbox (badness 10000) in paragraph at lines 2117--2121 \T1/pcr/m/n/10 double / dpstrf . f$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 htt ps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and [2367] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2164--2164 []\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m atrix"), ...)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2172--2172 [] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(list( NULL), dn[2L]),[] [2368] [2369] Underfull \hbox (badness 10000) in paragraph at lines 2303--2310 []\T1/ptm/m/n/10 a [][]fi-nite[][][] num-ber. The ma-trix that is fac-tor-ized is []\T1/pcr/m/n/10 A + Imult * Underfull \hbox (badness 1946) in paragraph at lines 2303--2310 \T1/pcr/m/n/10 - diag(abs(A))) []\T1/ptm/m/n/10 en-sures that []\T1/pcr/m/n/10 A + Imult * diag(nrow(A)) []\T1/ptm/m/n/10 is di- [2370] Underfull \hbox (badness 10000) in paragraph at lines 2350--2363 []\T1/ptm/m/n/10 An ob-ject rep-re-sent-ing the fac-tor-iza-tion, in-her-it-ing from vir-tual class Underfull \hbox (badness 10000) in paragraph at lines 2366--2370 \T1/pcr/m/n/10 double / dpstrf . f$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 htt ps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and Underfull \hbox (badness 1917) in paragraph at lines 2371--2375 []\T1/ptm/m/n/10 The CHOLMOD source code; see [][]$\T1/pcr/m/n/10 https : / / g ithub . com / DrTimothyAldenDavis / Underfull \hbox (badness 8132) in paragraph at lines 2371--2375 \T1/pcr/m/n/10 SuiteSparse$[][]\T1/ptm/m/n/10 , no-tably the header file `\T1/p cr/m/n/10 CHOLMOD/Include/cholmod.h\T1/ptm/m/n/10 ' defin-ing [2371] Underfull \vbox (badness 10000) has occurred while \output is active [2372] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2488--2488 [] \T1/pcr/m/n/9 list(simpl1 = Cholesky(A4, perm = TRUE, super = FALSE, L DL = TRUE),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2489--2489 [] \T1/pcr/m/n/9 simpl0 = Cholesky(A4, perm = TRUE, super = FALSE, L DL = FALSE),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2490--2490 [] \T1/pcr/m/n/9 super0 = Cholesky(A4, perm = TRUE, super = TRUE )),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2492--2492 [] \T1/pcr/m/n/9 list(simpl1 = Cholesky(A4, perm = FALSE, super = FALSE, L DL = TRUE),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2493--2493 [] \T1/pcr/m/n/9 simpl0 = Cholesky(A4, perm = FALSE, super = FALSE, L DL = FALSE),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2494--2494 [] \T1/pcr/m/n/9 super0 = Cholesky(A4, perm = FALSE, super = TRUE )))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2498--2498 []\T1/pcr/m/n/9 rapply2 <- function(object, f, ...) rapply(object, f, , , how = "list", ...)[] Underfull \vbox (badness 10000) has occurred while \output is active [2373] Overfull \hbox (42.18039pt too wide) in paragraph at lines 2565--2565 [] \T1/pcr/m/n/9 x = c(1, 6, 38, 10, 60, 103, -4, 6, -32, -247, -2, - 16, -128, -2, -67))[] [2374] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2661--2661 [] \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4), j=c(2:4,1), x = 2, dimnames=dns))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2665--2665 [] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE, dimnames=dns))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2672--2672 [] \T1/pcr/m/n/9 a. <- sparseMatrix(i=4:1, j=1:4, dimnames=list(n4, n4), repr ="T") # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[] [2375] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colMeans} ) has been already used, duplicate ignored \relax l.2747 ...asA{colMeans}{colSums-methods}{colMeans} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colSums}) has been already used, duplicate ignored \relax l.2755 \aliasA{colSums}{colSums-methods}{colSums} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowMeans} ) has been already used, duplicate ignored \relax l.2762 ...asA{rowMeans}{colSums-methods}{rowMeans} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowSums}) has been already used, duplicate ignored \relax l.2770 \aliasA{rowSums}{colSums-methods}{rowSums} [2376] Underfull \hbox (badness 2922) in paragraph at lines 2822--2826 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i n-her-it-ing from Underfull \hbox (badness 1728) in paragraph at lines 2822--2826 \T1/ptm/m/n/10 class [][][]\T1/pcr/m/n/10 sparseVector[][][][]\T1/ptm/m/n/10 . Only ap-pli-ca-ble when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 is in-her-it-ing fr om a Underfull \hbox (badness 1237) in paragraph at lines 2833--2836 [][][]\T1/pcr/m/n/10 dimnames[][][](x) []\T1/ptm/m/n/10 are only kept (as [][][ ]\T1/pcr/m/n/10 names[][][](v)[]\T1/ptm/m/n/10 ) when the re-sult-ing []\T1/pcr /m/n/10 v []\T1/ptm/m/n/10 is [][][]\T1/pcr/m/n/10 numeric[][][][]\T1/ptm/m/n/1 0 , since [2377] [2378] Underfull \hbox (badness 3547) in paragraph at lines 2994--2997 []\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when [2379] [2380] [2381] [2382] [2383] Underfull \hbox (badness 10000) in paragraph at lines 3402--3405 []\T1/pcr/m/n/10 signature(from = "denseLU", logarithm = "logical")[]\T1/ptm/m/ n/10 : com- [2384] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3457--3457 []\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m atrix"), ...)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 3464--3464 [] \T1/pcr/m/n/9 new( "pMatrix", Dim = c(n, n), Dimnames = c(dn[ 1L], list(NULL)),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3467--3467 [] \T1/pcr/m/n/9 new("dtrMatrix", Dim = c(n, n), Dimnames = list( NULL, NULL),[] [2385] Overfull \hbox (31.3804pt too wide) in paragraph at lines 3470--3470 [] \T1/pcr/m/n/9 new("dtrMatrix", Dim = c(n, n), Dimnames = c(lis t(NULL), dn[2L]),[] [2386] Underfull \hbox (badness 7379) in paragraph at lines 3598--3600 []\T1/pcr/m/n/10 signature(x = "dgCMatrix")[]\T1/ptm/m/n/10 : com-putes the LU de-com-po-si-tion of a square [2387] [2388] [2389] Underfull \hbox (badness 4846) in paragraph at lines 3819--3823 []\T1/ptm/m/n/10 Note that both []\T1/pcr/m/n/10 new(.) []\T1/ptm/m/n/10 and [] [][]\T1/pcr/m/n/10 spMatrix[][][] []\T1/ptm/m/n/10 con-struc-tors for []\T1/pcr /m/n/10 "dgTMatrix" []\T1/ptm/m/n/10 (and other Underfull \hbox (badness 2717) in paragraph at lines 3824--3828 []\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can be stored in more than one pos-si-ble [2390] Underfull \hbox (badness 5231) in paragraph at lines 3869--3874 []\T1/ptm/m/n/10 Construct a for-mally di-ag-o-nal [][][]\T1/pcr/m/n/10 Matrix[ ][][][]\T1/ptm/m/n/10 , i.e., an ob-ject in-her-it-ing from vir-tual class Overfull \hbox (84.78088pt too wide) in paragraph at lines 3880--3880 []\T1/pcr/m/n/10 .sparseDiagonal(n, x = NULL, uplo = "U", shape = "t", unitri = TRUE, kind, cols)[] [2391] Underfull \hbox (badness 10000) in paragraph at lines 3936--3939 []\T1/pcr/m/n/10 .trDiagonal() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 .symDiagon al() []\T1/ptm/m/n/10 are sim-ple wrap-pers, for Underfull \hbox (badness 6792) in paragraph at lines 3936--3939 []\T1/pcr/m/n/10 .sparseDiagonal(shape = "t") []\T1/ptm/m/n/10 and []\T1/pcr/m/ n/10 .sparseDiagonal(shape = "s")[]\T1/ptm/m/n/10 , re-spec- [2392] Underfull \hbox (badness 3646) in paragraph at lines 4013--4016 []\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 dimnames[][][][]\T1/ptm/m/n/10 , a [] [][]\T1/pcr/m/n/10 list[][][][]\T1/ptm/m/n/10 , see the [][][]\T1/pcr/m/n/10 Ma trix[][][] []\T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally Underfull \hbox (badness 6542) in paragraph at lines 4048--4052 []\T1/pcr/m/n/10 signature(x = "diagonalMatrix")[]\T1/ptm/m/n/10 : all these gr oup meth-ods re-turn a Underfull \hbox (badness 4518) in paragraph at lines 4057--4063 []\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")[]\T1/ptm/m/n/10 : the re-sult is from class [2393] Underfull \hbox (badness 10000) in paragraph at lines 4064--4068 []\T1/pcr/m/n/10 (object = "diagonalMatrix")[]\T1/ptm/m/n/10 : Re-turns an ob-j ect of S3 class Underfull \hbox (badness 2318) in paragraph at lines 4074--4078 [][][]\T1/pcr/m/n/10 Diagonal[][][]() []\T1/ptm/m/n/10 as con-struc-tor of thes e ma-tri-ces, and [][][]\T1/pcr/m/n/10 isDiagonal[][][][]\T1/ptm/m/n/10 . [][][ ]\T1/pcr/m/n/10 ddiMatrix[][][] []\T1/ptm/m/n/10 and [2394] [2395] [2396] Underfull \hbox (badness 10000) in paragraph at lines 4331--4333 []\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")[]\T1/ptm/m/n/10 : this group con-tains [2397] [2398] Overfull \hbox (69.18036pt too wide) in paragraph at lines 4475--4475 []\T1/pcr/m/n/9 stopifnot(all.equal(S9p0, S9p))# same as as default, but diffe rent from the random one[] [2399] Underfull \hbox (badness 2469) in paragraph at lines 4590--4593 []\T1/pcr/m/n/10 signature(x = "dpoMatrix")[]\T1/ptm/m/n/10 : Re-turns the [][] []\T1/pcr/m/n/10 determinant[][][] []\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 x[]\T1/ ptm/m/n/10 , via [2400] Underfull \hbox (badness 10000) in paragraph at lines 4613--4618 []\T1/ptm/m/n/10 Currently the va-lid-ity meth-ods for these classes such as Underfull \hbox (badness 2020) in paragraph at lines 4613--4618 [][][]\T1/pcr/m/n/10 getValidity[][][](getClass("dpoMatrix")) []\T1/ptm/m/n/10 for ef-fi-ciency rea-sons only check the di- Underfull \hbox (badness 1748) in paragraph at lines 4619--4628 \T1/pcr/m/n/10 error=identity), "error") []\T1/ptm/m/n/10 . In-deed, when \T1/p tm/m/it/10 co-erc-ing \T1/ptm/m/n/10 to these classes, a ver-sion Underfull \hbox (badness 1590) in paragraph at lines 4619--4628 \T1/ptm/m/n/10 of [][][]\T1/pcr/m/n/10 Cholesky[][][]() []\T1/ptm/m/n/10 or [][ ][]\T1/pcr/m/n/10 chol[][][]() []\T1/ptm/m/n/10 is typ-i-cally used, e.g., see []\T1/pcr/m/n/10 selectMethod("coerce", Underfull \hbox (badness 6675) in paragraph at lines 4675--4682 []\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 Matrix[][][][]\T1/ptm/m/n/10 , typ-i-ca lly in-her-it-ing from vir-tual class [][][]\T1/pcr/m/n/10 sparseMatrix[][][][] \T1/ptm/m/n/10 . Underfull \hbox (badness 6493) in paragraph at lines 4675--4682 [][][]\T1/pcr/m/n/10 denseMatrix[][][] []\T1/ptm/m/n/10 and tra-di-tional vec-t ors and ma-tri-ces are co-erced to [2401] Underfull \hbox (badness 10000) in paragraph at lines 4690--4698 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing if the re-sult must in-herit from vi r-tual class Underfull \hbox (badness 1365) in paragraph at lines 4690--4698 [][][]\T1/pcr/m/n/10 CsparseMatrix[][][][]\T1/ptm/m/n/10 . If []\T1/pcr/m/n/10 FALSE []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 in-her-its from [][][]\T1/pcr/m/n/10 RsparseMatrix[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4713--4716 []\T1/ptm/m/n/10 Function [][][]\T1/pcr/m/n/10 sparseMatrix[][][][]\T1/ptm/m/n/ 10 , for con-struct-ing ob-jects in-her-it-ing from vir-tual class [2402] Underfull \hbox (badness 10000) in paragraph at lines 4757--4761 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10 new("dsCMatrix", ...) []\T1/ptm/m/n/10 or Underfull \hbox (badness 2103) in paragraph at lines 4757--4761 []\T1/pcr/m/n/10 new("dsTMatrix", ...)[]\T1/ptm/m/n/10 , or au-to-mat-i-cally v ia e.g., []\T1/pcr/m/n/10 as(*, "symmetricMatrix")[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1571) in paragraph at lines 4807--4810 []\T1/pcr/m/n/10 signature(x = "dsCMatrix", pivot = "logical")[]\T1/ptm/m/n/10 : Re-turns (and stores) the [2403] [2404] Underfull \hbox (badness 10000) in paragraph at lines 4949--4954 []\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "dMatrix"[]\T1/ptm/m/n/10 , by class [] \T1/pcr/m/n/10 "dsparseMatrix"[]\T1/ptm/m/n/10 , class []\T1/pcr/m/n/10 "sparse Matrix"[]\T1/ptm/m/n/10 , by Underfull \hbox (badness 6961) in paragraph at lines 4949--4954 \T1/ptm/m/n/10 class []\T1/pcr/m/n/10 "dsparseMatrix" []\T1/ptm/m/n/10 or []\T1 /pcr/m/n/10 "RsparseMatrix"[]\T1/ptm/m/n/10 ; class []\T1/pcr/m/n/10 "compMatri x" []\T1/ptm/m/n/10 by class Underfull \hbox (badness 1400) in paragraph at lines 4961--4964 []\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")[]\T1/ptm/m/n/10 : if []\T1/pcr/m/n/10 uplo == [2405] Underfull \hbox (badness 10000) in paragraph at lines 5013--5015 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10 new("dsyMatrix", ...) []\T1/ptm/m/n/10 or Underfull \hbox (badness 1365) in paragraph at lines 5049--5052 []\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")[]\T1/ptm/m/n/10 , or []\T1/pcr/m/n/10 x = "dsyMatrix" [2406] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5095--5095 []\T1/pcr/m/n/9 stopifnot(all(S1 == S2)) # equal "seen as matrix", but differ internally :[] [2407] [2408] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5201--5201 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim = c(5L, 5L),[] Underfull \hbox (badness 3635) in paragraph at lines 5256--5260 []\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ddenseMatrix"[]\T1/ptm/m/n/10 , di-rec tly. Class []\T1/pcr/m/n/10 "triangularMatrix"[]\T1/ptm/m/n/10 , di-rectly. Cla ss Underfull \hbox (badness 10000) in paragraph at lines 5265--5268 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")[]\T1/ptm/m/n/10 : Ma-trix mul-ti-pli-ca-tion; Underfull \hbox (badness 10000) in paragraph at lines 5268--5272 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")[]\T1/ptm/m/n /10 : the [2409] [2410] [2411] [2412] Underfull \hbox (badness 10000) in paragraph at lines 5524--5526 []\T1/ptm/m/n/10 a ma-trix fac-tor-iza-tion, typ-i-cally in-her-it-ing from vir -tual class Overfull \hbox (29.27832pt too wide) in paragraph at lines 5543--5543 [] \T1/pcr/m/n/10 all.equal(as(x, "matrix"), as(Reduce(\TS1/cmtt/m/n/10 `\T 1/pcr/m/n/10 %*%\TS1/cmtt/m/n/10 `\T1/pcr/m/n/10 , expand2(y)), "matrix")) Overfull \hbox (37.71342pt too wide) in alignment at lines 5574--5574 [] [] [2413] Underfull \hbox (badness 7064) in paragraph at lines 5602--5619 []\T1/pcr/m/n/10 signature(x = "p?BunchKaufman")[]\T1/ptm/m/n/10 : ex-pands the fac-tor-iza-tion $\OML/cmm/m/it/10 A \OT1/cmr/m/n/10 = Underfull \hbox (badness 3000) in paragraph at lines 5631--5638 []\T1/pcr/m/n/10 signature(x = "denseLU")[]\T1/ptm/m/n/10 : ex-pands the fac-to r-iza-tion $\OML/cmm/m/it/10 A \OT1/cmr/m/n/10 = \OML/cmm/m/it/10 P[]LU$ \T1/pt m/m/n/10 as Underfull \hbox (badness 2735) in paragraph at lines 5647--5654 []\T1/pcr/m/n/10 signature(x = "CHMfactor")[]\T1/ptm/m/n/10 : as []\T1/pcr/m/n/ 10 expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/pcr/m/n/10 list(P, L)[]\T1/p tm/m/n/10 . Underfull \hbox (badness 1337) in paragraph at lines 5654--5669 []\T1/pcr/m/n/10 signature(x = "sparseLU")[]\T1/ptm/m/n/10 : as []\T1/pcr/m/n/1 0 expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/pcr/m/n/10 list(P, L, U, Underfull \hbox (badness 2680) in paragraph at lines 5654--5669 \T1/pcr/m/n/10 Q)[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 expand(x)[["Q"]] []\T1/ptm /m/n/10 and []\T1/pcr/m/n/10 expand2(x)[["P2."]] []\T1/ptm/m/n/10 rep-re-sent t he same per- Underfull \hbox (badness 5374) in paragraph at lines 5654--5669 \T1/ptm/m/n/10 mu-ta-tion ma-trix $\OML/cmm/m/it/10 P[]$ \T1/ptm/m/n/10 but hav e op-po-site []\T1/pcr/m/n/10 margin []\T1/ptm/m/n/10 slots and in-verted []\T1 /pcr/m/n/10 perm []\T1/ptm/m/n/10 slots. Underfull \hbox (badness 2073) in paragraph at lines 5669--5674 []\T1/pcr/m/n/10 signature(x = "denseLU")[]\T1/ptm/m/n/10 : as []\T1/pcr/m/n/10 expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/pcr/m/n/10 list(L, U, P)[]\T1/ ptm/m/n/10 . [2414] [2415] [2416] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5881--5881 []\T1/pcr/m/n/9 str(pores <- readMM(system.file("external/pores_1.mtx", packag e = "Matrix")))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5882--5882 []\T1/pcr/m/n/9 str(utm <- readHB(system.file("external/utm300.rua" , packag e = "Matrix")))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5883--5883 []\T1/pcr/m/n/9 str(lundA <- readMM(system.file("external/lund_a.mtx" , packag e = "Matrix")))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5884--5884 []\T1/pcr/m/n/9 str(lundA <- readHB(system.file("external/lund_a.rsa" , packag e = "Matrix")))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5885--5885 []\T1/pcr/m/n/9 ## https://math.nist.gov/MatrixMarket/data/Harwell-Boeing/coun terx/counterx.htm[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5886--5886 []\T1/pcr/m/n/9 str(jgl <- readMM(system.file("external/jgl009.mtx" , packag e = "Matrix")))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5892--5892 []\T1/pcr/m/n/9 u. <- url("https://www.cise.ufl.edu/research/sparse/RB/Boeing/ msc00726.tar.gz")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5897--5897 []\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary dir./folder:[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5900--5900 []\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[] [2417] Overfull \hbox (58.38037pt too wide) in paragraph at lines 5910--5910 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume nts to sparseMatrix():[] [2418] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5972--5972 [] \T1/pcr/m/n/9 all.equal(facmul(x, nm, y, trans = TRUE, left = TRUE), crossprod(L, y))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5973--5973 [] \T1/pcr/m/n/9 all.equal(facmul(x, nm, y, trans = TRUE, left = FALSE), t crossprod(y, L))[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6052--6052 []\T1/pcr/m/n/10 .diag2dense(from, kind = ".", shape = "t", packed = FALSE, up lo = "U")[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 6054--6054 []\T1/pcr/m/n/10 .m2dense(from, class = ".ge", uplo = "U", diag = "N", trans = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6057--6057 []\T1/pcr/m/n/10 .diag2sparse(from, kind = ".", shape = "t", repr = "C", uplo = "U")[] [2419] Overfull \hbox (18.78088pt too wide) in paragraph at lines 6059--6059 []\T1/pcr/m/n/10 .m2sparse(from, class = ".gC", uplo = "U", diag = "N", trans = FALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 6131--6133 []\T1/ptm/m/n/10 a string in []\T1/pcr/m/n/10 c("trace", "sumLog", "prod", "min ", "max", [2420] Underfull \hbox (badness 10000) in paragraph at lines 6206--6212 [][]\T1/pcr/m/n/10 .solve.dgC.*(a, b)[]\T1/ptm/b/n/10 : []\T1/pcr/m/n/10 .solv e.dgC.lu(a, b) []\T1/ptm/m/n/10 needs a square ma-trix []\T1/pcr/m/n/10 a[]\T1/ ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 6206--6212 []\T1/pcr/m/n/10 .solve.dgC.qr(a, b) []\T1/ptm/m/n/10 needs a ``long'' ma-trix []\T1/pcr/m/n/10 a[]\T1/ptm/m/n/10 , with []\T1/pcr/m/n/10 nrow(a) >= ncol(a)[] \T1/ptm/m/n/10 . [2421] Underfull \hbox (badness 10000) in paragraph at lines 6220--6229 [][]\T1/pcr/m/n/10 .updateCHMfactor(object, parent, mult)[]\T1/ptm/b/n/10 : [] \T1/pcr/m/n/10 .updateCHMfactor []\T1/ptm/m/n/10 up- Underfull \hbox (badness 10000) in paragraph at lines 6220--6229 \T1/ptm/m/n/10 dates []\T1/pcr/m/n/10 object []\T1/ptm/m/n/10 with the re-sult of Cholesky fac-tor-iz-ing []\T1/pcr/m/n/10 F(parent) + mult[1] * Underfull \hbox (badness 2443) in paragraph at lines 6220--6229 \T1/pcr/m/n/10 diag(nrow(parent))[]\T1/ptm/m/n/10 , i.e., []\T1/pcr/m/n/10 F(pa rent) []\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 mult[1] []\T1/ptm/m/n/10 times the iden-tity ma-trix, [2422] [2423] [2424] Underfull \hbox (badness 10000) in paragraph at lines 6486--6491 []\T1/ptm/m/n/10 Classes [][][]\T1/pcr/m/n/10 compMatrix[][][][]\T1/ptm/m/n/10 , and the non-general vir-tual classes: [][][]\T1/pcr/m/n/10 symmetricMatrix[][ ][][]\T1/ptm/m/n/10 , [2425] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.image}) h as been already used, duplicate ignored \relax l.6529 \aliasA{image}{image-methods}{image} [2426] [2427] Underfull \hbox (badness 4120) in paragraph at lines 6625--6628 []\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][ ][]\T1/pcr/m/n/10 dgTMatrix[][][] []\T1/ptm/m/n/10 class. Use Overfull \hbox (47.58038pt too wide) in paragraph at lines 6644--6644 []\T1/pcr/m/n/9 stopifnot(!is.null(leg <- imgC$legend), is.list(leg$right)) # failed for 2 days ..[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6664--6664 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col /row) indices:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 6670--6670 [] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, border.col=NA)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 6671--6671 [] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd =2, border.col=NA)[] Overfull \hbox (144.78027pt too wide) in paragraph at lines 6675--6675 []\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor der.col = adjustcolor("skyblue", 1/2))[] [2428] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6683--6683 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a nti-aliasing[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 6686--6686 [] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi ly zoom in and out[] [2429] Underfull \hbox (badness 10000) in paragraph at lines 6820--6823 []\T1/pcr/m/n/10 signature(x = "indMatrix", y = "Matrix") []\T1/ptm/m/n/10 and oth-ers listed by Underfull \hbox (badness 1286) in paragraph at lines 6820--6823 []\T1/pcr/m/n/10 showMethods("%*%", classes = "indMatrix")[]\T1/ptm/m/n/10 : ma -trix prod-ucts im-ple-mented Underfull \hbox (badness 10000) in paragraph at lines 6823--6826 []\T1/pcr/m/n/10 signature(from = "numeric", to = "indMatrix")[]\T1/ptm/m/n/10 : sup-port-ing typ-i-cal Underfull \hbox (badness 3375) in paragraph at lines 6826--6831 []\T1/pcr/m/n/10 signature(from = "list", to = "indMatrix")[]\T1/ptm/m/n/10 : s up-port-ing []\T1/pcr/m/n/10 indMatrix [2430] Underfull \hbox (badness 4156) in paragraph at lines 6837--6839 []\T1/pcr/m/n/10 signature(x = "indMatrix")[]\T1/ptm/m/n/10 : row and Underfull \hbox (badness 1337) in paragraph at lines 6843--6847 []\T1/pcr/m/n/10 signature(X = "indMatrix", Y = "indMatrix")[]\T1/ptm/m/n/10 : Kro-necker prod-uct of Underfull \hbox (badness 1776) in paragraph at lines 6853--6862 []\T1/ptm/m/n/10 Fabian Scheipl at `\T1/pcr/m/n/10 uni-muenchen.de\T1/ptm/m/n/1 0 ', build-ing on the ex-ist-ing class [][][]\T1/pcr/m/n/10 pMatrix[][][] []\T1 /ptm/m/n/10 af-ter Underfull \hbox (badness 1253) in paragraph at lines 6853--6862 \T1/ptm/m/n/10 a nice hike's con-ver-sa-tion with Mar-tin Maech-ler. Meth-ods f or [][][]\T1/pcr/m/n/10 crossprod[][][](x, y) []\T1/ptm/m/n/10 and [2431] Underfull \hbox (badness 1509) in paragraph at lines 6946--6948 []\T1/ptm/m/n/10 an in-te-ger off-set, in-di-cat-ing that the re-sult should be a per-mu-ta-tion of Underfull \hbox (badness 10000) in paragraph at lines 6973--6977 []\T1/pcr/m/n/10 invertPerm(p) []\T1/ptm/m/n/10 re-turns an in-te-ger vec-tor o f length []\T1/pcr/m/n/10 length(p) []\T1/ptm/m/n/10 such that Underfull \hbox (badness 4441) in paragraph at lines 6973--6977 []\T1/pcr/m/n/10 p[invertPerm(p)] []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 invertP erm(p)[p] []\T1/ptm/m/n/10 are both []\T1/pcr/m/n/10 seq_along(p)[]\T1/ptm/m/n/ 10 , i.e., the [2432] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7010--7010 []\T1/pcr/m/n/9 ## Product of transpositions (1 2)(2 1)(4 3)(6 8)(10 1) = (3 4 )(6 8)(1 10)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.anyNA}) h as been already used, duplicate ignored \relax l.7024 \aliasA{anyNA}{is.na-methods}{anyNA} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.finite }) has been already used, duplicate ignored \relax l.7031 ...asA{is.finite}{is.na-methods}{is.finite} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.infini te}) has been already used, duplicate ignored \relax l.7039 ...is.infinite}{is.na-methods}{is.infinite} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.na}) h as been already used, duplicate ignored \relax l.7047 \aliasA{is.na}{is.na-methods}{is.na} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.nan}) has been already used, duplicate ignored \relax l.7054 \aliasA{is.nan}{is.na-methods}{is.nan} [2433] [2434] [2435] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.isSymmetr ic}) has been already used, duplicate ignored \relax l.7213 ...etric}{isSymmetric-methods}{isSymmetric} Overfull \hbox (138.78088pt too wide) in paragraph at lines 7260--7260 []\T1/pcr/m/n/10 isSymmetric(object, checkDN = TRUE, tol = 100 * .Machine$doub le.eps, tol1 = 8 * tol, ...)[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 7262--7262 []\T1/pcr/m/n/10 isSymmetric(object, checkDN = TRUE, tol = 100 * .Machine$doub le.eps, ...)[] [2436] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7317--7317 []\T1/pcr/m/n/9 isSymmetric(as(M, "generalMatrix")) # still symmetric, even if not "formally"[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7321--7321 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs = TRUE) # includes S3 g eneric from base[] [2437] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7404--7404 []\T1/pcr/m/n/9 isTriangular(as(M, "generalMatrix")) # still triangular, even if not "formally"[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 7431--7431 []\T1/pcr/m/n/10 KhatriRao(X, Y = X, FUN = "*", sparseY = TRUE, make.dimnames = FALSE) [2438] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7507--7507 []\T1/pcr/m/n/9 stopifnot(all(K1 <- KhatriRao(nd, zm) == 0), identical(dim(K1) , c(12L, 4L)),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7508--7508 [] \T1/pcr/m/n/9 all(K2 <- KhatriRao(zm, nd) == 0), identical(dim(K2) , c(12L, 4L)))[] [2439] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7515--7515 [] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di mnames(Kmd)))[] [2440] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.kronecker }) has been already used, duplicate ignored \relax l.7589 ...kronecker}{kronecker-methods}{kronecker} Underfull \hbox (badness 1062) in paragraph at lines 7686--7689 []\T1/pcr/m/n/10 ldenseMatrix []\T1/ptm/m/n/10 is the vir-tual class of all den se \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both [2441] Underfull \hbox (badness 6063) in paragraph at lines 7712--7715 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-call y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2442 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.*,ndiMatr ix,Matrix.Rdash.method}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.7826 C lass \code{"\LinkA{sparseMatrix}{sparseMatrix.Rdash.class}"}, by cla... ] Underfull \hbox (badness 2635) in paragraph at lines 7873--7878 []\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ldenseMatrix"[]\T1/ptm/m/n/10 , di-rec tly. Class []\T1/pcr/m/n/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/ 10 "ldenseMatrix"[]\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 7873--7878 \T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "denseMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/10 "ldenseMatrix"[]\T1/ptm/m/n/10 . Class []\T1/pcr/m/n/10 "Matri x"[]\T1/ptm/m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 7881--7884 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ); use, e.g., [2443] Underfull \hbox (badness 10000) in paragraph at lines 7938--7948 []\T1/pcr/m/n/10 lsTMatrix[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 ltTMatrix[]\T 1/ptm/m/n/10 ) or in com-pressed column-oriented form (class Underfull \hbox (badness 1242) in paragraph at lines 7938--7948 [][][]\T1/pcr/m/n/10 CsparseMatrix[][][][]\T1/ptm/m/n/10 , sub-classes []\T1/pc r/m/n/10 lgCMatrix[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lsCMatrix[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 ltCMatrix[]\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\ T1/ptm/m/n/10 --in [2444] Underfull \hbox (badness 3179) in paragraph at lines 8020--8023 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cal ly equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2445] Underfull \hbox (badness 10000) in paragraph at lines 8105--8108 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ; use, e.g., [2446] Underfull \hbox (badness 10000) in paragraph at lines 8166--8169 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ; use, e.g., [2447] [2448] [2449] Underfull \hbox (badness 10000) in paragraph at lines 8404--8407 []\T1/ptm/m/n/10 vector of all non-zero en-tries of []\T1/pcr/m/n/10 x[]\T1/ptm /m/n/10 ; ex-ists \T1/ptm/b/n/10 only \T1/ptm/m/n/10 when []\T1/pcr/m/n/10 as(x , Underfull \hbox (badness 1490) in paragraph at lines 8426--8428 []\T1/pcr/m/n/10 mat2triplet() []\T1/ptm/m/n/10 is con-cep-tu-ally the \T1/ptm/ m/it/10 in-verse \T1/ptm/m/n/10 func-tion of [][][]\T1/pcr/m/n/10 spMatrix[][][ ] []\T1/ptm/m/n/10 and (one case of) [2450] pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rpcent.* .Rpcent.}) has been already used, duplicate ignored \relax l.8447 ...*\%}{matmult-methods}{.Rpcent.*.Rpcent.} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.crossprod }) has been already used, duplicate ignored \relax l.8521 ...A{crossprod}{matmult-methods}{crossprod} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tcrosspro d}) has been already used, duplicate ignored \relax l.8597 ...tcrossprod}{matmult-methods}{tcrossprod} Underfull \hbox (badness 1881) in paragraph at lines 8683--8689 \T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][][]\T1/ pcr/m/n/10 t[][][](.)[]\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn [2451] Underfull \hbox (badness 10000) in paragraph at lines 8752--8755 []\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")[]\T1/ptm/m/n/10 : Ma-trix mul-ti-pli-ca-tion; Underfull \hbox (badness 10000) in paragraph at lines 8755--8760 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and other sig-na-tures (use Underfull \hbox (badness 3557) in paragraph at lines 8755--8760 []\T1/pcr/m/n/10 showMethods("%*%", class="dtrMatrix")[]\T1/ptm/m/n/10 ): ma-tr ix mul-ti-pli-ca-tion. Mul-ti- Underfull \hbox (badness 6608) in paragraph at lines 8760--8764 \T1/ptm/m/n/10 sig-na-tures, use []\T1/pcr/m/n/10 showMethods("crossprod", clas s = "dgeMatrix")[]\T1/ptm/m/n/10 , ma-trix Underfull \hbox (badness 1552) in paragraph at lines 8770--8771 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and other sig-na- [2452] [2453] [2454] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det}) has been already used, duplicate ignored \relax l.8995 \aliasA{det}{Matrix-class}{det} Underfull \hbox (badness 1337) in paragraph at lines 9069--9072 []\T1/pcr/m/n/10 signature(x = "Matrix", value = "list")[]\T1/ptm/m/n/10 : set the []\T1/pcr/m/n/10 dimnames []\T1/ptm/m/n/10 to a Underfull \hbox (badness 10000) in paragraph at lines 9082--9085 [2455] Underfull \hbox (badness 10000) in paragraph at lines 9091--9093 []\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")[]\T1/ptm/m/n/10 : This re-lies on a cor-rect [2456] [2457] Underfull \hbox (badness 10000) in paragraph at lines 9260--9264 []\T1/pcr/m/n/10 CholeskyFactorization[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Bunch KaufmanFactorization[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 9283--9285 []\T1/pcr/m/n/10 signature(x = "MatrixFactorization", logarithm = Underfull \hbox (badness 10000) in paragraph at lines 9300--9303 []\T1/pcr/m/n/10 signature(obj = "MatrixFactorization")[]\T1/ptm/m/n/10 : re-tu rns []\T1/pcr/m/n/10 obj []\T1/ptm/m/n/10 with [2458] Underfull \hbox (badness 3019) in paragraph at lines 9312--9315 []\T1/ptm/m/n/10 Classes ex-tend-ing []\T1/pcr/m/n/10 CholeskyFactorization[]\T 1/ptm/m/n/10 , namely [][][]\T1/pcr/m/n/10 Cholesky[][][][]\T1/ptm/m/n/10 , [][ ][]\T1/pcr/m/n/10 pCholesky[][][][]\T1/ptm/m/n/10 , and Underfull \hbox (badness 10000) in paragraph at lines 9316--9318 []\T1/ptm/m/n/10 Classes ex-tend-ing []\T1/pcr/m/n/10 BunchKaufmanFactorization []\T1/ptm/m/n/10 , namely [][][]\T1/pcr/m/n/10 BunchKaufman[][][] []\T1/ptm/m/n /10 and Underfull \hbox (badness 10000) in paragraph at lines 9331--9334 []\T1/ptm/m/n/10 Generic func-tions [][][]\T1/pcr/m/n/10 expand1[][][] []\T1/pt m/m/n/10 and [][][]\T1/pcr/m/n/10 expand2[][][] []\T1/ptm/m/n/10 for con-struct -ing ma-trix fac-tors from Underfull \hbox (badness 1062) in paragraph at lines 9360--9363 []\T1/pcr/m/n/10 ndenseMatrix []\T1/ptm/m/n/10 is the vir-tual class of all den se \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both Underfull \hbox (badness 6063) in paragraph at lines 9392--9395 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-call y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2459] Underfull \hbox (badness 3312) in paragraph at lines 9449--9451 []\T1/ptm/m/n/10 logical in-di-cat-ing if []\T1/pcr/m/n/10 X <- (X + t(X))/2 [] \T1/ptm/m/n/10 should be done, af-ter []\T1/pcr/m/n/10 X <- [2460] [2461] Overfull \hbox (85.38034pt too wide) in paragraph at lines 9552--9552 [] \T1/pcr/m/n/9 all.equal(n.A.m, unname(as.matrix(n.A$mat)), tolerance = 1e -15)# seen rel.d.= 1.46e-16[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 9592--9592 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a ll in this example[] [2462] Underfull \hbox (badness 2635) in paragraph at lines 9645--9650 []\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ndenseMatrix"[]\T1/ptm/m/n/10 , di-rec tly. Class []\T1/pcr/m/n/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/ 10 "ndenseMatrix"[]\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 9645--9650 \T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "denseMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/10 "ndenseMatrix"[]\T1/ptm/m/n/10 . Class []\T1/pcr/m/n/10 "Matri x"[]\T1/ptm/m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 9653--9656 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ); use, e.g., [2463] Underfull \hbox (badness 2521) in paragraph at lines 9721--9727 []\T1/pcr/m/n/10 signature(from = "matrix", to = "nMatrix")[]\T1/ptm/m/n/10 : N ote that these co-er-cions [2464] Underfull \hbox (badness 1867) in paragraph at lines 9834--9836 []\T1/ptm/m/n/10 fast sim- [2465] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.norm}) ha s been already used, duplicate ignored \relax l.9876 \aliasA{norm}{norm-methods}{norm} [2466] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9971--9971 []\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9972--9972 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9973--9973 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Underfull \hbox (badness 2401) in paragraph at lines 10018--10028 []\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][][]\T1/pcr/m/n /10 TsparseMatrix[][][][]\T1/ptm/m/n/10 , sub-classes []\T1/pcr/m/n/10 ngTMatri x[]\T1/ptm/m/n/10 , [2467] Underfull \hbox (badness 3179) in paragraph at lines 10089--10092 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cal ly equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2468] Underfull \hbox (badness 10000) in paragraph at lines 10169--10172 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ; use, e.g., [2469] Underfull \hbox (badness 10000) in paragraph at lines 10233--10236 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ; use, e.g., [2470] [2471] Underfull \hbox (badness 10000) in paragraph at lines 10330--10332 []\T1/ptm/m/n/10 typically a []\T1/pcr/m/n/10 "packedMatrix"[]\T1/ptm/m/n/10 , though [2472] [2473] Underfull \hbox (badness 10000) in paragraph at lines 10547--10550 []\T1/pcr/m/n/10 signature(x = "pMatrix", y = "Matrix") []\T1/ptm/m/n/10 and ot h-ers listed by Underfull \hbox (badness 8189) in paragraph at lines 10547--10550 []\T1/pcr/m/n/10 showMethods("%*%", classes = "pMatrix")[]\T1/ptm/m/n/10 : ma-t rix prod-ucts im-ple-mented [2474] Underfull \hbox (badness 10000) in paragraph at lines 10550--10554 []\T1/pcr/m/n/10 signature(from = "numeric", to = "pMatrix")[]\T1/ptm/m/n/10 : sup-port-ing typ-i-cal Underfull \hbox (badness 2460) in paragraph at lines 10558--10564 []\T1/pcr/m/n/10 signature(a = "pMatrix", b = "missing")[]\T1/ptm/m/n/10 : the in-verse per-mu-ta-tion ma-trix, [2475] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10628--10628 [] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD iag = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10631--10631 []\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m ax.print")),[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10633--10633 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 10637--10637 []\T1/pcr/m/n/10 printSpMatrix2(x, digits = NULL, maxp = max(100L, getOption(" max.print")),[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10638--10638 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Underfull \hbox (badness 3989) in paragraph at lines 10663--10673 []\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of [] \T1/pcr/m/n/10 x []\T1/ptm/m/n/10 should Underfull \hbox (badness 10000) in paragraph at lines 10663--10673 \T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro m [2476] [2477] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr}) has been already used, duplicate ignored \relax l.10764 \aliasA{qr}{qr-methods}{qr} [2478] [2479] Overfull \hbox (25.98041pt too wide) in paragraph at lines 10896--10896 [] \T1/pcr/m/n/9 all.equal(qr.coef(qr.A1, b), drop(solve(crossprod(A1), cro ssprod(A1, b))))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10912--10912 [] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 qr.coef\TS1/pcr/m/n/9 ' \ T1/pcr/m/n/9 computes unique least squares solution of "nearby" problem[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10913--10913 [] \T1/pcr/m/n/9 ## Z x = b for some full rank Z ~ A, currently without war ning {FIXME} ![] Underfull \vbox (badness 10000) has occurred while \output is active [2480] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10956--10956 []\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m atrix"), ...)[] [2481] Underfull \hbox (badness 2005) in paragraph at lines 11008--11014 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of [][][]\T1/pcr/m/n/10 qr[][][](x, tol, Underfull \hbox (badness 10000) in paragraph at lines 11025--11028 []\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense []\T1/pcr/m/n/10 x[]\ T1/ptm/m/n/10 , it cor-re-sponds to [2482] Overfull \hbox (85.38034pt too wide) in paragraph at lines 11124--11124 []\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/ n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale free"[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 11140--11140 []\T1/pcr/m/n/9 sapply(meths, function(.m.) rankMatrix(M15, method = .m., tol = 1e-7)) # all 14[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 11147--11147 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # war ning+ ~1.5 sec (2013)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 11148--11148 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con siderably faster![] [2483] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h as been already used, duplicate ignored \relax l.11167 \aliasA{rcond}{rcond-methods}{rcond} [2484] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11283--11283 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not have full rank[] [2485] [2486] [2487] Underfull \hbox (badness 2150) in paragraph at lines 11476--11484 \T1/ptm/m/n/10 dices, if not []\T1/pcr/m/n/10 symmetric [][]sample.int[][][](nr ow*ncol, nnz)[]\T1/ptm/m/n/10 , then---if []\T1/pcr/m/n/10 rand.x []\T1/ptm/m/n /10 is not [2488] [2489] Underfull \hbox (badness 5147) in paragraph at lines 11633--11636 []\T1/ptm/m/n/10 Class [][][]\T1/pcr/m/n/10 SchurFactorization[][][][]\T1/ptm/m /n/10 , di-rectly. Class [][][]\T1/pcr/m/n/10 MatrixFactorization[][][][]\T1/pt m/m/n/10 , by class [2490] Underfull \hbox (badness 3179) in paragraph at lines 11648--11651 []\T1/pcr/m/n/10 signature(from = "Schur", logarithm = "logical")[]\T1/ptm/m/n/ 10 : com-putes [2491] [2492] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11813--11813 [] \T1/pcr/m/n/9 all.equal(e1, e3[order(Mod(e3), decreasing = TRUE)], toler ance = 1e-13)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solve}) h as been already used, duplicate ignored \relax l.11823 \aliasA{solve}{solve-methods}{solve} [2493] Overfull \hbox (90.78088pt too wide) in paragraph at lines 11947--11947 []\T1/pcr/m/n/10 solve(a, b, system = c("A", "LDLt", "LD", "DLt", "L", "Lt", " D", "P", "Pt"), ...)[] Underfull \hbox (badness 1147) in paragraph at lines 11959--11965 []\T1/ptm/m/n/10 a vec-tor, [][][]\T1/pcr/m/n/10 sparseVector[][][][]\T1/ptm/m/ n/10 , ma-trix, or [][][]\T1/pcr/m/n/10 Matrix[][][] []\T1/ptm/m/n/10 sat-is-fy -ing []\T1/pcr/m/n/10 NROW(b) == Underfull \hbox (badness 3460) in paragraph at lines 12009--12014 []\T1/ptm/m/n/10 Methods for dense []\T1/pcr/m/n/10 a []\T1/ptm/m/n/10 are buil t on 14 LA-PACK rou-tines: class []\T1/pcr/m/n/10 d..Matrix[]\T1/ptm/m/n/10 , w here [2494] Overfull \hbox (52.98038pt too wide) in paragraph at lines 12082--12082 []\T1/pcr/m/n/9 image(ia0 <- solve(a, tol = 0)) # checker board, dense [but re ally, a is singular!][] Overfull \hbox (25.98041pt too wide) in paragraph at lines 12086--12086 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] [2495] Underfull \hbox (badness 10000) in paragraph at lines 12109--12112 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, from a for-mu la and data frame Overfull \hbox (6.78088pt too wide) in paragraph at lines 12126--12126 [] \T1/pcr/m/n/10 drop.unused.levels = TRUE, repr = c("C", "R", "T"), giveCs parse)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 12128--12128 [] \T1/pcr/m/n/10 drop.unused.levels = TRUE, repr = c("C", "R", "T"), giveCs parse,[] Underfull \hbox (badness 1648) in paragraph at lines 12137--12139 []\T1/ptm/m/n/10 a data frame cre-ated with [][][]\T1/pcr/m/n/10 model.frame[][ ][][]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 10000) in paragraph at lines 12145--12148 []\T1/ptm/m/n/10 character string or []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or (co-er-ca-ble to) Underfull \hbox (badness 2591) in paragraph at lines 12145--12148 []\T1/pcr/m/n/10 "[][]sparseMatrix[][][]"[]\T1/ptm/m/n/10 , spec-i-fy-ing the c on-trasts to be ap-plied to the Underfull \hbox (badness 10000) in paragraph at lines 12156--12160 []\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for Underfull \hbox (badness 2828) in paragraph at lines 12156--12160 []\T1/pcr/m/n/10 sparse.model.matrix []\T1/ptm/m/n/10 has been changed to []\T1 /pcr/m/n/10 FALSE[]\T1/ptm/m/n/10 , 2010-07, for [2496] Underfull \hbox (badness 1668) in paragraph at lines 12171--12176 [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/ m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse Underfull \hbox (badness 3291) in paragraph at lines 12198--12203 []\T1/pcr/m/n/10 model.Matrix(sparse = TRUE) []\T1/ptm/m/n/10 from pack-age [][ ]\T1/ptm/b/n/10 Ma-trix-Mod-els[][] \T1/ptm/m/n/10 may be nowa-days be Underfull \hbox (badness 2073) in paragraph at lines 12198--12203 \T1/ptm/m/n/10 prefer-able to []\T1/pcr/m/n/10 sparse.model.matrix[]\T1/ptm/m/n /10 , as []\T1/pcr/m/n/10 model.Matrix []\T1/ptm/m/n/10 re-turns an ob-ject of class [2497] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12252--12252 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M) == c(0, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12253--12253 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M) == c(3, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12254--12254 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2498] Underfull \hbox (badness 2961) in paragraph at lines 12316--12319 []\T1/pcr/m/n/10 signature(from = "sparseLU", logarithm = "logical")[]\T1/ptm/m /n/10 : com- Overfull \hbox (9.78043pt too wide) in paragraph at lines 12359--12359 []\T1/pcr/m/n/9 A <- as(readMM(system.file("external", "pores_1.mtx", package = "Matrix")),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12370--12370 []\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m atrix"), ...)[] [2499] Overfull \hbox (20.58041pt too wide) in paragraph at lines 12377--12377 [] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(dn[1L ], list(NULL)),[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 12380--12380 [] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(list( NULL), dn[2L]),[] Underfull \hbox (badness 10000) in paragraph at lines 12405--12407 []\T1/ptm/m/n/10 This in-ter-face is rec-om-mended over di-rect con-struc-tion via calls such as Overfull \hbox (0.78088pt too wide) in paragraph at lines 12412--12412 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] [2500] Underfull \hbox (badness 2261) in paragraph at lines 12450--12456 \T1/ptm/m/n/10 of the sparse ma-trix re-sult, i.e., spec-i-fy-ing one of the vi r-tual classes [2501] Underfull \hbox (badness 10000) in paragraph at lines 12539--12542 []\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][][]\T1/pcr/m/n/10 xtabs[][][ ](*, sparse=TRUE)[]\T1/ptm/m/n/10 , for sparse ta-bles and Overfull \hbox (4.38043pt too wide) in paragraph at lines 12552--12552 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12556--12556 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12557--12557 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12562--12562 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims = c(10,20)))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12565--12565 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar e consistent[] [2502] Overfull \hbox (15.18042pt too wide) in paragraph at lines 12588--12588 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 12589--12589 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12615--12615 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep resentations.[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 12618--12618 [] \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack age = "SparseM"))) {[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12620--12620 [] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims = X@dimension)[] [2503] Underfull \hbox (badness 6842) in paragraph at lines 12710--12713 []\T1/pcr/m/n/10 (x = "sparseMatrix", logarithm=TRUE)[]\T1/ptm/m/n/10 : [][][]\ T1/pcr/m/n/10 determinant[][][]() []\T1/ptm/m/n/10 meth-ods Underfull \hbox (badness 10000) in paragraph at lines 12745--12749 [][][]\T1/pcr/m/n/10 sparseMatrix[][][][]\T1/ptm/m/n/10 , and its ref-er-ences, such as [][][]\T1/pcr/m/n/10 xtabs[][][](*, sparse=TRUE)[]\T1/ptm/m/n/10 , or [2504] [2505] Underfull \hbox (badness 2961) in paragraph at lines 12929--12932 []\T1/pcr/m/n/10 signature(from = "sparseQR", logarithm = "logical")[]\T1/ptm/m /n/10 : com- [2506] Underfull \hbox (badness 3229) in paragraph at lines 13007--13011 []\T1/ptm/m/n/10 The many aux-il-iary func-tions for QR fac-tor-iza-tions: [][] []\T1/pcr/m/n/10 qr.Q[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 qr.R[][][][] \T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 qr.X[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc r/m/n/10 qr.coef[][][][]\T1/ptm/m/n/10 , [2507] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13047--13047 []\T1/pcr/m/n/9 ae1 <- function(a, b, ...) all.equal(as(a, "matrix"), as(b, "m atrix"), ...)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 13055--13055 [] \T1/pcr/m/n/9 new("pMatrix", Dim = c(m, m), Dimnames = c(dn[1L ], list(NULL)),[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 13058--13058 [] \T1/pcr/m/n/9 new("pMatrix", Dim = c(n, n), Dimnames = c(list( NULL), dn[2L]),[] Underfull \vbox (badness 10000) has occurred while \output is active [2508] Overfull \hbox (42.18039pt too wide) in paragraph at lines 13077--13077 [] \T1/pcr/m/n/9 ae2(qrc <- qr.coef (qr.A, b), with(e.qr.A, solve(R1 %*% P 2., t(qrQ)) %*% b))[] Underfull \hbox (badness 5036) in paragraph at lines 13112--13114 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a [2509] Underfull \hbox (badness 2970) in paragraph at lines 13232--13238 []\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class []\T1/pcr/m/ n/10 "sparseVector" []\T1/ptm/m/n/10 has the five ac- Underfull \hbox (badness 3679) in paragraph at lines 13232--13238 \T1/ptm/m/n/10 tual daugh-ter classes []\T1/pcr/m/n/10 "dsparseVector"[]\T1/ptm /m/n/10 , []\T1/pcr/m/n/10 "isparseVector"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 " lsparseVector"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13277--13280 []\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") []\T1/ptm/m/ n/10 co-erces sparse [2510] Underfull \hbox (badness 10000) in paragraph at lines 13317--13322 []\T1/pcr/m/n/10 (x = "nsparseVector")[]\T1/ptm/m/n/10 : re-turn [][][]\T1/pcr/ m/n/10 logical[][][] []\T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 13332--13334 [][][]\T1/pcr/m/n/10 sparseVector[][][]() []\T1/ptm/m/n/10 for friendly con-str uc-tion of sparse vec-tors (apart from []\T1/pcr/m/n/10 as(*, [2511] Underfull \vbox (badness 10000) has occurred while \output is active [2512] Overfull \hbox (24.78088pt too wide) in paragraph at lines 13432--13432 []\T1/pcr/m/n/10 spMatrix(nrow, ncol, i = integer(0L), j = integer(0L), x = do uble(0L)) Underfull \hbox (badness 2310) in paragraph at lines 13459--13465 [][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) []\T1/ptm/m/n/10 for the more usual con-struc-tor of such ma-tri-ces. Then, [2513] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.[<.Rdash. }) has been already used, duplicate ignored \relax l.13511 ...\Rdash{}}{Subassign-methods}{[<.Rdash.} Underfull \hbox (badness 6910) in paragraph at lines 13598--13600 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2514] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.[}) has b een already used, duplicate ignored \relax l.13647 \aliasA{[}{Subscript-methods}{[} [2515] [2516] Underfull \hbox (badness 2591) in paragraph at lines 13780--13785 \T1/ptm/m/n/10 Classes [][][]\T1/pcr/m/n/10 triangularMatrix[][][][]\T1/ptm/m/n /10 , and, e.g., [][][]\T1/pcr/m/n/10 dsyMatrix[][][] []\T1/ptm/m/n/10 for nu-m eric \T1/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or [2517] Underfull \hbox (badness 2057) in paragraph at lines 13856--13858 []\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe r-ent ma-trix classes, use e.g., Underfull \hbox (badness 6396) in paragraph at lines 13865--13869 []\T1/pcr/m/n/10 symmpart(x) []\T1/ptm/m/n/10 re-turns a sym-met-ric ma-trix, i n-her-it-ing from [][][]\T1/pcr/m/n/10 symmetricMatrix[][][] []\T1/ptm/m/n/10 o r Underfull \hbox (badness 7722) in paragraph at lines 13870--13875 []\T1/pcr/m/n/10 skewpart(x) []\T1/ptm/m/n/10 re-turns a skew-symmetric ma-trix , in-her-it-ing from [][][]\T1/pcr/m/n/10 generalMatrix[][][][]\T1/ptm/m/n/10 , [2518] Underfull \hbox (badness 6641) in paragraph at lines 13947--13950 []\T1/ptm/m/n/10 Currently, [][][]\T1/pcr/m/n/10 Schur[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 isSymmetric[][][] []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 as () []\T1/ptm/m/n/10 (i.e. [][][]\T1/pcr/m/n/10 coerce[][][][]\T1/ptm/m/n/10 ) h ave meth-ods with [2519] Underfull \hbox (badness 5133) in paragraph at lines 13983--13987 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 "TsparseMatrix" []\T1/ptm/m/n/10 class is the vir-tual class of all sparse ma-tri-ces coded in Underfull \hbox (badness 2818) in paragraph at lines 13983--13987 \T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c re-ated from it. See [2520] Underfull \hbox (badness 1668) in paragraph at lines 14113--14116 [][][]\T1/pcr/m/n/10 pack[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 unpac k[][][][]\T1/ptm/m/n/10 ; its vir-tual "com-ple-ment" []\T1/pcr/m/n/10 "[][]pac kedMatrix[][][]"[]\T1/ptm/m/n/10 ; its proper sub-classes [2521] [2522] Underfull \hbox (badness 10000) in paragraph at lines 14224--14230 []\T1/ptm/m/n/10 GAL lat-tice file `\T1/pcr/m/n/10 usc_q.GAL\T1/ptm/m/n/10 ' (r e-trieved in 2008 from [2523] [2524] [2525]) (./boot-pkg.tex [2526] Chapter 18. [2527] [2528] [2529] [2530] [2531] [2532] [2533] Overfull \hbox (12.78088pt too wide) in paragraph at lines 532--532 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f" , "w"), [2534] Underfull \hbox (badness 1325) in paragraph at lines 570--577 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r e-quired. Pos-si-ble Underfull \hbox (badness 1275) in paragraph at lines 585--590 []\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m ulti-sample prob- [2535] [2536] [2537] Underfull \hbox (badness 1881) in paragraph at lines 826--828 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 6493) in paragraph at lines 853--857 [][][]\T1/pcr/m/n/10 boot.array[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 bo ot.ci[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 censboot[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 empinf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 j ack.after.boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 tilt.boot[][][][]\T 1/ptm/m/n/10 , [2538] Overfull \hbox (4.38043pt too wide) in paragraph at lines 887--887 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, data = nuke)[] Underfull \vbox (badness 10000) has occurred while \output is active [2539] [2540] [2541] Underfull \hbox (badness 1496) in paragraph at lines 1084--1093 []\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari- ance of the Underfull \hbox (badness 2005) in paragraph at lines 1084--1093 \T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i n-ter-vals. If it Underfull \hbox (badness 2343) in paragraph at lines 1084--1093 \T1/ptm/m/n/10 is not sup-plied and []\T1/pcr/m/n/10 length(index) []\T1/ptm/m/ n/10 is 2 then []\T1/pcr/m/n/10 var.t0 []\T1/ptm/m/n/10 de-faults to Underfull \hbox (badness 2150) in paragraph at lines 1105--1111 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa ult value is [2542] [2543] [2544] [2545] Underfull \hbox (badness 1571) in paragraph at lines 1445--1447 []\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis- [2546] [2547] [2548] [2549] [2550] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1738--1738 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix( 1,n,2), [2551] [2552] [2553] Underfull \vbox (badness 10000) has occurred while \output is active [2554] Overfull \hbox (31.3804pt too wide) in paragraph at lines 2013--2013 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4) + strata(ulcer),[] [2555] Underfull \hbox (badness 6268) in paragraph at lines 2084--2086 []\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch an-ning House. [2556] [2557] [2558] Underfull \hbox (badness 1565) in paragraph at lines 2338--2343 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori g-i-nal data set [2559] Underfull \hbox (badness 4595) in paragraph at lines 2363--2368 \T1/ptm/m/n/10 are passed un-changed ev-ery time []\T1/pcr/m/n/10 boot.out$stat istic []\T1/ptm/m/n/10 is called. Underfull \hbox (badness 1881) in paragraph at lines 2432--2434 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 2057) in paragraph at lines 2440--2441 [][][]\T1/pcr/m/n/10 boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 empinf[] [][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 k3.linear[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 linear.approx[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 saddle.distn[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 smooth.spline[][][][] \T1/ptm/m/n/10 , [2560] [2561] Underfull \hbox (badness 1077) in paragraph at lines 2536--2540 []\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of []\T1/pcr/m /n/10 n/((n-1)*(n-2)) []\T1/ptm/m/n/10 where []\T1/pcr/m/n/10 n []\T1/ptm/m/n/1 0 is the sam-ple Underfull \hbox (badness 1112) in paragraph at lines 2536--2540 \T1/ptm/m/n/10 size, if []\T1/pcr/m/n/10 unbiased []\T1/ptm/m/n/10 is []\T1/pcr /m/n/10 FALSE []\T1/ptm/m/n/10 then a mul-ti-plier of []\T1/pcr/m/n/10 1/n []\T 1/ptm/m/n/10 is used. This is mul-ti-plied by [2562] [2563] [2564] [2565] [2566] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2895--2895 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25, Overfull \hbox (18.78088pt too wide) in paragraph at lines 2897--2897 []\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25,[] [2567] [2568] [2569] Underfull \hbox (badness 3861) in paragraph at lines 3105--3108 [][][]\T1/pcr/m/n/10 boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 boot.arr ay[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 boot.ci[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 control[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 jack .after.boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 linear.approx[][][][]\ T1/ptm/m/n/10 , [2570] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3158--3158 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1 :ncol(mat)) [2571] [2572] [2573] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3378--3378 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling [2574] [2575] [2576] [2577] [2578] [2579] [2580] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3838--3838 [] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q = NULL)[] [2581] [2582] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3977--3977 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 = grav.z0[3])[] [2583] [2584] [2585] [2586] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4259--4259 []\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz e data as in [2587] [2588] Underfull \hbox (badness 10000) in paragraph at lines 4362--4364 []\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o f Underfull \hbox (badness 1430) in paragraph at lines 4371--4375 \T1/ptm/m/n/10 If []\T1/pcr/m/n/10 t0 []\T1/ptm/m/n/10 is sup-plied but nei-the r []\T1/pcr/m/n/10 t []\T1/ptm/m/n/10 nor []\T1/pcr/m/n/10 L []\T1/ptm/m/n/10 a re sup-plied then []\T1/pcr/m/n/10 t0 []\T1/ptm/m/n/10 is set to [2589] [2590] [2591] [2592] [2593] [2594] [2595] [2596] [2597] Underfull \hbox (badness 3000) in paragraph at lines 4959--4962 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2598] [2599] [2600] [2601] Underfull \hbox (badness 2293) in paragraph at lines 5238--5241 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5238--5241 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2602] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5317--5317 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat a = grav1[, 2])[] [2603] [2604] [2605] [2606] [2607] [2608] [2609] [2610] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5866--5866 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c ity.sp1$spa[1][] [2611] Underfull \hbox (badness 1127) in paragraph at lines 5988--6006 []\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less than []\T1/pcr/m/n/10 min(alpha)/10[]\T1/ptm/m/n/10 , then [2612] Underfull \hbox (badness 2837) in paragraph at lines 6021--6024 []\T1/ptm/m/n/10 The re-turned value is an ob-ject of class []\T1/pcr/m/n/10 "s addle.distn"[]\T1/ptm/m/n/10 . See the help file for [2613] [2614] [2615] [2616] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6306--6306 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and Wright (1991). [2617] [2618] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6495--6495 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling Overfull \hbox (20.58041pt too wide) in paragraph at lines 6497--6497 []\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t ilting was used[] [2619] [2620] [2621] Underfull \hbox (badness 1596) in paragraph at lines 6742--6746 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m ent ex-pected by [2622] [2623] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6902--6902 [] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha = c(0.05, 0.95),[] [2624] [2625] [2626] [2627] [2628] [2629] [2630] [2631]) (./class-pkg.tex [2632] Chapter 19. [2633] [2634] [2635] [2636] [2637] [2638] [2639] [2640] [2641] [2642] [2643] [2644] [2645] [2646] Overfull \hbox (42.18039pt too wide) in paragraph at lines 1006--1006 [] \T1/pcr/m/n/9 alpha = list(seq(0.05, 0, length.out = 1e4), seq(0.02, 0, length.out = 1e5)),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1007--1007 [] \T1/pcr/m/n/9 radii = list(seq(8, 1, length.out = 1e4), seq(4, 1, length .out = 1e5)))[] [2647] [2648]) (./cluster-pkg.tex Chapter 20. [2649] [2650] [2651] Overfull \hbox (42.18039pt too wide) in paragraph at lines 253--253 [] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met hod = 0.5)[iC]) ,[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 254--254 [] \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, -.5))[iC]),[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 255--255 [] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, +.5))[iC]))[] [2652] [2653] [2654] [2655] Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519 [] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot = axes,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 523--523 [] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5, ...)[] [2656] [2657] Overfull \hbox (66.78088pt too wide) in paragraph at lines 638--638 [] \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c orrect.d = TRUE)[] [2658] Underfull \hbox (badness 3078) in paragraph at lines 692--695 []\T1/ptm/m/n/10 Setting this to []\T1/pcr/m/n/10 FALSE []\T1/ptm/m/n/10 saves mem-ory (and hence time), but dis-ables [2659] [2660] Underfull \hbox (badness 2941) in paragraph at lines 795--798 [][][]\T1/pcr/m/n/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-en ces; [][][]\T1/pcr/m/n/10 clara.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 pam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 partition.object[][][][]\ T1/ptm/m/n/10 , [2661] Overfull \hbox (9.78043pt too wide) in paragraph at lines 838--838 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo r this seed):[] Underfull \hbox (badness 10000) in paragraph at lines 885--887 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2662] Overfull \hbox (24.78088pt too wide) in paragraph at lines 950--950 [] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code =3), ...)[] [2663] Underfull \hbox (badness 4872) in paragraph at lines 996--998 []\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is Underfull \hbox (badness 1342) in paragraph at lines 1010--1014 []\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in 2012, [2664] Underfull \hbox (badness 10000) in paragraph at lines 1102--1104 [][][]$\T1/pcr/m/n/10 https : / / bioconductor . org / packages / 3 . 12 / bioc / html / SAGx . html$[][] \T1/ptm/m/n/10 Dep-re- [2665] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1126--1126 [] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE. factor = SEf)))[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 1143--1143 []\T1/pcr/m/n/9 ## You can manually set it before running this : doExtras < - TRUE # or FALSE[] Underfull \vbox (badness 10000) has occurred while \output is active [2666] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1181--1181 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap() ==> k = 1 clust er is optimal")[] Underfull \hbox (badness 4144) in paragraph at lines 1213--1217 []\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 does not have a []\T1 /pcr/m/n/10 diss []\T1/ptm/m/n/10 nor a []\T1/pcr/m/n/10 data []\T1/ptm/m/n/10 com-po-nent, e.g., for [2667] Overfull \hbox (60.78088pt too wide) in paragraph at lines 1289--1289 [] \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1, cex.txt = cex,[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1295--1295 [] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin t variability."),[] [2668] [2669] [2670] Underfull \hbox (badness 10000) in paragraph at lines 1482--1485 Underfull \hbox (badness 10000) in paragraph at lines 1499--1503 [][][]\T1/pcr/m/n/10 princomp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cmds cale[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pam[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 clara[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 daisy[][ ][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 par[][][][]\T1/ptm/m/n/10 , [][][]\T 1/pcr/m/n/10 identify[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cov.mve[][][ ][]\T1/ptm/m/n/10 , Overfull \hbox (31.3804pt too wide) in paragraph at lines 1523--1523 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a nd label ellipses[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1533--1533 [] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i dent. only points[] [2671] Underfull \hbox (badness 5741) in paragraph at lines 1573--1576 []\T1/pcr/m/n/10 coefHier() []\T1/ptm/m/n/10 di-rectly in-ter-faces to the un-d er-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only [2672] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1642--1642 [] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa rnType,[] [2673] Underfull \hbox (badness 1552) in paragraph at lines 1691--1693 []\T1/ptm/b/n/10 A\T1/ptm/m/n/10 symmetric bi-nary vari-able, aka []\T1/pcr/m/n /10 "A" []\T1/ptm/m/n/10 in re-sult []\T1/pcr/m/n/10 Types[]\T1/ptm/m/n/10 , se e Underfull \hbox (badness 1629) in paragraph at lines 1705--1709 []\T1/ptm/b/n/10 I\T1/ptm/m/n/10 nterval scaled -- the \T1/ptm/b/n/10 de-fault \T1/ptm/m/n/10 for all nu-meric Underfull \hbox (badness 3746) in paragraph at lines 1705--1709 \T1/ptm/m/n/10 (incl []\T1/pcr/m/n/10 integer[]\T1/ptm/m/n/10 ) columns of []\T 1/pcr/m/n/10 x[]\T1/ptm/m/n/10 , aka []\T1/pcr/m/n/10 "I" []\T1/ptm/m/n/10 in r e-sult []\T1/pcr/m/n/10 Types[]\T1/ptm/m/n/10 , see [2674] Underfull \hbox (badness 1540) in paragraph at lines 1781--1789 \T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1 0 w[]^^N[]$\T1/ptm/m/n/10 , where $\OML/cmm/m/it/10 w[]$[]\T1/pcr/m/n/10 = [2675] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1870--1870 []\T1/pcr/m/n/9 ## Example 2 in reference, extended --- different ways of "m ixed" / "gower":[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1874--1874 []\T1/pcr/m/n/9 summary(d0 <- daisy(flower)) # -> the first 3 {0,1} treate d as *N*ominal[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 1875--1875 []\T1/pcr/m/n/9 summary(dS123 <- daisy(flower, type = list(symm = 1:3))) # fi rst 3 treated as *S*ymmetric[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1876--1876 []\T1/pcr/m/n/9 stopifnot(dS123 == d0) # i.e., *S*ymmetric <==> *N*ominal {fo r 2-level factor}[] Overfull \hbox (106.98032pt too wide) in paragraph at lines 1880--1880 []\T1/pcr/m/n/9 summary(dA123 <- daisy(flowerN)) # .. all 3 logicals treated * A*symmetric binary (w/ warning)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1882--1882 []\T1/pcr/m/n/9 summary(dA13 <- daisy(flower, type = list(asymm = c(1, 3), ord ratio = 7)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1890--1890 []\T1/pcr/m/n/9 summary(dN <- daisy(Nflow)) # w/ warning: treated binary .. 1: 3 as interval[] Overfull \hbox (117.7803pt too wide) in paragraph at lines 1891--1891 []\T1/pcr/m/n/9 ## Still, using Euclidean/Manhattan distance for {0-1} *is* id entical to treating them as "N" :[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 1907--1907 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st and = FALSE, [2676] [2677] [2678] [2679] [2680] Underfull \hbox (badness 10000) in paragraph at lines 2228--2231 Underfull \hbox (badness 3179) in paragraph at lines 2242--2248 [][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] []\T1/ptm/m/n/10 which is also the [][][]\T1/pcr/m/n/10 predict[][][] []\T1/ptm/m/n/10 method for []\T1/pcr/m/n/1 0 ellipsoid []\T1/ptm/m/n/10 ob-jects. [2681] [2682] Underfull \hbox (badness 10000) in paragraph at lines 2400--2403 [][][]\T1/pcr/m/n/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-en ces; [][][]\T1/pcr/m/n/10 fanny.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 partition.object[][][][]\T1/ptm/m/n/10 , [2683] Underfull \hbox (badness 1292) in paragraph at lines 2468--2471 []\T1/ptm/m/n/10 named vec-tor with []\T1/pcr/m/n/10 iterations[]\T1/ptm/m/n/10 , the num-ber of it-er-a-tions needed and [2684] Underfull \hbox (badness 6675) in paragraph at lines 2477--2479 []\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl us-ter-ing, see Underfull \hbox (badness 10000) in paragraph at lines 2500--2503 [][][]\T1/pcr/m/n/10 fanny[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.f anny[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 dissimilarity.object[][][][]\ T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 partition.object[][][][]\T1/ptm/m/n/10 , [2685] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2575--2575 [] \T1/pcr/m/n/9 "4" = "red", "5" = "blue")[levels(f lowerN$color)][] Overfull \hbox (90.78033pt too wide) in paragraph at lines 2576--2576 []\T1/pcr/m/n/9 levels(flowerN$soil) <- c("1" = "dry", "2" = "normal", "3" = "wet")[levels(flowerN$soil)][] [2686] Overfull \hbox (48.78088pt too wide) in paragraph at lines 2639--2639 []\T1/pcr/m/n/10 medoids(x, clustering, diss = inherits(x, "dist"), USE.NAMES = FALSE, ...) [2687] Overfull \hbox (69.18036pt too wide) in paragraph at lines 2686--2686 [] \T1/pcr/m/n/9 stopifnot(length(cl.k) == nrow(votes.repub), 1 <= cl.k, cl.k <= k, table(cl.k) >= 2)[] [2688] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2791--2791 []\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/ 9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[] [2689] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2870--2870 [] \T1/pcr/m/n/10 variant = c("original", "o_1", "o_2", "f_3", "f_4", "f_5" , "faster"),[] [2690] [2691] [2692] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3099--3099 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro und (1, 16):[] [2693] [2694] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3202--3202 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co l.axis = "red")[] [2695] [2696] [2697] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3398--3398 [] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x $ac, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3399--3399 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2698] Underfull \hbox (badness 10000) in paragraph at lines 3466--3469 []\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via []\T1/pcr/m /n/10 pltree() []\T1/ptm/m/n/10 is pro-vided by []\T1/pcr/m/n/10 dg <- [2699] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3516--3516 [] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3517--3517 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2700] [2701] [2702] Underfull \hbox (badness 10000) in paragraph at lines 3702--3705 []\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 does not have a []\T1 /pcr/m/n/10 diss []\T1/ptm/m/n/10 com-po-nent as for [][][]\T1/pcr/m/n/10 pam[] [][](*, Underfull \hbox (badness 1448) in paragraph at lines 3702--3705 \T1/pcr/m/n/10 keep.diss=FALSE)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 dist []\T1/p tm/m/n/10 must be the dis-sim-i-lar-ity if a clus-plot is [2703] Underfull \hbox (badness 10000) in paragraph at lines 3765--3770 [][][]\T1/pcr/m/n/10 partition.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n /10 clusplot.partition[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 clusplot.de fault[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pam[][][][]\T1/ptm/m/n/10 , [2704] Underfull \hbox (badness 1748) in paragraph at lines 3827--3832 \T1/ptm/m/n/10 dis-patches to [][][]\T1/pcr/m/n/10 plot.hclust[][][](..)[]\T1/p tm/m/n/10 . If more flex-i-ble plots are needed, con-sider []\T1/pcr/m/n/10 xx <- Underfull \hbox (badness 6268) in paragraph at lines 3839--3842 [][][]\T1/pcr/m/n/10 agnes[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 agnes.o bject[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 diana[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 diana.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/1 0 hclust[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 par[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.agnes[][][][]\T1/ptm/m/n/10 , [2705] [2706] [2707] Underfull \hbox (badness 10000) in paragraph at lines 4024--4027 [][][]\T1/pcr/m/n/10 summary.agnes[][][] []\T1/ptm/m/n/10 pro-duc-ing more out- put; [][][]\T1/pcr/m/n/10 agnes[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 ag nes.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/ n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4055--4058 [][][]\T1/pcr/m/n/10 summary.clara[][][] []\T1/ptm/m/n/10 pro-duc-ing more out- put; [][][]\T1/pcr/m/n/10 clara[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cl ara.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/ n/10 , [2708] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4108--4108 [] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right = TRUE, ...)[] [2709] Underfull \hbox (badness 2035) in paragraph at lines 4119--4121 []\T1/ptm/m/n/10 a []\T1/pcr/m/n/10 dissimilarity []\T1/ptm/m/n/10 ob-ject or a []\T1/pcr/m/n/10 summary.dissimilarity []\T1/ptm/m/n/10 one for [2710] [2711] [2712] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4312--4312 [] \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w idth "* s[i]),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 4314--4314 [] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat = TRUE, ...)[] [2713] [2714] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4456--4456 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus ter-wise coloring[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4465--4465 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4467--4467 [] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma in")); frame()[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 4470--4470 []\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol denrod4", "gray20")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4472--4472 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE,[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4479--4479 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro wnames == indices[] [2715] [2716] [2717] [2718] [2719] [2720] [2721] Underfull \hbox (badness 10000) in paragraph at lines 4853--4859 []\T1/ptm/m/n/10 Our ver-sion of the []\T1/pcr/m/n/10 xclara []\T1/ptm/m/n/10 i s slightly more rounded than the one from Underfull \hbox (badness 10000) in paragraph at lines 4869--4871 []\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file `\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side Overfull \hbox (52.98038pt too wide) in paragraph at lines 4882--4882 []\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10 01:2000}, {2001:3000} Overfull \hbox (9.78043pt too wide) in paragraph at lines 4884--4884 []\T1/pcr/m/n/9 p.ID <- c(78, 1411, 2535) ## PAM\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s medoid indices == pam(xclara, 3)$id.med[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4894--4894 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o bservations:[] [2722] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4898--4898 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? - - Robust range:[] [2723]) (./codetools-pkg.tex [2724] Chapter 21. Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16 [] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17 [] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = !all,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18 [] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress Undefined,[] [2725] Underfull \hbox (badness 10000) in paragraph at lines 65--70 []\T1/pcr/m/n/10 checkUsageEnv []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 checkUsage Package []\T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply [2726] Overfull \hbox (18.78088pt too wide) in paragraph at lines 118--118 []\T1/pcr/m/n/10 makeConstantFolder(..., leaf, handler, call, exit, isLocal, f oldable,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 121--121 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e nterInternal,[] [2727] [2728] [2729]) (./foreign-pkg.tex [2730] Chapter 22. Underfull \hbox (badness 10000) in paragraph at lines 33--37 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of a Data Underfull \hbox (badness 10000) in paragraph at lines 33--37 \T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able as [][]$\T1/p cr/m/n/10 https : / / support . Underfull \hbox (badness 10000) in paragraph at lines 33--37 \T1/pcr/m/n/10 sas . com / content / dam / SAS / support / en / technical-[]pap ers / Overfull \hbox (74.28088pt too wide) in paragraph at lines 33--37 \T1/pcr/m/n/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[]s et-[]in-[]sas-[]transport-[]xport-[]format . [2731] Underfull \hbox (badness 1231) in paragraph at lines 67--70 []\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr om, or a [2732] [2733] Underfull \hbox (badness 3601) in paragraph at lines 237--245 []\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude []\T1/pcr/m /n/10 "datalabel"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "time.stamp"[]\T1/ptm/m/n/ 10 , [2734] Overfull \hbox (12.78088pt too wide) in paragraph at lines 295--295 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates = FALSE, [2735] [2736] [2737] Overfull \hbox (48.78088pt too wide) in paragraph at lines 461--461 [] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t o.data.frame,[] [2738] Overfull \hbox (30.78088pt too wide) in paragraph at lines 462--462 [] \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen d", "no"),[] Underfull \hbox (badness 2846) in paragraph at lines 505--514 []\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif- fer-ent lev- Underfull \hbox (badness 3746) in paragraph at lines 505--514 \T1/ptm/m/n/10 els. For []\T1/pcr/m/n/10 "append" []\T1/ptm/m/n/10 (the de-faul t), the first orig-i-nal value la-bel is Underfull \hbox (badness 2269) in paragraph at lines 505--514 \T1/ptm/m/n/10 kept while fur-ther du-pli-cated la-bels are re-named to []\T1/p cr/m/n/10 paste0(label, Underfull \hbox (badness 10000) in paragraph at lines 515--518 []\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with du- Underfull \hbox (badness 10000) in paragraph at lines 515--518 \T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault []\T1/pcr/m/n/10 "_dup licated_"[]\T1/ptm/m/n/10 ) if [2739] Underfull \hbox (badness 10000) in paragraph at lines 549--557 []\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 https : / / learn . microsoft . com / en-[]us / windows / win32 / intl / Underfull \hbox (badness 7613) in paragraph at lines 567--573 []\T1/ptm/m/n/10 There may be at-tributes []\T1/pcr/m/n/10 "label.table" []\T1/ ptm/m/n/10 and []\T1/pcr/m/n/10 "variable.labels"[]\T1/ptm/m/n/10 . At-tribute [2740] Overfull \hbox (20.58041pt too wide) in paragraph at lines 622--622 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg ument settings.[] Overfull \hbox (112.38031pt too wide) in paragraph at lines 623--623 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to R factor labels) are uncomplete,[] [2741] Overfull \hbox (9.78043pt too wide) in paragraph at lines 656--656 []\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ ate variables[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 660--660 []\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt h=w), "\n"))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 667--667 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, collapse="")[] [2742] [2743] Underfull \hbox (badness 10000) in paragraph at lines 811--812 Overfull \hbox (4.38043pt too wide) in paragraph at lines 821--821 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f oreign")[1])[] [2744] Underfull \hbox (badness 10000) in paragraph at lines 868--872 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of a Data Underfull \hbox (badness 10000) in paragraph at lines 868--872 \T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able at [][]$\T1/p cr/m/n/10 https : / / support . Underfull \hbox (badness 10000) in paragraph at lines 868--872 \T1/pcr/m/n/10 sas . com / content / dam / SAS / support / en / technical-[]pap ers / Overfull \hbox (74.28088pt too wide) in paragraph at lines 868--872 \T1/pcr/m/n/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[]s et-[]in-[]sas-[]transport-[]xport-[]format . [2745] Overfull \hbox (24.78088pt too wide) in paragraph at lines 899--899 [] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G lobalEnv) [2746] Overfull \hbox (0.78088pt too wide) in paragraph at lines 963--963 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute (x))) [2747] [2748] Underfull \hbox (badness 10000) in paragraph at lines 1075--1076 [][][]$\T1/pcr/m/n/10 https : / / www . clicketyclick . dk / databases / xbase / format / data _ types . Overfull \hbox (24.78088pt too wide) in paragraph at lines 1111--1111 [] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", "codes"))[] [2749] [2750] Underfull \hbox (badness 10000) in paragraph at lines 1268--1274 []\T1/ptm/m/n/10 The work for this func-tion is done by []\T1/pcr/m/n/10 foreig n:::writeForeignStata[]\T1/ptm/m/n/10 , [2751] Underfull \hbox (badness 2088) in paragraph at lines 1294--1297 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 package="SPSS"[]\T1/ptm/m/n/10 , as a sid e ef-fect, the dec-i-mal in-di-ca-tor is al-ways set by []\T1/pcr/m/n/10 SET [2752]) (./lattice-pkg.tex Chapter 23. [2753] Underfull \hbox (badness 2073) in paragraph at lines 117--121 \T1/ptm/m/n/10 pro-vide a holis-tic in-tro-duc-tion to the Trel-lis paradigm: [ ][]$\T1/pcr/m/n/10 http : / / web . archive . org / Underfull \hbox (badness 10000) in paragraph at lines 117--121 \T1/pcr/m/n/10 web / 20081020164041 / http : / / cm . bell-[]labs . com / cm / ms / departments / sia / [2754] [2755] Overfull \hbox (12.78088pt too wide) in paragraph at lines 291--291 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 295--295 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .xyplot"),[] [2756] Overfull \hbox (42.78088pt too wide) in paragraph at lines 306--306 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul t.dotplot"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 316--316 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.barchart"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 327--327 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.stripplot"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 351--351 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Underfull \vbox (badness 10000) has occurred while \output is active [2757] Overfull \hbox (30.78088pt too wide) in paragraph at lines 355--355 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .bwplot"),[] [2758] [2759] [2760] Underfull \hbox (badness 1221) in paragraph at lines 676--679 []\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as ar-gu-ments to [2761] [2762] [2763] [2764] Underfull \hbox (badness 2005) in paragraph at lines 1014--1026 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of fac-tors will be Underfull \hbox (badness 1199) in paragraph at lines 1014--1026 \T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a use-ful lay-out. [2765] [2766] Underfull \hbox (badness 1661) in paragraph at lines 1127--1133 []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 y []\T1/ptm/m/n/10 sho uld be num-bers be-tween 0 and 1, giv-ing co-or-di-nates [2767] Underfull \hbox (badness 1097) in paragraph at lines 1253--1255 []\T1/ptm/m/n/10 Logical flag, whether leg-end should have a Underfull \hbox (badness 1917) in paragraph at lines 1267--1268 []\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to [2768] [2769] [2770] Underfull \hbox (badness 1540) in paragraph at lines 1507--1513 []\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][][]\T1/pcr/m/ n/10 plot.trellis[][][][]\T1/ptm/m/n/10 , [2771] Underfull \hbox (badness 10000) in paragraph at lines 1594--1611 [][][]\T1/pcr/m/n/10 panel.dotplot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.stripplot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.superpose[] [][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.loess[][][][]\T1/ptm/m/n/10 , [2772] Underfull \vbox (badness 10000) has occurred while \output is active [2773] Overfull \hbox (36.7804pt too wide) in paragraph at lines 1682--1682 [] \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar dSprays$rowpos))),[] [2774] Underfull \hbox (badness 2012) in paragraph at lines 1736--1738 []\T1/ptm/m/n/10 additional ar-gu-ments passed to [][][]\T1/pcr/m/n/10 xyplot[] [][][]\T1/ptm/m/n/10 , which may pass them on to Underfull \hbox (badness 6808) in paragraph at lines 1766--1770 []\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p assed to Underfull \hbox (badness 10000) in paragraph at lines 1783--1786 []\T1/ptm/m/n/10 style set-tings be-yond the stan-dard []\T1/pcr/m/n/10 col[]\T 1/ptm/m/n/10 , []\T1/pcr/m/n/10 lty[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lwd[]\T1 /ptm/m/n/10 , etc; see [2775] Underfull \hbox (badness 10000) in paragraph at lines 1836--1838 []\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix An-drews [2776] [2777] [2778] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2077--2077 [] \T1/pcr/m/n/10 auto.key = lattice.getOption("default.args")$auto .key,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2090--2090 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl ot"),[] Underfull \vbox (badness 10000) has occurred while \output is active [2779] Underfull \hbox (badness 10000) in paragraph at lines 2169--2172 []\T1/ptm/m/n/10 When []\T1/pcr/m/n/10 breaks []\T1/ptm/m/n/10 is un-spec-i-fie d, the value of Underfull \hbox (badness 1320) in paragraph at lines 2169--2172 []\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") []\T1/ptm/m/n/10 is firs t checked. If [2780] [2781] [2782] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2374--2374 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2378--2378 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .qqmath"),[] [2783] [2784] [2785] [2786] [2787] Overfull \hbox (60.78088pt too wide) in paragraph at lines 2737--2737 [] \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev elplot.raster")[] [2788] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2769--2769 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl ot"),[] Underfull \vbox (badness 10000) has occurred while \output is active [2789] Underfull \hbox (badness 2913) in paragraph at lines 2848--2853 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when []\T1/ pcr/m/n/10 x []\T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 2848--2853 []\T1/pcr/m/n/10 row.values []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 column.values []\T1/ptm/m/n/10 must have the same lengths as [2790] [2791] Underfull \hbox (badness 6758) in paragraph at lines 2976--2980 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be Underfull \hbox (badness 7576) in paragraph at lines 2976--2980 \T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][][]\T1/pcr/m/n/10 grid.ra ster[][][][]\T1/ptm/m/n/10 . See also Underfull \hbox (badness 10000) in paragraph at lines 2982--2984 []\T1/ptm/m/n/10 Logical flag, passed to [][][]\T1/pcr/m/n/10 rasterGrob[][][] []\T1/ptm/m/n/10 when Underfull \hbox (badness 1609) in paragraph at lines 3034--3040 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti ons should be used, Underfull \hbox (badness 2772) in paragraph at lines 3034--3040 \T1/ptm/m/n/10 both for the false color im-age and the color key (if present). Ef- Underfull \hbox (badness 1400) in paragraph at lines 3034--3040 \T1/ptm/m/n/10 fec-tively, set-ting this to []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n /10 changes the de-fault panel func-tion from Underfull \hbox (badness 2486) in paragraph at lines 3058--3062 []\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for the de-fault panel func-tion [2792] [2793] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3163--3163 [] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3164--3164 [] \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3165--3165 [] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite = TRUE),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3176--3176 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. cloud"),[] [2794] Overfull \hbox (66.78088pt too wide) in paragraph at lines 3191--3191 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.wireframe"),[] [2795] Underfull \hbox (badness 2913) in paragraph at lines 3256--3261 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when []\T1/ pcr/m/n/10 x []\T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 3256--3261 []\T1/pcr/m/n/10 row.values []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 column.values []\T1/ptm/m/n/10 must have the same lengths as [2796] [2797] [2798] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.parallel} ) has been already used, duplicate ignored \relax l.3545 \aliasA{parallel}{B\_08\_splom}{parallel} [2799] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3587--3587 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. splom"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3610--3610 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.parallel"),[] Underfull \vbox (badness 10000) has occurred while \output is active [2800] [2801] [2802] [2803] [2804] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3947--3947 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt( var(x))) [2805] Underfull \hbox (badness 2277) in paragraph at lines 4033--4037 []\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault set-tings by Underfull \hbox (badness 2435) in paragraph at lines 4033--4037 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2806] [2807] Overfull \hbox (120.78088pt too wide) in paragraph at lines 4130--4130 [] \T1/pcr/m/n/10 symbol = palette.colors(palette = "Okabe-Ito") [c(6, 2, 4, 7, 3, 5, 8)],[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 4132--4132 [] \T1/pcr/m/n/10 region = hcl.colors(14, palette = "YlGnBu", re v = TRUE),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4139--4139 [] \T1/pcr/m/n/10 reference = "gray90", bg = "transparent", fg = " black",[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 4140--4140 [] \T1/pcr/m/n/10 strip.bg = rep("gray95", 7), strip.fg = rep("gra y70", 7),[] [2808] [2809] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4283--4283 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict = FALSE) Underfull \hbox (badness 1173) in paragraph at lines 4292--4296 []\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un- spec-i-fied in Underfull \hbox (badness 3219) in paragraph at lines 4319--4321 []\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i s-sued when Underfull \hbox (badness 1728) in paragraph at lines 4336--4340 []\T1/pcr/m/n/10 theme[]\T1/ptm/m/n/10 ). These are used to mod-ify the cur-ren t set-tings (ob-tained by [2810] Underfull \hbox (badness 5161) in paragraph at lines 4401--4405 []\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in []\T1/pcr/m/n/10 trell is.settings []\T1/ptm/m/n/10 has not been fi-nal-ized, Underfull \hbox (badness 4913) in paragraph at lines 4401--4405 \T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca n be ob-tained by [2811] [2812] Underfull \hbox (badness 1067) in paragraph at lines 4519--4529 []\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. []\T1/pcr/m/n/10 col []\T1/ptm/m/n/ 10 is used for com-po-nents []\T1/pcr/m/n/10 "plot.symbol"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4519--4529 []\T1/pcr/m/n/10 "plot.line"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "plot.polygon"[ ]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "superpose.symbol"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1735) in paragraph at lines 4519--4529 []\T1/pcr/m/n/10 "superpose.line"[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 "super pose.polygon"[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 col.points Underfull \hbox (badness 10000) in paragraph at lines 4519--4529 []\T1/ptm/m/n/10 over-rides []\T1/pcr/m/n/10 col[]\T1/ptm/m/n/10 , but is used only for []\T1/pcr/m/n/10 "plot.symbol" []\T1/ptm/m/n/10 and Underfull \hbox (badness 5231) in paragraph at lines 4519--4529 []\T1/pcr/m/n/10 "superpose.symbol"[]\T1/ptm/m/n/10 . Sim-i-larly, []\T1/pcr/m/ n/10 col.line []\T1/ptm/m/n/10 over-rides []\T1/pcr/m/n/10 col []\T1/ptm/m/n/10 for Underfull \hbox (badness 1701) in paragraph at lines 4544--4547 []\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents []\T1/pcr/m/n/10 pl ot.symbol[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 plot.polygon[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4547--4549 []\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents []\T1/pcr/m/n/10 plot.polygon []\T1/ptm/m/n/10 and [2813] [2814] Underfull \hbox (badness 2932) in paragraph at lines 4690--4695 []\T1/pcr/m/n/10 auto.key[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 aspect[]\T1/ptm/m/ n/10 , []\T1/pcr/m/n/10 between[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 grid[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 skip[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 strip[]\T1/ ptm/m/n/10 , []\T1/pcr/m/n/10 xscale.components[]\T1/ptm/m/n/10 , [2815] [2816] [2817] [2818] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4966--4966 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab = "Height")[] [2819] [2820] [2821] Underfull \hbox (badness 10000) in paragraph at lines 5153--5156 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 trellis[]\T1/ptm/m/n/10 , by de-fault plot-ted by []\T1/pcr/m/n/10 print.trellis[]\T1/ptm/m/n/10 . [2822] Underfull \hbox (badness 1442) in paragraph at lines 5285--5288 []\T1/pcr/m/n/10 plot.shingle []\T1/ptm/m/n/10 dis-plays the ranges of shin-gle s via rect-an-gles. []\T1/pcr/m/n/10 print.shingle []\T1/ptm/m/n/10 and [2823] [2824] [2825] [2826] [2827] [2828] Underfull \hbox (badness 3646) in paragraph at lines 5624--5627 [][][]\T1/pcr/m/n/10 Lattice[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 draw. key[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 trellis.par.get[][][][]\T1/ptm /m/n/10 , and [][][]\T1/pcr/m/n/10 xyplot[][][][]\T1/ptm/m/n/10 , specif-i-call y the en-try for Overfull \hbox (36.78088pt too wide) in paragraph at lines 5654--5654 [] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh ich.given],[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5655--5655 [] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which .given],[] [2829] Underfull \hbox (badness 10000) in paragraph at lines 5743--5746 []\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i -zon-tal. Underfull \hbox (badness 2103) in paragraph at lines 5743--5746 []\T1/pcr/m/n/10 horizontal=FALSE []\T1/ptm/m/n/10 is use-ful for strips on the left of pan-els us-ing [2830] Underfull \hbox (badness 1635) in paragraph at lines 5769--5774 []\T1/pcr/m/n/10 strip.default []\T1/ptm/m/n/10 is called for its side-effect, which is to draw a strip ap-pro-pri-ate for [2831] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5920--5920 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la bels,[] [2832] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5934--5934 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose "), ...)[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5935--5935 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos e"), ...)[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5938--5938 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location" , "toplevel",[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5941--5941 [] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig ht", "page"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 5943--5943 [] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in side"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5949--5949 [] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi ch.given",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5950--5950 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5951--5951 [] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi ch.panel",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5952--5952 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5953--5953 [] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co lumn",[] Underfull \hbox (badness 10000) in paragraph at lines 5969--5971 []\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of Underfull \hbox (badness 2376) in paragraph at lines 5980--5982 []\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point. De-faults to [2833] [2834] Underfull \hbox (badness 2538) in paragraph at lines 6105--6109 \T1/ptm/m/n/10 For []\T1/pcr/m/n/10 trellis.focus[]\T1/ptm/m/n/10 , the de-faul t is []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 in in-ter-ac-tive mode, and Underfull \hbox (badness 4205) in paragraph at lines 6116--6123 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 panel.identify.qqmath[]\T1/ptm/m/n/10 , e x-tra pa-ram-e-ters are passed on to Underfull \hbox (badness 4792) in paragraph at lines 6116--6123 []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 trellis.switchFocus[]\T1/ptm/m/n/10 , the se are used (in com-bi-na-tion with [2835] [2836] Underfull \hbox (badness 10000) in paragraph at lines 6269--6273 [][][]\T1/pcr/m/n/10 identify[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Latt ice[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.trellis[][][][]\T1/ptm/m /n/10 , [][][]\T1/pcr/m/n/10 trellis.currentLayout[][][][]\T1/ptm/m/n/10 , [2837] [2838] Underfull \hbox (badness 4242) in paragraph at lines 6416--6421 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- [2839] [2840] Underfull \hbox (badness 3601) in paragraph at lines 6532--6537 []\T1/ptm/m/n/10 Creates Box and Whisker plot of []\T1/pcr/m/n/10 x []\T1/ptm/m /n/10 for ev-ery level of []\T1/pcr/m/n/10 y []\T1/ptm/m/n/10 (or the other way round Underfull \hbox (badness 2486) in paragraph at lines 6532--6537 \T1/ptm/m/n/10 if []\T1/pcr/m/n/10 horizontal=FALSE[]\T1/ptm/m/n/10 ). By de-fa ult, the ac-tual box-plot statis-tics are cal-cu-lated us-ing [2841] Overfull \hbox (60.78088pt too wide) in paragraph at lines 6620--6620 [] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co lors")$palette,[] [2842] [2843] [2844] Underfull \hbox (badness 10000) in paragraph at lines 6819--6823 []\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The Underfull \hbox (badness 10000) in paragraph at lines 6824--6826 []\T1/ptm/m/n/10 numeric, be-tween 0 and 1, giv-ing a min-i-mum sat-u-ra-tion i n [2845] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6920--6920 [] \T1/pcr/m/n/9 shade.colors.palette = makeShadePalette(hcl.colors(1 0, "Inferno"),[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6923--6923 [] \T1/pcr/m/n/9 shade.colors.palette = makeShadePalette(hcl.colors(1 0, "Dark Mint"),[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6926--6926 [] \T1/pcr/m/n/9 shade.colors.palette = makeShadePalette(hcl.colors(1 0, "Harmonic"),[] [2846] [2847] [2848] [2849] [2850] [2851] Underfull \hbox (badness 1320) in paragraph at lines 7288--7295 []\T1/pcr/m/n/10 panel.levelplot.raster []\T1/ptm/m/n/10 is an al-ter-na-tive p anel func-tion that uses the raster draw- Underfull \hbox (badness 1715) in paragraph at lines 7288--7295 \T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more ef-fi-cient. When us-ing [2852] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7363--7363 [] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = NULL,[] [2853] Underfull \hbox (badness 10000) in paragraph at lines 7393--7397 []\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments to Underfull \hbox (badness 1584) in paragraph at lines 7393--7397 []\T1/pcr/m/n/10 diag.panel.splom []\T1/ptm/m/n/10 to know what ar-gu-ments thi s func-tion is passed [2854] Underfull \hbox (badness 10000) in paragraph at lines 7498--7501 \T1/ptm/m/n/10 and []\T1/pcr/m/n/10 diag.panel []\T1/ptm/m/n/10 from []\T1/pcr/ m/n/10 panel.pairs[]\T1/ptm/m/n/10 . Cur-rently ig-nored by Overfull \hbox (101.58032pt too wide) in paragraph at lines 7523--7523 [] \T1/pcr/m/n/9 function(i,j) hcl.colors(11)[i+j-1]) ## rainbow( 11, start=.12, end=.5)[i+j-1])[] [2855] [2856] Underfull \hbox (badness 2012) in paragraph at lines 7664--7667 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2857] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7710--7710 [] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta ils.n = 50))[] [2858] [2859] [2860] Underfull \hbox (badness 1939) in paragraph at lines 7899--7907 []\T1/pcr/m/n/10 "lm" []\T1/ptm/m/n/10 adds a lin-ear re-gres-sion line (same a s [][][]\T1/pcr/m/n/10 panel.lmline[][][][]\T1/ptm/m/n/10 , ex-cept Underfull \hbox (badness 1163) in paragraph at lines 7899--7907 \T1/ptm/m/n/10 for de-fault graph-i-cal pa-ram-e-ters). []\T1/pcr/m/n/10 "loess " []\T1/ptm/m/n/10 adds a loess fit (same as Underfull \hbox (badness 2772) in paragraph at lines 7922--7925 []\T1/ptm/m/n/10 Most gen-er-ally, []\T1/pcr/m/n/10 grid []\T1/ptm/m/n/10 can b e a list of ar-gu-ments to be sup-plied to [2861] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7993--7993 [] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y = c(1/6, 4/6)),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8003--8003 [] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d raw = FALSE),[] [2862] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8088--8088 [] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam e.type)[] [2863] Overfull \hbox (84.78088pt too wide) in paragraph at lines 8107--8107 [] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ide ntifier, name.type)[] [2864] [2865] Overfull \hbox (63.78036pt too wide) in paragraph at lines 8246--8246 []\T1/pcr/m/n/9 xyplot(y ~ x, d, panel = panel.rect, col = 4, alpha = 0.5, wid th = 0.1, height = 0.1)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8253--8253 []\T1/pcr/m/n/9 xyplot(y ~ x, d, panel = panel.polygon, col = 4, alpha = 0.5, rule = "evenodd")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8255--8255 []\T1/pcr/m/n/9 ## Example adapted from https://journal.r-project.org/articles /RJ-2012-017/[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8259--8259 []\T1/pcr/m/n/9 xyplot(y ~ x, data = d, panel = panel.polygon, rule = "none", col = "grey")[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8260--8260 []\T1/pcr/m/n/9 xyplot(y ~ x, data = d, panel = panel.polypath, rule = "windin g", col = "grey")[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8261--8261 []\T1/pcr/m/n/9 xyplot(y ~ x, data = d, panel = panel.polypath, rule = "evenod d", col = "grey")[] [2866] Overfull \hbox (66.78088pt too wide) in paragraph at lines 8324--8324 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden tifier = "grid")[] [2867] Underfull \hbox (badness 1436) in paragraph at lines 8379--8385 []\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c al pa-ram-e-ters for [2868] Overfull \hbox (42.18039pt too wide) in paragraph at lines 8509--8509 [] \T1/pcr/m/n/9 panel.superpose(x, y, ..., panel.groups = panel.ave rage, grid = FALSE,[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8523--8523 [] \T1/pcr/m/n/9 args = list(mean = mean(x), sd = sd(x)), ...)[] [2869] [2870] [2871] [2872] [2873] [2874] [2875] Underfull \hbox (badness 10000) in paragraph at lines 8948--8951 []\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to []\T1/pcr/m/n/10 panel.super pose Underfull \hbox (badness 10000) in paragraph at lines 8948--8951 []\T1/ptm/m/n/10 from []\T1/pcr/m/n/10 panel.superpose.2[]\T1/ptm/m/n/10 , and to []\T1/pcr/m/n/10 panel.groups []\T1/ptm/m/n/10 from [2876] [2877] Overfull \hbox (24.78088pt too wide) in paragraph at lines 9123--9123 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st ack, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9124--9124 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin t, ...)[] [2878] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9136--9136 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr ipts, ...)[] Underfull \hbox (badness 3118) in paragraph at lines 9155--9158 []\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. []\T1/pcr/m/n/10 type [ ]\T1/ptm/m/n/10 has a dif-fer-ent mean-ing in [2879] Underfull \hbox (badness 1515) in paragraph at lines 9231--9235 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2880] [2881] Underfull \hbox (badness 6316) in paragraph at lines 9337--9342 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in [2882] Overfull \hbox (47.58038pt too wide) in paragraph at lines 9447--9447 [] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b ottom$labels$labels)[] [2883] [2884] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9586--9586 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su nspot.year)),[] [2885] Underfull \hbox (badness 1028) in paragraph at lines 9645--9649 \T1/pcr/m/n/10 condition []\T1/ptm/m/n/10 for 2-D, and []\T1/pcr/m/n/10 left, r ight.x, right.y, left.name, right.x.name, [2886] [2887] [2888] [2889] [2890] [2891] [2892] Underfull \hbox (badness 7238) in paragraph at lines 10109--10113 []\T1/ptm/m/n/10 Factor with lev-els []\T1/pcr/m/n/10 "Svansota"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "No. 462"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Manchuria"[] \T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "No. 475"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10109--10113 []\T1/pcr/m/n/10 "Velvet"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Peatland"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "Glabron"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "No. 4 57"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Wisconsin No. 38"[]\T1/ptm/m/n/10 , [2893] [2894] [2895] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma} ) has been already used, duplicate ignored \relax l.10340 \aliasA{melanoma}{H\_melanoma}{melanoma} [2896] [2897] [2898] Underfull \hbox (badness 10000) in paragraph at lines 10502--10507 \T1/pcr/m/n/10 diseases[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Diabetes[]\T1/ptm/m/ n/10 , []\T1/pcr/m/n/10 Flu and pneumonia[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 He art disease[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Lower Overfull \hbox (9.78043pt too wide) in paragraph at lines 10575--10575 [] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list( columns = 2),[] [2899] [2900]) (./mgcv-pkg.tex Chapter 24. [2901] [2902] Overfull \hbox (6.78088pt too wide) in paragraph at lines 160--160 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL, Overfull \hbox (18.78088pt too wide) in paragraph at lines 163--163 [] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret e=FALSE,[] [2903] Overfull \hbox (48.78088pt too wide) in paragraph at lines 165--165 [] \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in tercept=NULL,[] Underfull \hbox (badness 1142) in paragraph at lines 185--189 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 210--215 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2904] [2905] [2906] [2907] Underfull \hbox (badness 10000) in paragraph at lines 379--386 [][][]\T1/pcr/m/n/10 mgcv.parallel[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gamObject[][][][]\T1 /ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/ptm/m/n/10 , [][][]\T1 /pcr/m/n/10 smooth.terms[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 379--386 [][][]\T1/pcr/m/n/10 linear.functional.terms[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][] [][]predict. gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 379--386 [][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 g am.side[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.selection[][][][]\T1/p tm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][][]\T1/ptm /m/n/10 , [2908] Overfull \hbox (4.38043pt too wide) in paragraph at lines 422--422 []\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2 ,bs=bs,k=k)+[] [2909] [2910] [2911] Underfull \hbox (badness 2922) in paragraph at lines 634--635 []\T1/ptm/m/n/10 The link func-tion: one of []\T1/pcr/m/n/10 "logit"[]\T1/ptm/m /n/10 , []\T1/pcr/m/n/10 "probit"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cloglog" []\T1/ptm/m/n/10 and [2912] [2913] Underfull \hbox (badness 1406) in paragraph at lines 704--705 []\T1/ptm/m/n/10 The MKL BLAS is mut-lithreaded by de-fault. Un-der linux set-t ing en-vi-ron-ment vari-able [2914] [2915] Underfull \hbox (badness 1158) in paragraph at lines 814--816 []\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe n us-ing pe-nal-ized re-gres-sion [2916] Underfull \hbox (badness 1259) in paragraph at lines 877--878 []\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro -duc-tion with R (2nd edi-tion). [2917] Underfull \vbox (badness 10000) has occurred while \output is active [2918] [2919] [2920] [2921] [2922] [2923] [2924] [2925] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1337--1337 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1338--1338 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1355--1355 [] \T1/pcr/m/n/9 plot(b$y[oy],rs[oy,ii[1]],ylim=c(-3,3),type="l",ylab="scor e residuals",[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1367--1367 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor +rx+obstruct[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1376--1376 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in d]),type="l",[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1378--1378 [] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind]) ,lwd=2,col=i)[] Underfull \vbox (badness 10000) has occurred while \output is active [2926] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1409--1409 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights= d,data=surv)[] Underfull \vbox (badness 10000) has occurred while \output is active [2927] [2928] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1492--1492 [] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid), initial = 0,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1503--1503 [] \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][ nrow(um)] <- 1[] Underfull \vbox (badness 10000) has occurred while \output is active [2929] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1542--1542 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter polate to te[] [2930] [2931] [2932] [2933] [2934] [2935] [2936] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1939--1939 []\T1/pcr/m/n/9 bd <- bam(y~s(x0)+ s(x1) + s(x1,fac,bs="sz",k=5)+s(x2,k=20),di screte=TRUE)[] [2937] [2938] [2939] [2940] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2174--2174 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str ict=FALSE) [2941] [2942] [2943] [2944] [2945] [2946] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2579--2579 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL,[] Underfull \hbox (badness 1728) in paragraph at lines 2591--2594 []\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][][]\T1/pcr/m/n /10 formula.gam[][][] []\T1/ptm/m/n/10 and also Underfull \hbox (badness 1142) in paragraph at lines 2604--2608 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2947] Underfull \hbox (badness 1043) in paragraph at lines 2630--2636 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2948] [2949] [2950] Underfull \hbox (badness 1043) in paragraph at lines 2795--2801 \T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v en-tion mech-a-nism de-scribed in [2951] [2952] Underfull \hbox (badness 10000) in paragraph at lines 2933--2939 [][][]\T1/pcr/m/n/10 mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gamObject[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/pt m/m/n/10 , [][][]\T1/pcr/m/n/10 smooth.terms[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2933--2939 [][][]\T1/pcr/m/n/10 linear.functional.terms[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][] [][]predict. gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2933--2939 [][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 g am.side[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.selection[][][][]\T1/p tm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][][]\T1/ptm /m/n/10 , [2953] Underfull \vbox (badness 10000) has occurred while \output is active [2954] Underfull \vbox (badness 10000) has occurred while \output is active [2955] [2956] [2957] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3250--3250 []\T1/pcr/m/n/10 gam.control(nthreads=1,ncv.threads=1,irls.reg=0.0,epsilon = 1 e-07, [2958] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3251--3251 [] \T1/pcr/m/n/10 maxit = 200,mgcv.tol=1e-7,mgcv.half=15, trace = F ALSE,[] [2959] [2960] [2961] [2962] [2963] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3591--3591 [] \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco l(x)),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3594--3594 [] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol (x)),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3595--3595 [] \T1/pcr/m/n/10 pearson.extra=0,dev.extra=0,n.true=-1,Sl=NULL,nei=NU LL,...)[] [2964] [2965] [2966] [2967] [2968] [2969] [2970] [2971] Underfull \hbox (badness 5189) in paragraph at lines 4073--4077 []\T1/ptm/m/n/10 Random ef-fects can be added to []\T1/pcr/m/n/10 gam []\T1/ptm /m/n/10 mod-els us-ing []\T1/pcr/m/n/10 s(...,bs="re") []\T1/ptm/m/n/10 terms ( see [2972] [2973] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4190--4190 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Underfull \vbox (badness 10000) has occurred while \output is active [2974] [2975] [2976] Underfull \hbox (badness 1184) in paragraph at lines 4360--4364 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2977] [2978] [2979] [2980] [2981] [2982] [2983] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4806--4806 [] \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i d=1)+s(x1,id=1)+[] [2984] [2985] [2986] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4956--4956 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, d1b = 0, [2987] [2988] Underfull \hbox (badness 1142) in paragraph at lines 5083--5087 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2989] Underfull \hbox (badness 10000) in paragraph at lines 5155--5164 []\T1/ptm/m/n/10 In the event of []\T1/pcr/m/n/10 lme []\T1/ptm/m/n/10 con-ver- gence fail-ures, con-sider mod-i-fy-ing [2990] [2991] Underfull \hbox (badness 5970) in paragraph at lines 5272--5278 [][][]\T1/pcr/m/n/10 magic[][][] []\T1/ptm/m/n/10 for an al-ter-na-tive for cor -re-lated data, [][][]\T1/pcr/m/n/10 te[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.gam[][][][]\T1/ptm /m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 1418) in paragraph at lines 5272--5278 [][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 n egbin[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 vis.gam[][][][]\T1/ptm/m/n/1 0 ,[][][]\T1/pcr/m/n/10 pdTens[][][][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 gamm4 [ ]\T1/ptm/m/n/10 ( [][]$\T1/pcr/m/n/10 https : / / cran . r-[]project . [2992] Underfull \vbox (badness 10000) has occurred while \output is active [2993] [2994] [2995] [2996] Underfull \hbox (badness 1577) in paragraph at lines 5622--5625 []\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see [] [][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 ar-gu-ment Underfull \hbox (badness 2181) in paragraph at lines 5629--5630 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2997] [2998] [2999] [3000] [3001] [3002] [3003] [3004] [3005] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6127--6127 []\T1/pcr/m/n/10 ginla(G,A=NULL,nk=16,nb=100,J=1,interactive=FALSE,integ=0,app rox=0) Underfull \hbox (badness 6708) in paragraph at lines 6133--6134 []\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by []\T1/pcr/m/n/10 gam(.. .,fit=FALSE) []\T1/ptm/m/n/10 or [3006] [3007] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6182--6182 [] \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d ata. A simple[] [3008] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6207--6207 [] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j] ,lty=lty[j])[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6236--6236 [] \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo r comparison[] [3009] [3010] [3011] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6358--6358 [] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r norm(100)*.4[] [3012] [3013] [3014] [3015] [3016] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6695--6695 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n a.action, Overfull \hbox (36.78088pt too wide) in paragraph at lines 6697--6697 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona lize=FALSE)[] Underfull \hbox (badness 1142) in paragraph at lines 6718--6722 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [3017] [3018] [3019] [3020] [3021] [3022] [3023] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7037--7037 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999, all.derivs=FALSE) [3024] [3025] [3026] Underfull \vbox (badness 10000) has occurred while \output is active [3027] Underfull \vbox (badness 10000) has occurred while \output is active [3028] [3029] [3030] Overfull \hbox (52.98038pt too wide) in paragraph at lines 7469--7469 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want to rule the world.",[] [3031] Overfull \hbox (36.78088pt too wide) in paragraph at lines 7496--7496 [] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y), nthreads=1)[] [3032] [3033] [3034] [3035] [3036] [3037] Underfull \vbox (badness 4805) has occurred while \output is active [3038] [3039] [3040] Underfull \hbox (badness 1242) in paragraph at lines 8050--8051 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [3041] [3042] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8137--8137 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt ion with bam...[] [3043] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8200--8200 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate d covariates[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8219--8219 [] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]] ,na.rm=TRUE)[] [3044] [3045] [3046] [3047] [3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055] [3056] [3057] [3058] [3059] [3060] [3061] [3062] [3063] [3064] Underfull \vbox (badness 10000) has occurred while \output is active [3065] [3066] Underfull \hbox (badness 10000) in paragraph at lines 9538--9541 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: []\T1/pcr/m/n/10 Dim .pdIndot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 coef.pdIdnot[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 9538--9541 []\T1/pcr/m/n/10 corMatrix.pdIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 logDet.pd Idnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdConstruct.pdIdnot[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3118) in paragraph at lines 9538--9541 []\T1/pcr/m/n/10 pdFactor.pdIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdMatrix.p dIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 solve.pdIdnot[]\T1/ptm/m/n/10 , []\T1 /pcr/m/n/10 summary.pdIdnot[]\T1/ptm/m/n/10 . [3067] Underfull \hbox (badness 10000) in paragraph at lines 9594--9597 []\T1/ptm/m/n/10 These func-tions ([]\T1/pcr/m/n/10 pdTens[]\T1/ptm/m/n/10 , [] \T1/pcr/m/n/10 pdConstruct.pdTens[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdFactor.p dTens[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3108) in paragraph at lines 9594--9597 []\T1/pcr/m/n/10 pdMatrix.pdTens[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 coef.pdTens []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 summary.pdTens[]\T1/ptm/m/n/10 ) would n ot nor-mally be [3068] [3069] [3070] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9814--9814 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s cale=-1,[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 9818--9818 [] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi ds=FALSE,[] [3071] [3072] [3073] Underfull \hbox (badness 1629) in paragraph at lines 9974--9979 []\T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is some-times to clone the [3074] [3075] [3076] [3077] Overfull \hbox (84.78088pt too wide) in paragraph at lines 10186--10186 [] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread s=1,gc.level=0,...)[] Underfull \hbox (badness 1062) in paragraph at lines 10223--10227 []\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 type=="terms" []\T1/ptm/m/n/10 or []\T1/pc r/m/n/10 type="iterms" []\T1/ptm/m/n/10 then terms (smooth or para- [3078] [3079] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10356--10356 [] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL L,...)[] [3080] [3081] [3082] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10517--10517 []\T1/pcr/m/n/9 x1 <- seq(.2,.8,length=m1);x2 <- seq(.2,.8,length=m2) ## margi nal grid points[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10518--10518 []\T1/pcr/m/n/9 df <- data.frame(x0=rep(.5,n),x1=rep(x1,m2),x2=rep(x2,each=m1) ,x3=rep(0,n))[] [3083] Underfull \vbox (badness 10000) has occurred while \output is active [3084] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10637--10637 [] \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s mooth deriv i[] [3085] Underfull \hbox (badness 1205) in paragraph at lines 10675--10676 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 10675--10676 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for Underfull \hbox (badness 1975) in paragraph at lines 10681--10686 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [3086] Underfull \hbox (badness 1205) in paragraph at lines 10765--10766 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 10765--10766 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [3087] Underfull \hbox (badness 10000) in paragraph at lines 10834--10837 []\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from Underfull \hbox (badness 2057) in paragraph at lines 10834--10837 [][][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][][]\T1/ptm/m/n/10 , al -though el-e-ments []\T1/pcr/m/n/10 X []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 S [ ]\T1/ptm/m/n/10 are not needed, [3088] [3089] [3090] Underfull \hbox (badness 1253) in paragraph at lines 10964--10966 []\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion cri-te-rion re-ported is one of GCV, [3091] [3092] [3093] [3094] [3095] Underfull \hbox (badness 1946) in paragraph at lines 11217--11224 []\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef- fects in a GAM in the same Underfull \hbox (badness 2221) in paragraph at lines 11217--11224 \T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre s-sion terms. This method Underfull \hbox (badness 2042) in paragraph at lines 11217--11224 \T1/ptm/m/n/10 can be used with [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 by mak-ing use of []\T1/pcr/m/n/10 s(...,bs="re") []\T1/ptm/m/n/10 terms in a model: see Underfull \hbox (badness 2846) in paragraph at lines 11225--11228 []\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the []\T1/pcr/m/n /10 paraPen []\T1/ptm/m/n/10 ar-gu-ment to [][][]\T1/pcr/m/n/10 gam[][][] []\T1 /ptm/m/n/10 can be used: Underfull \hbox (badness 5862) in paragraph at lines 11225--11228 \T1/ptm/m/n/10 see [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/ptm/m/n/10 . If s mooth-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g. [3096] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11291--11291 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11301--11301 []\T1/pcr/m/n/9 ## The effect of the new factor levels (or any interaction inv olving them)[] [3097] Underfull \hbox (badness 10000) in paragraph at lines 11332--11335 []\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of []\T1/pcr/m/n/ 10 "deviance"[]\T1/ptm/m/n/10 , [3098] [3099] [3100] [3101] [3102] Overfull \hbox (36.78088pt too wide) in paragraph at lines 11634--11634 []\T1/pcr/m/n/10 s(..., k=-1,fx=FALSE,bs="tp",m=NA,by=NA,xt=NULL,id=NULL,sp=NU LL,pc=NULL) [3103] [3104] [3105] [3106] [3107] [3108] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12007--12007 [] \T1/pcr/m/n/9 true <- mu + (del * sigma) * sinh((1/del) * asinh(qnorm(qq)) + (eps/del))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12021--12021 []\T1/pcr/m/n/9 b <- gam(list(accel~s(times, k=20, bs = "ad"), ~s(times, k = 1 0), ~1, ~1),[] Underfull \vbox (badness 10000) has occurred while \output is active [3109] [3110] Underfull \hbox (badness 3861) in paragraph at lines 12123--12126 []\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to model ma-trix X, or, if Overfull \hbox (36.78088pt too wide) in paragraph at lines 12132--12132 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, cov = TRUE,[] [3111] Underfull \hbox (badness 10000) in paragraph at lines 12149--12153 []\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 inverse==TRUE []\T1/ptm/m/n/10 and []\T1/p cr/m/n/10 both.sides==FALSE []\T1/ptm/m/n/10 then the re- Underfull \hbox (badness 10000) in paragraph at lines 12189--12193 []\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 inverse==TRUE []\T1/ptm/m/n/10 and []\T1/p cr/m/n/10 both.sides==FALSE []\T1/ptm/m/n/10 then the re- [3112] [3113] [3114] Overfull \hbox (20.58041pt too wide) in paragraph at lines 12333--12333 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$ vectors[,ind]))[] Underfull \hbox (badness 1975) in paragraph at lines 12344--12349 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [3115] Underfull \hbox (badness 1803) in paragraph at lines 12421--12425 \T1/ptm/m/n/10 The last en-try will be the []\T1/pcr/m/n/10 by []\T1/ptm/m/n/10 vari-able, if []\T1/pcr/m/n/10 object$by []\T1/ptm/m/n/10 is not []\T1/pcr/m/n /10 "NA"[]\T1/ptm/m/n/10 . Underfull \hbox (badness 1502) in paragraph at lines 12433--12445 []\T1/pcr/m/n/10 cs.smooth.spec []\T1/ptm/m/n/10 (cu-bic re-gres-sion splines w ith shrinkage-to-zero); []\T1/pcr/m/n/10 cc.smooth.spec [3116] Underfull \hbox (badness 2401) in paragraph at lines 12450--12454 []\T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able . Plot meth-ods can be Underfull \hbox (badness 2970) in paragraph at lines 12450--12454 \T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for []\T1/pc r/m/n/10 mgcv:::plot.sos.smooth[]\T1/ptm/m/n/10 , [3117] [3118] [3119] Underfull \hbox (badness 6876) in paragraph at lines 12645--12651 [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use adap-tive smooths of on e or two vari-ables, spec-i-fied via terms like [3120] Underfull \hbox (badness 10000) in paragraph at lines 12686--12687 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3121] [3122] Underfull \hbox (badness 10000) in paragraph at lines 12804--12805 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3123] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12858--12858 [] \T1/pcr/m/n/9 b <- gam(y~s(x0,bs=bs,m=c(4,2))+s(x1,bs=bs)+s(x2,k=15,bs=bs, m=c(4,3,0))+[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12870--12870 [] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5, 1.5) (black)[] [3124] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12882--12882 [] \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions and intervals[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12887--12887 [] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i ntervals away[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12893--12893 [] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w ild and wide[] Overfull \hbox (3.70428pt too wide) in paragraph at lines 12894--12894 [] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/cmtt/m/n/9 `\T1 /pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] [3125] Underfull \hbox (badness 10000) in paragraph at lines 12963--12965 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a Underfull \hbox (badness 10000) in paragraph at lines 12963--12965 \T1/ptm/m/n/10 term []\T1/pcr/m/n/10 s(...,bs="cr",...)[]\T1/ptm/m/n/10 , []\T1 /pcr/m/n/10 s(...,bs="cs",...) []\T1/ptm/m/n/10 or [3126] [3127] Underfull \hbox (badness 10000) in paragraph at lines 13093--13094 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3128] [3129] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13174--13174 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first deriv penalty[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13175--13175 []\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi ed 2nd deriv[] [3130] [3131] Underfull \hbox (badness 10000) in paragraph at lines 13328--13329 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3132] [3133] [3134] [3135] [3136] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13578--13578 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m ethod="REML")[] [3137] Underfull \hbox (badness 10000) in paragraph at lines 13639--13641 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3138] [3139] Underfull \hbox (badness 10000) in paragraph at lines 13798--13801 []\T1/ptm/m/n/10 For the []\T1/pcr/m/n/10 smooth.construct []\T1/ptm/m/n/10 met hod a smooth spec-i-fi-ca-tion ob- Underfull \hbox (badness 3312) in paragraph at lines 13798--13801 \T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term []\T1/pcr/m/n/10 s(x,...,bs ="re",)[]\T1/ptm/m/n/10 . For the Underfull \hbox (badness 7099) in paragraph at lines 13798--13801 []\T1/pcr/m/n/10 predict.Matrix []\T1/ptm/m/n/10 method an ob-ject of class []\ T1/pcr/m/n/10 "random.effect" [3140] [3141] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13884--13884 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with 2 variances[] [3142] Underfull \hbox (badness 10000) in paragraph at lines 13929--13935 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a Underfull \hbox (badness 7832) in paragraph at lines 13929--13935 []\T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) []\T1/ptm/m/n/10 term in a []\T1/pcr/m/n/10 gam []\T1/ptm/m/n/10 for- [3143] [3144] [3145] Overfull \hbox (36.7804pt too wide) in paragraph at lines 14144--14144 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] Underfull \vbox (badness 10000) has occurred while \output is active [3146] Underfull \vbox (badness 10000) has occurred while \output is active [3147] Underfull \hbox (badness 10000) in paragraph at lines 14247--14255 [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths on th e sphere, via terms like Underfull \hbox (badness 10000) in paragraph at lines 14273--14274 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3148] [3149] [3150] Underfull \hbox (badness 7613) in paragraph at lines 14418--14421 []\T1/ptm/m/n/10 method an ob-ject of class []\T1/pcr/m/n/10 "sz.interaction" [ ]\T1/ptm/m/n/10 pro-duced by the [3151] Underfull \hbox (badness 1546) in paragraph at lines 14439--14440 []\T1/ptm/m/n/10 The terms can have a smooth-ing pa-ram-e-ter per smooth, or a sin-gle smooth-ing pa-ram-e- Overfull \hbox (128.58029pt too wide) in paragraph at lines 14485--14485 []\T1/pcr/m/n/9 b <- gam(y ~ s(x)+s(f1,x,bs="sz")+s(f2,x,bs="sz")+s(f1,f2,x,bs ="sz",id=1),data=dat,method="REML")[] [3152] [3153] [3154] Underfull \hbox (badness 3396) in paragraph at lines 14631--14634 [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths of an y num-ber of vari-ables, spec-i-fied via terms like Underfull \hbox (badness 10000) in paragraph at lines 14676--14678 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3155] [3156] [3157] [3158] [3159] [3160] Underfull \hbox (badness 10000) in paragraph at lines 14967--14969 []\T1/pcr/m/n/10 bs="fs" []\T1/ptm/m/n/10 A spe-cial smoother class (see [3161] Underfull \hbox (badness 10000) in paragraph at lines 15001--15005 [][][]\T1/pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][][]\ T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 t2[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 tprs[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Duchon.spline[][][][]\T 1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cubic.regression.spline[][][][]\T1/ptm/m/n/ 10 , Underfull \hbox (badness 10000) in paragraph at lines 15001--15005 [][][]\T1/pcr/m/n/10 p.spline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 d.sp line[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 mrf[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 soap[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Spherical .Spline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 adaptive.smooth[][][][]\T1 /ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 15001--15005 [][][]\T1/pcr/m/n/10 user.defined.smooth[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/ m/n/10 smooth.construct.re.smooth.spec[][][][]\T1/ptm/m/n/10 , [3162] [3163] [3164] [3165] [3166] Underfull \hbox (badness 2158) in paragraph at lines 15291--15291 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [3167] Overfull \hbox (48.78088pt too wide) in paragraph at lines 15370--15370 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0, centre=FALSE)[] [3168] [3169] Overfull \hbox (12.78088pt too wide) in paragraph at lines 15504--15504 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars "),...)[] [3170] [3171] Underfull \hbox (badness 4846) in paragraph at lines 15635--15638 []\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or es-ti-ma-tors if [3172] [3173] [3174] [3175] [3176] [3177] [3178] [3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186] [3187] [3188] [3189] [3190] [3191] Overfull \hbox (120.78088pt too wide) in paragraph at lines 16853--16853 []\T1/pcr/m/n/10 vcov(object, sandwich=FALSE, freq = FALSE, dispersion = NULL, unconditional=FALSE, ...)[] [3192] Underfull \hbox (badness 1715) in paragraph at lines 16875--16876 []\T1/ptm/m/n/10 Basically, just ex-tracts []\T1/pcr/m/n/10 object$Ve[]\T1/ptm/ m/n/10 , []\T1/pcr/m/n/10 object$Vp []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 object $Vc []\T1/ptm/m/n/10 (if avail-able) from a [3193] [3194] [3195] Overfull \hbox (54.78088pt too wide) in paragraph at lines 17065--17065 []\T1/pcr/m/n/10 XWXd(X,w,k,ks,ts,dt,v,qc,nthreads=1,drop=NULL,ar.stop=-1,ar.r ow=-1,ar.w=-1, Overfull \hbox (48.78088pt too wide) in paragraph at lines 17067--17067 []\T1/pcr/m/n/10 XWyd(X,w,y,k,ks,ts,dt,v,qc,drop=NULL,ar.stop=-1,ar.row=-1,ar. w=-1,lt=NULL)[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17069--17069 []\T1/pcr/m/n/10 diagXVXd(X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,rt= NULL)[] [3196] Underfull \hbox (badness 10000) in paragraph at lines 17089--17090 []\T1/ptm/m/n/10 Negative to ig-nore. Oth-er-wise sum rows Underfull \hbox (badness 1668) in paragraph at lines 17089--17090 []\T1/pcr/m/n/10 (ar.stop[i-1]+1):ar.stop[i] []\T1/ptm/m/n/10 of the rows se-le cted by []\T1/pcr/m/n/10 ar.row [3197] Underfull \vbox (badness 10000) has occurred while \output is active [3198] [3199] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17277--17277 []\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li near predictor,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17278--17278 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun ded in regions[] [3200] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17290--17290 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val ues, to check we[] [3201] [3202] [3203]) (./nlme-pkg.tex [3204] Chapter 25. [3205] Underfull \hbox (badness 1009) in paragraph at lines 84--93 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3206] Underfull \hbox (badness 1009) in paragraph at lines 174--183 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3207] [3208] [3209] [3210] [3211] Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454 [] \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [3212] [3213] Overfull \hbox (20.58041pt too wide) in paragraph at lines 595--595 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 --------------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 611--611 []\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n on-sensical!)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 614--614 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 --------------------------- ---------------[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 621--621 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 --------------------------- ---------------[] [3214] [3215] [3216] [3217] [3218] [3219] [3220] [3221] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1085--1085 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil lary fissure"),[] [3222] Underfull \hbox (badness 5446) in paragraph at lines 1147--1149 []\T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel .htm[]\T1/ptm/m/n/10 ', the first edi-tion of [3223] [3224] [3225] [3226] [3227] [3228] [3229] Underfull \hbox (badness 10000) in paragraph at lines 1626--1629 [][][]\T1/pcr/m/n/10 lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fixed. effects.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 ranef.lmList[][][][ ]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.ranef.lmList[][][][]\T1/ptm/m/n/10 , [3230] Underfull \hbox (badness 3780) in paragraph at lines 1643--1645 []\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a ted with each com-po-nent of the [3231] [3232] [3233] [3234] [3235] Underfull \hbox (badness 2042) in paragraph at lines 1992--1998 \T1/ptm/m/n/10 is in-ner to the []\T1/pcr/m/n/10 displayLevel []\T1/ptm/m/n/10 group-ing fac-tor. If equal to []\T1/pcr/m/n/10 TRUE[]\T1/ptm/m/n/10 , [3236] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2054--2054 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla pse = "Dog")[] [3237] Underfull \hbox (badness 1132) in paragraph at lines 2143--2145 []\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac ted us-ing the [3238] [3239] Underfull \hbox (badness 4168) in paragraph at lines 2254--2260 [][][]\T1/pcr/m/n/10 ACF.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corAR MA[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/pcr/m/n/10 Dim.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 , [3240] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2279--2279 [] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [3241] [3242] [3243] [3244] [3245] [3246] [3247] [3248] Underfull \hbox (badness 10000) in paragraph at lines 2845--2849 [][][]\T1/pcr/m/n/10 corFactor[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cor Matrix.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 recalc.corStruct[ ][][][]\T1/ptm/m/n/10 , [3249] [3250] [3251] [3252] [3253] [3254 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.corMatrix .corCompSymm}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.3188 ...trix(cs1, covariate = 1:4, corr = FALSE) ] [3255] [3256] [3257] [3258] [3259] [3260] Underfull \hbox (badness 6493) in paragraph at lines 3580--3588 [][][]\T1/pcr/m/n/10 corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corGau s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corLin[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 corRatio[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corSp her[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][][]\T 1/ptm/m/n/10 , [3261] [3262] [3263] [3264] [3265] [3266] [3267] [3268] [3269] [3270] [3271] [3272] [3273] [3274] [3275] [3276] [3277] [3278] [3279] [3280] [3281] [3282] [3283] [3284] Underfull \hbox (badness 10000) in paragraph at lines 5160--5164 [][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/p cr/m/n/10 getCovariate.data.frame[][][][]\T1/ptm/m/n/10 , [3285] [3286] [3287] [3288] [3289] [3290] [3291] Underfull \hbox (badness 10000) in paragraph at lines 5592--5595 [][][]\T1/pcr/m/n/10 getGroupsFormula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n /10 getGroups.data.frame[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 getGroups .gls[][][][]\T1/ptm/m/n/10 , [3292] [3293] [3294] [3295] [3296] [3297] [3298] [3299] [3300] Underfull \hbox (badness 2799) in paragraph at lines 6098--6104 \T1/ptm/m/n/10 covariance ma-trix, ei-ther []\T1/pcr/m/n/10 "random.effects" [] \T1/ptm/m/n/10 for the random-effects [3301] Underfull \hbox (badness 7133) in paragraph at lines 6159--6163 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in [ ]\T1/pcr/m/n/10 model[]\T1/ptm/m/n/10 , [3302] Underfull \hbox (badness 2057) in paragraph at lines 6248--6259 [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gl sControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 glsObject[][][][]\T1/ptm/ m/n/10 , [][][]\T1/pcr/m/n/10 glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 plot.gls[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.gls[][][][] \T1/ptm/m/n/10 , [3303] Underfull \hbox (badness 10000) in paragraph at lines 6312--6314 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3304] [3305] [3306] [3307] Underfull \hbox (badness 7133) in paragraph at lines 6560--6564 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in [ ]\T1/pcr/m/n/10 model[]\T1/ptm/m/n/10 , [3308] Underfull \hbox (badness 10000) in paragraph at lines 6659--6665 [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gn lsControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gnlsObject[][][][]\T1/pt m/m/n/10 , [][][]\T1/pcr/m/n/10 gnlsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc r/m/n/10 predict.gnls[][][][]\T1/ptm/m/n/10 , Overfull \hbox (54.78088pt too wide) in paragraph at lines 6686--6686 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min Scale = 0.001, [3309] Underfull \hbox (badness 10000) in paragraph at lines 6724--6726 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3310] [3311] [3312] [3313] Underfull \hbox (badness 10000) in paragraph at lines 6995--7002 [][][]\T1/pcr/m/n/10 formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gappl y[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gsummary[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.nff GroupedData[][][][]\T1/ptm/m/n/10 , [3314] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7013--7013 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla ry fissure" ),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7018--7018 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted from object[] Underfull \hbox (badness 2875) in paragraph at lines 7040--7042 []\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a []\T1/pcr/m/n/10 gr oupedData []\T1/ptm/m/n/10 ob-ject or a [3315] [3316] [3317] Underfull \hbox (badness 10000) in paragraph at lines 7255--7260 [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr /m/n/10 Initialize.lmeStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initi alize.glsStruct[][][][]\T1/ptm/m/n/10 , [3318] [3319] [3320] Underfull \hbox (badness 1997) in paragraph at lines 7406--7414 []\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial -iza-tion and op-ti- Underfull \hbox (badness 2205) in paragraph at lines 7406--7414 \T1/ptm/m/n/10 miza-tion al-go-rithms used in []\T1/pcr/m/n/10 lme[]\T1/ptm/m/n /10 . De-faults to []\T1/pcr/m/n/10 list(niterEM=20, Underfull \hbox (badness 3118) in paragraph at lines 7429--7432 [][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initializ e.reStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.corStruct[][ ][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.varFunc[][][][]\T1/ptm/m/ n/10 , [3321] [3322] [3323] Underfull \hbox (badness 3354) in paragraph at lines 7645--7647 []\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when []\T1/pcr/m/n/ 10 which []\T1/ptm/m/n/10 is not equal to [3324] [3325] [3326] [3327] [3328] [3329] [3330] [3331] Underfull \hbox (badness 10000) in paragraph at lines 8173--8190 [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lm e.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lme.groupedData[][][][]\T 1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lmeControl[][][][]\T1/ptm/m/n/10 , [][][]\T 1/pcr/m/n/10 lmeObject[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8173--8190 [][][]\T1/pcr/m/n/10 lmeStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lmL ist[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/pcr/m/n/10 plot.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 qqnorm.lme[][][][]\T1/ ptm/m/n/10 , [3332] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8216--8216 [] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data = TRUE)[] Underfull \hbox (badness 1642) in paragraph at lines 8225--8247 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3333] [3334] [3335] [3336] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8490--8490 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni terEM = 25, [3337] Underfull \hbox (badness 10000) in paragraph at lines 8538--8540 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Overfull \hbox (9.78043pt too wide) in paragraph at lines 8582--8582 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3338] [3339] [3340] [3341] [3342] [3343] [3344] [3345] [3346] [3347] [3348] [3349] Underfull \hbox (badness 10000) in paragraph at lines 9345--9352 [][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 ,[][][]\T1/pcr/m/n/10 gls[][][][ ]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logLik.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logLik.glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 logLik.lmeStruct[][][][]\T1/ptm/m/n/10 , Overfull \hbox (4.38043pt too wide) in paragraph at lines 9356--9356 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me thod = "ML") [3350] [3351] [3352] [3353] [3354] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9707 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Matrix.1} ) has been already used, duplicate ignored \relax l.9707 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3355] Underfull \hbox (badness 10000) in paragraph at lines 9727--9730 []\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a s Underfull \hbox (badness 3108) in paragraph at lines 9771--9774 []\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive -definite Underfull \hbox (badness 2521) in paragraph at lines 9771--9774 \T1/ptm/m/n/10 ma-trix rep-re-sented by []\T1/pcr/m/n/10 object[]\T1/ptm/m/n/10 . Must have the same di-men-sions as [3356] [3357] [3358] [3359] [3360] [3361] [3362] [3363] [3364] [3365] [3366] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10451--10451 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights, [3367] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10455--10455 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights,[] Underfull \hbox (badness 1596) in paragraph at lines 10484--10510 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3368] [3369] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10638--10638 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights,[] [3370] [3371] [3372] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10789--10789 [] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma = NULL, ...)[] Underfull \hbox (badness 2213) in paragraph at lines 10800--10805 []\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][][]\T1/pcr/m/n/10 nlmi nb[][][] []\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 iter.max[]\T1/ptm/m/n/10 ) or the [ ][][]\T1/pcr/m/n/10 nlm[][][] Underfull \hbox (badness 6961) in paragraph at lines 10822--10826 []\T1/ptm/m/n/10 a log-i-cal value passed as the []\T1/pcr/m/n/10 trace []\T1/p tm/m/n/10 to [][][]\T1/pcr/m/n/10 nlminb[][][](.., control= [3373] Underfull \hbox (badness 10000) in paragraph at lines 10841--10843 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3374] [3375] [3376] [3377] Overfull \hbox (96.18033pt too wide) in paragraph at lines 11137--11137 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* message instead of one *each*[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 11138--11138 []\T1/pcr/m/n/9 mat.class <- class(matrix(1)) # ("matrix", "array") for R >= 4 .0.0; ("matrix" in older R)[] [3378] [3379] [3380] [3381] [3382] [3383] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11528--11528 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo nt)), .. lme(*)) [3384] [3385] [3386] [3387] [3388] [3389] Underfull \hbox (badness 6268) in paragraph at lines 11915--11925 [][][]\T1/pcr/m/n/10 pdBlocked[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdC ompSymm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdDiag[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 pdFactor[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdIdent[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 pdMatrix[][][][]\T1/ptm/m/n/10 , [3390] [3391] [3392] [3393] Underfull \hbox (badness 10000) in paragraph at lines 12176--12182 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 coef.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdBlocked[][][][]\T1 /ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 pdConstruct[][][][]\T1/ptm/m/n/10 , [3394] [3395] [3396] [3397] [3398] Underfull \hbox (badness 6876) in paragraph at lines 12498--12500 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 value []\T1/ptm/m/n/10 is an \T1/ptm/m/it/ 10 ini-tial-ized []\T1/pcr/m/n/10 pdMat []\T1/ptm/m/n/10 ob-ject, []\T1/pcr/m/n /10 object []\T1/ptm/m/n/10 will be con-structed from [3399] [3400] Underfull \hbox (badness 2452) in paragraph at lines 12654--12661 [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdC ompSymm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdDiag[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 pdIdent[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdNatural[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdSymm[][][][]\T1/ptm/m/ n/10 , [][][]\T1/pcr/m/n/10 reStruct[][][][]\T1/ptm/m/n/10 , [3401] Underfull \hbox (badness 10000) in paragraph at lines 12720--12726 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdFactor[][][][]\T1/p tm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 pdMatrix.reStruct[][][][]\T1/ptm/m/n/10 , [3402] [3403] [3404] [3405] [3406] [3407] [3408] [3409] [3410] Overfull \hbox (25.98041pt too wide) in paragraph at lines 13309--13309 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo nt)), .. lme(*)) [3411] [3412] [3413] [3414] [3415] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13674--13674 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 0, id = 0.05)[] [3416] Underfull \hbox (badness 10000) in paragraph at lines 13701--13704 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nffGroupe dData[]\T1/ptm/m/n/10 , rep-re-sent-ing a [3417] Underfull \hbox (badness 1838) in paragraph at lines 13744--13751 []\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If []\T1/pcr/m/ n/10 TRUE []\T1/ptm/m/n/10 and ei-ther []\T1/pcr/m/n/10 inner Underfull \hbox (badness 3713) in paragraph at lines 13744--13751 []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 innerGroups []\T1/ptm/m/n/10 are non-[]\T1 /pcr/m/n/10 NULL[]\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent []\T1/pcr/m/n/ 10 inner Overfull \hbox (12.78088pt too wide) in paragraph at lines 13801--13801 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect, panel,[] [3418] Underfull \hbox (badness 10000) in paragraph at lines 13808--13811 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nfnGroupe dData[]\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 2469) in paragraph at lines 13808--13811 []\T1/pcr/m/n/10 groupedData []\T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-vari-ate and a sin-gle [3419] Underfull \hbox (badness 10000) in paragraph at lines 13916--13919 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nmGrouped Data[]\T1/ptm/m/n/10 , rep-re-sent-ing a [3420] [3421] Underfull \hbox (badness 10000) in paragraph at lines 14010--14012 [][][]\T1/pcr/m/n/10 groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 c ollapse.groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.nfnGroupe dData[][][][]\T1/ptm/m/n/10 , [3422] [3423] [3424] [3425] [3426] [3427] [3428] [3429] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14534--14534 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female", "Male","Male"),[] [3430] [3431] [3432] [3433] [3434] [3435] [3436] [3437] [3438] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.random.ef fects}) has been already used, duplicate ignored \relax l.15187 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.random.ef fects.1}) has been already used, duplicate ignored \relax l.15187 ...Extract Random Effects}{random.effects} [3439] [3440] [3441] [3442] [3443] [3444] [3445] [3446] [3447] [3448] Underfull \hbox (badness 2126) in paragraph at lines 15826--15830 []\T1/ptm/m/n/10 Charles F. Minto, Thomas W. Schnider and Steven L. Shafer (199 7). Phar-ma-coki-net- [3449] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15834--15834 []\T1/pcr/m/n/9 plot(Remifentanil, type = "l", lwd = 2) # shows the 65 patient s\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 remi profiles Overfull \hbox (31.3804pt too wide) in paragraph at lines 15853--15853 [] \T1/pcr/m/n/9 stopifnot(all.equal(BSA, Wt^{0.425} * Ht^{0.725} * 0.00718 4, tol = 1.5e-5),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15854--15854 [] \T1/pcr/m/n/9 all.equal(LBM, LBMfn(Wt, Ht, Sex), tol = 7e-7)[] [3450] Underfull \hbox (badness 1009) in paragraph at lines 15884--15893 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3451] [3452] Overfull \hbox (66.78088pt too wide) in paragraph at lines 16031--16031 [] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi st = FALSE, ...)[] [3453] [3454] [3455] [3456] [3457] Underfull \hbox (badness 10000) in paragraph at lines 16366--16372 [][][]\T1/pcr/m/n/10 groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 l me[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 solve.reStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 summary.reStruct[][][][]\T1/ptm/m/n/10 , [3458] Overfull \hbox (18.78088pt too wide) in paragraph at lines 16398--16398 [] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG en, ...)[] [3459] [3460] [3461] [3462] [3463] [3464] [3465] Underfull \hbox (badness 1728) in paragraph at lines 16885--16888 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3466] [3467] [3468] [3469] [3470] Underfull \hbox (badness 1803) in paragraph at lines 17219--17228 \T1/pcr/m/n/10 of an Identity" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pdIdent[]\ T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "General Positive-Definite, Underfull \hbox (badness 10000) in paragraph at lines 17219--17228 \T1/pcr/m/n/10 Natural Parametrization" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 p dNatural[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "General Underfull \hbox (badness 7888) in paragraph at lines 17219--17228 \T1/pcr/m/n/10 Positive-Definite" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pdSymm[ ]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 data.class(object) [3471] Underfull \hbox (badness 10000) in paragraph at lines 17290--17291 []\T1/pcr/m/n/10 "Constant plus power of variance Underfull \hbox (badness 10000) in paragraph at lines 17291--17292 []\T1/pcr/m/n/10 "Constant plus proportion of variance [3472] [3473] [3474] [3475] Underfull \hbox (badness 10000) in paragraph at lines 17541--17549 [][][]\T1/pcr/m/n/10 varComb[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varCo nstPower[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varConstProp[][][][]\T1/p tm/m/n/10 , [][][]\T1/pcr/m/n/10 varExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 varFixed[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varIdent[][][][]\T1 /ptm/m/n/10 , [3476] [3477] [3478] [3479] Overfull \hbox (4.38043pt too wide) in paragraph at lines 17813--17813 []\T1/pcr/m/n/9 # Generate some synthetic data using the two-component error m odel and use Overfull \hbox (25.98041pt too wide) in paragraph at lines 17815--17815 []\T1/pcr/m/n/9 # overparameterisation in the case of a constant term in the v ariance function[] [3480] [3481] [3482] [3483] [3484] [3485] Underfull \hbox (badness 10000) in paragraph at lines 18251--18261 [][][]\T1/pcr/m/n/10 Variogram.corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n /10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.co rLin[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18251--18261 [][][]\T1/pcr/m/n/10 Variogram.corRatio[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 Variogram.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogr am.corSpher[][][][]\T1/ptm/m/n/10 , [3486] Underfull \hbox (badness 3579) in paragraph at lines 18289--18294 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3487] Underfull \hbox (badness 3579) in paragraph at lines 18353--18358 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3488] Underfull \hbox (badness 3579) in paragraph at lines 18416--18421 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3489] Underfull \hbox (badness 1577) in paragraph at lines 18477--18479 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 "[][]corR atio[][][]"[]\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal Underfull \hbox (badness 3579) in paragraph at lines 18479--18484 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3490] Underfull \hbox (badness 3579) in paragraph at lines 18542--18547 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence Underfull \hbox (badness 10000) in paragraph at lines 18575--18584 [][][]\T1/pcr/m/n/10 corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Va riogram[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.default[][][][]\ T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.corExp[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18575--18584 [][][]\T1/pcr/m/n/10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 Variogram.corLin[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.co rRatio[][][][]\T1/ptm/m/n/10 , [3491] Underfull \hbox (badness 3579) in paragraph at lines 18614--18619 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3492] [3493] Underfull \hbox (badness 1009) in paragraph at lines 18760--18769 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3494] [3495] Underfull \hbox (badness 1009) in paragraph at lines 18892--18901 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3496] [3497] [3498] [3499] [3500] [3501] [3502] [3503] [3504]) (./nnet-pkg.tex Chapter 26. pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom} ) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom. 1}) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} [3505] Overfull \hbox (12.78088pt too wide) in paragraph at lines 71--71 [] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored = FALSE,[] [3506] [3507] [3508] Overfull \hbox (15.18042pt too wide) in paragraph at lines 371--371 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3509] Overfull \hbox (4.38043pt too wide) in paragraph at lines 428--428 []\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c( 0,0,1),50)),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 431--431 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay =5e-4, maxit=200)[] [3510] [3511] Overfull \hbox (15.18042pt too wide) in paragraph at lines 511--511 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3512]) (./rpart-pkg.tex Chapter 27. [3513] [3514] [3515] [3516] Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse = TRUE, ...)[] [3517] Underfull \hbox (badness 2351) in paragraph at lines 349--353 \T1/ptm/m/n/10 age: []\T1/pcr/m/n/10 pretty = 0 []\T1/ptm/m/n/10 im-plies []\T1 /pcr/m/n/10 minlength = 0L[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pretty = NULL []\ T1/ptm/m/n/10 im-plies [3518] [3519] [3520] Underfull \hbox (badness 1442) in paragraph at lines 592--598 []\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 FALSE[]\T1/ptm/m/n/10 , the leaf nodes wil l be at the hor-i-zon-tal plot co-or-di-nates of [3521] [3522] Overfull \hbox (0.78088pt too wide) in paragraph at lines 738--738 [] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep = ""),[] Underfull \hbox (badness 10000) in paragraph at lines 771--775 []\T1/ptm/m/n/10 Logical. If []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 (de-fault), adds to the la-bel Underfull \hbox (badness 1142) in paragraph at lines 771--775 \T1/pcr/m/n/10 #events level1/ #events level2/ \T1/ptm/m/n/10 etc. for method [ ]\T1/pcr/m/n/10 class[]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 n [3523] [3524] [3525] Overfull \hbox (25.98041pt too wide) in paragraph at lines 915--915 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie s, probabilities[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 934--934 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d igits"),[] [3526] [3527] [3528] [3529] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1180--1180 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m ethod, Overfull \hbox (12.78088pt too wide) in paragraph at lines 1181--1181 [] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos t, ...)[] Underfull \hbox (badness 2846) in paragraph at lines 1243--1245 []\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the []\T1/pcr/m/n /10 rpart []\T1/ptm/m/n/10 al-go-rithm. See [3530] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1287--1287 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the text is clipped[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1303--1303 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c p = 0.01, Overfull \hbox (60.78088pt too wide) in paragraph at lines 1304--1304 [] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,[] [3531] [3532] [3533] [3534] [3535] [3536] [3537] Underfull \hbox (badness 1565) in paragraph at lines 1760--1763 []\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val- ues are `[]\T1/pcr/m/n/10 diploid[]\T1/ptm/m/n/10 ', [3538] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1854--1854 [] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,[] [3539] [3540] [3541]) (./spatial-pkg.tex [3542] Chapter 28. [3543] [3544] [3545] [3546] [3547] [3548] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3549] [3550] [3551] [3552] [3553] [3554] [3555] [3556] [3557] [3558] [3559] [3560] [3561]) (./survival-pkg.tex [3562] Chapter 29. [3563] [3564] Overfull \hbox (31.3804pt too wide) in paragraph at lines 173--173 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data = lung, nmin = 1[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 192--192 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t he last point[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 195--195 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a nd Grambsch.[] [3565] [3566] Underfull \hbox (badness 6412) in paragraph at lines 284--286 []\T1/ptm/m/n/10 an op-tional list or vec-tor of group-ing el-e-ments, each as long as [3567] [3568] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has been already used, duplicate ignored \relax l.384 ... Myelogenous Leukemia survival data}{aml} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml.1}) h as been already used, duplicate ignored \relax l.384 ... Myelogenous Leukemia survival data}{aml} [3569] Overfull \hbox (9.78043pt too wide) in paragraph at lines 485--485 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da ta = ovarian) Overfull \hbox (4.38043pt too wide) in paragraph at lines 487--487 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d ata=ovarian)[] [3570] Overfull \hbox (6.78088pt too wide) in paragraph at lines 525--525 [] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog), lung)[] [3571] [3572] [3573] [3574] Overfull \hbox (20.58041pt too wide) in paragraph at lines 773--773 []\T1/pcr/m/n/9 py <- pseudo(survfit(Surv(time, status) ~1, lung), time=730) # 2 year survival Overfull \hbox (30.78088pt too wide) in paragraph at lines 789--789 []\T1/pcr/m/n/10 brier(fit, times, newdata, ties = TRUE, detail = FALSE, timef ix = TRUE, [3575] [3576] Overfull \hbox (48.78088pt too wide) in paragraph at lines 872--872 [] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan", "II.Borgan"),[] [3577] [3578] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1015--1015 [] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz e=stratsizes,[] [3579] [3580] Underfull \hbox (badness 1097) in paragraph at lines 1186--1188 []\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi al and negative-binomial data. [3581] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1206--1206 []\T1/pcr/m/n/9 ppois(4, 10.24153) #chance of seeing 4 or fewer events wit h large rate[] [3582] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1321--1321 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat um), data=infert) [3583] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1382--1382 []\T1/pcr/m/n/9 marginal.model <- coxph(Surv(time, status) ~ rx, data= rats, c luster=litter, pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colon}) h as been already used, duplicate ignored \relax l.1388 ...erapy for Stage B/C colon cancer}{colon} [3584] [3585] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1488--1488 [] \T1/pcr/m/n/10 influence=0, ranks = FALSE, reverse=FALSE, timefix=TRUE, ke epstrata=10, ...)[] [3586] [3587] [3588] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1714--1714 []\T1/pcr/m/n/9 options(na.action = na.exclude) # predict all 1384 obs, incl uding missing[] [3589] [3590] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1808--1808 []\T1/pcr/m/n/10 cox.zph(fit, transform="km", terms=TRUE, singledf=FALSE, glob al=TRUE) [3591] [3592] [3593] [3594] Underfull \hbox (badness 10000) in paragraph at lines 2124--2139 []\T1/ptm/m/n/10 One user mis-take that has re-cently arisen is to slav-ishly f ol-low the ad-vice of Underfull \hbox (badness 7486) in paragraph at lines 2124--2139 \T1/ptm/m/n/10 some cod-ing guides and prepend []\T1/pcr/m/n/10 survival:: []\T 1/ptm/m/n/10 onto ev-er-thing, in-clud-ing the spe- Underfull \hbox (badness 10000) in paragraph at lines 2124--2139 \T1/ptm/m/n/10 cial terms, e.g., []\T1/pcr/m/n/10 survival::coxph(survival:Surv (time, status) ~ age + [3595] Underfull \hbox (badness 3861) in paragraph at lines 2219--2223 [][][]\T1/pcr/m/n/10 coxph.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 coxphms.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 coxph.control[][][] []\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cluster[][][][]\T1/ptm/m/n/10 , [][][]\ T1/pcr/m/n/10 strata[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Surv[][][][]\ T1/ptm/m/n/10 , [3596] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2274--2274 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix =TRUE)[] [3597] [3598] [3599] [3600] [3601] [3602] [3603] [3604] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2902--2902 [] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" " exponential"[] [3605] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2943--2943 []\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass, etype, [3606] [3607] [3608] [3609] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3187--3187 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t df = 5,[] [3610] [3611] [3612] [3613] Underfull \hbox (badness 1019) in paragraph at lines 3449--3451 []\T1/ptm/m/n/10 outcome: []\T1/pcr/m/n/10 censor[]\T1/ptm/m/n/10 , []\T1/pcr/m /n/10 thymic lymphoma[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 reticulum cell sarcoma other [3614] [3615] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3593--3593 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt y(id), kidney) [3616] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3628--3628 [] \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre ssion", "death")))[] Underfull \hbox (badness 1389) in paragraph at lines 3642--3644 []\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan -Meier plot gen-er-ated with Overfull \hbox (12.78088pt too wide) in paragraph at lines 3653--3653 [] \T1/pcr/m/n/10 conf.type = c("log", "log-log", "plain", "logit", "ar csin"),[] [3617] [3618] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3787--3787 [] \T1/pcr/m/n/9 rmap=list(sex=sex, age=age*365.35, year=as.Da te(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/01/01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3619] [3620] Overfull \hbox (467.89665pt too wide) in alignment at lines 3928--3928 [] [] [3621] [3622] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4050--4050 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential ly the same.[] [3623] [3624] [3625] [3626] [3627] [3628] [3629] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4496--4496 [] \T1/pcr/m/n/9 entry.dt = as.Date(paste("2011", 1:10, "5" , sep=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 -\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3630] [3631] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4646--4646 []\T1/pcr/m/n/9 tdata <- data.frame(x= lung$age, y = 10*log(lung$age-35) + rno rm(228, 0, 2))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4651--4651 []\T1/pcr/m/n/9 knots <- unlist(attributes(fit1$model[[2]])[c(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Boundary.knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )])[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4655--4655 []\T1/pcr/m/n/9 unname(coef(fit1)[-1] - coef(fit1)[1]) # differences: yhat[2: 4] - yhat[1][] [3632] [3633] [3634] [3635] [3636] [3637] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4986--4986 [] \T1/pcr/m/n/10 xlab="Time", ylab, lty=1:2, col=1, lwd=1, hr=FALSE, p lot=TRUE, ...)[] [3638] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5075--5075 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca le=1,[] [3639] [3640] [3641] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5305--5305 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), collapse,[] [3642] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5431--5431 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] [3643] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5439--5439 [] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means , na.rm=TRUE)[] [3644] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5525--5525 []\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival is at +infinity[] [3645] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5603--5603 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars"), expand=FALSE , ...)[] [3646] Underfull \hbox (badness 1852) in paragraph at lines 5675--5677 []\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.survfit"[]\T1/pt m/m/n/10 , which is the re-sult of the [3647] [3648] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5801--5801 []\T1/pcr/m/n/10 pseudo(fit, times, type, addNA=TRUE, data.frame=FALSE, minus1 =FALSE, ...) [3649] [3650] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5912--5912 []\T1/pcr/m/n/9 rhat <- predict(rfit, newdata=expand.grid(ph.ecog=0:3, sex=1:2 ), se.fit=TRUE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5924--5924 []\T1/pcr/m/n/9 # the estimate for ph.ecog=3 is very unstable (n=1), pseudoval ues smooth it.[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5926--5926 []\T1/pcr/m/n/9 # In all the above we should be using the robust variance, e.g ., svyglm, but[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5950--5950 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me thod, Overfull \hbox (36.78088pt too wide) in paragraph at lines 5951--5951 [] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co mbine, ...)[] [3651] [3652] [3653] Overfull \hbox (30.78088pt too wide) in paragraph at lines 6114--6114 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] [3654] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6216--6216 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age + sex, mgus,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6237--6237 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50 ,60,70,100)) +[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6239--6239 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5 0,60,70,100)) +[] [3655] [3656] [3657] [3658] [3659] [3660] [3661] Overfull \hbox (42.78088pt too wide) in paragraph at lines 6705--6705 [] \T1/pcr/m/n/10 collapse=FALSE, weighted= (type %in% c("dfbeta", "dfbe tas")), ...)[] [3662] [3663] [3664] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6887--6887 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb etas",[] Underfull \hbox (badness 1043) in paragraph at lines 6899--6902 []\T1/pcr/m/n/10 "dfbetas"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "working"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "ldcase"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lsresp "[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ldshape"[]\T1/ptm/m/n/10 , and [3665] [3666] [3667] [3668] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7206--7206 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the ta=5), lung)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7207--7207 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog , theta=1), lung)[] [3669] [3670] [3671] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7391--7391 []\T1/pcr/m/n/10 rttright(formula, data, weights, subset, na.action, times, id , timefix = TRUE, [3672] Overfull \hbox (42.18039pt too wide) in paragraph at lines 7474--7474 []\T1/pcr/m/n/9 cdf <- cdf[!duplicated(aml$time[index], fromLast=TRUE)] # rem ove duplicate times[] [3673] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7478--7478 []\T1/pcr/m/n/9 wt2 <- rttright(Surv(dtime, death) ~ hormon, rotterdam, times= 365*c(3, 5))[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) has been already used, duplicate ignored \relax l.7482 ...ata from a soldering experiment}{solder} [3674] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7588--7588 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1, col = 1, [3675] [3676] [3677] [3678] [3679] [3680] Overfull \hbox (42.78088pt too wide) in paragraph at lines 7954--7954 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r r =expected,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 7955--7955 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli ne = FALSE,[] [3681] [3682] [3683] [3684] Overfull \hbox (54.78088pt too wide) in paragraph at lines 8272--8272 [] \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/ 10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/ n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[] [3685] [3686] [3687] [3688] Underfull \hbox (badness 1253) in paragraph at lines 8561--8564 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 median[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 quantile []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 plot []\T1/ptm/m/n/10 meth-ods first con-struct a sur-vival curve us-ing [3689] [3690] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8691--8691 []\T1/pcr/m/n/10 survcheck(formula, data, subset, na.action, id, istate, istat e0="(s0)", [3691] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8814--8814 []\T1/pcr/m/n/10 survcondense(formula, data, subset, weights, na.action= na.pa ss, id, [3692] [3693] [3694] Overfull \hbox (36.7804pt too wide) in paragraph at lines 9013--9013 [] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1 , year=accept.dt),[] [3695] Overfull \hbox (24.78088pt too wide) in paragraph at lines 9038--9038 [] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv idual.h",[] Underfull \hbox (badness 1038) in paragraph at lines 9080--9086 []\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre -dicted sur-vival [3696] Overfull \hbox (48.78088pt too wide) in paragraph at lines 9132--9132 [] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d t-entry.dt)),[] [3697] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9218--9218 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival by 1/2 years[] [3698] [3699] [3700] Underfull \hbox (badness 10000) in paragraph at lines 9438--9443 [][][]\T1/pcr/m/n/10 survfit.formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 survfit.coxph[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 survfit.object[][ ][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.survfit[][][][]\T1/ptm/m/n/10 , Overfull \hbox (12.78088pt too wide) in paragraph at lines 9458--9458 [] \T1/pcr/m/n/10 se.fit=TRUE, conf.int=.95, individual=FALSE, stype=2, ctype,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9459--9459 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] [3701] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9464--9464 [] \T1/pcr/m/n/10 se.fit=FALSE, conf.int=.95, individual=FALSE, stype=2 , ctype,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9465--9465 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] [3702] [3703] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9688--9688 [] \T1/pcr/m/n/10 stype=1, ctype=1, id, cluster, robust, istate, timefi x=TRUE,[] [3704] [3705] Underfull \hbox (badness 2653) in paragraph at lines 9822--9827 \T1/pcr/m/n/10 ctype=1[]\T1/ptm/m/n/10 , "fleming-harrington" which is equiv-a- lent to []\T1/pcr/m/n/10 stype=2, [3706] [3707] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9962--9962 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3708] [3709] [3710] [3711] [3712] Overfull \hbox (30.78088pt too wide) in paragraph at lines 10349--10349 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, Underfull \hbox (badness 1354) in paragraph at lines 10390--10394 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3713] Overfull \hbox (60.78088pt too wide) in paragraph at lines 10436--10436 []\T1/pcr/m/n/10 survConcordance(formula, data, weights, subset, na.action) # use concordance [3714] [3715] Underfull \hbox (badness 2035) in paragraph at lines 10600--10607 \T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][][]\T1/pcr/m/n/10 su rvreg.distributions[][][][]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 10600--10607 \T1/ptm/m/n/10 These in-clude []\T1/pcr/m/n/10 "weibull"[]\T1/ptm/m/n/10 , []\T 1/pcr/m/n/10 "exponential"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "gaussian"[]\T1/p tm/m/n/10 , Underfull \hbox (badness 1297) in paragraph at lines 10600--10607 []\T1/pcr/m/n/10 "logistic"[]\T1/ptm/m/n/10 ,[]\T1/pcr/m/n/10 "lognormal" []\T1 /ptm/m/n/10 and []\T1/pcr/m/n/10 "loglogistic"[]\T1/ptm/m/n/10 . Oth-er-wise, i t is [3716] [3717] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10690--10690 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3718] [3719] Overfull \hbox (31.3804pt too wide) in paragraph at lines 10847--10847 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3720] [3721] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10979--10979 [] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x ^2*temp -1))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 10982--10982 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3722] [3723] [3724] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11158--11158 []\T1/pcr/m/n/9 pfit2 <- pyears(Surv(years, death) ~ fgrp + agegrp, scale =100 0, data=test)[] [3725] [3726] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11316--11316 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic al trial plus[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11317--11317 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11323--11323 [] \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day , alk.phos))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 11325--11325 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil i), data=pbc2)[] [3727] [3728] [3729] [3730] [3731] [3732] [3733] Overfull \hbox (12.78088pt too wide) in paragraph at lines 11766--11766 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l inear",[] [3734] [3735] [3736]) (./fullrefman.ind [3737] [3738] [3739] [3740] [3741] [3742] [3743] [3744] [3745] [3746] [3747] [3748] [3749] [3750] [3751] [3752] [3753] [3754] [3755] [3756] [3757] [3758] [3759] [3760] [3761] [3762] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2691--2693 []| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2693--2695 []| \T1/pcr/m/n/10 smooth.construct.bs.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2695--2697 []| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2697--2699 []| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2699--2701 []| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2701--2703 []| \T1/pcr/m/n/10 smooth.construct.gp.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (25.3567pt too wide) in paragraph at lines 2703--2705 []| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2705--2707 []| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 , 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paragraph at lines 3355--3357 []| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 3357--3359 []| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 3359--3361 []| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (25.3567pt too wide) in paragraph at lines 3361--3363 []| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 3363--3365 []| \T1/pcr/m/n/10 smooth.construct.sz.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 3365--3367 []| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (43.3567pt too wide) in paragraph at lines 3367--3369 []| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 3369--3371 []| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , [3769] [3770] Overfull \hbox (19.3567pt too wide) in paragraph at lines 3525--3527 []| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , [3771] [3772] [3773] [3774] [3775] [3776] [3777] [3778] [3779] Overfull \hbox (20.8567pt too wide) in paragraph at lines 4759--4761 []\T1/pcr/m/n/10 [,Matrix,index,index,logical-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 4761--4763 []\T1/pcr/m/n/10 [,Matrix,index,index,missing-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 4763--4765 []\T1/pcr/m/n/10 [,Matrix,index,missing,logical-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 4765--4767 []\T1/pcr/m/n/10 [,Matrix,index,missing,missing-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 4767--4769 []\T1/pcr/m/n/10 [,Matrix,lMatrix,missing,missing-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 4769--4771 []\T1/pcr/m/n/10 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Arith,sparseVector,ddenseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 6162--6164 []\T1/pcr/m/n/10 Arith,sparseVector,dgeMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 6164--6166 []\T1/pcr/m/n/10 Arith,sparseVector,sparseVector-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 6166--6168 []\T1/pcr/m/n/10 Arith,triangularMatrix,diagonalMatrix-method [3790] [3791] [3792] Overfull \hbox (32.8567pt too wide) in paragraph at lines 6667--6669 []\T1/pcr/m/n/10 aspell_write_personal_dictionary_file [3793] Overfull \hbox (46.01662pt too wide) in paragraph at lines 6852--6854 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [3794] [3795] Overfull \hbox (10.01662pt too wide) in paragraph at lines 7299--7301 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3796] [3797] Overfull \hbox (2.8567pt too wide) in paragraph at lines 7773--7775 []\T1/pcr/m/n/10 chol2inv,triangularMatrix-method [3798] Overfull \hbox (2.8567pt too wide) in paragraph at lines 7818--7820 []\T1/pcr/m/n/10 Cholesky,triangularMatrix-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 7825--7827 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3799] [3800] [3801] Overfull \hbox (50.8567pt too wide) in paragraph at lines 8331--8333 []\T1/pcr/m/n/10 coerce,atomicVector,dsparseVector-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 8333--8335 []\T1/pcr/m/n/10 coerce,atomicVector,sparseVector-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 8335--8337 []\T1/pcr/m/n/10 coerce,BunchKaufman,dtrMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 8337--8339 []\T1/pcr/m/n/10 coerce,CHMsimpl,dtCMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 8339--8341 []\T1/pcr/m/n/10 coerce,CHMsuper,dgCMatrix-method Overfull \hbox (2.8567pt too 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coerce,matrix,CsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8405--8407 []\T1/pcr/m/n/10 coerce,Matrix,ddenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8407--8409 []\T1/pcr/m/n/10 coerce,matrix,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 8409--8411 []\T1/pcr/m/n/10 coerce,Matrix,denseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 8411--8413 []\T1/pcr/m/n/10 coerce,matrix,denseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 8415--8417 []\T1/pcr/m/n/10 coerce,Matrix,diagonalMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 8417--8419 []\T1/pcr/m/n/10 coerce,matrix,diagonalMatrix-method [3802] Overfull \hbox (14.8567pt too wide) in paragraph at lines 8431--8433 []\T1/pcr/m/n/10 coerce,Matrix,dsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8433--8435 []\T1/pcr/m/n/10 coerce,matrix,dsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8435--8437 []\T1/pcr/m/n/10 coerce,Matrix,generalMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8437--8439 []\T1/pcr/m/n/10 coerce,matrix,generalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8447--8449 []\T1/pcr/m/n/10 coerce,Matrix,ldenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8449--8451 []\T1/pcr/m/n/10 coerce,matrix,ldenseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8455--8457 []\T1/pcr/m/n/10 coerce,Matrix,lsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8457--8459 []\T1/pcr/m/n/10 coerce,matrix,lsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8469--8471 []\T1/pcr/m/n/10 coerce,Matrix,ndenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8471--8473 []\T1/pcr/m/n/10 coerce,matrix,ndenseMatrix-method 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paragraph at lines 8501--8503 []\T1/pcr/m/n/10 coerce,Matrix,sparseVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8503--8505 []\T1/pcr/m/n/10 coerce,matrix,sparseVector-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 8505--8507 []\T1/pcr/m/n/10 coerce,Matrix,symmetricMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 8507--8509 []\T1/pcr/m/n/10 coerce,matrix,symmetricMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 8509--8511 []\T1/pcr/m/n/10 coerce,Matrix,triangularMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 8511--8513 []\T1/pcr/m/n/10 coerce,matrix,triangularMatrix-method [3803] Overfull \hbox (14.8567pt too wide) in paragraph at lines 8513--8515 []\T1/pcr/m/n/10 coerce,Matrix,TsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8515--8517 []\T1/pcr/m/n/10 coerce,matrix,TsparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 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[]\T1/pcr/m/n/10 coerce,matrix.csc,CsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8537--8539 []\T1/pcr/m/n/10 coerce,matrix.csc,dgCMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 8541--8543 []\T1/pcr/m/n/10 coerce,matrix.csc,RsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 8543--8545 []\T1/pcr/m/n/10 coerce,matrix.csc,sparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 8545--8547 []\T1/pcr/m/n/10 coerce,matrix.csc,TsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 8547--8549 []\T1/pcr/m/n/10 coerce,matrix.csr,CsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8549--8551 []\T1/pcr/m/n/10 coerce,matrix.csr,dgCMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8551--8553 []\T1/pcr/m/n/10 coerce,matrix.csr,dgRMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 8555--8557 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coerce,sparseVector,CsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 8587--8589 []\T1/pcr/m/n/10 coerce,sparseVector,denseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8589--8591 []\T1/pcr/m/n/10 coerce,sparseVector,dsparseVector-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8591--8593 []\T1/pcr/m/n/10 coerce,sparseVector,generalMatrix-method [3804] Overfull \hbox (50.8567pt too wide) in paragraph at lines 8593--8595 []\T1/pcr/m/n/10 coerce,sparseVector,isparseVector-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8595--8597 []\T1/pcr/m/n/10 coerce,sparseVector,lsparseVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8597--8599 []\T1/pcr/m/n/10 coerce,sparseVector,Matrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8599--8601 []\T1/pcr/m/n/10 coerce,sparseVector,nsparseVector-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8601--8603 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coerce,vector,ndenseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8643--8645 []\T1/pcr/m/n/10 coerce,vector,nsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8645--8647 []\T1/pcr/m/n/10 coerce,vector,nsparseVector-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8647--8649 []\T1/pcr/m/n/10 coerce,vector,RsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8649--8651 []\T1/pcr/m/n/10 coerce,vector,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8651--8653 []\T1/pcr/m/n/10 coerce,vector,sparseVector-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8653--8655 []\T1/pcr/m/n/10 coerce,vector,TsparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 8655--8657 []\T1/pcr/m/n/10 coerce,vector,unpackedMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8657--8659 []\T1/pcr/m/n/10 coerce,vector,zsparseVector-method [3805] Overfull \hbox (62.8567pt too wide) in paragraph at lines 8782--8784 []\T1/pcr/m/n/10 Compare,CsparseMatrix,CsparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8788--8790 []\T1/pcr/m/n/10 Compare,lgeMatrix,lgeMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8800--8802 []\T1/pcr/m/n/10 Compare,ngeMatrix,ngeMatrix-method Overfull \hbox (86.8567pt too wide) in paragraph at lines 8814--8816 []\T1/pcr/m/n/10 Compare,triangularMatrix,diagonalMatrix-method [3806] [3807] [3808] Overfull \hbox (8.8567pt too wide) in paragraph at lines 9351--9353 []\T1/pcr/m/n/10 crossprod,ANY,sparseVector-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 9353--9355 []\T1/pcr/m/n/10 crossprod,CsparseMatrix,CsparseMatrix-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 9355--9357 []\T1/pcr/m/n/10 crossprod,CsparseMatrix,denseMatrix-method Overfull \hbox (80.8567pt too wide) in paragraph at lines 9357--9359 []\T1/pcr/m/n/10 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[]\T1/pcr/m/n/10 derivedDefaultMethodWithTrace-class Overfull \hbox (44.8567pt too wide) in paragraph at lines 9972--9974 []\T1/pcr/m/n/10 determinant,BunchKaufman,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 9974--9976 []\T1/pcr/m/n/10 determinant,CHMfactor,logical-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 9976--9978 []\T1/pcr/m/n/10 determinant,Cholesky,logical-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 9978--9980 []\T1/pcr/m/n/10 determinant,denseLU,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 9980--9982 []\T1/pcr/m/n/10 determinant,dgCMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 9982--9984 []\T1/pcr/m/n/10 determinant,dgeMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 9984--9986 []\T1/pcr/m/n/10 determinant,dgRMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 9986--9988 []\T1/pcr/m/n/10 determinant,dgTMatrix,logical-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 9988--9990 []\T1/pcr/m/n/10 determinant,diagonalMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 9990--9992 []\T1/pcr/m/n/10 determinant,dpoMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 9992--9994 []\T1/pcr/m/n/10 determinant,dppMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 9994--9996 []\T1/pcr/m/n/10 determinant,dsCMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 9996--9998 []\T1/pcr/m/n/10 determinant,dspMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 9998--10000 []\T1/pcr/m/n/10 determinant,dsRMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 10000--10002 []\T1/pcr/m/n/10 determinant,dsTMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 10002--10004 []\T1/pcr/m/n/10 determinant,dsyMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 10004--10006 []\T1/pcr/m/n/10 determinant,indMatrix,logical-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 10006--10008 []\T1/pcr/m/n/10 determinant,Matrix,logical-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 10008--10010 []\T1/pcr/m/n/10 determinant,Matrix,missing-method [3812] Overfull \hbox (86.8567pt too wide) in paragraph at lines 10010--10012 []\T1/pcr/m/n/10 determinant,MatrixFactorization,missing-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 10010--10012 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , Overfull \hbox (50.8567pt too wide) in paragraph at lines 10012--10014 []\T1/pcr/m/n/10 determinant,pBunchKaufman,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 10014--10016 []\T1/pcr/m/n/10 determinant,pCholesky,logical-method Overfull \hbox (14.8567pt too wide) 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MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , Overfull \hbox (8.8567pt too wide) in paragraph at lines 10392--10394 []\T1/pcr/m/n/10 dimnames<-,compMatrix,list-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 10394--10396 []\T1/pcr/m/n/10 dimnames<-,compMatrix,NULL-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 10400--10402 []\T1/pcr/m/n/10 dimnames<-,MatrixFactorization,list-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 10400--10402 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3814] Overfull \hbox (62.8567pt too wide) in paragraph at lines 10402--10404 []\T1/pcr/m/n/10 dimnames<-,MatrixFactorization,NULL-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 10402--10404 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3815] Overfull \hbox (46.01662pt too wide) in paragraph at lines 10753--10755 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [3816] [3817] [3818] [3819] [3820] Overfull \hbox (80.8567pt too wide) in paragraph at lines 11720--11722 []\T1/pcr/m/n/10 forceSymmetric,CsparseMatrix,character-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 11722--11724 []\T1/pcr/m/n/10 forceSymmetric,CsparseMatrix,missing-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 11724--11726 []\T1/pcr/m/n/10 forceSymmetric,denseMatrix,character-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 11726--11728 []\T1/pcr/m/n/10 forceSymmetric,denseMatrix,missing-method Overfull \hbox (86.8567pt too wide) in paragraph at lines 11728--11730 []\T1/pcr/m/n/10 forceSymmetric,diagonalMatrix,character-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 11730--11732 []\T1/pcr/m/n/10 forceSymmetric,diagonalMatrix,missing-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 11732--11734 []\T1/pcr/m/n/10 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kronecker,TsparseMatrix,Matrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 14358--14360 []\T1/pcr/m/n/10 kronecker,TsparseMatrix,TsparseMatrix-method [3834] Overfull \hbox (8.8567pt too wide) in paragraph at lines 14569--14571 []\T1/pcr/m/n/10 length,MatrixFactorization-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 14569--14571 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3835] [3836] [3837] Overfull \hbox (50.8567pt too wide) in paragraph at lines 15190--15192 []\T1/pcr/m/n/10 Logic,CsparseMatrix,CsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15196--15198 []\T1/pcr/m/n/10 Logic,dMatrix,sparseVector-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 15198--15200 []\T1/pcr/m/n/10 Logic,ldenseMatrix,lsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 15200--15202 []\T1/pcr/m/n/10 Logic,lgCMatrix,lgCMatrix-method Overfull \hbox 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wide) in paragraph at lines 15232--15234 []\T1/pcr/m/n/10 Logic,ngeMatrix,ngeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15242--15244 []\T1/pcr/m/n/10 Logic,nMatrix,sparseVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15250--15252 []\T1/pcr/m/n/10 Logic,sparseVector,dMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15252--15254 []\T1/pcr/m/n/10 Logic,sparseVector,lMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15254--15256 []\T1/pcr/m/n/10 Logic,sparseVector,nMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 15256--15258 []\T1/pcr/m/n/10 Logic,sparseVector,sparseVector-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 15258--15260 []\T1/pcr/m/n/10 Logic,triangularMatrix,diagonalMatrix-method [3838] [3839] Overfull \hbox (10.01662pt too wide) in paragraph at lines 15563--15565 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3840] [3841] [3842] Overfull \hbox (52.01662pt too wide) in paragraph at lines 16340--16342 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , [3843] [3844] [3845] Overfull \hbox (8.8567pt too wide) in paragraph at lines 16944--16946 []\T1/pcr/m/n/10 nonstandardGenericWithTrace-class Overfull \hbox (8.8567pt too wide) in paragraph at lines 16965--16967 []\T1/pcr/m/n/10 norm,denseMatrix,character-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 16967--16969 []\T1/pcr/m/n/10 norm,diagonalMatrix,character-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 16973--16975 []\T1/pcr/m/n/10 norm,sparseMatrix,character-method [3846] Overfull \hbox (26.8567pt too wide) in paragraph at lines 17252--17254 []\T1/pcr/m/n/10 Ops,atomicVector,sparseVector-method [3847] Overfull \hbox (8.8567pt too wide) in paragraph at lines 17270--17272 []\T1/pcr/m/n/10 Ops,ddiMatrix,sparseMatrix-method Overfull \hbox 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Ops,sparseVector,atomicVector-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 17398--17400 []\T1/pcr/m/n/10 Ops,sparseVector,sparseVector-method [3849] Overfull \hbox (46.01662pt too wide) in paragraph at lines 17607--17609 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (77.3567pt too wide) in paragraph at lines 17639--17641 []\T1/pcr/m/n/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , [3850] [3851] [3852] [3853] [3854] [3855] Overfull \hbox (46.01662pt too wide) in paragraph at lines 18982--18984 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 18985--18987 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 18987--18989 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 18989--18991 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 18991--18993 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.fs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 18993--18995 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (52.01662pt too wide) in paragraph at lines 18995--18997 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 18997--18999 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 18999--19001 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.re.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19001--19003 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (52.01662pt too wide) in paragraph at lines 19005--19007 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19007--19009 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 19009--19011 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.sz.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19011--19013 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19013--19015 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19015--19017 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19017--19019 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [3856] [3857] Overfull \hbox (4.01662pt too wide) in paragraph at lines 19367--19369 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19441--19443 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [3858] [3859] [3860] Overfull \hbox (10.01662pt too wide) in paragraph at lines 19913--19915 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , Overfull \hbox (8.8567pt too wide) in paragraph at lines 19919--19921 []\T1/pcr/m/n/10 qr.coef,sparseQR,dgeMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 19929--19931 []\T1/pcr/m/n/10 qr.fitted,sparseQR,dgeMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19931--19933 []\T1/pcr/m/n/10 qr.fitted,sparseQR,Matrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19933--19935 []\T1/pcr/m/n/10 qr.fitted,sparseQR,matrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19935--19937 []\T1/pcr/m/n/10 qr.fitted,sparseQR,vector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19945--19947 []\T1/pcr/m/n/10 qr.qty,sparseQR,dgeMatrix-method [3861] Overfull \hbox (14.8567pt too wide) in paragraph at lines 19970--19972 []\T1/pcr/m/n/10 qr.resid,sparseQR,dgeMatrix-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 20105--20107 []\T1/pcr/m/n/10 R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE [3862] [3863] Overfull \hbox (14.8567pt too wide) in paragraph at lines 20383--20385 []\T1/pcr/m/n/10 rcond,denseMatrix,character-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 20385--20387 []\T1/pcr/m/n/10 rcond,diagonalMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20387--20389 []\T1/pcr/m/n/10 rcond,indMatrix,character-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 20391--20393 []\T1/pcr/m/n/10 rcond,sparseMatrix,character-method [3864] [3865] [3866] [3867] [3868] Overfull \hbox (10.01662pt too wide) in paragraph at lines 21396--21398 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3869] Overfull \hbox (32.8567pt too wide) in paragraph at lines 21765--21767 []\T1/pcr/m/n/10 show,BunchKaufmanFactorization-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 21765--21767 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , Overfull \hbox (8.8567pt too wide) in paragraph at lines 21767--21769 []\T1/pcr/m/n/10 show,CholeskyFactorization-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 21767--21769 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , Overfull \hbox (26.8567pt too wide) in paragraph at lines 21781--21783 []\T1/pcr/m/n/10 show,genericFunctionWithTrace-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 21783--21785 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , Overfull \hbox (10.01662pt too wide) in paragraph at lines 21785--21787 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , Overfull \hbox (32.8567pt too wide) in paragraph at lines 21789--21791 []\T1/pcr/m/n/10 show,MethodDefinitionWithTrace-method [3870] Overfull \hbox (20.8567pt too wide) in paragraph at lines 21793--21795 []\T1/pcr/m/n/10 show,MethodWithNextWithTrace-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 21799--21801 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , Overfull \hbox (14.8567pt too wide) in paragraph at lines 21801--21803 []\T1/pcr/m/n/10 show,refClassRepresentation-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 21807--21809 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3871] Overfull \hbox (46.01662pt too wide) in paragraph at lines 22049--22051 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 22051--22053 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 22054--22056 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (5.3567pt too wide) in paragraph at lines 22062--22063 []\T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 22071--22073 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (5.3567pt too wide) in paragraph at lines 22075--22076 []\T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 22076--22078 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (23.3567pt too wide) in paragraph at lines 22083--22087 []\T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 22088--22090 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.tp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [3872] Overfull \hbox (46.01662pt too wide) in paragraph at lines 22139--22141 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10 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Transcript written on fullrefman.log. make[1]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/doc/manual' make: [Makefile:294: install-pdf] Error 2 (ignored) make[1]: Entering directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/include' make[1]: 'Rmath.h' is up to date. make[1]: Leaving directory '/tmp/archlinux-ci/r-archlinuxrb-build-oWJ08klY/r/src/R-4.3.3/src/include' ==> Tidying install... -> Removing empty directories... -> Removing libtool files... -> Purging unwanted files... -> Removing static library files... -> Stripping unneeded symbols from binaries and libraries... -> Compressing man and info pages... ==> Checking for packaging issues... ==> WARNING: Package contains reference to $srcdir usr/share/doc/R/NEWS.pdf ==> Creating package "r"... -> Generating .PKGINFO file... -> Generating .BUILDINFO file... -> Generating .MTREE file... -> Compressing package... ==> Leaving fakeroot environment. ==> Finished making: r 4.3.3-2 (Thu Apr 3 16:51:31 2025)