Mon May 1 04:47:03 UTC 2023 I: starting to build probabel/bookworm/amd64 on jenkins on '2023-05-01 04:46' Mon May 1 04:47:03 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_13/18256/console.log Mon May 1 04:47:03 UTC 2023 I: Downloading source for bookworm/probabel=0.5.0+dfsg-6 --2023-05-01 04:47:04-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/probabel/probabel_0.5.0%2bdfsg-6.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2338 (2.3K) [text/prs.lines.tag] Saving to: ‘probabel_0.5.0+dfsg-6.dsc’ 0K .. 100% 194M=0s 2023-05-01 04:47:04 (194 MB/s) - ‘probabel_0.5.0+dfsg-6.dsc’ saved [2338/2338] Mon May 1 04:47:04 UTC 2023 I: probabel_0.5.0+dfsg-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: probabel Binary: probabel, probabel-examples Architecture: any-amd64 any-i386 m68k sh4 all Version: 0.5.0+dfsg-6 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , L.C. Karssen , Pranav Ballaney Homepage: http://www.genabel.org Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/probabel Vcs-Git: https://salsa.debian.org/med-team/probabel.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libeigen3-dev, texlive-latex-base, texlive-latex-extra, texlive-latex-recommended, texlive-fonts-recommended, r-cran-survival , debhelper Package-List: probabel deb science optional arch=any-amd64,any-i386,m68k,sh4,x32 probabel-examples deb science optional arch=all Checksums-Sha1: de12edeb7b37edcfe5c0e68b05d2fbc4bb2a08aa 1774384 probabel_0.5.0+dfsg.orig.tar.xz ce224abc401f6e89330a291a10bd0104c914dbf7 7944 probabel_0.5.0+dfsg-6.debian.tar.xz Checksums-Sha256: 610daf84ba8883b5908cd125c6c117068cfbac38ee486d496622b1d9e0726ca3 1774384 probabel_0.5.0+dfsg.orig.tar.xz a4bcc8028ad72292f96588b87c1930251fcc6a4a9a4e8ad31e579ffc9213c120 7944 probabel_0.5.0+dfsg-6.debian.tar.xz Files: efdfa6dab47edc3b8dd5deb1f6717b9b 1774384 probabel_0.5.0+dfsg.orig.tar.xz 12182c02fa34f70ccb817083075f35d2 7944 probabel_0.5.0+dfsg-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmITaO8RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGcNg//fW1YmUG48k3igd0Ieoh8not9wY/tq7An Xy6SX5sEAhtRQzkc52iEALk4y4uwoclCWRHoUd74nSYku5mKb+2gcwCSqHRPx4Yo lWEaV5QnzjJ2IZvV4j14fkXv+3/1v2vAsXjO3nVTMUJR6LQA2nHns9RSVAuAJTVU DB5PVuDO05UIenIguMNbmQQ2i23PnMTjkQRjGwb09Fx12y9L2H7HFPEFh8jIY5sU iWvavfpkYOgkd5MkHIAh4Q5x7SQKvUPNjH6T7/5maDQnlVC4ngg7cwxCi+P1xsgJ LI+6EW+9k91wbyylxPvjNdn5vGeRzGNFKw505gXZ8U/95p07RFEGNJcwjlR5Pa2O jMRlOvyifXSHvh1I4BCdolM4O45HtkXO5CcaK9fFjNNMIzrgAARSgLTDm/5PPd5I i+3CLsEUHrH9m0LCNmoZjPcelAgureRFi4FQlQlYZ/p99dFLOgwNCLq6DtKqd/Sb vlDW7PWMEf8+fcTieLYnhmX6vKqzzhDl8KgBmGVyH9IsR9OariSiuZYO/xo+AsYa 4/GhYjxRTfNo0F0vNbo9mhwsnixDKnGgcyaTLN73D2NTOOyFQG7bqHMw0gN2h9RW XQkD7fbw9JOwRIFZ5DKQ7ehwqk5VUS5DsG1XLDfcLQwkIb0sdrvg8rPcNjcbmhXI ytvjy2sp3V0= =z2tG -----END PGP SIGNATURE----- Mon May 1 04:47:04 UTC 2023 I: Checking whether the package is not for us Mon May 1 04:47:04 UTC 2023 I: Starting 1st build on remote node ionos11-amd64.debian.net. Mon May 1 04:47:04 UTC 2023 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Mon May 1 04:54:00 UTC 2023 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Apr 30 16:47:06 -12 2023 I: pbuilder-time-stamp: 1682916426 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [probabel_0.5.0+dfsg-6.dsc] I: copying [./probabel_0.5.0+dfsg.orig.tar.xz] I: copying [./probabel_0.5.0+dfsg-6.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Feb 20 22:26:55 2022 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./probabel_0.5.0+dfsg-6.dsc: no acceptable signature found dpkg-source: info: extracting probabel in probabel-0.5.0+dfsg dpkg-source: info: unpacking probabel_0.5.0+dfsg.orig.tar.xz dpkg-source: info: unpacking probabel_0.5.0+dfsg-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying examples.patch dpkg-source: info: applying c++11.patch dpkg-source: info: applying ignore_failing_build_time_test.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/618402/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='da82b80e40f342389e9ae584b591983d' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='618402' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.QEWqOl0Q/pbuilderrc_Mn1n --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QEWqOl0Q/b1 --logfile b1/build.log probabel_0.5.0+dfsg-6.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 09:23 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:23 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 04:31 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar -rwxr-xr-x 1 root root 14520 Nov 2 04:31 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/618402/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libeigen3-dev, texlive-latex-base, texlive-latex-extra, texlive-latex-recommended, texlive-fonts-recommended, r-cran-survival, debhelper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libeigen3-dev; however: Package libeigen3-dev is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-base; however: Package texlive-latex-base is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however: Package texlive-latex-extra is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-recommended; however: Package texlive-latex-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however: Package texlive-fonts-recommended is not installed. pbuilder-satisfydepends-dummy depends on r-cran-survival; however: Package r-cran-survival is not installed. pbuilder-satisfydepends-dummy depends on debhelper; however: Package debhelper is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-lmodern{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libapache-pom-java{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcommons-logging-java{a} libcommons-parent-java{a} libcurl4{a} libdatrie1{a} libdebhelper-perl{a} libdeflate0{a} libeigen3-dev{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontbox-java{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libice6{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} libkpathsea6{a} liblapack3{a} libldap-2.5-0{a} liblerc4{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpdfbox-java{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpng16-16{a} libpsl5{a} libptexenc1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsm6{a} libssh2-1{a} libsub-override-perl{a} libsynctex2{a} libtcl8.6{a} libteckit0{a} libtexlua53-5{a} libtexluajit2{a} libthai-data{a} libthai0{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp7{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxi6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxss1{a} libxt6{a} libzzip-0-13{a} m4{a} man-db{a} media-types{a} openssl{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} preview-latex-style{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} r-base-core{a} r-cran-lattice{a} r-cran-matrix{a} r-cran-survival{a} readline-common{a} sensible-utils{a} t1utils{a} tex-common{a} texlive-base{a} texlive-binaries{a} texlive-fonts-recommended{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} ucf{a} unzip{a} x11-common{a} xdg-utils{a} zip{a} The following packages are RECOMMENDED but will NOT be installed: curl default-jre dvisvgm libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libspreadsheet-parseexcel-perl libx11-protocol-perl lmodern lynx publicsuffix r-base-dev r-doc-html r-recommended ruby shared-mime-info tex-gyre texlive-plain-generic tipa tk wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 139 newly installed, 0 to remove and 0 not upgraded. Need to get 176 MB of archives. After unpacking 547 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.8-1 [1407 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-4 [399 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libapache-pom-java all 29-2 [5276 B] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2 [292 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2 [759 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 libcommons-logging-java all 1.2-3 [62.4 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-9 [386 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 libpkgconf3 amd64 1.8.1-1 [36.1 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 libfontbox-java all 1:1.8.16-2 [211 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 libkpathsea6 amd64 2022.20220321.62855-5 [152 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 libpaper1 amd64 1.1.29 [12.5 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 libpaper-utils amd64 1.1.29 [8868 B] Get: 104 http://deb.debian.org/debian bookworm/main amd64 libpdfbox-java all 1:1.8.16-2 [5205 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 libptexenc1 amd64 2022.20220321.62855-5 [43.5 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 libsynctex2 amd64 2022.20220321.62855-5 [59.6 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 libteckit0 amd64 2.5.11+ds1-1+b1 [335 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 libtexlua53-5 amd64 2022.20220321.62855-5 [111 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 libtexluajit2 amd64 2022.20220321.62855-5 [246 kB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.1 [285 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-5 [316 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get: 116 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB] Get: 117 http://deb.debian.org/debian bookworm/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB] Get: 118 http://deb.debian.org/debian bookworm/main amd64 libxmu6 amd64 2:1.1.3-3 [60.1 kB] Get: 119 http://deb.debian.org/debian bookworm/main amd64 libxpm4 amd64 1:3.5.12-1.1 [48.4 kB] Get: 120 http://deb.debian.org/debian bookworm/main amd64 libxaw7 amd64 2:1.0.14-1 [201 kB] Get: 121 http://deb.debian.org/debian bookworm/main amd64 libxi6 amd64 2:1.8-1+b1 [84.2 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 libzzip-0-13 amd64 0.13.72+dfsg.1-1.1 [58.3 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 tex-common all 6.18 [32.5 kB] Get: 124 http://deb.debian.org/debian bookworm/main amd64 preview-latex-style all 12.2-1 [201 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 zip amd64 3.0-13 [230 kB] Get: 126 http://deb.debian.org/debian bookworm/main amd64 unzip amd64 6.0-28 [166 kB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 128 http://deb.debian.org/debian bookworm/main amd64 r-base-core amd64 4.2.2.20221110-2 [26.0 MB] Get: 129 http://deb.debian.org/debian bookworm/main amd64 r-cran-lattice amd64 0.20-45-3 [1177 kB] Get: 130 http://deb.debian.org/debian bookworm/main amd64 r-cran-matrix amd64 1.5-3-1 [3822 kB] Get: 131 http://deb.debian.org/debian bookworm/main amd64 r-cran-survival amd64 3.5-3-1 [5910 kB] Get: 132 http://deb.debian.org/debian bookworm/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get: 133 http://deb.debian.org/debian bookworm/main amd64 texlive-binaries amd64 2022.20220321.62855-5 [10.5 MB] Get: 134 http://deb.debian.org/debian bookworm/main amd64 texlive-base all 2022.20230122-3 [21.9 MB] Get: 135 http://deb.debian.org/debian bookworm/main amd64 texlive-fonts-recommended all 2022.20230122-3 [4988 kB] Get: 136 http://deb.debian.org/debian bookworm/main amd64 texlive-latex-base all 2022.20230122-3 [1182 kB] Get: 137 http://deb.debian.org/debian bookworm/main amd64 texlive-latex-recommended all 2022.20230122-3 [8880 kB] Get: 138 http://deb.debian.org/debian bookworm/main amd64 texlive-pictures all 2022.20230122-3 [15.8 MB] Get: 139 http://deb.debian.org/debian bookworm/main amd64 texlive-latex-extra all 2022.20230122-3 [19.2 MB] Fetched 176 MB in 6s (29.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19912 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../3-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20346 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_3.0.8-1_amd64.deb ... Unpacking openssl (3.0.8-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../005-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../008-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../011-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package ucf. Preparing to unpack .../013-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package m4. Preparing to unpack .../014-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../015-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../016-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../017-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../018-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../019-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../020-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../021-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../022-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../023-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../024-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../025-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. 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Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../033-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../034-libbrotli1_1.0.9-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b6) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../035-libpng16-16_1.6.39-2_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.39-2) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../036-libfreetype6_2.12.1+dfsg-4_amd64.deb ... Unpacking libfreetype6:amd64 (2.12.1+dfsg-4) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../037-fonts-dejavu-core_2.37-6_all.deb ... Unpacking fonts-dejavu-core (2.37-6) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../038-fontconfig-config_2.14.1-4_amd64.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/probabel-0.5.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../probabel_0.5.0+dfsg-6_source.changes dpkg-buildpackage: info: source package probabel dpkg-buildpackage: info: source version 0.5.0+dfsg-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/probabel-0.5.0+dfsg' dh_auto_configure -- --disable-silent-rules --with-eigen-include-path=/usr/include/eigen3 ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --disable-silent-rules --with-eigen-include-path=/usr/include/eigen3 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... 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R configure: building of the PDF of the user manual from LaTeX source is enabled checking for pdflatex... pdflatex checking for doxygen... no configure: Doxygen not found - Not generating code documentation configure: building of palinear is enabled configure: building of palogist is enabled configure: building of pacoxph is enabled checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating doc/Makefile config.status: creating examples/Makefile config.status: creating checks/Makefile config.status: creating checks/R-tests/Makefile config.status: creating src/config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/probabel-0.5.0+dfsg' dh_auto_build make -j15 make[1]: Entering directory '/build/probabel-0.5.0+dfsg' Making all in src make[2]: Entering directory '/build/probabel-0.5.0+dfsg/src' make all-am make[3]: Entering directory '/build/probabel-0.5.0+dfsg/src' g++ -DHAVE_CONFIG_H -I. -DLINEAR -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-main.o `test -f 'main.cpp' || echo './'`main.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-invsigma.o `test -f 'invsigma.cpp' || echo './'`invsigma.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-gendata.o `test -f 'gendata.cpp' || echo './'`gendata.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-eigen_mematrix.o `test -f 'eigen_mematrix.cpp' || echo './'`eigen_mematrix.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-command_line_settings.o `test -f 'command_line_settings.cpp' || echo './'`command_line_settings.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-reg1.o `test -f 'reg1.cpp' || echo './'`reg1.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-usage.o `test -f 'usage.cpp' || echo './'`usage.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-utilities.o `test -f 'utilities.cpp' || echo './'`utilities.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-phedata.o `test -f 'phedata.cpp' || echo './'`phedata.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-regdata.o `test -f 'regdata.cpp' || echo './'`regdata.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-maskedmatrix.o `test -f 'maskedmatrix.cpp' || echo './'`maskedmatrix.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-main_functions_dump.o `test -f 'main_functions_dump.cpp' || echo './'`main_functions_dump.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palinear-mlinfo.o `test -f 'mlinfo.cpp' || echo './'`mlinfo.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-main.o `test -f 'main.cpp' || echo './'`main.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-invsigma.o `test -f 'invsigma.cpp' || echo './'`invsigma.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-gendata.o `test -f 'gendata.cpp' || echo './'`gendata.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-eigen_mematrix.o `test -f 'eigen_mematrix.cpp' || echo './'`eigen_mematrix.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-command_line_settings.o `test -f 'command_line_settings.cpp' || echo './'`command_line_settings.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-reg1.o `test -f 'reg1.cpp' || echo './'`reg1.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-usage.o `test -f 'usage.cpp' || echo './'`usage.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-utilities.o `test -f 'utilities.cpp' || echo './'`utilities.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-phedata.o `test -f 'phedata.cpp' || echo './'`phedata.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-regdata.o `test -f 'regdata.cpp' || echo './'`regdata.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-maskedmatrix.o `test -f 'maskedmatrix.cpp' || echo './'`maskedmatrix.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-main_functions_dump.o `test -f 'main_functions_dump.cpp' || echo './'`main_functions_dump.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o palogist-mlinfo.o `test -f 'mlinfo.cpp' || echo './'`mlinfo.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palogist-AbstractMatrix.o `test -f 'fvlib/AbstractMatrix.cpp' || echo './'`fvlib/AbstractMatrix.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palogist-CastUtils.o `test -f 'fvlib/CastUtils.cpp' || echo './'`fvlib/CastUtils.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palogist-convert_util.o `test -f 'fvlib/convert_util.cpp' || echo './'`fvlib/convert_util.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palogist-FileVector.o `test -f 'fvlib/FileVector.cpp' || echo './'`fvlib/FileVector.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palogist-FilteredMatrix.o `test -f 'fvlib/FilteredMatrix.cpp' || echo './'`fvlib/FilteredMatrix.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palogist-frutil.o `test -f 'fvlib/frutil.cpp' || echo './'`fvlib/frutil.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palogist-Logger.o `test -f 'fvlib/Logger.cpp' || echo './'`fvlib/Logger.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palogist-RealHandlerWrapper.o `test -f 'fvlib/RealHandlerWrapper.cpp' || echo './'`fvlib/RealHandlerWrapper.cpp In file included from /usr/include/stdio.h:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, from /usr/include/c++/12/bits/basic_string.h:3960, from /usr/include/c++/12/string:53, from fvlib/convert_util.cpp:2: In function 'int sprintf(char*, const char*, ...)', inlined from 'void text2fvf(std::string, std::string, std::string, std::string, std::string, int, int, long unsigned int, long unsigned int, int, int, short unsigned int, bool, std::string)' at fvlib/convert_util.cpp:299:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin___sprintf_chk(char*, int, long unsigned int, const char*, ...)' In function 'int sprintf(char*, const char*, ...)', inlined from 'void text2fvf(std::string, std::string, std::string, std::string, std::string, int, int, long unsigned int, long unsigned int, int, int, short unsigned int, bool, std::string)' at fvlib/convert_util.cpp:307:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin___sprintf_chk(char*, int, long unsigned int, const char*, ...)' g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palogist-ReusableFileHandle.o `test -f 'fvlib/ReusableFileHandle.cpp' || echo './'`fvlib/ReusableFileHandle.cpp g++ -DHAVE_CONFIG_H -I. -DLOGISTIC -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palogist-Transposer.o `test -f 'fvlib/Transposer.cpp' || echo './'`fvlib/Transposer.cpp /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In function 'int sprintf(char*, const char*, ...)', inlined from 'void text2fvf(std::string, std::string, std::string, std::string, std::string, int, int, long unsigned int, long unsigned int, int, int, short unsigned int, bool, std::string)' at fvlib/convert_util.cpp:299:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-coxfit2.o `test -f 'coxfit2.c' || echo './'`coxfit2.c gcc -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-chinv2.o `test -f 'chinv2.c' || echo './'`chinv2.c gcc -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-cholesky2.o `test -f 'cholesky2.c' || echo './'`cholesky2.c gcc -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-chsolve2.o `test -f 'chsolve2.c' || echo './'`chsolve2.c gcc -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-dmatrix.o `test -f 'dmatrix.c' || echo './'`dmatrix.c g++ -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-main.o `test -f 'main.cpp' || echo './'`main.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-invsigma.o `test -f 'invsigma.cpp' || echo './'`invsigma.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-gendata.o `test -f 'gendata.cpp' || echo './'`gendata.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-eigen_mematrix.o `test -f 'eigen_mematrix.cpp' || echo './'`eigen_mematrix.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-command_line_settings.o `test -f 'command_line_settings.cpp' || echo './'`command_line_settings.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-reg1.o `test -f 'reg1.cpp' || echo './'`reg1.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-usage.o `test -f 'usage.cpp' || echo './'`usage.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-utilities.o `test -f 'utilities.cpp' || echo './'`utilities.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-phedata.o `test -f 'phedata.cpp' || echo './'`phedata.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-regdata.o `test -f 'regdata.cpp' || echo './'`regdata.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-maskedmatrix.o `test -f 'maskedmatrix.cpp' || echo './'`maskedmatrix.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-main_functions_dump.o `test -f 'main_functions_dump.cpp' || echo './'`main_functions_dump.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-mlinfo.o `test -f 'mlinfo.cpp' || echo './'`mlinfo.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/pacoxph-AbstractMatrix.o `test -f 'fvlib/AbstractMatrix.cpp' || echo './'`fvlib/AbstractMatrix.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/pacoxph-CastUtils.o `test -f 'fvlib/CastUtils.cpp' || echo './'`fvlib/CastUtils.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/pacoxph-convert_util.o `test -f 'fvlib/convert_util.cpp' || echo './'`fvlib/convert_util.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/pacoxph-FileVector.o `test -f 'fvlib/FileVector.cpp' || echo './'`fvlib/FileVector.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/pacoxph-FilteredMatrix.o `test -f 'fvlib/FilteredMatrix.cpp' || echo './'`fvlib/FilteredMatrix.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/pacoxph-frutil.o `test -f 'fvlib/frutil.cpp' || echo './'`fvlib/frutil.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/pacoxph-Logger.o `test -f 'fvlib/Logger.cpp' || echo './'`fvlib/Logger.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/pacoxph-RealHandlerWrapper.o `test -f 'fvlib/RealHandlerWrapper.cpp' || echo './'`fvlib/RealHandlerWrapper.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/pacoxph-ReusableFileHandle.o `test -f 'fvlib/ReusableFileHandle.cpp' || echo './'`fvlib/ReusableFileHandle.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/pacoxph-Transposer.o `test -f 'fvlib/Transposer.cpp' || echo './'`fvlib/Transposer.cpp g++ -DHAVE_CONFIG_H -I. -DCOXPH -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pacoxph-coxph_data.o `test -f 'coxph_data.cpp' || echo './'`coxph_data.cpp In file included from /usr/include/stdio.h:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, from /usr/include/c++/12/bits/basic_string.h:3960, from /usr/include/c++/12/string:53, from fvlib/convert_util.cpp:2: In function 'int sprintf(char*, const char*, ...)', inlined from 'void text2fvf(std::string, std::string, std::string, std::string, std::string, int, int, long unsigned int, long unsigned int, int, int, short unsigned int, bool, std::string)' at fvlib/convert_util.cpp:299:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin___sprintf_chk(char*, int, long unsigned int, const char*, ...)' In function 'int sprintf(char*, const char*, ...)', inlined from 'void text2fvf(std::string, std::string, std::string, std::string, std::string, int, int, long unsigned int, long unsigned int, int, int, short unsigned int, bool, std::string)' at fvlib/convert_util.cpp:307:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin___sprintf_chk(char*, int, long unsigned int, const char*, ...)' g++ -DHAVE_CONFIG_H -I. -DLINEAR -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palinear-AbstractMatrix.o `test -f 'fvlib/AbstractMatrix.cpp' || echo './'`fvlib/AbstractMatrix.cpp /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In function 'int sprintf(char*, const char*, ...)', inlined from 'void text2fvf(std::string, std::string, std::string, std::string, std::string, int, int, long unsigned int, long unsigned int, int, int, short unsigned int, bool, std::string)' at fvlib/convert_util.cpp:299:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -DLINEAR -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palinear-CastUtils.o `test -f 'fvlib/CastUtils.cpp' || echo './'`fvlib/CastUtils.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palinear-convert_util.o `test -f 'fvlib/convert_util.cpp' || echo './'`fvlib/convert_util.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palinear-FileVector.o `test -f 'fvlib/FileVector.cpp' || echo './'`fvlib/FileVector.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palinear-FilteredMatrix.o `test -f 'fvlib/FilteredMatrix.cpp' || echo './'`fvlib/FilteredMatrix.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palinear-frutil.o `test -f 'fvlib/frutil.cpp' || echo './'`fvlib/frutil.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palinear-Logger.o `test -f 'fvlib/Logger.cpp' || echo './'`fvlib/Logger.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palinear-RealHandlerWrapper.o `test -f 'fvlib/RealHandlerWrapper.cpp' || echo './'`fvlib/RealHandlerWrapper.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palinear-ReusableFileHandle.o `test -f 'fvlib/ReusableFileHandle.cpp' || echo './'`fvlib/ReusableFileHandle.cpp g++ -DHAVE_CONFIG_H -I. -DLINEAR -I/usr/include/eigen3 -Wdate-time -D_FORTIFY_SOURCE=2 -D_NOT_R_FILEVECTOR -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fvlib/palinear-Transposer.o `test -f 'fvlib/Transposer.cpp' || echo './'`fvlib/Transposer.cpp In file included from /usr/include/stdio.h:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, from /usr/include/c++/12/bits/basic_string.h:3960, from /usr/include/c++/12/string:53, from fvlib/convert_util.cpp:2: In function 'int sprintf(char*, const char*, ...)', inlined from 'void text2fvf(std::string, std::string, std::string, std::string, std::string, int, int, long unsigned int, long unsigned int, int, int, short unsigned int, bool, std::string)' at fvlib/convert_util.cpp:299:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin___sprintf_chk(char*, int, long unsigned int, const char*, ...)' In function 'int sprintf(char*, const char*, ...)', inlined from 'void text2fvf(std::string, std::string, std::string, std::string, std::string, int, int, long unsigned int, long unsigned int, int, int, short unsigned int, bool, std::string)' at fvlib/convert_util.cpp:307:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin___sprintf_chk(char*, int, long unsigned int, const char*, ...)' /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In function 'int sprintf(char*, const char*, ...)', inlined from 'void text2fvf(std::string, std::string, std::string, std::string, std::string, int, int, long unsigned int, long unsigned int, int, int, short unsigned int, bool, std::string)' at fvlib/convert_util.cpp:299:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o palinear palinear-main.o palinear-invsigma.o palinear-gendata.o palinear-eigen_mematrix.o palinear-command_line_settings.o palinear-reg1.o palinear-usage.o palinear-utilities.o palinear-phedata.o palinear-regdata.o palinear-maskedmatrix.o palinear-main_functions_dump.o palinear-mlinfo.o fvlib/palinear-AbstractMatrix.o fvlib/palinear-CastUtils.o fvlib/palinear-convert_util.o fvlib/palinear-FileVector.o fvlib/palinear-FilteredMatrix.o fvlib/palinear-frutil.o fvlib/palinear-Logger.o fvlib/palinear-RealHandlerWrapper.o fvlib/palinear-ReusableFileHandle.o fvlib/palinear-Transposer.o g++ -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o palogist palogist-main.o palogist-invsigma.o palogist-gendata.o palogist-eigen_mematrix.o palogist-command_line_settings.o palogist-reg1.o palogist-usage.o palogist-utilities.o palogist-phedata.o palogist-regdata.o palogist-maskedmatrix.o palogist-main_functions_dump.o palogist-mlinfo.o fvlib/palogist-AbstractMatrix.o fvlib/palogist-CastUtils.o fvlib/palogist-convert_util.o fvlib/palogist-FileVector.o fvlib/palogist-FilteredMatrix.o fvlib/palogist-frutil.o fvlib/palogist-Logger.o fvlib/palogist-RealHandlerWrapper.o fvlib/palogist-ReusableFileHandle.o fvlib/palogist-Transposer.o g++ -I ../src/include -g -O2 -ffile-prefix-map=/build/probabel-0.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o pacoxph pacoxph-coxfit2.o pacoxph-chinv2.o pacoxph-cholesky2.o pacoxph-chsolve2.o pacoxph-dmatrix.o pacoxph-main.o pacoxph-invsigma.o pacoxph-gendata.o pacoxph-eigen_mematrix.o pacoxph-command_line_settings.o pacoxph-reg1.o pacoxph-usage.o pacoxph-utilities.o pacoxph-phedata.o pacoxph-regdata.o pacoxph-maskedmatrix.o pacoxph-main_functions_dump.o pacoxph-mlinfo.o fvlib/pacoxph-AbstractMatrix.o fvlib/pacoxph-CastUtils.o fvlib/pacoxph-convert_util.o fvlib/pacoxph-FileVector.o fvlib/pacoxph-FilteredMatrix.o fvlib/pacoxph-frutil.o fvlib/pacoxph-Logger.o fvlib/pacoxph-RealHandlerWrapper.o fvlib/pacoxph-ReusableFileHandle.o fvlib/pacoxph-Transposer.o pacoxph-coxph_data.o make[3]: Leaving directory '/build/probabel-0.5.0+dfsg/src' make[2]: Leaving directory '/build/probabel-0.5.0+dfsg/src' Making all in doc make[2]: Entering directory '/build/probabel-0.5.0+dfsg/doc' === Making ProbABEL_manual.aux file === pdflatex ./ProbABEL_manual.tex This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./ProbABEL_manual.tex LaTeX2e <2022-11-01> patch level 1 L3 programming layer <2023-01-16> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2022/07/02 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/svgnam.def)) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty) (/usr/share/texlive/texmf-dist/tex/latex/titleref/titleref.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) No file ProbABEL_manual.toc. [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) [2] Overfull \hbox (7.36137pt too wide) in paragraph at lines 171--174 \T1/cmr/m/n/12 Prob-A-BEL web page ([][]$\T1/cmtt/m/n/12 http : / / www . genab el . org / packages / ProbABEL$[][]\T1/cmr/m/n/12 ). LaTeX Warning: Reference `sec:obtain' on page 3 undefined on input line 181. [3] Overfull \hbox (123.30513pt too wide) in paragraph at lines 238--241 \T1/cmtt/m/n/12 ProbABEL\T1/cmr/m/n/12 . Let's in-stall in a sub-di-rec-tory of your home di-rec-tory, e.g. \T1/cmtt/m/n/12 /home/yourusername/ProbABEL\T1/cmr /m/n/12 : Overfull \hbox (4.73831pt too wide) in paragraph at lines 268--272 []\T1/cmr/m/n/12 If all went well you will find the ex-e-cutable pro-grams (\T1 /cmtt/m/n/12 palinear\T1/cmr/m/n/12 , \T1/cmtt/m/n/12 palogist\T1/cmr/m/n/12 , [4] Overfull \hbox (1.38382pt too wide) in paragraph at lines 274--279 \T1/cmtt/m/n/12 ProbABEL \T1/cmr/m/n/12 takes three files as in-put: a file con -tain-ing SNP in-for-ma-tion (e.g. the [5] LaTeX Warning: Reference `sec:runanalysis' on page 6 undefined on input line 35 3. [6] Overfull \hbox (12.56972pt too wide) in paragraph at lines 377--384 []\T1/cmr/m/n/12 In the case of lin-ear or lo-gis-tic re-gres-sion (pro-grams \ T1/cmtt/m/n/12 palinear \T1/cmr/m/n/12 and \T1/cmtt/m/n/12 palogist\T1/cmr/m/n/ 12 , Overfull \hbox (14.44846pt too wide) in paragraph at lines 377--384 \T1/cmr/m/n/12 lin-ear re-gres-sion anal-y-sis fol-low here (also to be found i n \T1/cmtt/m/n/12 examples/height.txt\T1/cmr/m/n/12 ) [7] [8] Overfull \hbox (5.0841pt too wide) in paragraph at lines 454--458 []\T1/cmr/m/n/12 There are in to-tal 11 com-mand line op-tions you can spec-ify to the \T1/cmtt/m/n/12 ProbABEL [9] LaTeX Warning: Reference `ssec:dosein' on page 10 undefined on input line 503. LaTeX Warning: Reference `ssec:phenoin' on page 10 undefined on input line 505. LaTeX Warning: Reference `ssec:infoin' on page 10 undefined on input line 507. 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[13] [14] Overfull \hbox (4.6171pt too wide) in paragraph at lines 746--750 \T1/cmr/m/n/12 After in-stalling \T1/cmtt/m/n/12 ProbABEL \T1/cmr/m/n/12 you ca n find the \T1/cmtt/m/n/12 prepare_data.R \T1/cmr/m/n/12 file in the \T1/cmtt/m /n/12 scripts [15] [16] Overfull \hbox (8.33644pt too wide) in paragraph at lines 848--850 []\T1/cmr/m/n/12 Secondly, the Wald test can be used; for that the in-verse var iance-covariance [17] [18] LaTeX Warning: Reference `eq:expectation' on page 19 undefined on input line 94 4. LaTeX Warning: Reference `kinship' on page 19 undefined on input line 956. [19] [20] [21] No file ProbABEL_manual.ind. [22] (./ProbABEL_manual.aux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecti1200 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecti1200 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecti1200.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecti.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/extextit.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exileast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exilwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exilig.mf Ok [25] [26] [27] [28] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exitalp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exillett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exidigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exiligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.07143pt) Font metrics written on ecti1200.tfm. Output written on ecti1200.600gf (256 characters, 63048 bytes). Transcript written on ecti1200.log. mktexpk: /build/probabel-0.5.0+dfsg/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ecti1200.600pk: successfully generated. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `ProbABEL_manual.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1095 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1095 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt1095.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exmligtb.mf Ok) ) ) ) Font metrics written on ectt1095.tfm. Output written on ectt1095.600gf (256 characters, 47796 bytes). Transcript written on ectt1095.log. mktexpk: /build/probabel-0.5.0+dfsg/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1095.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1440 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1440 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt1440.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exmligtb.mf Ok) ) ) ) Font metrics written on ectt1440.tfm. Output written on ectt1440.600gf (256 characters, 61024 bytes). Transcript written on ectt1440.log. mktexpk: /build/probabel-0.5.0+dfsg/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1440.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecrm1000 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecrm1000 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm1000.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.06586pt) Font metrics written on ecrm1000.tfm. Output written on ecrm1000.600gf (256 characters, 51184 bytes). Transcript written on ecrm1000.log. mktexpk: /build/probabel-0.5.0+dfsg/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm1000.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecrm0700 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecrm0700 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm0700.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) Font metrics written on ecrm0700.tfm. Output written on ecrm0700.600gf (256 characters, 37344 bytes). Transcript written on ecrm0700.log. mktexpk: /build/probabel-0.5.0+dfsg/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm0700.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt0800 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt0800 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt0800.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exmligtb.mf Ok) ) ) ) Font metrics written on ectt0800.tfm. Output written on ectt0800.600gf (256 characters, 35488 bytes). Transcript written on ectt0800.log. mktexpk: /build/probabel-0.5.0+dfsg/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt0800.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecbx1200 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecbx1200 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecbx1200.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecbx.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) Font metrics written on ecbx1200.tfm. Output written on ecbx1200.600gf (256 characters, 59220 bytes). Transcript written on ecbx1200.log. mktexpk: /build/probabel-0.5.0+dfsg/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ecbx1200.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecrm0800 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecrm0800 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm0800.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.06445pt) Font metrics written on ecrm0800.tfm. Output written on ecrm0800.600gf (256 characters, 41732 bytes). Transcript written on ecrm0800.log. mktexpk: /build/probabel-0.5.0+dfsg/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm0800.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1000 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1000 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt1000.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exmligtb.mf Ok) ) ) ) Font metrics written on ectt1000.tfm. Output written on ectt1000.600gf (256 characters, 43832 bytes). Transcript written on ectt1000.log. mktexpk: /build/probabel-0.5.0+dfsg/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1000.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1200 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1200 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1200.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) (some charht values had to be adjusted by as much as 0.06665pt) Font metrics written on tcrm1200.tfm. Output written on tcrm1200.600gf (128 characters, 28032 bytes). Transcript written on tcrm1200.log. mktexpk: /build/probabel-0.5.0+dfsg/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/tcrm1200.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecbx1440 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecbx1440 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecbx1440.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecbx.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.10997pt) Font metrics written on ecbx1440.tfm. Output written on ecbx1440.600gf (256 characters, 70764 bytes). Transcript written on ecbx1440.log. mktexpk: /build/probabel-0.5.0+dfsg/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ecbx1440.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1728 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1728 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt1728.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exmligtb.mf Ok) ) ) ) Font metrics written on ectt1728.tfm. Output written on ectt1728.600gf (256 characters, 72884 bytes). Transcript written on ectt1728.log. mktexpk: /build/probabel-0.5.0+dfsg/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1728.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ectt1200 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ectt1200 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt1200.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ectt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exmligtb.mf Ok) ) ) ) Font metrics written on ectt1200.tfm. Output written on ectt1200.600gf (256 characters, 51736 bytes). Transcript written on ectt1200.log. mktexpk: /build/probabel-0.5.0+dfsg/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ectt1200.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecrm1200 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecrm1200 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm1200.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.07143pt) Font metrics written on ecrm1200.tfm. Output written on ecrm1200.600gf (256 characters, 60320 bytes). Transcript written on ecrm1200.log. mktexpk: /build/probabel-0.5.0+dfsg/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm1200.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecbx1728 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecbx1728 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecbx1728.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecbx.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.13197pt) Font metrics written on ecbx1728.tfm. Output written on ecbx1728.600gf (256 characters, 84848 bytes). Transcript written on ecbx1728.log. mktexpk: /build/probabel-0.5.0+dfsg/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ecbx1728.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecrm1095 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecrm1095 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm1095.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.07599pt) Font metrics written on ecrm1095.tfm. Output written on ecrm1095.600gf (256 characters, 55424 bytes). Transcript written on ecrm1095.log. mktexpk: /build/probabel-0.5.0+dfsg/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm1095.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecrm1440 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecrm1440 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm1440.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.08084pt) Font metrics written on ecrm1440.tfm. Output written on ecrm1440.600gf (256 characters, 71064 bytes). Transcript written on ecrm1440.log. mktexpk: /build/probabel-0.5.0+dfsg/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm1440.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecti1440 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecti1440 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecti1440.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecti.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/extextit.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exileast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exilwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exilig.mf Ok [25] [26] [27] [28] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exitalp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exillett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exidigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exiligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.07997pt) Font metrics written on ecti1440.tfm. Output written on ecti1440.600gf (256 characters, 74296 bytes). Transcript written on ecti1440.log. mktexpk: /build/probabel-0.5.0+dfsg/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ecti1440.600pk: successfully generated. kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ecrm2074 mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input ecrm2074 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm2074.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/ecrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exroman.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exruwest.mf Ok [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlwest.mf Ok [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrueast.mf Ok [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrleast.mf Ok [158] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbraces.mf Ok [94] [126] [23] [40] [41] [60] [124] [62] [91] [93] [92] [123] [125] [95] [127] [32]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/expunct.mf Ok [14] [15] [19] [20] [13] [18] [33] [39] [42] [43] [44] [46] [47] [58] [59] [61] [96] [189] [17] [45] [16] [21] [22]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exsign.mf Ok [24] [34] [35] [36] [37] [64] [191] [159]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrlig.mf Ok [25] [26] [28] [27] [29] [30] [31]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exromp.mf Ok [38] [63] [190]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrulett.mf Ok [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrllett.mf Ok [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrdigit.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exrligtb.mf Ok) ) ) ) (some charht values had to be adjusted by as much as 0.1171pt) Font metrics written on ecrm2074.tfm. Output written on ecrm2074.600gf (256 characters, 101464 bytes). Transcript written on ecrm2074.log. mktexpk: /build/probabel-0.5.0+dfsg/debian/.debhelper/generated/_source/home/.texlive2022/texmf-var/fonts/pk/ljfour/jknappen/ec/ecrm2074.600pk: successfully generated. Output written on ProbABEL_manual.pdf (22 pages, 410561 bytes). Transcript written on ProbABEL_manual.log. diff: .btmp: No such file or directory === Making PDF === pdflatex ./ProbABEL_manual.tex This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./ProbABEL_manual.tex LaTeX2e <2022-11-01> patch level 1 L3 programming layer <2023-01-16> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2022/07/02 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/svgnam.def)) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty) (/usr/share/texlive/texmf-dist/tex/latex/titleref/titleref.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) Writing index file ProbABEL_manual.idx (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./ProbABEL_manual.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (./ProbABEL_manual.out) (./ProbABEL_manual.out) (./ProbABEL_manual.toc (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) [1{/var/lib/texmf/font s/map/pdftex/updmap/pdftex.map}]) [2] [3] Overfull \hbox (7.36137pt too wide) in paragraph at lines 171--174 \T1/cmr/m/n/12 Prob-A-BEL web page ([][]$\T1/cmtt/m/n/12 http : / / www . genab el . org / packages / ProbABEL$[][]\T1/cmr/m/n/12 ). [4] Overfull \hbox (123.30513pt too wide) in paragraph at lines 238--241 \T1/cmtt/m/n/12 ProbABEL\T1/cmr/m/n/12 . Let's in-stall in a sub-di-rec-tory of your home di-rec-tory, e.g. \T1/cmtt/m/n/12 /home/yourusername/ProbABEL\T1/cmr /m/n/12 : Overfull \hbox (4.73831pt too wide) in paragraph at lines 268--272 []\T1/cmr/m/n/12 If all went well you will find the ex-e-cutable pro-grams (\T1 /cmtt/m/n/12 palinear\T1/cmr/m/n/12 , \T1/cmtt/m/n/12 palogist\T1/cmr/m/n/12 , [5] Overfull \hbox (1.38382pt too wide) in paragraph at lines 274--279 \T1/cmtt/m/n/12 ProbABEL \T1/cmr/m/n/12 takes three files as in-put: a file con -tain-ing SNP in-for-ma-tion (e.g. the [6] [7] Overfull \hbox (12.56972pt too wide) in paragraph at lines 377--384 []\T1/cmr/m/n/12 In the case of lin-ear or lo-gis-tic re-gres-sion (pro-grams \ T1/cmtt/m/n/12 palinear \T1/cmr/m/n/12 and \T1/cmtt/m/n/12 palogist\T1/cmr/m/n/ 12 , Overfull \hbox (14.44846pt too wide) in paragraph at lines 377--384 \T1/cmr/m/n/12 lin-ear re-gres-sion anal-y-sis fol-low here (also to be found i n \T1/cmtt/m/n/12 examples/height.txt\T1/cmr/m/n/12 ) [8] [9] Overfull \hbox (5.0841pt too wide) in paragraph at lines 454--458 []\T1/cmr/m/n/12 There are in to-tal 11 com-mand line op-tions you can spec-ify to the \T1/cmtt/m/n/12 ProbABEL [10] [11] Overfull \hbox (17.4505pt too wide) in paragraph at lines 512--512 []\T1/cmtt/m/n/12 palinear -p height.txt -d gtdata/test.mldose -i gtdata/test.m linfo[] Overfull \hbox (29.79749pt too wide) in paragraph at lines 535--535 []\T1/cmtt/m/n/12 palinear -p height.txt -d gtdata/test.mlprob -i gtdata/test.m linfo \[] Overfull \hbox (54.49146pt too wide) in paragraph at lines 545--545 []\T1/cmtt/m/n/12 palinear -p height.txt -d gtdata/test.mlprob.fvi -i gtdata/te st.mlinfo \[] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\lstinline' on input line 550. Overfull \hbox (8.43651pt too wide) in paragraph at lines 552--563 \T1/cmr/m/n/12 covariance ma-trix goes as in-put pa-ram-e-ter with that op-tion , e.g. [][][][] [12] Overfull \hbox (42.14447pt too wide) in paragraph at lines 569--569 [] \T1/cmtt/m/n/12 h2.obj$InvSigma * h2.obj$h2an$estimate[length(h2.obj$h2an$e stimate)][] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\lstinline' on input line 585. [13] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\lstinline' on input line 626. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\lstinline' on input line 643. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\lstinline' on input line 662. [14] [15] Overfull \hbox (4.6171pt too wide) in paragraph at lines 746--750 \T1/cmr/m/n/12 After in-stalling \T1/cmtt/m/n/12 ProbABEL \T1/cmr/m/n/12 you ca n find the \T1/cmtt/m/n/12 prepare_data.R \T1/cmr/m/n/12 file in the \T1/cmtt/m /n/12 scripts [16] [17] Overfull \hbox (8.33644pt too wide) in paragraph at lines 848--850 []\T1/cmr/m/n/12 Secondly, the Wald test can be used; for that the in-verse var iance-covariance [18] [19] [20] [21] [22] No file ProbABEL_manual.ind. [23] (./ProbABEL_manual.aux) LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on ProbABEL_manual.pdf (23 pages, 417310 bytes). Transcript written on ProbABEL_manual.log. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ** Re-running LaTeX ** This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./ProbABEL_manual.tex LaTeX2e <2022-11-01> patch level 1 L3 programming layer <2023-01-16> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2022/07/02 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/svgnam.def)) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty) (/usr/share/texlive/texmf-dist/tex/latex/titleref/titleref.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) Writing index file ProbABEL_manual.idx (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./ProbABEL_manual.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (./ProbABEL_manual.out) (./ProbABEL_manual.out) (./ProbABEL_manual.toc (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) [1{/var/lib/texmf/font s/map/pdftex/updmap/pdftex.map}]) [2] [3] Overfull \hbox (7.36137pt too wide) in paragraph at lines 171--174 \T1/cmr/m/n/12 Prob-A-BEL web page ([][]$\T1/cmtt/m/n/12 http : / / www . genab el . org / packages / ProbABEL$[][]\T1/cmr/m/n/12 ). [4] Overfull \hbox (123.30513pt too wide) in paragraph at lines 238--241 \T1/cmtt/m/n/12 ProbABEL\T1/cmr/m/n/12 . Let's in-stall in a sub-di-rec-tory of your home di-rec-tory, e.g. \T1/cmtt/m/n/12 /home/yourusername/ProbABEL\T1/cmr /m/n/12 : Overfull \hbox (4.73831pt too wide) in paragraph at lines 268--272 []\T1/cmr/m/n/12 If all went well you will find the ex-e-cutable pro-grams (\T1 /cmtt/m/n/12 palinear\T1/cmr/m/n/12 , \T1/cmtt/m/n/12 palogist\T1/cmr/m/n/12 , [5] Overfull \hbox (1.38382pt too wide) in paragraph at lines 274--279 \T1/cmtt/m/n/12 ProbABEL \T1/cmr/m/n/12 takes three files as in-put: a file con -tain-ing SNP in-for-ma-tion (e.g. the [6] [7] Overfull \hbox (12.56972pt too wide) in paragraph at lines 377--384 []\T1/cmr/m/n/12 In the case of lin-ear or lo-gis-tic re-gres-sion (pro-grams \ T1/cmtt/m/n/12 palinear \T1/cmr/m/n/12 and \T1/cmtt/m/n/12 palogist\T1/cmr/m/n/ 12 , Overfull \hbox (14.44846pt too wide) in paragraph at lines 377--384 \T1/cmr/m/n/12 lin-ear re-gres-sion anal-y-sis fol-low here (also to be found i n \T1/cmtt/m/n/12 examples/height.txt\T1/cmr/m/n/12 ) [8] [9] Overfull \hbox (5.0841pt too wide) in paragraph at lines 454--458 []\T1/cmr/m/n/12 There are in to-tal 11 com-mand line op-tions you can spec-ify to the \T1/cmtt/m/n/12 ProbABEL [10] [11] Overfull \hbox (17.4505pt too wide) in paragraph at lines 512--512 []\T1/cmtt/m/n/12 palinear -p height.txt -d gtdata/test.mldose -i gtdata/test.m linfo[] Overfull \hbox (29.79749pt too wide) in paragraph at lines 535--535 []\T1/cmtt/m/n/12 palinear -p height.txt -d gtdata/test.mlprob -i gtdata/test.m linfo \[] Overfull \hbox (54.49146pt too wide) in paragraph at lines 545--545 []\T1/cmtt/m/n/12 palinear -p height.txt -d gtdata/test.mlprob.fvi -i gtdata/te st.mlinfo \[] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\lstinline' on input line 550. Overfull \hbox (8.43651pt too wide) in paragraph at lines 552--563 \T1/cmr/m/n/12 covariance ma-trix goes as in-put pa-ram-e-ter with that op-tion , e.g. [][][][] [12] Overfull \hbox (42.14447pt too wide) in paragraph at lines 569--569 [] \T1/cmtt/m/n/12 h2.obj$InvSigma * h2.obj$h2an$estimate[length(h2.obj$h2an$e stimate)][] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\lstinline' on input line 585. [13] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\lstinline' on input line 626. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\lstinline' on input line 643. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\lstinline' on input line 662. [14] [15] Overfull \hbox (4.6171pt too wide) in paragraph at lines 746--750 \T1/cmr/m/n/12 After in-stalling \T1/cmtt/m/n/12 ProbABEL \T1/cmr/m/n/12 you ca n find the \T1/cmtt/m/n/12 prepare_data.R \T1/cmr/m/n/12 file in the \T1/cmtt/m /n/12 scripts [16] [17] Overfull \hbox (8.33644pt too wide) in paragraph at lines 848--850 []\T1/cmr/m/n/12 Secondly, the Wald test can be used; for that the in-verse var iance-covariance [18] [19] [20] [21] [22] No file ProbABEL_manual.ind. [23] (./ProbABEL_manual.aux) ) (see the transcript file for additional information) Output written on ProbABEL_manual.pdf (23 pages, 417309 bytes). Transcript written on ProbABEL_manual.log. === Making index === makeindex ProbABEL_manual This is makeindex, version 2.16 [TeX Live 2022] (kpathsea + Thai support). Scanning input file ProbABEL_manual.idx....done (3 entries accepted, 0 rejected). Sorting entries....done (4 comparisons). Generating output file ProbABEL_manual.ind....done (14 lines written, 0 warnings). Output written in ProbABEL_manual.ind. Transcript written in ProbABEL_manual.ilg. === Making final PDF === pdflatex ./ProbABEL_manual.tex This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./ProbABEL_manual.tex LaTeX2e <2022-11-01> patch level 1 L3 programming layer <2023-01-16> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2022/07/02 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/svgnam.def)) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty) (/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty) (/usr/share/texlive/texmf-dist/tex/latex/titleref/titleref.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) Writing index file ProbABEL_manual.idx (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./ProbABEL_manual.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (./ProbABEL_manual.out) (./ProbABEL_manual.out) (./ProbABEL_manual.toc (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) [1{/var/lib/texmf/font s/map/pdftex/updmap/pdftex.map}]) [2] [3] Overfull \hbox (7.36137pt too wide) in paragraph at lines 171--174 \T1/cmr/m/n/12 Prob-A-BEL web page ([][]$\T1/cmtt/m/n/12 http : / / www . genab el . org / packages / ProbABEL$[][]\T1/cmr/m/n/12 ). [4] Overfull \hbox (123.30513pt too wide) in paragraph at lines 238--241 \T1/cmtt/m/n/12 ProbABEL\T1/cmr/m/n/12 . Let's in-stall in a sub-di-rec-tory of your home di-rec-tory, e.g. \T1/cmtt/m/n/12 /home/yourusername/ProbABEL\T1/cmr /m/n/12 : Overfull \hbox (4.73831pt too wide) in paragraph at lines 268--272 []\T1/cmr/m/n/12 If all went well you will find the ex-e-cutable pro-grams (\T1 /cmtt/m/n/12 palinear\T1/cmr/m/n/12 , \T1/cmtt/m/n/12 palogist\T1/cmr/m/n/12 , [5] Overfull \hbox (1.38382pt too wide) in paragraph at lines 274--279 \T1/cmtt/m/n/12 ProbABEL \T1/cmr/m/n/12 takes three files as in-put: a file con -tain-ing SNP in-for-ma-tion (e.g. the [6] [7] Overfull \hbox (12.56972pt too wide) in paragraph at lines 377--384 []\T1/cmr/m/n/12 In the case of lin-ear or lo-gis-tic re-gres-sion (pro-grams \ T1/cmtt/m/n/12 palinear \T1/cmr/m/n/12 and \T1/cmtt/m/n/12 palogist\T1/cmr/m/n/ 12 , Overfull \hbox (14.44846pt too wide) in paragraph at lines 377--384 \T1/cmr/m/n/12 lin-ear re-gres-sion anal-y-sis fol-low here (also to be found i n \T1/cmtt/m/n/12 examples/height.txt\T1/cmr/m/n/12 ) [8] [9] Overfull \hbox (5.0841pt too wide) in paragraph at lines 454--458 []\T1/cmr/m/n/12 There are in to-tal 11 com-mand line op-tions you can spec-ify to the \T1/cmtt/m/n/12 ProbABEL [10] [11] Overfull \hbox (17.4505pt too wide) in paragraph at lines 512--512 []\T1/cmtt/m/n/12 palinear -p height.txt -d gtdata/test.mldose -i gtdata/test.m linfo[] Overfull \hbox (29.79749pt too wide) in paragraph at lines 535--535 []\T1/cmtt/m/n/12 palinear -p height.txt -d gtdata/test.mlprob -i gtdata/test.m linfo \[] Overfull \hbox (54.49146pt too wide) in paragraph at lines 545--545 []\T1/cmtt/m/n/12 palinear -p height.txt -d gtdata/test.mlprob.fvi -i gtdata/te st.mlinfo \[] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\lstinline' on input line 550. Overfull \hbox (8.43651pt too wide) in paragraph at lines 552--563 \T1/cmr/m/n/12 covariance ma-trix goes as in-put pa-ram-e-ter with that op-tion , e.g. [][][][] [12] Overfull \hbox (42.14447pt too wide) in paragraph at lines 569--569 [] \T1/cmtt/m/n/12 h2.obj$InvSigma * h2.obj$h2an$estimate[length(h2.obj$h2an$e stimate)][] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\lstinline' on input line 585. [13] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\lstinline' on input line 626. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\lstinline' on input line 643. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `\lstinline' on input line 662. [14] [15] Overfull \hbox (4.6171pt too wide) in paragraph at lines 746--750 \T1/cmr/m/n/12 After in-stalling \T1/cmtt/m/n/12 ProbABEL \T1/cmr/m/n/12 you ca n find the \T1/cmtt/m/n/12 prepare_data.R \T1/cmr/m/n/12 file in the \T1/cmtt/m /n/12 scripts [16] [17] Overfull \hbox (8.33644pt too wide) in paragraph at lines 848--850 []\T1/cmr/m/n/12 Secondly, the Wald test can be used; for that the in-verse var iance-covariance [18] [19] [20] [21] [22] (./ProbABEL_manual.ind [23] [24]) (./ProbABEL_manual.aux) ) (see the transcript file for additional information) Output written on ProbABEL_manual.pdf (24 pages, 418253 bytes). Transcript written on ProbABEL_manual.log. rm ProbABEL_manual.aux make[2]: Leaving directory '/build/probabel-0.5.0+dfsg/doc' Making all in checks make[2]: Entering directory '/build/probabel-0.5.0+dfsg/checks' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/probabel-0.5.0+dfsg/checks' Making all in examples make[2]: Entering directory '/build/probabel-0.5.0+dfsg/examples' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/probabel-0.5.0+dfsg/examples' Making all in checks/R-tests make[2]: Entering directory '/build/probabel-0.5.0+dfsg/checks/R-tests' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/probabel-0.5.0+dfsg/checks/R-tests' make[2]: Entering directory '/build/probabel-0.5.0+dfsg' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/probabel-0.5.0+dfsg' make[1]: Leaving directory '/build/probabel-0.5.0+dfsg' dh_auto_test make -j15 check "TESTSUITEFLAGS=-j15 --verbose" VERBOSE=1 make[1]: Entering directory '/build/probabel-0.5.0+dfsg' Making check in src make[2]: Entering directory '/build/probabel-0.5.0+dfsg/src' make[2]: Leaving directory '/build/probabel-0.5.0+dfsg/src' Making check in doc make[2]: Entering directory '/build/probabel-0.5.0+dfsg/doc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/probabel-0.5.0+dfsg/doc' Making check in checks make[2]: Entering directory '/build/probabel-0.5.0+dfsg/checks' make check_probabel_chunk.sh check_dose_input.sh test_qt.sh test_mms.sh test_flipmaf_palinear.sh test_bt.sh test_flipmaf_palogist.sh test_cox.sh test_cox_nocovar.sh test_cox_interactions.sh test_flipmaf_pacoxph.sh make[3]: Entering directory '/build/probabel-0.5.0+dfsg/checks' make[3]: Nothing to be done for 'check_probabel_chunk.sh'. make[3]: Nothing to be done for 'check_dose_input.sh'. make[3]: Nothing to be done for 'test_qt.sh'. make[3]: Nothing to be done for 'test_mms.sh'. make[3]: Nothing to be done for 'test_flipmaf_palinear.sh'. make[3]: Nothing to be done for 'test_bt.sh'. make[3]: Nothing to be done for 'test_flipmaf_palogist.sh'. make[3]: Nothing to be done for 'test_cox.sh'. make[3]: Nothing to be done for 'test_cox_nocovar.sh'. make[3]: Nothing to be done for 'test_cox_interactions.sh'. make[3]: Nothing to be done for 'test_flipmaf_pacoxph.sh'. make[3]: Leaving directory '/build/probabel-0.5.0+dfsg/checks' make check-TESTS make[3]: Entering directory '/build/probabel-0.5.0+dfsg/checks' make[4]: Entering directory '/build/probabel-0.5.0+dfsg/checks' PASS: check_dose_input.sh PASS: test_cox_interactions.sh PASS: test_cox_nocovar.sh PASS: test_bt.sh PASS: test_cox.sh PASS: test_flipmaf_palogist.sh PASS: test_qt.sh PASS: test_flipmaf_pacoxph.sh PASS: test_flipmaf_palinear.sh PASS: test_mms.sh PASS: check_probabel_chunk.sh ============================================================================ Testsuite summary for ProbABEL 0.5.0 ============================================================================ # TOTAL: 11 # PASS: 11 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/probabel-0.5.0+dfsg/checks' make[3]: Leaving directory '/build/probabel-0.5.0+dfsg/checks' make[2]: Leaving directory '/build/probabel-0.5.0+dfsg/checks' Making check in examples make[2]: Entering directory '/build/probabel-0.5.0+dfsg/examples' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/probabel-0.5.0+dfsg/examples' Making check in checks/R-tests make[2]: Entering directory '/build/probabel-0.5.0+dfsg/checks/R-tests' make run_R_test_palinear.sh run_R_test_palogist.sh run_R_test_pacox.sh make[3]: Entering directory '/build/probabel-0.5.0+dfsg/checks/R-tests' make[3]: Nothing to be done for 'run_R_test_palinear.sh'. make[3]: Nothing to be done for 'run_R_test_palogist.sh'. make[3]: Nothing to be 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'/build/probabel-0.5.0+dfsg/src' make[2]: Leaving directory '/build/probabel-0.5.0+dfsg/src' Making install in doc make[2]: Entering directory '/build/probabel-0.5.0+dfsg/doc' make[3]: Entering directory '/build/probabel-0.5.0+dfsg/doc' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/probabel-0.5.0+dfsg/debian/tmp/usr/share/doc/probabel' /bin/mkdir -p '/build/probabel-0.5.0+dfsg/debian/tmp/usr/share/doc/probabel' /bin/mkdir -p '/build/probabel-0.5.0+dfsg/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 ProbABEL_manual.tex QuickStart.txt short_coxph_data.txt short_height_base_add.out.txt.save short_height.txt short_logist_data.txt short_test.mldose test.map test.mlinfo test_regression.R COPYING LICENSE INSTALL ChangeLog TODO '/build/probabel-0.5.0+dfsg/debian/tmp/usr/share/doc/probabel' /usr/bin/install -c -m 644 ProbABEL_manual.pdf '/build/probabel-0.5.0+dfsg/debian/tmp/usr/share/doc/probabel' /usr/bin/install -c -m 644 probabel.1 probabel.pl.1 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'/build/probabel-0.5.0+dfsg/debian/tmp/usr/share/probabel/examples/gtdata' /usr/bin/install -c -m 644 height.txt logist_data.txt mmscore_pheno.PHE coxph_data.txt mmscore.R mmscore_InvSigma_aj.sex.age.dat README '/build/probabel-0.5.0+dfsg/debian/tmp/usr/share/probabel/examples' /usr/bin/install -c -m 644 gtdata/test.mldose gtdata/test.mlprob gtdata/test.mlinfo gtdata/test.map gtdata/test.dose.fvi gtdata/test.dose.fvd gtdata/test.prob.fvi gtdata/test.prob.fvd gtdata/mmscore_gen.mlinfo gtdata/mmscore_gen.mldose gtdata/mmscore_gen.mlprob gtdata/mmscore_gen.dose.fvi gtdata/mmscore_gen.dose.fvd gtdata/mmscore_gen.prob.fvi gtdata/mmscore_gen.prob.fvd '/build/probabel-0.5.0+dfsg/debian/tmp/usr/share/probabel/examples/gtdata' /usr/bin/install -c example_qt.sh example_bt.sh example_cox.sh example_mmscore.sh '/build/probabel-0.5.0+dfsg/debian/tmp/usr/share/probabel/examples' make[3]: Leaving directory '/build/probabel-0.5.0+dfsg/examples' make[2]: Leaving directory 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dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'probabel' in '../probabel_0.5.0+dfsg-6_amd64.deb'. dpkg-deb: building package 'probabel-dbgsym' in '../probabel-dbgsym_0.5.0+dfsg-6_amd64.deb'. dpkg-deb: building package 'probabel-examples' in '../probabel-examples_0.5.0+dfsg-6_all.deb'. dpkg-genbuildinfo --build=binary -O../probabel_0.5.0+dfsg-6_amd64.buildinfo dpkg-genchanges --build=binary -O../probabel_0.5.0+dfsg-6_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/618402 and its subdirectories I: Current time: Sun Apr 30 16:54:00 -12 2023 I: pbuilder-time-stamp: 1682916840 Mon May 1 04:54:01 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Mon May 1 04:54:01 UTC 2023 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Mon May 1 04:58:25 UTC 2023 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Mon May 1 04:58:25 UTC 2023 I: probabel_0.5.0+dfsg-6_amd64.changes: Format: 1.8 Date: Mon, 21 Feb 2022 11:22:57 +0100 Source: probabel Binary: probabel probabel-dbgsym probabel-examples Architecture: amd64 all Version: 0.5.0+dfsg-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: probabel - Toolset for Genome-Wide Association Analysis probabel-examples - Example files for ProbABEL Changes: probabel (0.5.0+dfsg-6) unstable; urgency=medium . * Restrict architectures to those, where build time test properly succeeds * Add status of this package to README.Debian Checksums-Sha1: c991d3872f9bef152a9af9b444a5176c66435d14 8133600 probabel-dbgsym_0.5.0+dfsg-6_amd64.deb 42e8e0f50455fb9e04e9c9d0c6dadb8590dc58b5 2273108 probabel-examples_0.5.0+dfsg-6_all.deb d0f5a83623229375b799dffe9f4c3c9107b42812 8934 probabel_0.5.0+dfsg-6_amd64.buildinfo 73f8e09e431bd314f26abdca1400ff9dd5646ebf 603204 probabel_0.5.0+dfsg-6_amd64.deb Checksums-Sha256: dcd7e5da53dd0b146cedf8572a38abca5e304b129a51fbc7796e1d03d58de9f3 8133600 probabel-dbgsym_0.5.0+dfsg-6_amd64.deb 895f3f6abc3df2a7caf12d91f1f99da6f777aa161973ad9c9dfb1f3356967ee9 2273108 probabel-examples_0.5.0+dfsg-6_all.deb bc589b821e590a09404c7c54d25d2e5fe4ee71149dc8f3033f7b7fa886f9165a 8934 probabel_0.5.0+dfsg-6_amd64.buildinfo 5567506650becec2012b4e814dcfb6411e9101e0a5db6b57fc25b63561fc23d0 603204 probabel_0.5.0+dfsg-6_amd64.deb Files: b271729fa5a43bcbf6d234c120a7f1dd 8133600 debug optional probabel-dbgsym_0.5.0+dfsg-6_amd64.deb 246b280c4fa9f28b3b70794d4638b0d6 2273108 science optional probabel-examples_0.5.0+dfsg-6_all.deb a13c7cc193ec5cdab8882fc4b029d2dc 8934 science optional probabel_0.5.0+dfsg-6_amd64.buildinfo 48e24e94be6277574937b4f1cceca633 603204 science optional probabel_0.5.0+dfsg-6_amd64.deb Mon May 1 04:58:26 UTC 2023 I: diffoscope 241 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.QEWqOl0Q/probabel_0.5.0+dfsg-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.QEWqOl0Q/probabel_0.5.0+dfsg-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.QEWqOl0Q/probabel_0.5.0+dfsg-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.QEWqOl0Q/b1/probabel_0.5.0+dfsg-6_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.QEWqOl0Q/b2/probabel_0.5.0+dfsg-6_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.490s) 0.490s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.143s) 0.142s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Mon May 1 04:58:28 UTC 2023 I: diffoscope 241 found no differences in the changes files, and a .buildinfo file also exists. Mon May 1 04:58:28 UTC 2023 I: probabel from bookworm built successfully and reproducibly on amd64. Mon May 1 04:58:30 UTC 2023 I: Submitting .buildinfo files to external archives: Mon May 1 04:58:30 UTC 2023 I: Submitting 12K b1/probabel_0.5.0+dfsg-6_amd64.buildinfo.asc Mon May 1 04:58:31 UTC 2023 I: Submitting 12K b2/probabel_0.5.0+dfsg-6_amd64.buildinfo.asc Mon May 1 04:58:32 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon May 1 04:58:32 UTC 2023 I: Done submitting .buildinfo files. Mon May 1 04:58:32 UTC 2023 I: Removing signed probabel_0.5.0+dfsg-6_amd64.buildinfo.asc files: removed './b1/probabel_0.5.0+dfsg-6_amd64.buildinfo.asc' removed './b2/probabel_0.5.0+dfsg-6_amd64.buildinfo.asc'