Thu Aug 15 18:27:12 UTC 2024 I: starting to build wise/unstable/i386 on jenkins on '2024-08-15 18:27' Thu Aug 15 18:27:12 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_15/32721/console.log Thu Aug 15 18:27:12 UTC 2024 I: Downloading source for unstable/wise=2.4.1-25 --2024-08-15 18:27:12-- http://deb.debian.org/debian/pool/main/w/wise/wise_2.4.1-25.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2305 (2.3K) [text/prs.lines.tag] Saving to: ‘wise_2.4.1-25.dsc’ 0K .. 100% 320M=0s 2024-08-15 18:27:12 (320 MB/s) - ‘wise_2.4.1-25.dsc’ saved [2305/2305] Thu Aug 15 18:27:13 UTC 2024 I: wise_2.4.1-25.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: wise Binary: wise, wise-doc, wise-data Architecture: any all Version: 2.4.1-25 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille Homepage: https://www.ebi.ac.uk/~birney/wise2/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/wise Vcs-Git: https://salsa.debian.org/med-team/wise.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev, libfl-dev Package-List: wise deb science optional arch=any wise-data deb doc optional arch=all wise-doc deb doc optional arch=all Checksums-Sha1: 50215e0541ed043d2ee44463da1b1a0d5272d724 3410178 wise_2.4.1.orig.tar.gz 97c02fec57cc662f7cf6aba621da09971dc009fa 39944 wise_2.4.1-25.debian.tar.xz Checksums-Sha256: 0aec5e30739110783517a429606249fc6c5fd0d65171c1a6d79ecc5ff81d2935 3410178 wise_2.4.1.orig.tar.gz 1d5eafd21cab385e75f51f6b1c869e8be80e7845a21d7f1653d200704e80768c 39944 wise_2.4.1-25.debian.tar.xz Files: 9e90132c19a653831ce63b5af7f08302 3410178 wise_2.4.1.orig.tar.gz 15f80c4850dd04e2edc1c09c2fbeb7e2 39944 wise_2.4.1-25.debian.tar.xz Dgit: f2b00df5d7344f58a5d22bf48375199853de79af debian archive/debian/2.4.1-25 https://git.dgit.debian.org/wise -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAma929kUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdo2IA//S9vC+AlihkfUIS6zTvidnXqc4DRV 3FJXopi6jvnT6TgrmgY3gwtov/2E9LwunADy2BdTpYMXWDo0wWX50z+45nRGgE1K 0U392SUgDIl8fzXIqd/tlWeRY6W7BMA3EGyMzQba//0bqygsrN1mUCTjQXL833UX EvLQgo2oJvIxDoArtA7GkDsGQiVx9Rm3tPGpgxPY3HKonyiTMPeIEJXej0Vw1TuE sSvmq3k+PqhvyQ8hej5wZp5S24lTwJp3BSUhP9GFf5fWJ+Q6WHGYO98fEuZtHTtB W97M330ip2g8WbyTST+FQ8daCr+FpDy6lB/HM9iQhUmWYFX+EwW9qfZfreCbgLhE DFTTb4a6qmv7n3HOt5voZJn1E1hN733jbavSHWTl+8qmRXjxDmbBPFrLJ8eiBUG+ G4GrrN6EidZqzsEpaz6JeCkEuRNIrXBni4JapJd6C4Kbq/3/0JugM4j16Gj5NI4j JDZRj437dbE5+98vtO489Nj/X5iFwAPWUkp+n7tBnqVlzAdxZPHtZhMgfPRnUwbB SCwxDnyAhBvaUwHqkiUSH7Su93XnCmcQaW2fQthdmXRgwfwmiOw9En1bxVdoev7e QKiYhiKw9UDZE8Dh24Re+kSWDsCFihFVhlt7qz9FGG4P4s6xwSAu0P3kuRhSpM+t ilzFsKuRQEK15qM= =wPEk -----END PGP SIGNATURE----- Thu Aug 15 18:27:13 UTC 2024 I: Checking whether the package is not for us Thu Aug 15 18:27:13 UTC 2024 I: Starting 1st build on remote node infom07-i386.debian.net. Thu Aug 15 18:27:13 UTC 2024 I: Preparing to do remote build '1' on infom07-i386.debian.net. Thu Aug 15 18:30:50 UTC 2024 I: Deleting $TMPDIR on infom07-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Aug 15 06:27:15 -12 2024 I: pbuilder-time-stamp: 1723746435 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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: using eatmydata during job I: Copying source file I: copying [wise_2.4.1-25.dsc] I: copying [./wise_2.4.1.orig.tar.gz] I: copying [./wise_2.4.1-25.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Aug 15 10:43:37 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./wise_2.4.1-25.dsc: no acceptable signature found dpkg-source: info: extracting wise in wise-2.4.1 dpkg-source: info: unpacking wise_2.4.1.orig.tar.gz dpkg-source: info: unpacking wise_2.4.1-25.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 01_welcome-csh.patch dpkg-source: info: applying 02_isnumber.patch dpkg-source: info: applying 03_doc-nodycache.patch dpkg-source: info: applying 04_wise2-pdflatex-update.patch dpkg-source: info: applying 05_glib2.patch dpkg-source: info: applying 06_getline.patch dpkg-source: info: applying 07_ld--as-needed.patch dpkg-source: info: applying 08_mayhem.patch dpkg-source: info: applying 09_dnal-add-return-statement.patch dpkg-source: info: applying 10_fix_path_to_data_files.patch dpkg-source: info: applying 11_consistent_manual_dates.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying cross.patch dpkg-source: info: applying implicit-function-declaration.patch dpkg-source: info: applying executable-is-script.patch dpkg-source: info: applying gcc-14.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/28329/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='741d8c05739244158a4f4da020b36d76' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='28329' 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.arrGDNNn/pbuilderrc_Wr9O --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.arrGDNNn/b1 --logfile b1/build.log wise_2.4.1-25.dsc' SUDO_GID='111' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom07-i386 6.1.0-23-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.99-1 (2024-07-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/28329/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: i386 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), texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev, libfl-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19712 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 texlive-latex-base; however: Package texlive-latex-base is not installed. pbuilder-satisfydepends-dummy depends on texlive-extra-utils; however: Package texlive-extra-utils is not installed. pbuilder-satisfydepends-dummy depends on hevea; however: Package hevea is not installed. pbuilder-satisfydepends-dummy depends on docbook-to-man; however: Package docbook-to-man is not installed. pbuilder-satisfydepends-dummy depends on libglib2.0-dev; however: Package libglib2.0-dev is not installed. pbuilder-satisfydepends-dummy depends on libfl-dev; however: Package libfl-dev 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} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docbook{a} docbook-to-man{a} dwz{a} file{a} flex{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lmodern{a} fonts-urw-base35{a} gettext{a} gettext-base{a} ghostscript{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libblkid-dev{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcups2t64{a} libdatrie1{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi-dev{a} libfile-homedir-perl{a} libfile-stripnondeterminism-perl{a} libfile-which-perl{a} libfl-dev{a} libfl2{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libgirepository-2.0-0{a} libglib2.0-0t64{a} libglib2.0-bin{a} libglib2.0-data{a} libglib2.0-dev{a} libglib2.0-dev-bin{a} libgraphite2-3{a} libgs-common{a} libgs10{a} libgs10-common{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libice6{a} libicu72{a} libidn12{a} libijs-0.35{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libjs-jquery{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libmime-charset-perl{a} libmount-dev{a} libmpfi0{a} libnsl2{a} libopenjp2-7{a} libosp5{a} libpaper-utils{a} libpaper1{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpng16-16t64{a} libpotrace0{a} libptexenc1{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} libselinux1-dev{a} libsepol-dev{a} libsharpyuv0{a} libsm6{a} libsombok3{a} libsynctex2{a} libsysprof-capture-4-dev{a} libteckit0{a} libtexlua53-5{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libunicode-linebreak-perl{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} libxi6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6t64{a} libyaml-tiny-perl{a} libzzip-0-13t64{a} lmodern{a} m4{a} man-db{a} media-types{a} netbase{a} opensp{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} poppler-data{a} python3{a} python3-minimal{a} python3-packaging{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sgml-data{a} t1utils{a} tex-common{a} texlive-base{a} texlive-binaries{a} texlive-extra-utils{a} texlive-latex-base{a} texlive-luatex{a} texlive-plain-generic{a} tzdata{a} ucf{a} uuid-dev{a} x11-common{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl dbus dvisvgm fonts-droid-fallback javascript-common krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl liblog-log4perl-perl libltdl-dev libmail-sendmail-perl libnet-dbus-perl libx11-protocol-perl lynx ruby shared-mime-info texlive-latex-recommended wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 169 newly installed, 0 to remove and 0 not upgraded. Need to get 232 MB of archives. After unpacking 578 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: hevea but it is not installable The following actions will resolve these dependencies: Install the following packages: 1) hevea [2.36-2+b2 (unstable)] 2) hicolor-icon-theme [0.18-1 (unstable)] 3) imagemagick [8:6.9.13.12+dfsg1-1 (unstable)] 4) imagemagick-6-common [8:6.9.13.12+dfsg1-1 (unstable)] 5) imagemagick-6.q16 [8:6.9.13.12+dfsg1-1 (unstable)] 6) libdav1d7 [1.4.3-1 (unstable)] 7) libde265-0 [1.0.15-1+b2 (unstable)] 8) libfftw3-double3 [3.3.10-1+b3 (unstable)] 9) libheif-plugin-dav1d [1.18.1-1 (unstable)] 10) libheif-plugin-libde265 [1.18.1-1 (unstable)] 11) libheif1 [1.18.1-1 (unstable)] 12) liblqr-1-0 [0.4.2-2.1+b1 (unstable)] 13) libltdl7 [2.4.7-7+b1 (unstable)] 14) libmagickcore-6.q16-7t64 [8:6.9.13.12+dfsg1-1 (unstable)] 15) libmagickwand-6.q16-7t64 [8:6.9.13.12+dfsg1-1 (unstable)] 16) libnetpbm11t64 [2:11.07.00-2 (unstable)] 17) libraw23t64 [0.21.2-2.1 (unstable)] 18) libstdlib-ocaml [5.2.0-2 (unstable)] 19) libwebpdemux2 [1.4.0-0.1 (unstable)] 20) libwebpmux3 [1.4.0-0.1 (unstable)] 21) netpbm [2:11.07.00-2 (unstable)] 22) ocaml-base [5.2.0-2 (unstable)] The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docbook{a} docbook-to-man{a} dwz{a} file{a} flex{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lmodern{a} fonts-urw-base35{a} gettext{a} gettext-base{a} ghostscript{a} groff-base{a} hevea{a} hicolor-icon-theme{a} imagemagick{a} imagemagick-6-common{a} imagemagick-6.q16{a} intltool-debian{a} libarchive-zip-perl{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libblkid-dev{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcups2t64{a} libdatrie1{a} libdav1d7{a} libdbus-1-3{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi-dev{a} libfftw3-double3{a} libfile-homedir-perl{a} libfile-stripnondeterminism-perl{a} libfile-which-perl{a} libfl-dev{a} libfl2{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libgirepository-2.0-0{a} libglib2.0-0t64{a} libglib2.0-bin{a} libglib2.0-data{a} libglib2.0-dev{a} libglib2.0-dev-bin{a} libgraphite2-3{a} libgs-common{a} libgs10{a} libgs10-common{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libice6{a} libicu72{a} libidn12{a} libijs-0.35{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libjs-jquery{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} liblerc4{a} liblqr-1-0{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmagickcore-6.q16-7t64{a} libmagickwand-6.q16-7t64{a} libmime-charset-perl{a} libmount-dev{a} libmpfi0{a} libnetpbm11t64{a} libnsl2{a} libopenjp2-7{a} libosp5{a} libpaper-utils{a} libpaper1{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpng16-16t64{a} libpotrace0{a} libptexenc1{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libraw23t64{a} libreadline8t64{a} libselinux1-dev{a} libsepol-dev{a} libsharpyuv0{a} libsm6{a} libsombok3{a} libstdlib-ocaml{a} libsynctex2{a} libsysprof-capture-4-dev{a} libteckit0{a} libtexlua53-5{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libunicode-linebreak-perl{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6t64{a} libyaml-tiny-perl{a} libzzip-0-13t64{a} lmodern{a} m4{a} man-db{a} media-types{a} netbase{a} netpbm{a} ocaml-base{a} opensp{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} poppler-data{a} python3{a} python3-minimal{a} python3-packaging{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sgml-data{a} t1utils{a} tex-common{a} texlive-base{a} texlive-binaries{a} texlive-extra-utils{a} texlive-latex-base{a} texlive-luatex{a} texlive-plain-generic{a} tzdata{a} ucf{a} uuid-dev{a} x11-common{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl dbus dvisvgm fonts-droid-fallback javascript-common krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libheif-plugin-aomenc libheif-plugin-x265 liblog-log4perl-perl libltdl-dev libmagickcore-6.q16-7-extra libmail-sendmail-perl libnet-dbus-perl libx11-protocol-perl lynx ruby shared-mime-info texlive-latex-recommended wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 191 newly installed, 0 to remove and 0 not upgraded. Need to get 242 MB of archives. After unpacking 612 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 flex i386 2.6.4-8.2+b2 [415 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 libfftw3-double3 i386 3.3.10-1+b3 [635 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.2-1 [107 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b4 [309 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 libpng16-16t64 i386 1.6.43-5 [286 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 libfreetype6 i386 2.13.2+dfsg-1+b4 [449 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 libfontenc1 i386 1:1.1.8-1 [23.1 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 x11-common all 1:7.7+23.1 [216 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 13 http://deb.debian.org/debian unstable/main i386 xfonts-utils i386 1:7.7+6 [95.2 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 15 http://deb.debian.org/debian unstable/main i386 fontconfig-config i386 2.15.0-1.1 [317 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 libfontconfig1 i386 2.15.0-1.1 [401 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 libsharpyuv0 i386 1.4.0-0.1 [113 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 libdav1d7 i386 1.4.3-1 [327 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 libheif-plugin-dav1d i386 1.18.1-1 [10.8 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 libde265-0 i386 1.0.15-1+b2 [199 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 libheif-plugin-libde265 i386 1.18.1-1 [14.5 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 libheif1 i386 1.18.1-1 [360 kB] Get: 23 http://deb.debian.org/debian unstable/main i386 libjbig0 i386 2.1-6.1+b1 [31.8 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 libjpeg62-turbo i386 1:2.1.5-3 [169 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 liblcms2-2 i386 2.14-2+b1 [165 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 libglib2.0-0t64 i386 2.81.1-3 [1567 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 liblqr-1-0 i386 0.4.2-2.1+b1 [31.8 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 libltdl7 i386 2.4.7-7+b1 [395 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 libopenjp2-7 i386 2.5.0-2+b3 [197 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 libraw23t64 i386 0.21.2-2.1 [407 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 libdeflate0 i386 1.21-1 [48.0 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 liblerc4 i386 4.0.0+ds-4+b1 [180 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 libwebp7 i386 1.4.0-0.1 [318 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 libtiff6 i386 4.5.1+git230720-4 [338 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 libwebpdemux2 i386 1.4.0-0.1 [111 kB] Get: 36 http://deb.debian.org/debian unstable/main i386 libwebpmux3 i386 1.4.0-0.1 [125 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 libxau6 i386 1:1.0.9-1+b1 [18.5 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 libxdmcp6 i386 1:1.1.2-3+b1 [24.8 kB] Get: 39 http://deb.debian.org/debian unstable/main i386 libxcb1 i386 1.17.0-2 [148 kB] Get: 40 http://deb.debian.org/debian unstable/main i386 libx11-data all 2:1.8.7-1 [328 kB] Get: 41 http://deb.debian.org/debian unstable/main i386 libx11-6 i386 2:1.8.7-1+b1 [822 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-5 [9550 kB] Get: 44 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg-3+b1 [704 kB] Get: 45 http://deb.debian.org/debian unstable/main i386 imagemagick-6-common all 8:6.9.13.12+dfsg1-1 [67.3 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 libmagickcore-6.q16-7t64 i386 8:6.9.13.12+dfsg1-1 [1767 kB] Get: 47 http://deb.debian.org/debian unstable/main i386 libmagickwand-6.q16-7t64 i386 8:6.9.13.12+dfsg1-1 [298 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 poppler-data all 0.4.12-1 [1601 kB] Get: 49 http://deb.debian.org/debian unstable/main i386 libpython3.12-minimal i386 3.12.5-1 [812 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 python3.12-minimal i386 3.12.5-1 [2240 kB] Get: 51 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.12.5-1 [26.7 kB] Get: 52 http://deb.debian.org/debian unstable/main i386 media-types all 10.1.0 [26.9 kB] Get: 53 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 tzdata all 2024a-4 [255 kB] Get: 55 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.1-1 [23.1 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 58 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-3 [9432 B] Get: 59 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 60 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 61 http://deb.debian.org/debian unstable/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 62 http://deb.debian.org/debian unstable/main i386 libtirpc3t64 i386 1.3.4+ds-1.3 [90.2 kB] Get: 63 http://deb.debian.org/debian unstable/main i386 libnsl2 i386 1.3.0-3+b2 [42.4 kB] Get: 64 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-4 [69.3 kB] Get: 65 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-4 [171 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 libpython3.12-stdlib i386 3.12.5-1 [1978 kB] Get: 67 http://deb.debian.org/debian unstable/main i386 python3.12 i386 3.12.5-1 [666 kB] Get: 68 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.12.5-1 [9588 B] Get: 69 http://deb.debian.org/debian unstable/main i386 python3 i386 3.12.5-1 [27.6 kB] Get: 70 http://deb.debian.org/debian unstable/main i386 sgml-base all 1.31 [15.4 kB] Get: 71 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3 [314 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3 [114 kB] Get: 74 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3 [42.9 kB] Get: 75 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 76 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-5 [1196 kB] Get: 78 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.2-7 [101 kB] Get: 79 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 man-db i386 2.12.1-3 [1422 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 ucf all 3.0043+nmu1 [55.2 kB] Get: 82 http://deb.debian.org/debian unstable/main i386 autoconf all 2.71-3 [332 kB] Get: 83 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 84 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 85 http://deb.debian.org/debian unstable/main i386 autopoint all 0.22.5-2 [723 kB] Get: 86 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.18 [89.6 kB] Get: 87 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-7 [517 kB] Get: 88 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 89 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 90 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 91 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 92 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.191-2 [194 kB] Get: 93 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 94 http://deb.debian.org/debian unstable/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 96 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 97 http://deb.debian.org/debian unstable/main i386 debhelper all 13.18 [914 kB] Get: 98 http://deb.debian.org/debian unstable/main i386 xml-core all 0.19 [20.1 kB] Get: 99 http://deb.debian.org/debian unstable/main i386 sgml-data all 2.0.11+nmu1 [179 kB] Get: 100 http://deb.debian.org/debian unstable/main i386 docbook all 4.5-11 [126 kB] Get: 101 http://deb.debian.org/debian unstable/main i386 libosp5 i386 1.5.2-15 [1003 kB] Get: 102 http://deb.debian.org/debian unstable/main i386 opensp i386 1.5.2-15 [455 kB] Get: 103 http://deb.debian.org/debian unstable/main i386 docbook-to-man i386 1:2.0.0-47 [77.1 kB] Get: 104 http://deb.debian.org/debian unstable/main i386 fonts-lmodern all 2.005-1 [4540 kB] Get: 105 http://deb.debian.org/debian unstable/main i386 libgs-common all 10.03.1~dfsg-2 [148 kB] Get: 106 http://deb.debian.org/debian unstable/main i386 libgs10-common all 10.03.1~dfsg-2 [474 kB] Get: 107 http://deb.debian.org/debian unstable/main i386 libavahi-common-data i386 0.8-13+b2 [112 kB] Get: 108 http://deb.debian.org/debian unstable/main i386 libavahi-common3 i386 0.8-13+b2 [45.3 kB] Get: 109 http://deb.debian.org/debian unstable/main i386 libdbus-1-3 i386 1.14.10-4+b1 [217 kB] Get: 110 http://deb.debian.org/debian unstable/main i386 libavahi-client3 i386 0.8-13+b2 [49.3 kB] Get: 111 http://deb.debian.org/debian unstable/main i386 libcups2t64 i386 2.4.10-1 [265 kB] Get: 112 http://deb.debian.org/debian unstable/main i386 libidn12 i386 1.42-2 [81.3 kB] Get: 113 http://deb.debian.org/debian unstable/main i386 libijs-0.35 i386 0.35-15.1+b1 [15.7 kB] Get: 114 http://deb.debian.org/debian unstable/main i386 libjbig2dec0 i386 0.20-1+b2 [66.5 kB] Get: 115 http://deb.debian.org/debian unstable/main i386 libpaper1 i386 1.1.29+b1 [13.0 kB] Get: 116 http://deb.debian.org/debian unstable/main i386 libice6 i386 2:1.0.10-1+b1 [58.6 kB] Get: 117 http://deb.debian.org/debian unstable/main i386 libsm6 i386 2:1.2.3-1+b1 [33.9 kB] Get: 118 http://deb.debian.org/debian unstable/main i386 libxt6t64 i386 1:1.2.1-1.2 [193 kB] Get: 119 http://deb.debian.org/debian unstable/main i386 libgs10 i386 10.03.1~dfsg-2 [2687 kB] Get: 120 http://deb.debian.org/debian unstable/main i386 ghostscript i386 10.03.1~dfsg-2 [50.3 kB] Get: 121 http://deb.debian.org/debian unstable/main i386 libnetpbm11t64 i386 2:11.07.00-2 [188 kB] Get: 122 http://deb.debian.org/debian unstable/main i386 netpbm i386 2:11.07.00-2 [2080 kB] Get: 123 http://deb.debian.org/debian unstable/main i386 tex-common all 6.18 [32.5 kB] Get: 124 http://deb.debian.org/debian unstable/main i386 libpaper-utils i386 1.1.29+b1 [9280 B] Get: 125 http://deb.debian.org/debian unstable/main i386 libkpathsea6 i386 2024.20240313.70630+ds-4 [160 kB] Get: 126 http://deb.debian.org/debian unstable/main i386 libptexenc1 i386 2024.20240313.70630+ds-4 [50.0 kB] Get: 127 http://deb.debian.org/debian unstable/main i386 libsynctex2 i386 2024.20240313.70630+ds-4 [65.5 kB] Get: 128 http://deb.debian.org/debian unstable/main i386 libtexlua53-5 i386 2024.20240313.70630+ds-4 [129 kB] Get: 129 http://deb.debian.org/debian unstable/main i386 t1utils i386 1.41-4 [62.3 kB] Get: 130 http://deb.debian.org/debian unstable/main i386 libpixman-1-0 i386 0.42.2-1+b1 [555 kB] Get: 131 http://deb.debian.org/debian unstable/main i386 libxcb-render0 i386 1.17.0-2 [116 kB] Get: 132 http://deb.debian.org/debian unstable/main i386 libxcb-shm0 i386 1.17.0-2 [105 kB] Get: 133 http://deb.debian.org/debian unstable/main i386 libxrender1 i386 1:0.9.10-1.1+b1 [28.8 kB] Get: 134 http://deb.debian.org/debian unstable/main i386 libcairo2 i386 1.18.0-3+b1 [588 kB] Get: 135 http://deb.debian.org/debian unstable/main i386 libgraphite2-3 i386 1.3.14-2 [77.7 kB] Get: 136 http://deb.debian.org/debian unstable/main i386 libharfbuzz0b i386 9.0.0-1 [500 kB] Get: 137 http://deb.debian.org/debian unstable/main i386 libmpfi0 i386 1.5.4+ds-3 [38.5 kB] Get: 138 http://deb.debian.org/debian unstable/main i386 libpotrace0 i386 1.16-2+b1 [24.2 kB] Get: 139 http://deb.debian.org/debian unstable/main i386 libteckit0 i386 2.5.12+ds1-1 [284 kB] Get: 140 http://deb.debian.org/debian unstable/main i386 libxmu6 i386 2:1.1.3-3+b2 [60.5 kB] Get: 141 http://deb.debian.org/debian unstable/main i386 libxpm4 i386 1:3.5.17-1+b1 [57.8 kB] Get: 142 http://deb.debian.org/debian unstable/main i386 libxaw7 i386 2:1.0.14-1+b2 [208 kB] Get: 143 http://deb.debian.org/debian unstable/main i386 libxi6 i386 2:1.8.1-1 [81.0 kB] Get: 144 http://deb.debian.org/debian unstable/main i386 libzzip-0-13t64 i386 0.13.72+dfsg.1-1.3 [58.0 kB] Get: 145 http://deb.debian.org/debian unstable/main i386 texlive-binaries i386 2024.20240313.70630+ds-4 [8377 kB] Get: 146 http://deb.debian.org/debian unstable/main i386 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 147 http://deb.debian.org/debian unstable/main i386 texlive-base all 2024.20240706-1 [22.7 MB] Get: 148 http://deb.debian.org/debian unstable/main i386 hicolor-icon-theme all 0.18-1 [12.0 kB] Get: 149 http://deb.debian.org/debian unstable/main i386 imagemagick-6.q16 i386 8:6.9.13.12+dfsg1-1 [290 kB] Get: 150 http://deb.debian.org/debian unstable/main i386 imagemagick i386 8:6.9.13.12+dfsg1-1 [19.6 kB] Get: 151 http://deb.debian.org/debian unstable/main i386 libstdlib-ocaml i386 5.2.0-2 [503 kB] Get: 152 http://deb.debian.org/debian unstable/main i386 ocaml-base i386 5.2.0-2 [470 kB] Get: 153 http://deb.debian.org/debian unstable/main i386 hevea i386 2.36-2+b2 [898 kB] Get: 154 http://deb.debian.org/debian unstable/main i386 uuid-dev i386 2.40.2-7 [47.0 kB] Get: 155 http://deb.debian.org/debian unstable/main i386 libblkid-dev i386 2.40.2-7 [227 kB] Get: 156 http://deb.debian.org/debian unstable/main i386 libdatrie1 i386 0.2.13-3 [39.5 kB] Get: 157 http://deb.debian.org/debian unstable/main i386 libffi-dev i386 3.4.6-1 [57.8 kB] Get: 158 http://deb.debian.org/debian unstable/main i386 libfile-which-perl all 1.27-2 [15.1 kB] Get: 159 http://deb.debian.org/debian unstable/main i386 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 160 http://deb.debian.org/debian unstable/main i386 libfl2 i386 2.6.4-8.2+b2 [84.3 kB] Get: 161 http://deb.debian.org/debian unstable/main i386 libfl-dev i386 2.6.4-8.2+b2 [85.7 kB] Get: 162 http://deb.debian.org/debian unstable/main i386 libgirepository-2.0-0 i386 2.81.1-3 [142 kB] Get: 163 http://deb.debian.org/debian unstable/main i386 libglib2.0-data all 2.81.1-3 [1275 kB] Get: 164 http://deb.debian.org/debian unstable/main i386 libglib2.0-bin i386 2.81.1-3 [128 kB] Get: 165 http://deb.debian.org/debian unstable/main i386 python3-packaging all 24.1-1 [45.8 kB] Get: 166 http://deb.debian.org/debian unstable/main i386 libglib2.0-dev-bin i386 2.81.1-3 [172 kB] Get: 167 http://deb.debian.org/debian unstable/main i386 libsepol-dev i386 3.7-1 [405 kB] Get: 168 http://deb.debian.org/debian unstable/main i386 libpcre2-16-0 i386 10.42-4+b1 [244 kB] Get: 169 http://deb.debian.org/debian unstable/main i386 libpcre2-32-0 i386 10.42-4+b1 [233 kB] Get: 170 http://deb.debian.org/debian unstable/main i386 libpcre2-posix3 i386 10.42-4+b1 [55.8 kB] Get: 171 http://deb.debian.org/debian unstable/main i386 libpcre2-dev i386 10.42-4+b1 [759 kB] Get: 172 http://deb.debian.org/debian unstable/main i386 libselinux1-dev i386 3.5-2+b4 [165 kB] Get: 173 http://deb.debian.org/debian unstable/main i386 libmount-dev i386 2.40.2-7 [28.5 kB] Get: 174 http://deb.debian.org/debian unstable/main i386 libsysprof-capture-4-dev i386 46.0-2 [51.6 kB] Get: 175 http://deb.debian.org/debian unstable/main i386 libpkgconf3 i386 1.8.1-3 [38.2 kB] Get: 176 http://deb.debian.org/debian unstable/main i386 pkgconf-bin i386 1.8.1-3 [30.3 kB] Get: 177 http://deb.debian.org/debian unstable/main i386 pkgconf i386 1.8.1-3 [26.1 kB] Get: 178 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1 [915 kB] Get: 179 http://deb.debian.org/debian unstable/main i386 libglib2.0-dev i386 2.81.1-3 [1878 kB] Get: 180 http://deb.debian.org/debian unstable/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 181 http://deb.debian.org/debian unstable/main i386 libmime-charset-perl all 1.013.1-2 [34.0 kB] Get: 182 http://deb.debian.org/debian unstable/main i386 libthai-data all 0.1.29-2 [168 kB] Get: 183 http://deb.debian.org/debian unstable/main i386 libthai0 i386 0.1.29-2 [50.1 kB] Get: 184 http://deb.debian.org/debian unstable/main i386 libsombok3 i386 2.4.0-2+b1 [33.2 kB] Get: 185 http://deb.debian.org/debian unstable/main i386 libunicode-linebreak-perl i386 0.0.20190101-1+b6 [97.6 kB] Get: 186 http://deb.debian.org/debian unstable/main i386 libyaml-tiny-perl all 1.74-1 [30.7 kB] Get: 187 http://deb.debian.org/debian unstable/main i386 lmodern all 2.005-1 [9480 kB] Get: 188 http://deb.debian.org/debian unstable/main i386 texlive-latex-base all 2024.20240706-1 [1274 kB] Get: 189 http://deb.debian.org/debian unstable/main i386 texlive-luatex all 2024.20240706-1 [27.0 MB] Get: 190 http://deb.debian.org/debian unstable/main i386 texlive-plain-generic all 2024.20240706-2 [28.6 MB] Get: 191 http://deb.debian.org/debian unstable/main i386 texlive-extra-utils all 2024.20240706-2 [64.1 MB] Fetched 242 MB in 11s (21.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package m4. (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 ... 19712 files and directories currently installed.) Preparing to unpack .../00-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package flex. Preparing to unpack .../01-flex_2.6.4-8.2+b2_i386.deb ... Unpacking flex (2.6.4-8.2+b2) ... Selecting previously unselected package libfftw3-double3:i386. Preparing to unpack .../02-libfftw3-double3_3.3.10-1+b3_i386.deb ... Unpacking libfftw3-double3:i386 (3.3.10-1+b3) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../03-libexpat1_2.6.2-1_i386.deb ... Unpacking libexpat1:i386 (2.6.2-1) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../04-libbrotli1_1.1.0-2+b4_i386.deb ... Unpacking libbrotli1:i386 (1.1.0-2+b4) ... Selecting previously unselected package libpng16-16t64:i386. Preparing to unpack .../05-libpng16-16t64_1.6.43-5_i386.deb ... Unpacking libpng16-16t64:i386 (1.6.43-5) ... Selecting previously unselected package libfreetype6:i386. Preparing to unpack .../06-libfreetype6_2.13.2+dfsg-1+b4_i386.deb ... Unpacking libfreetype6:i386 (2.13.2+dfsg-1+b4) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../07-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. 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Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-4) ... Selecting previously unselected package libpython3.12-stdlib:i386. Preparing to unpack .../15-libpython3.12-stdlib_3.12.5-1_i386.deb ... Unpacking libpython3.12-stdlib:i386 (3.12.5-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.5-1_i386.deb ... Unpacking python3.12 (3.12.5-1) ... Selecting previously unselected package libpython3-stdlib:i386. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/wise-2.4.1/ && 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 > ../wise_2.4.1-25_source.changes dpkg-buildpackage: info: source package wise dpkg-buildpackage: info: source version 2.4.1-25 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/wise-2.4.1' /usr/bin/make -C src clean make[2]: Entering directory '/build/reproducible-path/wise-2.4.1/src' cd external ; /usr/bin/make clean make[3]: Entering directory '/build/reproducible-path/wise-2.4.1/src/external' (cd mott; make clean) make[4]: Entering directory '/build/reproducible-path/wise-2.4.1/src/external/mott' rm -f *.[oa] make[4]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/external/mott' make[3]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/external' if test -d dynlibsrc; then cd dynlibsrc ; rm -f *.[oa]; fi if test -d models; then cd models ; rm -f *.[oa]; fi if test -d base; then cd base ; rm -f *.[oa]; fi if test -d socket; then cd socket ; rm -f *.[oa]; fi if test -d dnaindex; then cd dnaindex ; rm -f *.[oa]; fi if test -d network; then cd network ; rm -f *.[oa]; fi if test -d dyc; then cd dyc ; rm -f *.[oa]; fi if test -d HMMer2; then cd HMMer2 ; rm -f *.[oa]; fi if test -d perl; then cd perl/Wise2/libs ; rm -f *.[oa]; fi if test -x perl/Wise2/Makefile; then cd perl/Wise2/ ; /usr/bin/make clean; fi if test -d oldbin; then rm -rf oldbin; fi if test -d bin; then echo 'moving binaries to oldbin'; mv -f bin oldbin; fi make[2]: Leaving directory '/build/reproducible-path/wise-2.4.1/src' /usr/bin/make -C debian/manpages.d clean make[2]: Entering directory '/build/reproducible-path/wise-2.4.1/debian/manpages.d' rm -f dba.1 dnal.1 estwise.1 estwisedb.1 genewise.1 genewisedb.1 genomewise.1 promoterwise.1 psw.1 pswdb.1 scanwise.1 scanwise_server.1 make[2]: Leaving directory '/build/reproducible-path/wise-2.4.1/debian/manpages.d' rm -f -r src/oldbin for i in dba psw dnal genomewise pswdb scanwise estwise genewise sywise genewisedb promoterwise pseudowise estwisedb; do rm -f src/models/$i; done rm -f src/network/scanwise_server rm -f docs/temp.tex rm -f docs/api.* rm -f docs/wise2.image.tex rm -f docs/*.pdf rm -f docs/*.aux rm -f docs/*.log rm -f docs/*.toc rm -f docs/*.pdf rm -f docs/*.dvi rm -f docs/*.ps rm -f docs/*.4ct rm -f docs/*.4tc rm -f docs/*.css rm -f docs/*.idv rm -f docs/*.lg rm -f docs/*.tmp rm -f docs/*.xref rm -f docs/*.haux rm -f docs/*.htoc rm -f docs/*.html rm -f -r docs/api rm -f -r docs/dynamite rm -f -r docs/wise2 dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/wise.substvars debian/wise-doc.substvars debian/wise-data.substvars debian/files rm -fr -- debian/wise/ debian/tmp/ debian/wise-doc/ debian/wise-data/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) make[1]: Leaving directory '/build/reproducible-path/wise-2.4.1' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/wise-2.4.1' # The dyc compiler is needed before building the all the rest. # Also, it pre-depends on the libwisebase library, otherwise # linking fails. dh_auto_build --sourcedirectory=src/base -- libwisebase.a cd src/base && make -j6 "INSTALL=install --strip-program=true" libwisebase.a make[2]: Entering directory '/build/reproducible-path/wise-2.4.1/src/base' cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wiseconfig.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wisestring.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wiseerror.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wisememman.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wisefile.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wiserandom.c wisefile.dy: In function ‘Wise2_myfclose’: wisefile.dy:72:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘FILE *’ [-Wformat=] 72 | fprintf(stderr,"Closing %d\n",ofp); | ^~~~~~~~~~~~~~ ~~~ | | | FILE * cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wisetime.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wiseoverlay.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wisestreaminterface.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread commandline.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread linesubs.c ar ru libwisebase.a wiseconfig.o wisestring.o wiseerror.o wisememman.o wisefile.o wiserandom.o wisetime.o wiseoverlay.o wisestreaminterface.o commandline.o linesubs.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libwisebase.a if test -x /bin/ranlib; then /bin/ranlib libwisebase.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisebase.a; else exit 0; fi make[2]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/base' dh_auto_build --sourcedirectory=src/dyc -- dyc cd src/dyc && make -j6 "INSTALL=install --strip-program=true" dyc make[2]: Entering directory '/build/reproducible-path/wise-2.4.1/src/dyc' cc -pthread -c -g -DUNIX -I../base/ -I../base/ dyc.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ dyna2.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ dynfile.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ wisec.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ dynafunc.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ module.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ type.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ method.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ dynadb.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ friend.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ inputfile.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ variable.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ modulefunc.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ api.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ display.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ dynashadow.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ labelmaster.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ ftext.c dynashadow.dy: In function ‘optimised_shadow_GenericMatrix’: dynashadow.dy:2180:31: warning: passing argument 2 of ‘write_main_shadow_block’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2180 | write_main_shadow_block(dfp,gm,"DC_OPT_SHADOW_MATRIX","mat","DC_OPT_SHADOW_SPECIAL","DC_OPT_SHADOW_MATRIX_SP","DC_OPT_SHADOW_SPECIAL_SP",7,TRUE,TRUE,0,TRUE); | ^~ In file included from dynashadow.c:4: dynashadow.h:163:60: note: expected ‘GenericMatrix *’ but argument is of type ‘const GenericMatrix *’ 163 | void write_main_shadow_block(DYNFILE * dfp,GenericMatrix * gm,char * matrixtag,char * pointer_tag,char * specialtag,char * shadow_main_tag,char * shadow_special_tag,int shadow_length,boolean shadow_on_special,boolean use_special,int debug,int use_shadow_pointer); | ~~~~~~~~~~~~~~~~^~ dynashadow.dy:2187:36: warning: passing argument 2 of ‘write_special_shadow_block’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2187 | write_special_shadow_block(dfp,gm,"DC_OPT_SHADOW_MATRIX","mat","DC_OPT_SHADOW_SPECIAL","DC_OPT_SHADOW_MATRIX_SP","DC_OPT_SHADOW_SPECIAL_SP",7,TRUE,0); | ^~ dynashadow.h:189:63: note: expected ‘GenericMatrix *’ but argument is of type ‘const GenericMatrix *’ 189 | void write_special_shadow_block(DYNFILE * dfp,GenericMatrix * gm,char * matrix,char * pointer_tag,char * special,char * shadow_main_tag,char * shadow_special_tag,int shadow_length,boolean shadow_on_special,int debug); | ~~~~~~~~~~~~~~~~^~ cc -pthread -c -g -DUNIX -I../base/ -I../base/ funcinfo.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ objectinfo.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ exprtree.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ compugen.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ docugen.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ input.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ dpimpl.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ dbthread.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ probal.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ telegraph.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ dynadebug.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ dyshatter.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ y.tab.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ lex.yy.c cc -o dyc dyc.o dyna2.o dynfile.o wisec.o dynafunc.o module.o type.o method.o dynadb.o friend.o inputfile.o variable.o modulefunc.o api.o display.o dynashadow.o labelmaster.o ftext.o funcinfo.o objectinfo.o exprtree.o compugen.o docugen.o input.o dpimpl.o dbthread.o probal.o telegraph.o dynadebug.o dyshatter.o y.tab.o lex.yy.o -ll -lwisebase -g -lm -L../base/ -lpthread make[2]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/dyc' PATH="$PATH:/build/reproducible-path/wise-2.4.1/src/dyc" \ dh_auto_build --sourcedirectory=src -- all cd src && make -j6 "INSTALL=install --strip-program=true" all make[2]: Entering directory '/build/reproducible-path/wise-2.4.1/src' (cd base ; make CC="cc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" libwisebase.a ) make[3]: Entering directory '/build/reproducible-path/wise-2.4.1/src/base' make[3]: 'libwisebase.a' is up to date. make[3]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/base' (cd HMMer2 ; make CC="cc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" libhmmer.a ) make[3]: Entering directory '/build/reproducible-path/wise-2.4.1/src/HMMer2' cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c alphabet.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c core_algorithms.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c debug.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c emit.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c emulation.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c histogram.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c hmmio.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c mathsupport.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c masks.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c misc.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c modelmakers.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c plan7.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c plan9.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c prior.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c tophits.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c trace.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c aligneval.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c alignio.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c cluster.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c dayhoff.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c file.c file.c: In function ‘EnvFileOpen’: file.c:159:26: warning: ‘%s’ directive writing up to 1022 bytes into a region of size between 1 and 1023 [-Wformat-overflow=] 159 | sprintf(full, "%s%c%s", s, DIRSLASH, fname); | ^~ In file included from /usr/include/stdio.h:980, from file.c:12: In function ‘sprintf’, inlined from ‘EnvFileOpen’ at file.c:159:7: /usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 2 and 2046 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c getopt.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c gnuregex.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c interleaved.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c iupac.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c msf.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c revcomp.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c selex.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c sqerror.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c sqio.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c sre_ctype.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c sre_math.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c sre_string.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c stack.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c translate.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c types.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c weight.c ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o emit.o emulation.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o prior.o tophits.o trace.o aligneval.o alignio.o cluster.o dayhoff.o file.o getopt.o gnuregex.o interleaved.o iupac.o msf.o revcomp.o selex.o sqerror.o sqio.o sre_ctype.o sre_math.o sre_string.o stack.o translate.o types.o weight.o a - alphabet.o a - core_algorithms.o a - debug.o a - emit.o a - emulation.o a - histogram.o a - hmmio.o a - mathsupport.o a - masks.o a - misc.o a - modelmakers.o a - plan7.o a - plan9.o a - prior.o a - tophits.o a - trace.o a - aligneval.o a - alignio.o a - cluster.o a - dayhoff.o a - file.o a - getopt.o a - gnuregex.o a - interleaved.o a - iupac.o a - msf.o a - revcomp.o a - selex.o a - sqerror.o a - sqio.o a - sre_ctype.o a - sre_math.o a - sre_string.o a - stack.o a - translate.o a - types.o a - weight.o if test -x /bin/ranlib; then /bin/ranlib libhmmer.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libhmmer.a; else exit 0; fi if test -x ranlib; then ranlib libhmmer.a; else exit 0; fi chmod 644 libhmmer.a make[3]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/HMMer2' (cd dynlibsrc ; make CC="cc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" libdyna.a ) make[3]: Entering directory '/build/reproducible-path/wise-2.4.1/src/dynlibsrc' cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ packaln.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ aln.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dnamatrix.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ probability.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ alnrange.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ alnconvert.c packaln.dy: In function ‘Wise2_read_simple_PackAln’: packaln.dy:88:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 88 | fgets(buffer,MAXLINE,ifp); | ^~~~~~~~~~~~~~~~~~~~~~~~~ aln.dy: In function ‘Wise2_mapped_ascii_AlnBlock’: aln.dy:867:19: warning: too many arguments for format [-Wformat-extra-args] 867 | fprintf(ofp," {%3.2f} ",(double)(*score_to_double)(cuml),cuml); | ^~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ basematrix.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ shattermatrix.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ matrixdebug.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dpenvelope.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dbsearchimpl.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dprunimpl.c matrixdebug.dy: In function ‘Wise2_user_DebugMatrix’: matrixdebug.dy:208:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 208 | fgets(buffer,MAXLINE,in); | ^~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ complexsequence.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ complexevalset.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ complexconsensi.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ sequence.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ sequencestream.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ seqalign.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hitlist.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hsp.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hspstream.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ codon.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ compmat.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ codonmatrix.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ codonmapper.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ sequencedb.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hscore.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ seqlookup.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ arrayseqlookup.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ genericindexresult.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ linkedlist_lookpos.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ singlenumberspace.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ histogram.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ searchstatinterface.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ searchstatlookup.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ proteindb.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ protein.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ pairbase.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ pairbaseseq.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ genomicdb.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ randommodel.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ randomdb.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ genomic.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ cdna.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ cdnadb.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dna.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ embl.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ genomicregion.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ gene.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ transcript.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ translation.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ btcanvas.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ asciibtcanvas.c genomicregion.dy: In function ‘Wise2_read_EMBL_FT_into_GenomicRegion’: genomicregion.dy:756:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 756 | fgets(buffer,maxlen,ifp); | ^~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dynlibcross.c ar ru libdyna.a packaln.o aln.o dnamatrix.o probability.o alnrange.o alnconvert.o basematrix.o shattermatrix.o matrixdebug.o dpenvelope.o dbsearchimpl.o dprunimpl.o complexsequence.o complexevalset.o complexconsensi.o sequence.o sequencestream.o seqalign.o hitlist.o hsp.o hspstream.o codon.o compmat.o codonmatrix.o codonmapper.o sequencedb.o hscore.o seqlookup.o arrayseqlookup.o genericindexresult.o linkedlist_lookpos.o singlenumberspace.o histogram.o searchstatinterface.o searchstatlookup.o proteindb.o protein.o pairbase.o pairbaseseq.o genomicdb.o randommodel.o randomdb.o genomic.o cdna.o cdnadb.o dna.o embl.o genomicregion.o gene.o transcript.o translation.o btcanvas.o asciibtcanvas.o dynlibcross.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libdyna.a if test -x /bin/ranlib; then /bin/ranlib libdyna.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna.a; else exit 0; fi make[3]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/dynlibsrc' (cd dynlibsrc ; make CC="cc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" libdyna_glib.a ) make[3]: Entering directory '/build/reproducible-path/wise-2.4.1/src/dynlibsrc' cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ subseqhash.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ intallocator.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ proteinstreamedindex.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ shadowseq.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ shadowseqindex.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hsphandler.c intallocator.dy: In function ‘Wise2_show_allocator_status_IntAllocator’: intallocator.dy:216:15: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘unsigned int’ [-Wformat=] 216 | fprintf(ofp,"%d blocks allocated, using %ld bytes\n",ia->current_allocated_block,ia->current_allocated_block * (sizeof(IntAllocatorHeader)+(sizeof(int)*ia->size)) * IntAllocator_BLOCKSIZE); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hspscaninterface.c shadowseqindex.dy: In function ‘Wise2_dump_stats_ShadowSequenceIndex’: shadowseqindex.dy:285:15: warning: format ‘%f’ expects argument of type ‘double’, but argument 4 has type ‘unsigned int’ [-Wformat=] 285 | fprintf(ofp,"Head memory %d [%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | unsigned int cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hsp2hitscan.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hsplookupscan.c hsp2hitscan.dy: In function ‘Wise2_one_off_two_hit_HSPscan_query_direct’: hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 210 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 210 | use.ru_utime.tv_sec, 211 | use.ru_utime.tv_sec/1000, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | long int hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 212 | use.ru_stime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘long int’ [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 213 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | long int hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 274 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 274 | use.ru_utime.tv_sec, 275 | use.ru_utime.tv_sec/1000, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | long int hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 276 | use.ru_stime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘long int’ [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 277 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | long int hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 287 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 287 | use.ru_utime.tv_sec, 288 | use.ru_utime.tv_sec/1000, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | long int hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 289 | use.ru_stime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘long int’ [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 290 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | long int hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 303 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 303 | use.ru_utime.tv_sec, 304 | use.ru_utime.tv_sec/1000, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | long int hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 305 | use.ru_stime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘long int’ [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 306 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | long int cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hsplookupthreaded.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hspthreadeddb.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hspscanruntime.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hsptwohitscan.c hspthreadeddb.dy: In function ‘Wise2_threadeddb_scan_worker’: hspthreadeddb.dy:154:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Wise2_HSPDatabaseSegment *’ [-Wformat=] 154 | fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ | | | Wise2_HSPDatabaseSegment * hsplookupthreaded.dy: In function ‘Wise2_one_off_ordered_HSPscan_scan_query_direct’: hsplookupthreaded.dy:263:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] 263 | fprintf(stderr,"retrieved array with %d elements\n",current_oph); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ | | | long int cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ proteinindexcons.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dnaindexcons.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ staticseq.c ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o hsplookupscan.o hsplookupthreaded.o hspthreadeddb.o hspscanruntime.o hsptwohitscan.o proteinindexcons.o dnaindexcons.o staticseq.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libdyna_glib.a if test -x /bin/ranlib; then /bin/ranlib libdyna_glib.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna_glib.a; else exit 0; fi make[3]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/dynlibsrc' (cd external ; make CC="cc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" all ) make[3]: Entering directory '/build/reproducible-path/wise-2.4.1/src/external' (cd mott; make CC="cc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread " all) make[4]: Entering directory '/build/reproducible-path/wise-2.4.1/src/external/mott' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mott_api.o mott_api.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gaplib.o gaplib.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../../dynlibsrc -I../../base wise2_mott_bridge.c ar ru libmott.a mott_api.o gaplib.o wise2_mott_bridge.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libmott.a if test -x /bin/ranlib; then /bin/ranlib libmott.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libmott.a; else exit 0; fi make[4]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/external/mott' make[3]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/external' (cd socket ; make CC="cc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" libwisesocket.a ) make[3]: Entering directory '/build/reproducible-path/wise-2.4.1/src/socket' cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ functionserver.c dyc -l -n Wise2_ -a _api.h -b _api.t -latex -perl functionclient.dy Warning Error Could not open [methods] for MethodTypeSet reading Warning Error You have no config file called 'methods'. This is bad news for dynamite matrices. I will attempt to compile, but you cannot use logical types. 'methods' should be either in the current directory, the $WISECONFIGDIR or your $WISEPERSONALDIR Warning Error You have 3 undocumented functions cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ anonobj.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ transferinterface.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ directsocketwrite.c functionserver.dy: In function ‘Wise2_main_loop_forking_FunctionServer’: functionserver.dy:129:11: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 129 | write(new_socket,buf,9); | ^~~~~~~~~~~~~~~~~~~~~~~ functionserver.dy:141:9: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 141 | write(new_socket,buf,6); | ^~~~~~~~~~~~~~~~~~~~~~~ functionserver.dy:183:9: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 183 | write(new_socket,buf,5); | ^~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ functionclient.c ar ru libwisesocket.a functionserver.o functionclient.o anonobj.o transferinterface.o directsocketwrite.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libwisesocket.a if test -x /bin/ranlib; then /bin/ranlib libwisesocket.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisesocket.a; else exit 0; fi make[3]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/socket' (cd dnaindex ; make CC="cc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" all ) make[3]: Entering directory '/build/reproducible-path/wise-2.4.1/src/dnaindex' cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_hash.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_count.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c kmer_assembly.dy: In function ‘Wise2_show_KmerAssemblyNode’: kmer_assembly.dy:296:15: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 296 | fprintf(ofp,"Node %ld of sequence %s \n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly.dy:302:17: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 302 | fprintf(ofp," ... prev ... %c, %d to %ld\n",node->prev[i]->base,node->prev[i]->sequence_label_len,node->prev[i]->prev->number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly.dy:309:17: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 309 | fprintf(ofp," ... next ... %c, %d to %ld\n",node->next[i]->base,node->next[i]->sequence_label_len,node->next[i]->next->number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly.dy: In function ‘Wise2_remove_sequence_label_KmerAssemblyLink’: kmer_assembly.dy:365:18: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘KmerAssemblyLink *’ [-Wformat=] 365 | fprintf(stderr," ...unable to remove label %ld from link %ld (%d labels)\n",label,kal,kal->sequence_label_len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ | | | KmerAssemblyLink * kmer_assembly.dy:367:20: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 367 | fprintf(stderr," [%ld] is %d label\n",kal->sequence_label[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c kmer_hash.dy: In function ‘Wise2_free_KmerHashIndex’: kmer_hash.dy:318:19: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 318 | fprintf(stderr, "min_kmer: %016lx\n", khi->min_kmer); | ^~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_hash.dy:319:19: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 319 | fprintf(stderr, "max_kmer: %016lx\n", khi->max_kmer); | ^~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_glib_index.dy: In function ‘Wise2_retrieve_by_kmer_KmerGlibIndex’: kmer_glib_index.dy:77:48: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 77 | return (void*) g_hash_table_lookup(kgi->hash,(gconstpointer)kmer); | ^ kmer_glib_index.dy: In function ‘Wise2_insert_by_kmer_KmerGlibIndex’: kmer_glib_index.dy:84:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 84 | g_hash_table_insert(kgi->hash,(gpointer)kmer,poi); | ^ kmer_glib_index.dy: In function ‘Wise2_retrieve_active_kmer_KmerGlibIndex’: kmer_glib_index.dy:124:40: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 124 | kgi->active_index[kgi->kmer_pos++] = (kmer_t) key; | ^ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models dnamapping.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c dyc -l -n Wise2_ -pthreads -dbtrace 5 -nocwarn kmer_assembly_untangler.dy Warning Error Could not open [methods] for MethodTypeSet reading Warning Error You have no config file called 'methods'. This is bad news for dynamite matrices. I will attempt to compile, but you cannot use logical types. 'methods' should be either in the current directory, the $WISECONFIGDIR or your $WISEPERSONALDIR Warning Error kmer_assembly_untangler.dy:24: For element long - got no good default. Returning 0 Warning Error You have 14 undocumented functions cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c kmer_assembly_error.dy: In function ‘Wise2_mark_tangles_KmerAssembly’: kmer_assembly_error.dy:93:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 93 | fprintf(stderr,"Marking node (%ld) [%s] as next tangled\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_error.dy:105:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 105 | fprintf(stderr,"Marking node (%ld) [%s] as prev tangled\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_error.dy: In function ‘Wise2_extend_indel_path_KmerAssembly’: kmer_assembly_error.dy:351:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int *’ [-Wformat=] 351 | fprintf(stderr,"in considering indel (%d, path %d), real (%c) and error (%c) do not agree at position %d,%d\n",delete_length,current_path,real->base,error->base,real_pos,error_pos); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | int * cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c dyc -l -n Wise2_ -pthreads -dbtrace 5 -nocwarn compressed_protein_index.dy Warning Error Could not open [methods] for MethodTypeSet reading Warning Error You have no config file called 'methods'. This is bad news for dynamite matrices. I will attempt to compile, but you cannot use logical types. 'methods' should be either in the current directory, the $WISECONFIGDIR or your $WISEPERSONALDIR Warning Error You have 16 undocumented functions cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c kmer_assembly_untangler.dy: In function ‘Wise2_untangle_KmerAssembly’: kmer_assembly_untangler.dy:120:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 120 | fprintf(stderr,"TANGLE: Node %ld, %s has forward %d and back %d links\n",node->number,buffer,node->next_len,node->prev_len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:141:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 141 | fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:141:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 141 | fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:157:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 157 | fprintf(stderr,"RESOLVED: Node %ld [%s] Fully untangled now...\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:159:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 159 | fprintf(stderr,"UNRESOLVED: Node %ld [%s] still tangled...\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy: In function ‘Wise2_old_attempt_forward_untangle_KmerAssembly’: kmer_assembly_untangler.dy:444:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 444 | fprintf(stderr,"looking at node %ld with path length %d, next length %d depth %d\n",current->next->number,pathlen,current->next->next_len,current->sequence_label_len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy: In function ‘Wise2_lift_forward_tangled_KmerAssemblyPath’: kmer_assembly_untangler.dy:753:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 6 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 753 | fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:753:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 8 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 753 | fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} make[3]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/dnaindex' (cd network ; make CC="cc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" all ) make[3]: Entering directory '/build/reproducible-path/wise-2.4.1/src/network' cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../socket -I../dynlibsrc -I../dnaindex wise_proteinindex_server.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../socket -I../dynlibsrc -I../dnaindex client_multihspscan.c wise_proteinindex_server.c: In function ‘show_version’: wise_proteinindex_server.c:28:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 28 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ cc -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase -Wl,-z,relro -Wl,-z,now -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0` -lpthread make[3]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/network' (cd models ; make CC="cc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" EXTRALIBS="-lm" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all ) make[3]: Entering directory '/build/reproducible-path/wise-2.4.1/src/models' cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ dnal.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ dnaalign.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ seqaligndisplay.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ psw.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ proteinsw.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ sw_wrap.c dnal.c: In function ‘show_version’: dnal.c:106:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 106 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ psw.c: In function ‘show_version’: psw.c:261:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 261 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ abc.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pba.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pswdb.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ dbac.c pswdb.c: In function ‘show_version’: pswdb.c:97:106: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 97 | fprintf(stdout,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ dbac.c: In function ‘show_version’: dbac.c:364:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 364 | fprintf(ofp," Compiled %s\n",COMPILE_DATE); | ^~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ dba.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ slimdba.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ bigdba.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ dbadisplay.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. estwise.c: In function ‘show_version’: estwise.c:559:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 559 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneparser21.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneparameter.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genestats.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewisehsp.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneutil.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneoutput.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ threestatemodel.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genefrequency.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ splicesitemodeler.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewise4.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewise6.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genestretch6.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewise21.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneloop21.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneloop6.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genephase6.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ gwlite.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ gwlitemodel.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ gwrap.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ matchsum.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estwrap.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewisemodel.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ phasemodel.c phasemodel.dy: In function ‘Wise2_read_fasta_PhasedProtein’: phasemodel.dy:241:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fgets(name,10000,ifp); | ^~~~~~~~~~~~~~~~~~~~~ phasemodel.dy:241:3: warning: ‘fgets’ writing 10000 bytes into a region of size 2000 overflows the destination [-Wstringop-overflow=] 241 | fgets(name,10000,ifp); | ^~~~~~~~~~~~~~~~~~~~~ phasemodel.dy:235:8: note: destination object ‘name’ of size 2000 235 | char name[2000]; | ^~~~ In file included from /usr/include/stdio.h:980, from ../base/wisebase.h:6, from ../dynlibsrc/probability.h:7, from geneparser21.h:6, from genewisemodel.h:6, from phasemodel.h:6, from phasemodel.c:4: /usr/include/i386-linux-gnu/bits/stdio2.h:196:1: note: in a call to function ‘fgets’ declared with attribute ‘access (write_only, 1, 2)’ 196 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream) | ^~~~~ In function ‘fgets’, inlined from ‘Wise2_read_fasta_PhasedProtein’ at phasemodel.dy:241:3: /usr/include/i386-linux-gnu/bits/stdio2.h:202:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 202 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ cdparser.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genedisplay.c genedisplay.dy: In function ‘Wise2_write_intron_desc’: genedisplay.dy:493:20: warning: too many arguments for format [-Wformat-extra-args] 493 | sprintf(buffer," Intron ??? ",in_number); | ^~~~~~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estwise3.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estslim3.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estloop3.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estfrag3.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estslimloop.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ gwquickdb.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ threestatedb.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pfamhmmer1db.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pwmdna.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewisemodeldb.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ seqhit.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ standardout.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneparser4.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estquick3.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread genewise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ genewise.c: In function ‘show_version’: genewise.c:860:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 860 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genomewise.c genewisedb.c: In function ‘show_version’: genewisedb.c:1005:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1005 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ genomewise.c: In function ‘show_version’: genomewise.c:18:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 18 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ estwisedb.c: In function ‘show_version’: estwisedb.c:838:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 838 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genomewise9.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genome_evidence.c dyc -l -D -n Wise2_ -a _api.h -b _api.t -latex -perl -pthreads -dbtrace 5 -nocwarn est_evidence.dy Warning Error Could not open [methods] for MethodTypeSet reading Warning Error You have no config file called 'methods'. This is bad news for dynamite matrices. I will attempt to compile, but you cannot use logical types. 'methods' should be either in the current directory, the $WISECONFIGDIR or your $WISEPERSONALDIR Warning Error You have not documented indicate_intron_used Warning Error You have not documented read_est_evidence Warning Error You have not documented new_est_GenomeEvidenceUnit Warning Error You have not documented est_utr5_start Warning Error You have not documented est_utr3_end Warning Error You have not documented est_start_pot Warning Error You have not documented est_stop_pot Warning Error You have not documented est_cds_frameshift Warning Error You have not documented est_cds_3SS Warning Error You have not documented est_cds_5SS Warning Error You have not documented est_intron_pot Warning Error You have not documented est_cds_pot Warning Error You have not documented est_3ss Warning Error You have not documented est_5ss Warning Error You have not documented est_utr_pot Warning Error You have 15 undocumented functions cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ sywise.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ sywise20.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ syexonmodel.c sywise.c: In function ‘show_version’: sywise.c:14:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 14 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pseudowise.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pseudowise7.c pseudowise.c: In function ‘show_version’: pseudowise.c:15:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 15 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` promoterwise.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ localdba.c promoterwise.c: In function ‘show_version’: promoterwise.c:17:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 17 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` localcishit.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ localcispara.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ motifmatrix.c motifmatrix.c: In function ‘Wise2_MotifConsMatrix_alloc_matrix’: motifmatrix.c:408:24: warning: assignment to ‘char’ from ‘void *’ makes integer from pointer without a cast [-Wint-conversion] 408 | for(i=0;i dba.1 docbook-to-man dnal.sgml > dnal.1 docbook-to-man estwise.sgml > estwise.1 docbook-to-man estwisedb.sgml > estwisedb.1 docbook-to-man genewise.sgml > genewise.1 docbook-to-man genewisedb.sgml > genewisedb.1 docbook-to-man genomewise.sgml > genomewise.1 docbook-to-man promoterwise.sgml > promoterwise.1 docbook-to-man psw.sgml > psw.1 docbook-to-man pswdb.sgml > pswdb.1 docbook-to-man scanwise.sgml > scanwise.1 docbook-to-man scanwise_server.sgml > scanwise_server.1 make[2]: Leaving directory '/build/reproducible-path/wise-2.4.1/debian/manpages.d' find src/models/ src/dynlibsrc/ -name '*.tex' -print0 | LC_ALL=C sort -z | xargs -0 cat | perl docs/gettex.pl > docs/temp.tex cat docs/wise2api.tex docs/temp.tex docs/apiend.tex > docs/api.tex sed -i 's/ sw_wrap / sw\\_wrap /' docs/api.tex sed -i 's/label{module_sequence\\_codon}/label{module_sequence_codon}/' docs/api.tex sed -i 's/Wise2::GeneParameter21_wrap/Wise2::GeneParameter21\\_wrap/' docs/api.tex cd docs && pdflatex api.tex This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./api.tex LaTeX2e <2024-06-01> patch level 2 L3 programming layer <2024-05-27> (/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def Entering LaTeX 2.09 COMPATIBILITY MODE ************************************************************* !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! This mode attempts to provide an emulation of the LaTeX 2.09 author environment so that OLD documents can be successfully processed. It should NOT be used for NEW documents! New documents should use Standard LaTeX conventions and start with the \documentclass command. Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style files that change any internal macros, especially not with those that change the FONT SELECTION or OUTPUT ROUTINES. Therefore such style files MUST BE UPDATED to use Current Standard LaTeX: LaTeX2e. If you suspect that you may be using such a style file, which is probably very, very old by now, then you should attempt to get it updated by sending a copy of this error message to the author of that file. ************************************************************* (/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2024/02/08 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file api.aux. (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] No file api.toc. [2] [3] Overfull \hbox (1.49698pt too wide) in paragraph at lines 109--109 [] \OT1/cmtt/m/n/10 print "You must give a file to revcom for a reverse to w ork!";[] [4] [5] LaTeX Warning: Reference `object_CodonTable' on page 6 undefined on input line 198. LaTeX Warning: Reference `object_Sequence' on page 6 undefined on input line 19 9. LaTeX Warning: Reference `object_CompMat' on page 6 undefined on input line 205 . LaTeX Warning: Reference `object_Sequence' on page 6 undefined on input line 20 6. LaTeX Warning: Reference `object_Protein' on page 6 undefined on input line 207 . LaTeX Warning: Reference `object_CompMat' on page 6 undefined on input line 208 . LaTeX Warning: Reference `module_sw_wrap' on page 6 undefined on input line 209 . LaTeX Warning: Reference `module_seqaligndisplay' on page 6 undefined on input line 210. LaTeX Warning: Reference `object_Protein' on page 6 undefined on input line 215 . LaTeX Warning: Reference `object_Sequence' on page 6 undefined on input line 21 5. [6] LaTeX Warning: Reference `object_ProteinDB' on page 7 undefined on input line 2 16. LaTeX Warning: Reference `object_ProteinDB' on page 7 undefined on input line 2 17. LaTeX Warning: Reference `module_sw_wrap' on page 7 undefined on input line 218 . LaTeX Warning: Reference `object_Hscore' on page 7 undefined on input line 219. LaTeX Warning: Reference `object_DataEntry' on page 7 undefined on input line 2 21. LaTeX Warning: Reference `object_ProteinDB' on page 7 undefined on input line 2 21. LaTeX Warning: Reference `object_Sequence' on page 7 undefined on input line 22 8. LaTeX Warning: Reference `object_Protein' on page 7 undefined on input line 229 . LaTeX Warning: Reference `object_Sequence' on page 7 undefined on input line 23 0. LaTeX Warning: Reference `object_Genomic' on page 7 undefined on input line 231 . LaTeX Warning: Reference `object_GeneFrequency' on page 7 undefined on input li ne 233. LaTeX Warning: Reference `object_CodonTable' on page 7 undefined on input line 234. LaTeX Warning: Reference `object_RandomModelDNA' on page 7 undefined on input l ine 235. LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 236. LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 237. Overfull \hbox (21.30891pt too wide) in paragraph at lines 237--238 []\OT1/cmr/m/n/10 Build an en-tire pa-ram-e-ter set for ge-newise us-ing Wise2: :GeneParameter21[]wrap LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 238. LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 239. [7] [8] [9] LaTeX Warning: Reference `module_gwrap' on page 10 undefined on input line 389. [10] LaTeX Warning: Reference `module_estwrap' on page 11 undefined on input line 39 1. LaTeX Warning: Reference `module_sw_wrap' on page 11 undefined on input line 39 3. LaTeX Warning: Reference `module_genedisplay' on page 11 undefined on input lin e 395. LaTeX Warning: Reference `module_seqaligndisplay' on page 11 undefined on input line 397. LaTeX Warning: Reference `module_threestatemodel' on page 11 undefined on input line 399. LaTeX Warning: Reference `module_threestatedb' on page 11 undefined on input li ne 400. LaTeX Warning: Reference `module_genefrequency' on page 11 undefined on input l ine 401. LaTeX Warning: Reference `module_geneparameter' on page 11 undefined on input l ine 402. LaTeX Warning: Reference `module_cdparser' on page 11 undefined on input line 4 03. LaTeX Warning: Reference `module_sequence' on page 11 undefined on input line 4 10. LaTeX Warning: Reference `module_sequencedb' on page 11 undefined on input line 411. LaTeX Warning: Reference `module_protein' on page 11 undefined on input line 41 2. LaTeX Warning: Reference `module_proteindb' on page 11 undefined on input line 413. LaTeX Warning: Reference `module_genomic' on page 11 undefined on input line 41 4. LaTeX Warning: Reference `module_genomicdb' on page 11 undefined on input line 415. LaTeX Warning: Reference `module_cdna' on page 11 undefined on input line 416. LaTeX Warning: Reference `module_cdnadb' on page 11 undefined on input line 417 . LaTeX Warning: Reference `module_probability' on page 11 undefined on input lin e 423. LaTeX Warning: Reference `module_codon' on page 11 undefined on input line 424. LaTeX Warning: Reference `module_compmat' on page 11 undefined on input line 42 5. LaTeX Warning: Reference `module_codonmat' on page 11 undefined on input line 4 26. LaTeX Warning: Reference `module_codonmapper' on page 11 undefined on input lin e 427. [11] LaTeX Warning: Reference `module_hscore' on page 12 undefined on input line 433 . LaTeX Warning: Reference `module_histogram' on page 12 undefined on input line 434. LaTeX Warning: Reference `module_dbimpl' on page 12 undefined on input line 435 . LaTeX Warning: Reference `module_aln' on page 12 undefined on input line 441. LaTeX Warning: Reference `module_packaln' on page 12 undefined on input line 44 2. LaTeX Warning: Reference `module_basematrix' on page 12 undefined on input line 443. LaTeX Warning: Reference `object_AlnBlock' on page 12 undefined on input line 4 51. LaTeX Warning: Reference `object_AlnColumn' on page 12 undefined on input line 453. LaTeX Warning: Reference `object_AlnUnit' on page 12 undefined on input line 45 5. LaTeX Warning: Reference `object_AlnSequence' on page 12 undefined on input lin e 457. LaTeX Warning: Reference `accessing_fields' on page 12 undefined on input line 464. Overfull \hbox (6.8248pt too wide) in paragraph at lines 475--482 \OT1/cmr/m/n/10 AlnBlock is the main rep-re-sen-ta-tion of align-ments from Dy- na-mite. Each AlnBlock [12] (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) LaTeX Warning: Reference `accessing_fields' on page 13 undefined on input line 513. [13] LaTeX Warning: Reference `accessing_fields' on page 14 undefined on input line 555. [14] LaTeX Warning: Reference `accessing_fields' on page 15 undefined on input line 623. [15] LaTeX Warning: Reference `object_AlnRange' on page 16 undefined on input line 6 52. LaTeX Warning: Reference `object_AlnRangeSet' on page 16 undefined on input lin e 654. LaTeX Warning: Reference `accessing_fields' on page 16 undefined on input line 661. LaTeX Warning: Reference `accessing_fields' on page 16 undefined on input line 688. [16] LaTeX Warning: Reference `object_cDNA' on page 17 undefined on input line 741. LaTeX Warning: Reference `accessing_fields' on page 17 undefined on input line 748. [17] [18] [19] LaTeX Warning: Reference `object_cDNADB' on page 20 undefined on input line 884 . LaTeX Warning: Reference `accessing_fields' on page 20 undefined on input line 924. [20] LaTeX Warning: Reference `object_CodonTable' on page 21 undefined on input line 1005. [21] [22] [23] [24] LaTeX Warning: Reference `accessing_fields' on page 25 undefined on input line 1213. [25] [26] [27] LaTeX Warning: Reference `object_CodonMapper' on page 28 undefined on input lin e 1363. LaTeX Warning: Reference `accessing_fields' on page 28 undefined on input line 1391. [28] Overfull \hbox (12.33003pt too wide) in paragraph at lines 1418--1419 []\OT1/cmtt/m/n/10 &Wise2::CodonMapper::sprinkle[]errors[]over[]CodonMapper (cm ,error) LaTeX Warning: Reference `object_ComplexSequence' on page 29 undefined on input line 1442. LaTeX Warning: Reference `object_ComplexSequenceEvalSet' on page 29 undefined o n input line 1444. LaTeX Warning: Reference `accessing_fields' on page 29 undefined on input line 1451. [29] LaTeX Warning: Reference `accessing_fields' on page 30 undefined on input line 1482. LaTeX Warning: Reference `object_CompMat' on page 30 undefined on input line 15 17. LaTeX Warning: Reference `accessing_fields' on page 30 undefined on input line 1524. [30] [31] LaTeX Warning: Reference `object_DBSearchImpl' on page 32 undefined on input li ne 1624. [32] LaTeX Warning: Reference `accessing_fields' on page 33 undefined on input line 1671. [33] LaTeX Warning: Reference `object_DnaMatrix' on page 34 undefined on input line 1736. LaTeX Warning: Reference `object_DnaProbMatrix' on page 34 undefined on input l ine 1738. [34] LaTeX Warning: Reference `accessing_fields' on page 35 undefined on input line 1799. LaTeX Warning: Reference `accessing_fields' on page 35 undefined on input line 1812. [35] LaTeX Warning: Reference `object_Gene' on page 36 undefined on input line 1844. LaTeX Warning: Reference `accessing_fields' on page 36 undefined on input line 1851. [36] [37] LaTeX Warning: Reference `object_Genomic' on page 38 undefined on input line 19 48. LaTeX Warning: Reference `object_GenomicRepeat' on page 38 undefined on input l ine 1950. [38] Overfull \hbox (0.5938pt too wide) in paragraph at lines 1989--1990 []\OT1/cmtt/m/n/10 Wise2[]Genomic[]from[]Sequence[]Nheuristic (seq,length[]of[] N) LaTeX Warning: Reference `accessing_fields' on page 39 undefined on input line 2038. [39] [40] LaTeX Warning: Reference `accessing_fields' on page 41 undefined on input line 2150. [41] LaTeX Warning: Reference `object_GenomicDB' on page 42 undefined on input line 2168. Overfull \hbox (65.9032pt too wide) in paragraph at lines 2175--2176 []\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB[]from[]single[]seq (gen,cses,score[]in []repeat[]coding) Overfull \hbox (43.1997pt too wide) in paragraph at lines 2176--2177 []\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB[]from[]single[]seq (gen,cses,score[]i n[]repeat[]coding) Overfull \hbox (41.12343pt too wide) in paragraph at lines 2192--2193 []\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[] cds[]score) Overfull \hbox (18.41994pt too wide) in paragraph at lines 2193--2194 []\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[ ]cds[]score) [42] LaTeX Warning: Reference `accessing_fields' on page 43 undefined on input line 2213. [43] LaTeX Warning: Reference `object_GenomicRegion' on page 44 undefined on input l ine 2298. LaTeX Warning: Reference `accessing_fields' on page 44 undefined on input line 2305. [44] Overfull \hbox (1.83012pt too wide) in paragraph at lines 2348--2349 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::read[]EMBL[]GenomicRegion[]file (file name) [45] Overfull \hbox (7.08008pt too wide) in paragraph at lines 2401--2402 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]ace[]GenomicRegion (gr,seq[]nam e,ofp) Overfull \hbox (3.5338pt too wide) in paragraph at lines 2426--2427 []\OT1/cmtt/m/n/10 Wise2[]show[]pretty[]GenomicRegion (gr,show[]supporting,ofp) Overfull \hbox (59.57962pt too wide) in paragraph at lines 2427--2428 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]pretty[]GenomicRegion (gr,show[ ]supporting,ofp) [46] [47] LaTeX Warning: Reference `object_Histogram' on page 48 undefined on input line 2505. [48] LaTeX Warning: Reference `accessing_fields' on page 49 undefined on input line 2553. Overfull \hbox (32.9967pt too wide) in paragraph at lines 2592--2592 [] \OT1/cmtt/m/n/10 b) cooperation with future versions of histogram.c would be possible.[] [49] [50] [51] Overfull \hbox (123.4428pt too wide) in paragraph at lines 2794--2795 []\OT1/cmtt/m/n/10 Wise2[]ExtremeValueSetHistogram (h,mu,lambda,lowbound,highbo und,wonka,ndegrees) Overfull \hbox (67.76958pt too wide) in paragraph at lines 2795--2796 []\OT1/cmtt/m/n/10 &Wise2::Histogram::set[]EVD (h,mu,lambda,lowbound,highbound, wonka,ndegrees) Overfull \hbox (33.66461pt too wide) in paragraph at lines 2797--2798 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->set[]EVD(mu,lambda,lowbound,highbound ,wonka,ndegrees) [52] [53] [54] LaTeX Warning: Reference `object_Hscore' on page 55 undefined on input line 293 0. LaTeX Warning: Reference `object_DataScore' on page 55 undefined on input line 2932. LaTeX Warning: Reference `object_DataEntry' on page 55 undefined on input line 2934. LaTeX Warning: Reference `accessing_fields' on page 55 undefined on input line 2961. Overfull \hbox (30.97293pt too wide) in paragraph at lines 2971--2972 []\OT1/cmr/m/n/10 should[]store Type [boolean (*should[]store)(int given[]score ,double in-ter-nal[]score[]level) [55] [56] [57] LaTeX Warning: Reference `accessing_fields' on page 58 undefined on input line 3162. [58] LaTeX Warning: Reference `accessing_fields' on page 59 undefined on input line 3188. LaTeX Warning: Reference `object_PackAln' on page 59 undefined on input line 32 29. [59] LaTeX Warning: Reference `object_PackAlnUnit' on page 60 undefined on input lin e 3231. LaTeX Warning: Reference `accessing_fields' on page 60 undefined on input line 3238. [60] LaTeX Warning: Reference `accessing_fields' on page 61 undefined on input line 3308. [61] [62] LaTeX Warning: Reference `object_Protein' on page 63 undefined on input line 34 31. LaTeX Warning: Reference `accessing_fields' on page 63 undefined on input line 3438. [63] LaTeX Warning: Reference `object_ProteinDB' on page 64 undefined on input line 3488. LaTeX Warning: Reference `accessing_fields' on page 64 undefined on input line 3545. [64] LaTeX Warning: Reference `object_RandomProteinDB' on page 65 undefined on input line 3590. LaTeX Warning: Reference `object_RandomDNADB' on page 65 undefined on input lin e 3592. LaTeX Warning: Reference `accessing_fields' on page 65 undefined on input line 3599. LaTeX Warning: Reference `accessing_fields' on page 65 undefined on input line 3620. [65] LaTeX Warning: Reference `object_RandomModelDNA' on page 66 undefined on input line 3642. LaTeX Warning: Reference `object_RandomModel' on page 66 undefined on input lin e 3644. LaTeX Warning: Reference `accessing_fields' on page 66 undefined on input line 3682. [66] LaTeX Warning: Reference `accessing_fields' on page 67 undefined on input line 3697. LaTeX Warning: Reference `object_Sequence' on page 67 undefined on input line 3 713. LaTeX Warning: Reference `object_SequenceSet' on page 67 undefined on input lin e 3715. [67] LaTeX Warning: Reference `accessing_fields' on page 68 undefined on input line 3779. [68] Overfull \hbox (16.34366pt too wide) in paragraph at lines 3839--3840 []\OT1/cmtt/m/n/10 Wise2[]force[]to[]dna[]Sequence (seq,fraction,number[]of[]co nver) [69] [70] [71] [72] [73] [74] LaTeX Warning: Reference `accessing_fields' on page 75 undefined on input line 4176. [75] [76] LaTeX Warning: Reference `object_SequenceDB' on page 77 undefined on input line 4265. LaTeX Warning: Reference `object_FileSource' on page 77 undefined on input line 4267. LaTeX Warning: Reference `accessing_fields' on page 77 undefined on input line 4294. [77] LaTeX Warning: Reference `accessing_fields' on page 78 undefined on input line 4355. LaTeX Warning: Reference `object_Exon' on page 78 undefined on input line 4381. LaTeX Warning: Reference `object_Transcript' on page 78 undefined on input line 4383. [78] LaTeX Warning: Reference `accessing_fields' on page 79 undefined on input line 4390. LaTeX Warning: Reference `accessing_fields' on page 79 undefined on input line 4413. [79] LaTeX Warning: Reference `object_Translation' on page 80 undefined on input lin e 4482. LaTeX Warning: Reference `accessing_fields' on page 80 undefined on input line 4489. Overfull \hbox (24.01358pt too wide) in paragraph at lines 4508--4515 \OT1/cmr/m/n/10 have any se-quence in it. When se-quence is asked for by get[]P rotein[]from[]Translation() [80] LaTeX Warning: Reference `object_cDNAParser' on page 81 undefined on input line 4549. [81] LaTeX Warning: Reference `accessing_fields' on page 82 undefined on input line 4579. LaTeX Warning: Reference `object_DnaStartEnd' on page 82 undefined on input lin e 4602. Overfull \hbox (62.7533pt too wide) in paragraph at lines 4609--4610 []\OT1/cmtt/m/n/10 Wise2[]make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap, text,dpri) Overfull \hbox (40.0498pt too wide) in paragraph at lines 4610--4611 []\OT1/cmtt/m/n/10 &Wise2::make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap ,text,dpri) [82] LaTeX Warning: Reference `accessing_fields' on page 83 undefined on input line 4655. Overfull \hbox (335.96082pt too wide) in paragraph at lines 4671--4672 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]sy n,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) Overfull \hbox (313.25732pt too wide) in paragraph at lines 4672--4673 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]s yn,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) [83] Overfull \hbox (329.87091pt too wide) in paragraph at lines 4698--4699 []\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp,c m,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri,palpoi) Overfull \hbox (270.41774pt too wide) in paragraph at lines 4699--4700 []\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp, cm,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri) [84] Overfull \hbox (265.40146pt too wide) in paragraph at lines 4732--4733 []\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,ct ,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri,palpoi) Overfull \hbox (205.94829pt too wide) in paragraph at lines 4733--4734 []\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,c t,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri) [85] Overfull \hbox (47.00343pt too wide) in paragraph at lines 4780--4781 []\OT1/cmtt/m/n/10 Wise2[]protein2genomic[]ascii[]display (alb,p,gen,ct,name,ma in,ofp) Overfull \hbox (24.29994pt too wide) in paragraph at lines 4781--4782 []\OT1/cmtt/m/n/10 &Wise2::protein2genomic[]ascii[]display (alb,p,gen,ct,name,m ain,ofp) [86] Overfull \hbox (188.7522pt too wide) in paragraph at lines 4801--4802 []\OT1/cmtt/m/n/10 Wise2[]protcdna[]ascii[]display (alb,protsequence,protname,p rotoff,cdna,ct,name,main,mult,ofp) Overfull \hbox (166.0487pt too wide) in paragraph at lines 4802--4803 []\OT1/cmtt/m/n/10 &Wise2::protcdna[]ascii[]display (alb,protsequence,protname, protoff,cdna,ct,name,main,mult,ofp) LaTeX Warning: Reference `object_GeneFrequency21' on page 87 undefined on input line 4830. LaTeX Warning: Reference `object_GeneConsensus' on page 87 undefined on input l ine 4832. LaTeX Warning: Reference `object_GeneSingleCons' on page 87 undefined on input line 4834. [87] LaTeX Warning: Reference `accessing_fields' on page 88 undefined on input line 4879. Overfull \hbox (1.40793pt too wide) in paragraph at lines 4893--4894 []\OT1/cmr/m/n/10 transition[GENEFREQUENCY21[]TRANSITION[]LEN] Type [dou-ble : Scalar] LaTeX Warning: Reference `accessing_fields' on page 88 undefined on input line 4906. [88] LaTeX Warning: Reference `accessing_fields' on page 89 undefined on input line 4921. LaTeX Warning: Reference `object_GeneParameter21' on page 89 undefined on input line 4937. LaTeX Warning: Reference `accessing_fields' on page 89 undefined on input line 4944. [89] LaTeX Warning: Reference `object_MatchSummarySet' on page 90 undefined on input line 4990. LaTeX Warning: Reference `object_MatchSummary' on page 90 undefined on input li ne 4992. LaTeX Warning: Reference `accessing_fields' on page 90 undefined on input line 4999. Overfull \hbox (71.7832pt too wide) in paragraph at lines 5014--5015 []\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]estwise (alb,qname,o ffset,target) Overfull \hbox (1.83012pt too wide) in paragraph at lines 5015--5016 []\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]es twise Overfull \hbox (62.22433pt too wide) in paragraph at lines 5017--5018 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->MatchSummarySet[]from[]AlnBlock[]estw ise(qname,offset,target) [90] Overfull \hbox (82.28311pt too wide) in paragraph at lines 5040--5041 []\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]genewise (alb,qname, protoff,target) Overfull \hbox (7.08008pt too wide) in paragraph at lines 5041--5042 []\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]ge newise Overfull \hbox (72.72424pt too wide) in paragraph at lines 5043--5044 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->MatchSummarySet[]from[]AlnBlock[]gene wise(qname,protoff,target) LaTeX Warning: Reference `accessing_fields' on page 91 undefined on input line 5065. [91] LaTeX Warning: Reference `object_PfamHmmer1DB' on page 92 undefined on input li ne 5107. LaTeX Warning: Reference `object_PfamHmmer1Entry' on page 92 undefined on input line 5109. LaTeX Warning: Reference `accessing_fields' on page 92 undefined on input line 5116. LaTeX Warning: Reference `accessing_fields' on page 92 undefined on input line 5152. [92] Overfull \hbox (92.78302pt too wide) in paragraph at lines 5174--5175 []\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]str[]align (alb,qname,query,tname,targ et,name,main,ofp) Overfull \hbox (70.07953pt too wide) in paragraph at lines 5175--5176 []\OT1/cmtt/m/n/10 &Wise2::write[]pretty[]str[]align (alb,qname,query,tname,tar get,name,main,ofp) [93] Overfull \hbox (3.5338pt too wide) in paragraph at lines 5217--5218 []\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]Protein[]align (alb,q,t,name,main,ofp) LaTeX Warning: Reference `object_DnaSequenceHitList' on page 94 undefined on in put line 5243. LaTeX Warning: Reference `object_SegmentHitList' on page 94 undefined on input line 5245. LaTeX Warning: Reference `object_SegmentHit' on page 94 undefined on input line 5247. [94] LaTeX Warning: Reference `accessing_fields' on page 95 undefined on input line 5254. Overfull \hbox (29.5499pt too wide) in paragraph at lines 5290--5291 []\OT1/cmtt/m/n/10 &Wise2::DnaSequenceHitList::read[]MSPcrunch[]DnaSequenceHitL ist (ifp) [95] LaTeX Warning: Reference `accessing_fields' on page 96 undefined on input line 5307. LaTeX Warning: Reference `accessing_fields' on page 96 undefined on input line 5320. Overfull \hbox (99.50298pt too wide) in paragraph at lines 5348--5349 []\OT1/cmtt/m/n/10 Wise2[]Align[]strings[]ProteinSmithWaterman (one,two,comp,ga p,ext,dpenv,dpri) Overfull \hbox (76.79948pt too wide) in paragraph at lines 5349--5350 []\OT1/cmtt/m/n/10 &Wise2::Align[]strings[]ProteinSmithWaterman (one,two,comp,g ap,ext,dpenv,dpri) [96] Overfull \hbox (110.00288pt too wide) in paragraph at lines 5373--5374 []\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinSmithWaterman (one,two,comp, gap,ext,dpenv,dpri) Overfull \hbox (87.2994pt too wide) in paragraph at lines 5374--5375 []\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinSmithWaterman (one,two,comp ,gap,ext,dpenv,dpri) Overfull \hbox (7.58401pt too wide) in paragraph at lines 5386--5387 []\OT1/cmr/m/n/10 [OWNER] new AlnBlock struc-ture rep-re-sent-ing the align-men t [AlnBlock [97] Overfull \hbox (68.00325pt too wide) in paragraph at lines 5407--5408 []\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext, dpenv,dpri) Overfull \hbox (45.29976pt too wide) in paragraph at lines 5408--5409 []\OT1/cmtt/m/n/10 &Wise2::Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext ,dpenv,dpri) Overfull \hbox (5.0038pt too wide) in paragraph at lines 5434--5435 []\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]ABC (one,two,comp,a,b,c,dpenv,dpri) [98] Overfull \hbox (47.00343pt too wide) in paragraph at lines 5455--5456 []\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpen v,dpri) Overfull \hbox (24.29994pt too wide) in paragraph at lines 5456--5457 []\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpe nv,dpri) Overfull \hbox (86.01088pt too wide) in paragraph at lines 5471--5474 \OT1/cmr/m/n/10 Align[]Sequences[]ProteinABC this func-tion is anal-o-gous to A lign[]Sequences[]ProteinSmithWaterman Overfull \hbox (240.62169pt too wide) in paragraph at lines 5478--5479 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,ex t,bits[]cutoff,report[]level,die[]on[]error,dbsi) Overfull \hbox (217.9182pt too wide) in paragraph at lines 5479--5480 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,e xt,bits[]cutoff,report[]level,die[]on[]error,dbsi) [99] Overfull \hbox (235.37173pt too wide) in paragraph at lines 5500--5501 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b,c ,bits[]cutoff,report[]level,die[]on[]error,dbsi) Overfull \hbox (212.66824pt too wide) in paragraph at lines 5501--5502 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b, c,bits[]cutoff,report[]level,die[]on[]error,dbsi) [100] Overfull \hbox (359.90063pt too wide) in paragraph at lines 5523--5524 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentry ,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) Overfull \hbox (337.19714pt too wide) in paragraph at lines 5524--5525 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentr y,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) LaTeX Warning: Reference `object_ThreeStateDB' on page 101 undefined on input l ine 5552. LaTeX Warning: Reference `accessing_fields' on page 101 undefined on input line 5559. [101] Overfull \hbox (15.42177pt too wide) in paragraph at lines 5587--5588 []\OT1/cmr/m/n/10 reload[]generic Type [Three-State-Model * (*reload[]generic)( ThreeStateDB * tdb,int Overfull \hbox (3.42192pt too wide) in paragraph at lines 5594--5595 []\OT1/cmr/m/n/10 dataentry[]add Type [boolean (*dataen-try[]add)(ThreeStateDB * tdb,DataEntry Overfull \hbox (41.78299pt too wide) in paragraph at lines 5598--5599 []\OT1/cmr/m/n/10 index[]generic Type [Three-State-Model * (*in-dex[]generic)(T hreeStateDB *tdb,DataEntry [102] Overfull \hbox (29.5499pt too wide) in paragraph at lines 5669--5670 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateDB::new[]proteindb[]ThreeStateDB (sdb,comp ,gap,ext) [103] [104] LaTeX Warning: Reference `object_ThreeStateModel' on page 105 undefined on inpu t line 5732. LaTeX Warning: Reference `object_ThreeStateUnit' on page 105 undefined on input line 5734. LaTeX Warning: Reference `accessing_fields' on page 105 undefined on input line 5775. [105] Overfull \hbox (16.10999pt too wide) in paragraph at lines 5802--5803 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]global[]model (tsm,prob[]int o[]model) Overfull \hbox (102.65288pt too wide) in paragraph at lines 5822--5823 []\OT1/cmtt/m/n/10 Wise2[]force[]weighted[]local[]model (tsm,prob[]into[]model, ratio[]start,ratio[]end) Overfull \hbox (169.19861pt too wide) in paragraph at lines 5823--5824 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]weighted[]local[]model (tsm, prob[]into[]model,ratio[]start,ratio[]end) Overfull \hbox (93.09401pt too wide) in paragraph at lines 5825--5826 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->force[]weighted[]local[]model(prob[]i nto[]model,ratio[]start,ratio[]end) Overfull \hbox (49.31339pt too wide) in paragraph at lines 5845--5846 []\OT1/cmtt/m/n/10 Wise2[]ThreeStateModel[]from[]half[]bit[]Sequence (pro,mat,r m,gap,ext) [106] Overfull \hbox (5.61008pt too wide) in paragraph at lines 5846--5847 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::ThreeStateModel[]from[]half[]bit[]S equence Overfull \hbox (39.75452pt too wide) in paragraph at lines 5848--5849 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->ThreeStateModel[]from[]half[]bit[]Seq uence(mat,rm,gap,ext) Overfull \hbox (51.38966pt too wide) in paragraph at lines 5872--5873 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::write[]HMMer[]1[]7[]ascii[]ThreeSta teModel (tsm,ofp) LaTeX Warning: Reference `accessing_fields' on page 107 undefined on input line 5890. [107] [108] (./api.aux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tctt1000 mkdir: cannot create directory ‘././nonexistent’: Permission denied mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tctt1000 This is METAFONT, Version 2.71828182 (TeX Live 2025/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tctt1000.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tctt.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]) ) ) ) Font metrics written on tctt1000.tfm. Output written on tctt1000.600gf (128 characters, 19540 bytes). Transcript written on tctt1000.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/tctt1000.600pk: successfully generated. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1000 mkdir: cannot create directory ‘././nonexistent’: Permission denied mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1000 This is METAFONT, Version 2.71828182 (TeX Live 2025/dev/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1000.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 0.06943pt) Font metrics written on tcrm1000.tfm. Output written on tcrm1000.600gf (128 characters, 23548 bytes). Transcript written on tcrm1000.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/tcrm1000.600pk: successfully generated. Output written on api.pdf (108 pages, 304193 bytes). Transcript written on api.log. cd docs && pdflatex api.tex This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./api.tex LaTeX2e <2024-06-01> patch level 2 L3 programming layer <2024-05-27> (/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def Entering LaTeX 2.09 COMPATIBILITY MODE ************************************************************* !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! This mode attempts to provide an emulation of the LaTeX 2.09 author environment so that OLD documents can be successfully processed. It should NOT be used for NEW documents! New documents should use Standard LaTeX conventions and start with the \documentclass command. Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style files that change any internal macros, especially not with those that change the FONT SELECTION or OUTPUT ROUTINES. Therefore such style files MUST BE UPDATED to use Current Standard LaTeX: LaTeX2e. If you suspect that you may be using such a style file, which is probably very, very old by now, then you should attempt to get it updated by sending a copy of this error message to the author of that file. ************************************************************* (/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2024/02/08 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./api.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./api.toc [2] [3] [4] [5] [6] [7] [8] [9]) [10] [11] Overfull \hbox (1.49698pt too wide) in paragraph at lines 109--109 [] \OT1/cmtt/m/n/10 print "You must give a file to revcom for a reverse to w ork!";[] [12] [13] [14] LaTeX Warning: Reference `object_GeneFrequency' on page 15 undefined on input l ine 233. LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 236. LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 237. Overfull \hbox (21.30891pt too wide) in paragraph at lines 237--238 []\OT1/cmr/m/n/10 Build an en-tire pa-ram-e-ter set for ge-newise us-ing Wise2: :GeneParameter21[]wrap LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 238. LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 239. [15] [16] [17] LaTeX Warning: Reference `module_gwrap' on page 18 undefined on input line 389. [18] LaTeX Warning: Reference `module_codonmat' on page 19 undefined on input line 4 26. [19] LaTeX Warning: Reference `module_dbimpl' on page 20 undefined on input line 435 . Overfull \hbox (6.8248pt too wide) in paragraph at lines 475--482 \OT1/cmr/m/n/10 AlnBlock is the main rep-re-sen-ta-tion of align-ments from Dy- na-mite. Each AlnBlock [20] (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] Overfull \hbox (12.33003pt too wide) in paragraph at lines 1418--1419 []\OT1/cmtt/m/n/10 &Wise2::CodonMapper::sprinkle[]errors[]over[]CodonMapper (cm ,error) [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] Overfull \hbox (0.5938pt too wide) in paragraph at lines 1989--1990 []\OT1/cmtt/m/n/10 Wise2[]Genomic[]from[]Sequence[]Nheuristic (seq,length[]of[] N) [47] [48] [49] Overfull \hbox (65.9032pt too wide) in paragraph at lines 2175--2176 []\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB[]from[]single[]seq (gen,cses,score[]in []repeat[]coding) Overfull \hbox (43.1997pt too wide) in paragraph at lines 2176--2177 []\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB[]from[]single[]seq (gen,cses,score[]i n[]repeat[]coding) Overfull \hbox (41.12343pt too wide) in paragraph at lines 2192--2193 []\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[] cds[]score) Overfull \hbox (18.41994pt too wide) in paragraph at lines 2193--2194 []\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[ ]cds[]score) [50] [51] [52] Overfull \hbox (1.83012pt too wide) in paragraph at lines 2348--2349 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::read[]EMBL[]GenomicRegion[]file (file name) [53] Overfull \hbox (7.08008pt too wide) in paragraph at lines 2401--2402 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]ace[]GenomicRegion (gr,seq[]nam e,ofp) Overfull \hbox (3.5338pt too wide) in paragraph at lines 2426--2427 []\OT1/cmtt/m/n/10 Wise2[]show[]pretty[]GenomicRegion (gr,show[]supporting,ofp) Overfull \hbox (59.57962pt too wide) in paragraph at lines 2427--2428 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]pretty[]GenomicRegion (gr,show[ ]supporting,ofp) [54] [55] [56] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2592--2592 [] \OT1/cmtt/m/n/10 b) cooperation with future versions of histogram.c would be possible.[] [57] [58] [59] Overfull \hbox (123.4428pt too wide) in paragraph at lines 2794--2795 []\OT1/cmtt/m/n/10 Wise2[]ExtremeValueSetHistogram (h,mu,lambda,lowbound,highbo und,wonka,ndegrees) Overfull \hbox (67.76958pt too wide) in paragraph at lines 2795--2796 []\OT1/cmtt/m/n/10 &Wise2::Histogram::set[]EVD (h,mu,lambda,lowbound,highbound, wonka,ndegrees) Overfull \hbox (33.66461pt too wide) in paragraph at lines 2797--2798 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->set[]EVD(mu,lambda,lowbound,highbound ,wonka,ndegrees) [60] [61] [62] Overfull \hbox (30.97293pt too wide) in paragraph at lines 2971--2972 []\OT1/cmr/m/n/10 should[]store Type [boolean (*should[]store)(int given[]score ,double in-ter-nal[]score[]level) [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] Overfull \hbox (16.34366pt too wide) in paragraph at lines 3839--3840 []\OT1/cmtt/m/n/10 Wise2[]force[]to[]dna[]Sequence (seq,fraction,number[]of[]co nver) [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] Overfull \hbox (24.01358pt too wide) in paragraph at lines 4508--4515 \OT1/cmr/m/n/10 have any se-quence in it. When se-quence is asked for by get[]P rotein[]from[]Translation() [88] [89] Overfull \hbox (62.7533pt too wide) in paragraph at lines 4609--4610 []\OT1/cmtt/m/n/10 Wise2[]make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap, text,dpri) Overfull \hbox (40.0498pt too wide) in paragraph at lines 4610--4611 []\OT1/cmtt/m/n/10 &Wise2::make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap ,text,dpri) [90] Overfull \hbox (335.96082pt too wide) in paragraph at lines 4671--4672 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]sy n,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) Overfull \hbox (313.25732pt too wide) in paragraph at lines 4672--4673 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]s yn,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) [91] Overfull \hbox (329.87091pt too wide) in paragraph at lines 4698--4699 []\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp,c m,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri,palpoi) Overfull \hbox (270.41774pt too wide) in paragraph at lines 4699--4700 []\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp, cm,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri) [92] Overfull \hbox (265.40146pt too wide) in paragraph at lines 4732--4733 []\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,ct ,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri,palpoi) Overfull \hbox (205.94829pt too wide) in paragraph at lines 4733--4734 []\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,c t,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri) [93] Overfull \hbox (47.00343pt too wide) in paragraph at lines 4780--4781 []\OT1/cmtt/m/n/10 Wise2[]protein2genomic[]ascii[]display (alb,p,gen,ct,name,ma in,ofp) Overfull \hbox (24.29994pt too wide) in paragraph at lines 4781--4782 []\OT1/cmtt/m/n/10 &Wise2::protein2genomic[]ascii[]display (alb,p,gen,ct,name,m ain,ofp) [94] Overfull \hbox (188.7522pt too wide) in paragraph at lines 4801--4802 []\OT1/cmtt/m/n/10 Wise2[]protcdna[]ascii[]display (alb,protsequence,protname,p rotoff,cdna,ct,name,main,mult,ofp) Overfull \hbox (166.0487pt too wide) in paragraph at lines 4802--4803 []\OT1/cmtt/m/n/10 &Wise2::protcdna[]ascii[]display (alb,protsequence,protname, protoff,cdna,ct,name,main,mult,ofp) [95] Overfull \hbox (1.40793pt too wide) in paragraph at lines 4893--4894 []\OT1/cmr/m/n/10 transition[GENEFREQUENCY21[]TRANSITION[]LEN] Type [dou-ble : Scalar] [96] [97] Overfull \hbox (71.7832pt too wide) in paragraph at lines 5014--5015 []\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]estwise (alb,qname,o ffset,target) Overfull \hbox (1.83012pt too wide) in paragraph at lines 5015--5016 []\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]es twise Overfull \hbox (62.22433pt too wide) in paragraph at lines 5017--5018 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->MatchSummarySet[]from[]AlnBlock[]estw ise(qname,offset,target) [98] Overfull \hbox (82.28311pt too wide) in paragraph at lines 5040--5041 []\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]genewise (alb,qname, protoff,target) Overfull \hbox (7.08008pt too wide) in paragraph at lines 5041--5042 []\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]ge newise Overfull \hbox (72.72424pt too wide) in paragraph at lines 5043--5044 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->MatchSummarySet[]from[]AlnBlock[]gene wise(qname,protoff,target) [99] [100] Overfull \hbox (92.78302pt too wide) in paragraph at lines 5174--5175 []\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]str[]align (alb,qname,query,tname,targ et,name,main,ofp) Overfull \hbox (70.07953pt too wide) in paragraph at lines 5175--5176 []\OT1/cmtt/m/n/10 &Wise2::write[]pretty[]str[]align (alb,qname,query,tname,tar get,name,main,ofp) [101] Overfull \hbox (3.5338pt too wide) in paragraph at lines 5217--5218 []\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]Protein[]align (alb,q,t,name,main,ofp) [102] Overfull \hbox (29.5499pt too wide) in paragraph at lines 5290--5291 []\OT1/cmtt/m/n/10 &Wise2::DnaSequenceHitList::read[]MSPcrunch[]DnaSequenceHitL ist (ifp) [103] Overfull \hbox (99.50298pt too wide) in paragraph at lines 5348--5349 []\OT1/cmtt/m/n/10 Wise2[]Align[]strings[]ProteinSmithWaterman (one,two,comp,ga p,ext,dpenv,dpri) Overfull \hbox (76.79948pt too wide) in paragraph at lines 5349--5350 []\OT1/cmtt/m/n/10 &Wise2::Align[]strings[]ProteinSmithWaterman (one,two,comp,g ap,ext,dpenv,dpri) [104] Overfull \hbox (110.00288pt too wide) in paragraph at lines 5373--5374 []\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinSmithWaterman (one,two,comp, gap,ext,dpenv,dpri) Overfull \hbox (87.2994pt too wide) in paragraph at lines 5374--5375 []\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinSmithWaterman (one,two,comp ,gap,ext,dpenv,dpri) Overfull \hbox (7.58401pt too wide) in paragraph at lines 5386--5387 []\OT1/cmr/m/n/10 [OWNER] new AlnBlock struc-ture rep-re-sent-ing the align-men t [AlnBlock [105] Overfull \hbox (68.00325pt too wide) in paragraph at lines 5407--5408 []\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext, dpenv,dpri) Overfull \hbox (45.29976pt too wide) in paragraph at lines 5408--5409 []\OT1/cmtt/m/n/10 &Wise2::Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext ,dpenv,dpri) Overfull \hbox (5.0038pt too wide) in paragraph at lines 5434--5435 []\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]ABC (one,two,comp,a,b,c,dpenv,dpri) [106] Overfull \hbox (47.00343pt too wide) in paragraph at lines 5455--5456 []\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpen v,dpri) Overfull \hbox (24.29994pt too wide) in paragraph at lines 5456--5457 []\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpe nv,dpri) Overfull \hbox (86.01088pt too wide) in paragraph at lines 5471--5474 \OT1/cmr/m/n/10 Align[]Sequences[]ProteinABC this func-tion is anal-o-gous to A lign[]Sequences[]ProteinSmithWaterman Overfull \hbox (240.62169pt too wide) in paragraph at lines 5478--5479 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,ex t,bits[]cutoff,report[]level,die[]on[]error,dbsi) Overfull \hbox (217.9182pt too wide) in paragraph at lines 5479--5480 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,e xt,bits[]cutoff,report[]level,die[]on[]error,dbsi) [107] Overfull \hbox (235.37173pt too wide) in paragraph at lines 5500--5501 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b,c ,bits[]cutoff,report[]level,die[]on[]error,dbsi) Overfull \hbox (212.66824pt too wide) in paragraph at lines 5501--5502 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b, c,bits[]cutoff,report[]level,die[]on[]error,dbsi) [108] Overfull \hbox (359.90063pt too wide) in paragraph at lines 5523--5524 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentry ,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) Overfull \hbox (337.19714pt too wide) in paragraph at lines 5524--5525 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentr y,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) [109] Overfull \hbox (15.42177pt too wide) in paragraph at lines 5587--5588 []\OT1/cmr/m/n/10 reload[]generic Type [Three-State-Model * (*reload[]generic)( ThreeStateDB * tdb,int Overfull \hbox (3.42192pt too wide) in paragraph at lines 5594--5595 []\OT1/cmr/m/n/10 dataentry[]add Type [boolean (*dataen-try[]add)(ThreeStateDB * tdb,DataEntry Overfull \hbox (41.78299pt too wide) in paragraph at lines 5598--5599 []\OT1/cmr/m/n/10 index[]generic Type [Three-State-Model * (*in-dex[]generic)(T hreeStateDB *tdb,DataEntry [110] Overfull \hbox (29.5499pt too wide) in paragraph at lines 5669--5670 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateDB::new[]proteindb[]ThreeStateDB (sdb,comp ,gap,ext) [111] [112] [113] Overfull \hbox (16.10999pt too wide) in paragraph at lines 5802--5803 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]global[]model (tsm,prob[]int o[]model) Overfull \hbox (102.65288pt too wide) in paragraph at lines 5822--5823 []\OT1/cmtt/m/n/10 Wise2[]force[]weighted[]local[]model (tsm,prob[]into[]model, ratio[]start,ratio[]end) Overfull \hbox (169.19861pt too wide) in paragraph at lines 5823--5824 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]weighted[]local[]model (tsm, prob[]into[]model,ratio[]start,ratio[]end) Overfull \hbox (93.09401pt too wide) in paragraph at lines 5825--5826 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->force[]weighted[]local[]model(prob[]i nto[]model,ratio[]start,ratio[]end) Overfull \hbox (49.31339pt too wide) in paragraph at lines 5845--5846 []\OT1/cmtt/m/n/10 Wise2[]ThreeStateModel[]from[]half[]bit[]Sequence (pro,mat,r m,gap,ext) [114] Overfull \hbox (5.61008pt too wide) in paragraph at lines 5846--5847 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::ThreeStateModel[]from[]half[]bit[]S equence Overfull \hbox (39.75452pt too wide) in paragraph at lines 5848--5849 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->ThreeStateModel[]from[]half[]bit[]Seq uence(mat,rm,gap,ext) Overfull \hbox (51.38966pt too wide) in paragraph at lines 5872--5873 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::write[]HMMer[]1[]7[]ascii[]ThreeSta teModel (tsm,ofp) [115] [116] (./api.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on api.pdf (116 pages, 318795 bytes). Transcript written on api.log. cd docs && pdflatex dynamite.tex This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./dynamite.tex LaTeX2e <2024-06-01> patch level 2 L3 programming layer <2024-05-27> (/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def Entering LaTeX 2.09 COMPATIBILITY MODE ************************************************************* !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! This mode attempts to provide an emulation of the LaTeX 2.09 author environment so that OLD documents can be successfully processed. It should NOT be used for NEW documents! New documents should use Standard LaTeX conventions and start with the \documentclass command. Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style files that change any internal macros, especially not with those that change the FONT SELECTION or OUTPUT ROUTINES. Therefore such style files MUST BE UPDATED to use Current Standard LaTeX: LaTeX2e. If you suspect that you may be using such a style file, which is probably very, very old by now, then you should attempt to get it updated by sending a copy of this error message to the author of that file. ************************************************************* (/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2024/02/08 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file dynamite.aux. (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] No file dynamite.toc. [2] [3] LaTeX Warning: Reference `own_objects' on page 4 undefined on input line 77. [4] [5] [6] Overfull \hbox (4.11092pt too wide) in paragraph at lines 253--257 \OT1/cmr/m/n/10 tri-bu-tion from 'ftp://ftp.sanger.ac.uk/pub/birney/dynamite/dy n.x.tar.Z' (where [7] [8] [9] [10] Overfull \hbox (48.74657pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 fprintf(ofp,"\npsw seq1 seq2\nBoth sequences in fasta format\n"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 * -g for gap value (an int) - rely on commandline error p rocessing[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 * -e for ext value (an int) - rely on commandline error p rocessing[] [11] Overfull \hbox (269.24464pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc e 2 %d",argc);[] [12] Overfull \hbox (22.4968pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 * or WISEPERSONALDIR if it is not present in the current directory.[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex plicit memory.[] [13] Overfull \hbox (59.24648pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext,NULL);[] Overfull \hbox (80.24629pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] [14] Overfull \hbox (48.74657pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex plicit memory.[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext,NULL);[] [15] Overfull \hbox (80.24629pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 639--639 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext);[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 654--654 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] [16] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 EPENLRKIFVGGLTSNTTDDLMREFYSQFGEITDIIVMR DPTTKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 EPE LRK+F+GGL+ TTD+ +R + Q+G +TD +VMR DP TKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMR DPNTKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 GFVTFSGKTEVDAAMKQRPHIIDGKTVDPKRAVPRDDKN RSESNVSTKR[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 GFVT++ EVDAAM RPH +DG+ V+PKRAV R+D R ++++ K+[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN GFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQ RPGAHLTVKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 LYVSGVREDHTEDMLTEYFTKYGTVTKSEIILDKATQKP RGFGFVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 ++V G++ED E L +YF +YG + EI+ D+ + K RGF FVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK RGFAFVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 HDSVDQCVLQKSHMVNGHRCDVRKGLSKDEMSKAQMNRD RETRGGRSRD[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 HDSVD+ V+QK H VNGH C+VRK LSK EM+ A ++ GRS[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN HDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASAS---- -SSQRGRSGS[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 GQRGGYNGGG-GGGGGWGGPAQRGGPGAYGGP-GGGGQG GYGGDYGG--[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 G GG GGG GG +G G G +GG GGGG G G G Y G[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN GNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYG GSGDGYNGFG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 GWGQQGGGGQGGWGGPQQQQGGG-GWGQQGGGGQGGWGG PQQQQQGGWG[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 G GGGG G GG + GG G+G QG G GG G GG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN NDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSG-YGGSGS YDSYNNGGGR[] [17] [18] Overfull \hbox (48.88945pt too wide) in paragraph at lines 793--795 []\OT1/cmr/m/n/10 The align-ment is the set of (i,j,) triples, where sta te is one of (Match,Insert,Delete) [19] [20] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] [21] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] [22] Overfull \hbox (32.64503pt too wide) in paragraph at lines 1015--1019 \OT1/cmr/m/n/10 and GE-NOMIC[]INTRON. No-tice how the source lines to and from GE-NOMIC[]INSERT Overfull \hbox (38.24666pt too wide) in paragraph at lines 1116--1116 []\OT1/cmtt/m/n/10 #define DnaMatrix_Score(dnamat,base1,base2) (dnamat->score[b ase1][base2])[] [23] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1116--1116 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_BASE(tar get,j))"[] [24] [25] Overfull \hbox (122.24593pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 fprintf(ofp,"\nest2gen est-seq genomic-seq\nBoth sequences in fasta format\n"[] [26] Overfull \hbox (269.24464pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] [27] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc e 2 %d",argc);[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a genomic one[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T he 'default' one[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI (= -infinity)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * We could build up something much better, using complexc onsensi and[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * other machinery, but not for now . See the genewi se code if you[] [28] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * cDNA2Gen has alot more parameter space than the paramet ers to this[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * program. Firstly we are treating errors similarly on ea ch side of the[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * Secondly there is a rather complex interaction between the gap/extension[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * of what is thought to be sequencing error and the intro ns. Here we have[] Overfull \hbox (64.49643pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * one more parameter, and intron open penalty, which can be set, to prevent[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * One good way to parameterise all this would be to have a probabilistic[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * model of the processes, derive probabilities and then m ap them to ints[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * (probability.h has got these mappings, such as Probabil ity2Score).[] Overfull \hbox (101.24611pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga p,-ext,-gap,-ext,0,NULL);[] Overfull \hbox (80.24629pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] [29] Overfull \hbox (74.99634pt too wide) in paragraph at lines 1342--1342 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga p,-ext,-gap,-ext,0);[] [30] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a genomic one[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T he 'default' one[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI (= -infinity)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * We could build up something much better, using complexc onsensi and[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * other machinery, but not for now . See the genewi se code if you[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 1 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GATGGT-TAT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GAT T T T[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2132 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GAT--TAT-T[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 49 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2178 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] [31] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 98 CAGTGGCAAGAAAAGGGGCTTTGCCT-TAGTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 CAGTGGCAAGAAAAGGGGCTTTGCCT T GTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2227 CAGTGGCAAGAAAAGGGGCTTTGCCTTT-GTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 146 CTCCGTGGATAAGATTGTCA TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 CTCCGTGGATAAGATTGTCA TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2275 CTCCGTGGATAAGATTGTCA<-2295:2387->TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 182 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2404 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 231 ATGGCTAGTGCTTCATCCAGCCAAAGAG GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 ATGGCTAGTGCTTCATCCAGCCAAAGAG GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2453 ATGGCTAGTGCTTCATCCAGCCAAAGAG<-2481:2566 ->GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 267 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2575 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2624 ACAACTTCGGTCGTGGAGGAAACTTCAGTGGTCGTG<-2 660:2793->[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 352 GTNG-CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GT G CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2794 GT-GGCTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 400 ATGGCTATAATGGATTTGGCAATGATG GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 ATGGCTATAATGGATTTGGCAATGATG GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2842 ATGGCTATAATGGATTTGGCAATGATG<-2869:3805- >GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 436 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG--tttat gcA-CAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG ++ + +A CAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3815 TTGGAGGTGGTGGAAGCTACAATGATTTTGGGAATT-A- -CAACAATCA[] [32] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 482 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3861 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 531 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3910 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 580 AAG GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 AAG GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3959 AAG<-3962:4251->GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] [33] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1572--1572 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1572--1572 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [34] [35] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1600--1600 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 1634--1634 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_MyProteinSW(seqone,seqtwo,mat,-12, -2,NULL);[] Overfull \hbox (127.49588pt too wide) in paragraph at lines 1634--1634 [] \OT1/cmtt/m/n/10 fprintf(stdout,"%d,%d are matched with score %d\n",uni t->i+1,unit->j+1,unit->score);[] [36] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1727--1727 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1727--1727 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [37] [38] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1849--1849 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1849--1849 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [39] Overfull \hbox (258.74474pt too wide) in paragraph at lines 1849--1849 [] \OT1/cmtt/m/n/10 calc="ALPHA_SEQ_SCORE(query,i) + ALPHA_SEQ_SCORE(target,j) + mat_alpha.comp[SEQ_POS(query,i)][SEQ_POS(target,j)]"[] [40] [41] Overfull \hbox (20.54509pt too wide) in paragraph at lines 1911--1912 []\OT1/cmr/m/n/10 The macro Dna-Ma-trix[]Score which is de-fined at the top of the cdna2genomic.dy Overfull \hbox (17.24684pt too wide) in paragraph at lines 1928--1928 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_CODON(ta rget,j))"[] [42] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1944--1944 [] \OT1/cmtt/m/n/10 Mis-type in argument 3 of DNA\_MAT\_SCORE: wanted [b ase] got [codon][] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1955--1955 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,j),GENOMIC_BASE(tar get,j))"[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1967--1967 [] \OT1/cmtt/m/n/10 For function CDNA\_BASE, you have arguments j and qu ery, which do not[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1967--1967 []\OT1/cmtt/m/n/10 expect to paired directly in a function. This is just a warn ing that[] [43] Overfull \hbox (17.24684pt too wide) in paragraph at lines 2014--2014 [] \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr ix",one);[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 2014--2014 [] \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr ix",two);[] [44] [45] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fprintf(stdout,"dbsearch [options] \n");[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 /** add more options here sometime, eg comp matrix and gap penalty*/[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 /** print out dbsearch options. We don't know here what im plementations are[] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 either possible or how they are specified. Of course, there is the problem[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 that we could clash our options with the dbsearchimpl options, but that[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 is not too likely, and this makes this program future proof wrt to new[] [46] Overfull \hbox (43.49661pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 * care about which implementation is used, and does not k now either (!)[] [47] Overfull \hbox (106.49606pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 /* 10 means a score cutoff of 10, -1 means don't report on stderr search progress */[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) != SEARCH_OK )[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing ungracefully");[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (174.74547pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fprintf(stdout,"Comparison to %s was %d score\n",out-> ds[i]->target->name,out->ds[i]->score);[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta rget);[] [48] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s",t emp->baseseq->name);[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs, mat,-12,-2,NULL);[] Overfull \hbox (101.24611pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query->n ame,temp->baseseq->name);[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 write_pretty_seq_align(alb,query,temp->baseseq,15,50,s tdout);[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2263--2263 [] \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) != SEARCH_OK )[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2263--2263 [] \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing ungracefully");[] [49] Overfull \hbox (1.49698pt too wide) in paragraph at lines 2292--2292 [] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta rget);[] [50] [51] [52] [53] [54] Overfull \hbox (1.32472pt too wide) in paragraph at lines 2528--2534 \OT1/cmr/m/n/10 de-scribed by a "state...endstate" multi-line block. Within eac h "state...endstate" [55] [56] [57] [58] [59] Overfull \hbox (1.75064pt too wide) in paragraph at lines 2772--2776 \OT1/cmr/m/n/10 Dy-na-mite file: for ex-am-ple the fol-low-ing er-ror was made by mistyp-ing ``MATCH'' Overfull \hbox (59.24648pt too wide) in paragraph at lines 2792--2792 [] \OT1/cmtt/m/n/10 In matrix ProteinSW - State MATCH asks for source MA TCH2 but there is[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 2792--2792 [] \OT1/cmtt/m/n/10 Failing simple cross-checks, aborting before calc-li ne parsing[] [60] [61] [62] (./dynamite.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on dynamite.pdf (62 pages, 221240 bytes). Transcript written on dynamite.log. cd docs && pdflatex dynamite.tex This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./dynamite.tex LaTeX2e <2024-06-01> patch level 2 L3 programming layer <2024-05-27> (/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def Entering LaTeX 2.09 COMPATIBILITY MODE ************************************************************* !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! This mode attempts to provide an emulation of the LaTeX 2.09 author environment so that OLD documents can be successfully processed. It should NOT be used for NEW documents! New documents should use Standard LaTeX conventions and start with the \documentclass command. Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style files that change any internal macros, especially not with those that change the FONT SELECTION or OUTPUT ROUTINES. Therefore such style files MUST BE UPDATED to use Current Standard LaTeX: LaTeX2e. If you suspect that you may be using such a style file, which is probably very, very old by now, then you should attempt to get it updated by sending a copy of this error message to the author of that file. ************************************************************* (/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2024/02/08 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./dynamite.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./dynamite.toc [2] Overfull \hbox (8.02837pt too wide) in paragraph at lines 50--50 [][] []\OT1/cmr/m/n/10 [Dynamite Level] Did not un-der-stand line [ source MAT CH]. ) [3] [4] [5] [6] [7] [8] Overfull \hbox (4.11092pt too wide) in paragraph at lines 253--257 \OT1/cmr/m/n/10 tri-bu-tion from 'ftp://ftp.sanger.ac.uk/pub/birney/dynamite/dy n.x.tar.Z' (where [9] [10] [11] [12] Overfull \hbox (48.74657pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 fprintf(ofp,"\npsw seq1 seq2\nBoth sequences in fasta format\n"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 * -g for gap value (an int) - rely on commandline error p rocessing[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 * -e for ext value (an int) - rely on commandline error p rocessing[] [13] Overfull \hbox (269.24464pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc e 2 %d",argc);[] [14] Overfull \hbox (22.4968pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 * or WISEPERSONALDIR if it is not present in the current directory.[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex plicit memory.[] [15] Overfull \hbox (59.24648pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext,NULL);[] Overfull \hbox (80.24629pt too wide) in paragraph at lines 588--588 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] [16] Overfull \hbox (48.74657pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex plicit memory.[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext,NULL);[] [17] Overfull \hbox (80.24629pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 639--639 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext);[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 654--654 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] [18] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 EPENLRKIFVGGLTSNTTDDLMREFYSQFGEITDIIVMR DPTTKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 EPE LRK+F+GGL+ TTD+ +R + Q+G +TD +VMR DP TKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMR DPNTKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 GFVTFSGKTEVDAAMKQRPHIIDGKTVDPKRAVPRDDKN RSESNVSTKR[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 GFVT++ EVDAAM RPH +DG+ V+PKRAV R+D R ++++ K+[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN GFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQ RPGAHLTVKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 LYVSGVREDHTEDMLTEYFTKYGTVTKSEIILDKATQKP RGFGFVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 ++V G++ED E L +YF +YG + EI+ D+ + K RGF FVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK RGFAFVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 HDSVDQCVLQKSHMVNGHRCDVRKGLSKDEMSKAQMNRD RETRGGRSRD[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 HDSVD+ V+QK H VNGH C+VRK LSK EM+ A ++ GRS[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN HDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASAS---- -SSQRGRSGS[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 GQRGGYNGGG-GGGGGWGGPAQRGGPGAYGGP-GGGGQG GYGGDYGG--[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 G GG GGG GG +G G G +GG GGGG G G G Y G[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN GNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYG GSGDGYNGFG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 GWGQQGGGGQGGWGGPQQQQGGG-GWGQQGGGGQGGWGG PQQQQQGGWG[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \OT1/cmtt/m/n/10 G GGGG G GG + GG G+G QG G GG G GG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN NDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSG-YGGSGS YDSYNNGGGR[] [19] [20] Overfull \hbox (48.88945pt too wide) in paragraph at lines 793--795 []\OT1/cmr/m/n/10 The align-ment is the set of (i,j,) triples, where sta te is one of (Match,Insert,Delete) [21] [22] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] [23] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] [24] Overfull \hbox (32.64503pt too wide) in paragraph at lines 1015--1019 \OT1/cmr/m/n/10 and GE-NOMIC[]INTRON. No-tice how the source lines to and from GE-NOMIC[]INSERT Overfull \hbox (38.24666pt too wide) in paragraph at lines 1116--1116 []\OT1/cmtt/m/n/10 #define DnaMatrix_Score(dnamat,base1,base2) (dnamat->score[b ase1][base2])[] [25] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1116--1116 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_BASE(tar get,j))"[] [26] [27] Overfull \hbox (122.24593pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 fprintf(ofp,"\nest2gen est-seq genomic-seq\nBoth sequences in fasta format\n"[] [28] Overfull \hbox (269.24464pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] [29] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc e 2 %d",argc);[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a genomic one[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T he 'default' one[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI (= -infinity)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * We could build up something much better, using complexc onsensi and[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * other machinery, but not for now . See the genewi se code if you[] [30] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * cDNA2Gen has alot more parameter space than the paramet ers to this[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * program. Firstly we are treating errors similarly on ea ch side of the[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * Secondly there is a rather complex interaction between the gap/extension[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * of what is thought to be sequencing error and the intro ns. Here we have[] Overfull \hbox (64.49643pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * one more parameter, and intron open penalty, which can be set, to prevent[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * One good way to parameterise all this would be to have a probabilistic[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * model of the processes, derive probabilities and then m ap them to ints[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 * (probability.h has got these mappings, such as Probabil ity2Score).[] Overfull \hbox (101.24611pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga p,-ext,-gap,-ext,0,NULL);[] Overfull \hbox (80.24629pt too wide) in paragraph at lines 1335--1335 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] [31] Overfull \hbox (74.99634pt too wide) in paragraph at lines 1342--1342 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga p,-ext,-gap,-ext,0);[] [32] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a genomic one[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T he 'default' one[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI (= -infinity)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * We could build up something much better, using complexc onsensi and[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 * other machinery, but not for now . See the genewi se code if you[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1379--1379 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 1 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GATGGT-TAT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GAT T T T[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2132 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GAT--TAT-T[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 49 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2178 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] [33] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 98 CAGTGGCAAGAAAAGGGGCTTTGCCT-TAGTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 CAGTGGCAAGAAAAGGGGCTTTGCCT T GTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2227 CAGTGGCAAGAAAAGGGGCTTTGCCTTT-GTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 146 CTCCGTGGATAAGATTGTCA TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 CTCCGTGGATAAGATTGTCA TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2275 CTCCGTGGATAAGATTGTCA<-2295:2387->TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 182 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2404 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 231 ATGGCTAGTGCTTCATCCAGCCAAAGAG GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 ATGGCTAGTGCTTCATCCAGCCAAAGAG GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2453 ATGGCTAGTGCTTCATCCAGCCAAAGAG<-2481:2566 ->GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 267 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2575 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2624 ACAACTTCGGTCGTGGAGGAAACTTCAGTGGTCGTG<-2 660:2793->[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 352 GTNG-CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GT G CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2794 GT-GGCTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 400 ATGGCTATAATGGATTTGGCAATGATG GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 ATGGCTATAATGGATTTGGCAATGATG GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2842 ATGGCTATAATGGATTTGGCAATGATG<-2869:3805- >GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 436 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG--tttat gcA-CAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG ++ + +A CAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3815 TTGGAGGTGGTGGAAGCTACAATGATTTTGGGAATT-A- -CAACAATCA[] [34] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 482 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3861 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 531 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3910 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 580 AAG GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 AAG GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3959 AAG<-3962:4251->GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] [35] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1572--1572 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1572--1572 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [36] [37] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1600--1600 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 1634--1634 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_MyProteinSW(seqone,seqtwo,mat,-12, -2,NULL);[] Overfull \hbox (127.49588pt too wide) in paragraph at lines 1634--1634 [] \OT1/cmtt/m/n/10 fprintf(stdout,"%d,%d are matched with score %d\n",uni t->i+1,unit->j+1,unit->score);[] [38] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1727--1727 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1727--1727 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [39] [40] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1849--1849 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1849--1849 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [41] Overfull \hbox (258.74474pt too wide) in paragraph at lines 1849--1849 [] \OT1/cmtt/m/n/10 calc="ALPHA_SEQ_SCORE(query,i) + ALPHA_SEQ_SCORE(target,j) + mat_alpha.comp[SEQ_POS(query,i)][SEQ_POS(target,j)]"[] [42] [43] Overfull \hbox (20.54509pt too wide) in paragraph at lines 1911--1912 []\OT1/cmr/m/n/10 The macro Dna-Ma-trix[]Score which is de-fined at the top of the cdna2genomic.dy Overfull \hbox (17.24684pt too wide) in paragraph at lines 1928--1928 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_CODON(ta rget,j))"[] [44] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1944--1944 [] \OT1/cmtt/m/n/10 Mis-type in argument 3 of DNA\_MAT\_SCORE: wanted [b ase] got [codon][] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1955--1955 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,j),GENOMIC_BASE(tar get,j))"[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1967--1967 [] \OT1/cmtt/m/n/10 For function CDNA\_BASE, you have arguments j and qu ery, which do not[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1967--1967 []\OT1/cmtt/m/n/10 expect to paired directly in a function. This is just a warn ing that[] [45] Overfull \hbox (17.24684pt too wide) in paragraph at lines 2014--2014 [] \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr ix",one);[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 2014--2014 [] \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr ix",two);[] [46] [47] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fprintf(stdout,"dbsearch [options] \n");[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 /** add more options here sometime, eg comp matrix and gap penalty*/[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 /** print out dbsearch options. We don't know here what im plementations are[] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 either possible or how they are specified. Of course, there is the problem[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 that we could clash our options with the dbsearchimpl options, but that[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 is not too likely, and this makes this program future proof wrt to new[] [48] Overfull \hbox (43.49661pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 * care about which implementation is used, and does not k now either (!)[] [49] Overfull \hbox (106.49606pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 /* 10 means a score cutoff of 10, -1 means don't report on stderr search progress */[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) != SEARCH_OK )[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing ungracefully");[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (174.74547pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fprintf(stdout,"Comparison to %s was %d score\n",out-> ds[i]->target->name,out->ds[i]->score);[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta rget);[] [50] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s",t emp->baseseq->name);[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs, mat,-12,-2,NULL);[] Overfull \hbox (101.24611pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query->n ame,temp->baseseq->name);[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 write_pretty_seq_align(alb,query,temp->baseseq,15,50,s tdout);[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2263--2263 [] \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) != SEARCH_OK )[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2263--2263 [] \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing ungracefully");[] [51] Overfull \hbox (1.49698pt too wide) in paragraph at lines 2292--2292 [] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta rget);[] [52] [53] [54] [55] [56] Overfull \hbox (1.32472pt too wide) in paragraph at lines 2528--2534 \OT1/cmr/m/n/10 de-scribed by a "state...endstate" multi-line block. Within eac h "state...endstate" [57] [58] [59] [60] [61] Overfull \hbox (1.75064pt too wide) in paragraph at lines 2772--2776 \OT1/cmr/m/n/10 Dy-na-mite file: for ex-am-ple the fol-low-ing er-ror was made by mistyp-ing ``MATCH'' Overfull \hbox (59.24648pt too wide) in paragraph at lines 2792--2792 [] \OT1/cmtt/m/n/10 In matrix ProteinSW - State MATCH asks for source MA TCH2 but there is[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 2792--2792 [] \OT1/cmtt/m/n/10 Failing simple cross-checks, aborting before calc-li ne parsing[] [62] [63] [64] (./dynamite.aux) LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on dynamite.pdf (64 pages, 224801 bytes). Transcript written on dynamite.log. cd docs && pdflatex wise2.tex This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./wise2.tex LaTeX2e <2024-06-01> patch level 2 L3 programming layer <2024-05-27> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2024/02/08 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file wise2.aux. (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] No file wise2.toc. [2] [3] [4] LaTeX Warning: Reference `genewise_large' on page 5 undefined on input line 110 . LaTeX Warning: Reference `estwise_large' on page 5 undefined on input line 113. Overfull \hbox (11.99689pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 This program is freely distributed under a GPL. See source d irectory[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 Copyright (c) GRL limited: portions of the code are from sep arate copyright[] [5] Overfull \hbox (32.9967pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 Warning: The bits scores is not probablistically correct for single seqs[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 roa1_drome 88 AQKSRPHKIDGRVVEPKRAVPRQ DID[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 A +RPHK+DGRVVEPKRAV R+ D[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 AMNARPHKVDGRVVEPKRAVSRE DSQ[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 HSHNRNPA 1867 gaagaccagggagggcaaggtagGTGAGTG Intron 2 TAGgtc[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 ctacgcaataggttacagctcga<0-----[1936 : 2 083]-0>aca[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 tgtagacggtaatgaagatccaa tta[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 roa1_drome 114 SPNAGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDIN IVIDKETGKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 P A TVKK+FVG +K+D +E +RDYF+ +G I I I+ D+ +GKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE IMTDRGSGKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 HSHNRNPA 2093 acggctagaaatgggaaggaggcccagttgctgaaggag aaagcgagaa[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 gcgcatctaatttggtaaacaaaatgaataaagatatta ttcaggggaa[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 aatccatgagatttctaactaatcaatttagtaatagta cgtcactcga[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 roa1_drome 163 RGFAFVEFDDYDPVDKVV QKQHQ[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 RGFAFV FDD+D VDK+V QK H[] [6] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 RGFAFVTFDDHDSVDKIV L:I[att] QKYHT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 HSHNRNPA 2240 agtgtgatggcgtggaagAGTAAGTA Intron 3 TAGTTcatca[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 ggtcttctaaaactaatt <1-----[2295 : 2387] -1> aaaac[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 gctctactcctccgtgtc gactt[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 tagaagatgactcaaatcgcccgag <1-----[2481 : 2793][] [7] [8] LaTeX Warning: Reference `sec:start_end' on page 9 undefined on input line 297. [9] LaTeX Warning: Reference `half_and_blast' on page 10 undefined on input line 34 6. [10] [11] LaTeX Warning: Reference `genewise_large' on page 12 undefined on input line 45 5. LaTeX Warning: Reference `estwise_large' on page 12 undefined on input line 455 . LaTeX Warning: Reference `compile_pthread' on page 12 undefined on input line 4 66. LaTeX Warning: Reference `half_and_blast' on page 12 undefined on input line 47 3. [12] LaTeX Warning: Reference `half_and_blast' on page 13 undefined on input line 51 3. [13] [14] LaTeX Warning: Reference `running_pthread' on page 15 undefined on input line 6 13. [15] [16] [17] LaTeX Warning: Reference `Figure:genewise21' on page 18 undefined on input line 708. [18] [19] [20] LaTeX Warning: Reference `Figure:genewise623' on page 21 undefined on input lin e 900. [21] Overfull \hbox (2.03789pt too wide) in paragraph at lines 965--968 []\OT1/cmr/m/n/10 Algorithms are named in two parts, \OT1/cmr/m/it/10 descripti ve-word state-number:transition- [22] [23] [24] [25] Overfull \hbox (68.08423pt too wide) in paragraph at lines 1108--1109 []\OT1/cmr/m/n/10 The half-wise pro-tein database, found at ftp://ftp.sanger.ac .uk/pub/birney/wise2/halfwise [26] LaTeX Warning: Reference `sec:commonmode' on page 27 undefined on input line 11 81. [27] LaTeX Warning: Reference `sec:start_end' on page 28 undefined on input line 121 0. [28] Overfull \hbox (42.24687pt too wide) in paragraph at lines 1268--1268 []\OT1/cmtt/m/n/10 pexon [] Overfull \hbox (42.24687pt too wide) in paragraph at lines 1268--1268 []\OT1/cmtt/m/n/10 pexon [] [29] LaTeX Warning: Reference `sec:alg' on page 30 undefined on input line 1276. Overfull \hbox (36.99692pt too wide) in paragraph at lines 1312--1312 []\OT1/cmtt/m/n/10 Bits Query start end Target start end idel s introns[] Overfull \hbox (5.4972pt too wide) in paragraph at lines 1312--1312 []\OT1/cmtt/m/n/10 230.57 roa1_drome 26 347 HSHNRNPA 1386 3963 0 6[] [30] [31] LaTeX Warning: Reference `sec:start_end' on page 32 undefined on input line 137 7. [32] [33] [34] LaTeX Warning: Reference `sec:start_end' on page 35 undefined on input line 146 9. [35] [36] LaTeX Warning: Reference `compile_pthread' on page 37 undefined on input line 1 561. [37] [38] [39] [40] [41] [42] (./wise2.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on wise2.pdf (42 pages, 213109 bytes). Transcript written on wise2.log. cd docs && pdflatex wise2.tex This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./wise2.tex LaTeX2e <2024-06-01> patch level 2 L3 programming layer <2024-05-27> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2024/02/08 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./wise2.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./wise2.toc [2]) [3] [4] [5] Overfull \hbox (11.99689pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 This program is freely distributed under a GPL. See source d irectory[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 Copyright (c) GRL limited: portions of the code are from sep arate copyright[] [6] Overfull \hbox (32.9967pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 Warning: The bits scores is not probablistically correct for single seqs[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 roa1_drome 88 AQKSRPHKIDGRVVEPKRAVPRQ DID[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 A +RPHK+DGRVVEPKRAV R+ D[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 AMNARPHKVDGRVVEPKRAVSRE DSQ[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 HSHNRNPA 1867 gaagaccagggagggcaaggtagGTGAGTG Intron 2 TAGgtc[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 ctacgcaataggttacagctcga<0-----[1936 : 2 083]-0>aca[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 tgtagacggtaatgaagatccaa tta[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 roa1_drome 114 SPNAGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDIN IVIDKETGKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 P A TVKK+FVG +K+D +E +RDYF+ +G I I I+ D+ +GKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE IMTDRGSGKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 HSHNRNPA 2093 acggctagaaatgggaaggaggcccagttgctgaaggag aaagcgagaa[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 gcgcatctaatttggtaaacaaaatgaataaagatatta ttcaggggaa[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 aatccatgagatttctaactaatcaatttagtaatagta cgtcactcga[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 roa1_drome 163 RGFAFVEFDDYDPVDKVV QKQHQ[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 RGFAFV FDD+D VDK+V QK H[] [7] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 RGFAFVTFDDHDSVDKIV L:I[att] QKYHT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 HSHNRNPA 2240 agtgtgatggcgtggaagAGTAAGTA Intron 3 TAGTTcatca[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 ggtcttctaaaactaatt <1-----[2295 : 2387] -1> aaaac[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 gctctactcctccgtgtc gactt[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 tagaagatgactcaaatcgcccgag <1-----[2481 : 2793][] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] LaTeX Warning: Reference `Figure:genewise21' on page 19 undefined on input line 708. [19] [20] [21] [22] Overfull \hbox (2.03789pt too wide) in paragraph at lines 965--968 []\OT1/cmr/m/n/10 Algorithms are named in two parts, \OT1/cmr/m/it/10 descripti ve-word state-number:transition- [23] [24] [25] [26] Overfull \hbox (68.08423pt too wide) in paragraph at lines 1108--1109 []\OT1/cmr/m/n/10 The half-wise pro-tein database, found at ftp://ftp.sanger.ac .uk/pub/birney/wise2/halfwise [27] [28] [29] Overfull \hbox (42.24687pt too wide) in paragraph at lines 1268--1268 []\OT1/cmtt/m/n/10 pexon [] Overfull \hbox (42.24687pt too wide) in paragraph at lines 1268--1268 []\OT1/cmtt/m/n/10 pexon [] [30] Overfull \hbox (36.99692pt too wide) in paragraph at lines 1312--1312 []\OT1/cmtt/m/n/10 Bits Query start end Target start end idel s introns[] Overfull \hbox (5.4972pt too wide) in paragraph at lines 1312--1312 []\OT1/cmtt/m/n/10 230.57 roa1_drome 26 347 HSHNRNPA 1386 3963 0 6[] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] (./wise2.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on wise2.pdf (43 pages, 215399 bytes). Transcript written on wise2.log. cd docs && hevea api.tex ./api.tex:2: Warning: Command not found: \pdftrailerid ./api.tex:233: Warning: Undefined label: 'object_GeneFrequency' ./api.tex:236: Warning: Undefined label: 'module_gwrap' ./api.tex:237: Warning: Undefined label: 'module_gwrap' ./api.tex:238: Warning: Undefined label: 'module_gwrap' ./api.tex:239: Warning: Undefined label: 'module_gwrap' ./api.tex:389: Warning: Undefined label: 'module_gwrap' ./api.tex:426: Warning: Undefined label: 'module_codonmat' ./api.tex:435: Warning: Undefined label: 'module_dbimpl' ./api.tex:476: Warning: Application of '\'' on ',' failed ./api.tex:629: Warning: Application of '\'' on 't' failed ./api.tex:631: Warning: Application of '\'' on 'b' failed ./api.tex:633: Warning: Application of '\'' on 'b' failed ./api.tex:1642: Warning: Application of '\'' on 't' failed ./api.tex:1660: Warning: Application of '\'' on 't' failed ./api.tex:1882: Warning: Application of '\'' on '.' failed ./api.tex:2441: Warning: Application of '\'' on 'b' failed ./api.tex:2847: Warning: Application of '\'' on 'h' failed ./api.tex:2847: Warning: Application of '\'' on 't' failed ./api.tex:4435: Warning: Application of '\'' on '.' failed ./api.tex:4952: Warning: Application of '\'' on 'd' failed ./api.tex:4952: Warning: Application of '\'' on 'd' failed ./api.tex:5809: Warning: Application of '\'' on 'f' failed ./api.tex:5809: Warning: Application of '\'' on '[' failed ./api.tex:5830: Warning: Application of '\'' on 'f' failed ./api.tex:5830: Warning: Application of '\'' on '[' failed cd docs && hevea api.tex ./api.tex:2: Warning: Command not found: \pdftrailerid ./api.tex:233: Warning: Undefined label: 'object_GeneFrequency' ./api.tex:236: Warning: Undefined label: 'module_gwrap' ./api.tex:237: Warning: Undefined label: 'module_gwrap' ./api.tex:238: Warning: Undefined label: 'module_gwrap' ./api.tex:239: Warning: Undefined label: 'module_gwrap' ./api.tex:389: Warning: Undefined label: 'module_gwrap' ./api.tex:426: Warning: Undefined label: 'module_codonmat' ./api.tex:435: Warning: Undefined label: 'module_dbimpl' ./api.tex:476: Warning: Application of '\'' on ',' failed ./api.tex:629: Warning: Application of '\'' on 't' failed ./api.tex:631: Warning: Application of '\'' on 'b' failed ./api.tex:633: Warning: Application of '\'' on 'b' failed ./api.tex:1642: Warning: Application of '\'' on 't' failed ./api.tex:1660: Warning: Application of '\'' on 't' failed ./api.tex:1882: Warning: Application of '\'' on '.' failed ./api.tex:2441: Warning: Application of '\'' on 'b' failed ./api.tex:2847: Warning: Application of '\'' on 'h' failed ./api.tex:2847: Warning: Application of '\'' on 't' failed ./api.tex:4435: Warning: Application of '\'' on '.' failed ./api.tex:4952: Warning: Application of '\'' on 'd' failed ./api.tex:4952: Warning: Application of '\'' on 'd' failed ./api.tex:5809: Warning: Application of '\'' on 'f' failed ./api.tex:5809: Warning: Application of '\'' on '[' failed ./api.tex:5830: Warning: Application of '\'' on 'f' failed ./api.tex:5830: Warning: Application of '\'' on '[' failed cd docs && hevea dynamite.tex ./dynamite.tex:2: Warning: Command not found: \pdftrailerid ./dynamite.tex:2618: Warning: Command not found: \+ ./dynamite.tex:2618: Warning: Command not found: \* ./dynamite.tex:2619: Warning: Command not found: \* ./dynamite.tex:2756: Warning: Application of '\"' on ')' failed ./dynamite.tex:2756: Warning: Application of '\"' on ')' failed cd docs && hevea dynamite.tex ./dynamite.tex:2: Warning: Command not found: \pdftrailerid ./dynamite.tex:2618: Warning: Command not found: \+ ./dynamite.tex:2618: Warning: Command not found: \* ./dynamite.tex:2619: Warning: Command not found: \* ./dynamite.tex:2756: Warning: Application of '\"' on ')' failed ./dynamite.tex:2756: Warning: Application of '\"' on ')' failed cd docs && hevea wise2.tex ./wise2.tex:3: Warning: Command not found: \pdftrailerid ./wise2.tex:241: Warning: \hbox ./wise2.tex:243: Warning: \hbox ./wise2.tex:245: Warning: \hbox ./wise2.tex:247: Warning: \hbox ./wise2.tex:249: Warning: \hbox ./wise2.tex:251: Warning: \hbox ./wise2.tex:253: Warning: \hbox ./wise2.tex:255: Warning: \hbox ./wise2.tex:263: Warning: \hbox ./wise2.tex:265: Warning: \hbox ./wise2.tex:267: Warning: \hbox ./wise2.tex:269: Warning: \hbox ./wise2.tex:271: Warning: \hbox ./wise2.tex:273: Warning: \hbox ./wise2.tex:275: Warning: \hbox ./wise2.tex:277: Warning: \hbox ./wise2.tex:708: Warning: Undefined label: 'Figure:genewise21' ./wise2.tex:712: Warning: Command not found: \leavevmode ./wise2.tex:904: Warning: Command not found: \leavevmode cd docs && hevea wise2.tex ./wise2.tex:3: Warning: Command not found: \pdftrailerid ./wise2.tex:241: Warning: \hbox ./wise2.tex:243: Warning: \hbox ./wise2.tex:245: Warning: \hbox ./wise2.tex:247: Warning: \hbox ./wise2.tex:249: Warning: \hbox ./wise2.tex:251: Warning: \hbox ./wise2.tex:253: Warning: \hbox ./wise2.tex:255: Warning: \hbox ./wise2.tex:263: Warning: \hbox ./wise2.tex:265: Warning: \hbox ./wise2.tex:267: Warning: \hbox ./wise2.tex:269: Warning: \hbox ./wise2.tex:271: Warning: \hbox ./wise2.tex:273: Warning: \hbox ./wise2.tex:275: Warning: \hbox ./wise2.tex:277: Warning: \hbox ./wise2.tex:708: Warning: Undefined label: 'Figure:genewise21' ./wise2.tex:712: Warning: Command not found: \leavevmode ./wise2.tex:904: Warning: Command not found: \leavevmode mkdir -p docs/api mkdir -p docs/dynamite mkdir -p docs/wise2 mv docs/api.html docs/api mv docs/dynamite.html docs/dynamite mv docs/wise2.html docs/wise2 dh_auto_build make[1]: Leaving directory '/build/reproducible-path/wise-2.4.1' rm -f debian/wise-data.debhelper.log debian/wise-doc.debhelper.log debian/wise.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/wise-2.4.1' echo "Since a patch was used to adapt the binaries to the Debian locations of data files the test suite will not run in the build directory any more." Since a patch was used to adapt the binaries to the Debian locations of data files the test suite will not run in the build directory any more. echo "A autopkgtest was added as compensation." A autopkgtest was added as compensation. # make -C src test make[1]: Leaving directory '/build/reproducible-path/wise-2.4.1' create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/wise.substvars debian/wise-doc.substvars debian/wise-data.substvars rm -fr -- debian/.debhelper/generated/wise/ debian/wise/ debian/tmp/ debian/.debhelper/generated/wise-doc/ debian/wise-doc/ debian/.debhelper/generated/wise-data/ debian/wise-data/ dh_installdirs install -m0755 -d debian/wise/usr/bin install -m0755 -d debian/wise-data/usr/share/wise dh_install install -m0755 -d debian/wise/usr/bin cp --reflink=auto -a ./src/bin/dba ./src/bin/dnal ./src/bin/estwise ./src/bin/estwisedb ./src/bin/genewise ./src/bin/genewisedb ./src/bin/promoterwise ./src/bin/psw ./src/bin/pswdb ./src/bin/scanwise ./src/bin/scanwise_server ./src/models/genomewise debian/wise/usr/bin/ install -m0755 -d debian/wise-data/usr/share/wise cp --reflink=auto -a ./wisecfg/BLOSUM30.bla ./wisecfg/BLOSUM45.bla ./wisecfg/BLOSUM62.bla ./wisecfg/BLOSUM80.bla ./wisecfg/aa.rnd ./wisecfg/cb.tmf ./wisecfg/codon.martian ./wisecfg/codon.table ./wisecfg/gene.stat ./wisecfg/gon120.bla ./wisecfg/gon160.bla ./wisecfg/gon200.bla ./wisecfg/gon250.bla ./wisecfg/gon350.bla ./wisecfg/human.gf ./wisecfg/human.gp ./wisecfg/human.stats ./wisecfg/idenity.bla ./wisecfg/methods ./wisecfg/pb.gf ./wisecfg/pombe.gf ./wisecfg/tm.pri ./wisecfg/wag55 ./wisecfg/wag65 ./wisecfg/wag75 ./wisecfg/wag85 ./wisecfg/wise.2 ./wisecfg/wise.per ./wisecfg/worm.gf debian/wise-data/usr/share/wise/ dh_installdocs install -m0755 -d debian/wise/usr/share/doc/wise install -m0755 -d debian/wise/usr/share/doc/wise cp --reflink=auto -a ./README debian/wise/usr/share/doc/wise cp --reflink=auto -a ./debian/tests/run-unit-test debian/wise/usr/share/doc/wise chmod -R u\+rw,go=rX debian/wise/usr/share/doc install -p -m0644 debian/README.Debian debian/wise/usr/share/doc/wise/README.Debian install -p -m0644 debian/copyright debian/wise/usr/share/doc/wise/copyright install -m0755 -d debian/wise-doc/usr/share/doc/wise-doc install -m0755 -d debian/wise-doc/usr/share/doc/wise cp --reflink=auto -a ./docs/api.pdf debian/wise-doc/usr/share/doc/wise cp --reflink=auto -a ./docs/dynamite.pdf debian/wise-doc/usr/share/doc/wise cp --reflink=auto -a ./docs/wise2.pdf debian/wise-doc/usr/share/doc/wise cd './docs/api/..' && find 'api' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/reproducible-path/wise-2.4.1/debian/wise-doc/usr/share/doc/wise cd './docs/dynamite/..' && find 'dynamite' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/reproducible-path/wise-2.4.1/debian/wise-doc/usr/share/doc/wise cd './docs/wise2/..' && find 'wise2' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/reproducible-path/wise-2.4.1/debian/wise-doc/usr/share/doc/wise chmod -R u\+rw,go=rX debian/wise-doc/usr/share/doc install -p -m0644 debian/copyright debian/wise-doc/usr/share/doc/wise-doc/copyright install -m0755 -d debian/wise-doc/usr/share/doc-base/ install -p -m0644 debian/wise-doc.doc-base.api debian/wise-doc/usr/share/doc-base/wise-doc.wise-api install -p -m0644 debian/wise-doc.doc-base.dynamite debian/wise-doc/usr/share/doc-base/wise-doc.wise-dynamite install -p -m0644 debian/wise-doc.doc-base.wise debian/wise-doc/usr/share/doc-base/wise-doc.wise install -m0755 -d debian/wise-data/usr/share/doc/wise-data install -p -m0644 debian/copyright debian/wise-data/usr/share/doc/wise-data/copyright dh_installchangelogs install -m0755 -d debian/wise-data/usr/share/doc/wise-data install -p -m0644 debian/.debhelper/generated/wise-data/dh_installchangelogs.dch.trimmed debian/wise-data/usr/share/doc/wise-data/changelog.Debian install -m0755 -d debian/wise/usr/share/doc/wise install -p -m0644 debian/.debhelper/generated/wise/dh_installchangelogs.dch.trimmed debian/wise/usr/share/doc/wise/changelog.Debian install -m0755 -d debian/wise-doc/usr/share/doc/wise-doc install -p -m0644 debian/.debhelper/generated/wise-doc/dh_installchangelogs.dch.trimmed debian/wise-doc/usr/share/doc/wise-doc/changelog.Debian debian/rules override_dh_installexamples-indep make[1]: Entering directory '/build/reproducible-path/wise-2.4.1' dh_installexamples install -m0755 -d debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/basic_cdna.out debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/basic_dna.out debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/basic_genomic.out debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/dna.db debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/estwise-db.out debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/genewise-db-lite.out debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/genewise-db.out debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/genewisedb-pfam.out debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/go.evi debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/go.out debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/HMM.ascii debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/HMM.binary debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/hmm_cdna.out debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/hmm_genomic.out debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/human.genomic debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/pep.fa debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/promoterwise.out debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/pswdb.out debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/pw.human debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/pw.mouse debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/road.pep debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/rrm.HMM debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/scanwisep.out debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/short.dna debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/short.pep debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/short.test debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/testman.pl debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/wrong.hmm debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/wrong.out debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/wrong_est.out debian/wise-data/usr/share/doc/wise-data/examples sed -i -e 's?"../bin/$do"?"$do"?' -e 's?#!/usr/local/bin/perl?/usr/bin/perl?' debian/wise-data/usr/share/doc/wise-data/examples/testman.pl make[1]: Leaving directory '/build/reproducible-path/wise-2.4.1' dh_installexamples -Nwise-doc -Nwise-data dh_installman install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/dba.1 debian/wise/usr/share/man/man1/dba.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/dnal.1 debian/wise/usr/share/man/man1/dnal.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/estwise.1 debian/wise/usr/share/man/man1/estwise.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/estwisedb.1 debian/wise/usr/share/man/man1/estwisedb.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/genewise.1 debian/wise/usr/share/man/man1/genewise.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/genewisedb.1 debian/wise/usr/share/man/man1/genewisedb.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/genomewise.1 debian/wise/usr/share/man/man1/genomewise.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/promoterwise.1 debian/wise/usr/share/man/man1/promoterwise.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/psw.1 debian/wise/usr/share/man/man1/psw.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/pswdb.1 debian/wise/usr/share/man/man1/pswdb.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/scanwise.1 debian/wise/usr/share/man/man1/scanwise.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/scanwise_server.1 debian/wise/usr/share/man/man1/scanwise_server.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/dba.1 debian/wise/usr/share/man/man1/dnal.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/estwise.1 debian/wise/usr/share/man/man1/estwisedb.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/genewise.1 debian/wise/usr/share/man/man1/genewisedb.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/psw.1 debian/wise/usr/share/man/man1/pswdb.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/genomewise.1 debian/wise/usr/share/man/man1/promoterwise.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/scanwise.1 debian/wise/usr/share/man/man1/scanwise_server.1 mv debian/wise/usr/share/man/man1/estwise.1.dh-new debian/wise/usr/share/man/man1/estwise.1 mv debian/wise/usr/share/man/man1/estwisedb.1.dh-new debian/wise/usr/share/man/man1/estwisedb.1 chmod 0644 -- debian/wise/usr/share/man/man1/estwise.1 debian/wise/usr/share/man/man1/estwisedb.1 mv debian/wise/usr/share/man/man1/genomewise.1.dh-new debian/wise/usr/share/man/man1/genomewise.1 mv debian/wise/usr/share/man/man1/promoterwise.1.dh-new debian/wise/usr/share/man/man1/promoterwise.1 chmod 0644 -- debian/wise/usr/share/man/man1/genomewise.1 debian/wise/usr/share/man/man1/promoterwise.1 mv debian/wise/usr/share/man/man1/dba.1.dh-new debian/wise/usr/share/man/man1/dba.1 mv debian/wise/usr/share/man/man1/dnal.1.dh-new debian/wise/usr/share/man/man1/dnal.1 chmod 0644 -- debian/wise/usr/share/man/man1/dba.1 debian/wise/usr/share/man/man1/dnal.1 mv debian/wise/usr/share/man/man1/scanwise.1.dh-new debian/wise/usr/share/man/man1/scanwise.1 mv debian/wise/usr/share/man/man1/scanwise_server.1.dh-new debian/wise/usr/share/man/man1/scanwise_server.1 chmod 0644 -- debian/wise/usr/share/man/man1/scanwise.1 debian/wise/usr/share/man/man1/scanwise_server.1 mv debian/wise/usr/share/man/man1/psw.1.dh-new debian/wise/usr/share/man/man1/psw.1 mv debian/wise/usr/share/man/man1/pswdb.1.dh-new debian/wise/usr/share/man/man1/pswdb.1 chmod 0644 -- debian/wise/usr/share/man/man1/psw.1 debian/wise/usr/share/man/man1/pswdb.1 mv debian/wise/usr/share/man/man1/genewise.1.dh-new debian/wise/usr/share/man/man1/genewise.1 mv debian/wise/usr/share/man/man1/genewisedb.1.dh-new debian/wise/usr/share/man/man1/genewisedb.1 chmod 0644 -- debian/wise/usr/share/man/man1/genewise.1 debian/wise/usr/share/man/man1/genewisedb.1 dh_perl dh_link dh_strip_nondeterminism dh_compress cd debian/wise cd debian/wise-doc cd debian/wise-data chmod a-x usr/share/doc/wise-data/changelog.Debian gzip -9nf usr/share/doc/wise-data/changelog.Debian chmod a-x usr/share/doc/wise/changelog.Debian usr/share/man/man1/dba.1 usr/share/man/man1/dnal.1 usr/share/man/man1/estwise.1 usr/share/man/man1/estwisedb.1 usr/share/man/man1/genewise.1 usr/share/man/man1/genewisedb.1 usr/share/man/man1/genomewise.1 usr/share/man/man1/promoterwise.1 usr/share/man/man1/psw.1 usr/share/man/man1/pswdb.1 usr/share/man/man1/scanwise.1 usr/share/man/man1/scanwise_server.1 cd '/build/reproducible-path/wise-2.4.1' gzip -9nf usr/share/doc/wise/changelog.Debian usr/share/man/man1/dba.1 usr/share/man/man1/dnal.1 usr/share/man/man1/estwise.1 usr/share/man/man1/estwisedb.1 usr/share/man/man1/genewise.1 usr/share/man/man1/genewisedb.1 usr/share/man/man1/genomewise.1 usr/share/man/man1/promoterwise.1 usr/share/man/man1/psw.1 usr/share/man/man1/pswdb.1 usr/share/man/man1/scanwise.1 usr/share/man/man1/scanwise_server.1 cd '/build/reproducible-path/wise-2.4.1' chmod a-x usr/share/doc/wise-doc/changelog.Debian usr/share/doc/wise/api.pdf usr/share/doc/wise/dynamite.pdf usr/share/doc/wise/wise2.pdf gzip -9nf usr/share/doc/wise-doc/changelog.Debian usr/share/doc/wise/api.pdf usr/share/doc/wise/dynamite.pdf usr/share/doc/wise/wise2.pdf cd '/build/reproducible-path/wise-2.4.1' rm -f debian/wise-data.debhelper.log debian/wise-doc.debhelper.log debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/wise-2.4.1' dh_fixperms find debian/wise ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/wise-data ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/wise-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/wise-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/wise-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wise-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/wise-data/usr/share/doc -type f -a -true -a ! -regex 'debian/wise-data/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wise-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wise/usr/share/doc -type f -a -true -a ! -regex 'debian/wise/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wise/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/wise-data/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/wise/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wise-data -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wise -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wise/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian -iname "*.hmm" -exec chmod -x \{\} \; make[1]: Leaving directory '/build/reproducible-path/wise-2.4.1' dh_missing dh_dwz -a install -m0755 -d debian/wise/usr/lib/debug/.dwz/i386-linux-gnu dwz -mdebian/wise/usr/lib/debug/.dwz/i386-linux-gnu/wise.debug -M/usr/lib/debug/.dwz/i386-linux-gnu/wise.debug -- debian/wise/usr/bin/dba debian/wise/usr/bin/dnal debian/wise/usr/bin/estwise debian/wise/usr/bin/estwisedb debian/wise/usr/bin/genewise debian/wise/usr/bin/genewisedb debian/wise/usr/bin/genomewise debian/wise/usr/bin/promoterwise debian/wise/usr/bin/psw debian/wise/usr/bin/pswdb debian/wise/usr/bin/scanwise debian/wise/usr/bin/scanwise_server objcopy --compress-debug-sections debian/wise/usr/lib/debug/.dwz/i386-linux-gnu/wise.debug chmod 0644 -- debian/wise/usr/lib/debug/.dwz/i386-linux-gnu/wise.debug dh_strip -a install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/be objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/be/428782ad2b76c9582c768d4a0bde250ce94ebc.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/be/428782ad2b76c9582c768d4a0bde250ce94ebc.debug strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewise objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/be/428782ad2b76c9582c768d4a0bde250ce94ebc.debug debian/wise/usr/bin/genewise install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/9e objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/9e/188079903d2ef30eec16461616818f33bf5d7f.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/9e/188079903d2ef30eec16461616818f33bf5d7f.debug strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwisedb objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/9e/188079903d2ef30eec16461616818f33bf5d7f.debug debian/wise/usr/bin/estwisedb install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b2 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dba debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b2/b81f4514d6d515a18485d64ce60a46680832cd.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b2/b81f4514d6d515a18485d64ce60a46680832cd.debug strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dba objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b2/b81f4514d6d515a18485d64ce60a46680832cd.debug debian/wise/usr/bin/dba install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d4 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/psw debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d4/5847b600ab5a6a8f6adeec8545789ab1b3434e.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d4/5847b600ab5a6a8f6adeec8545789ab1b3434e.debug strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/psw objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d4/5847b600ab5a6a8f6adeec8545789ab1b3434e.debug debian/wise/usr/bin/psw install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/66 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dnal debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/66/7657120013b02d53aae5dbeed4b615ab6e5356.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/66/7657120013b02d53aae5dbeed4b615ab6e5356.debug strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dnal objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/66/7657120013b02d53aae5dbeed4b615ab6e5356.debug debian/wise/usr/bin/dnal install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/15 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise_server debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/15/3d115572107bf39211a00d09943cb29d9dc405.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/15/3d115572107bf39211a00d09943cb29d9dc405.debug strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise_server objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/15/3d115572107bf39211a00d09943cb29d9dc405.debug debian/wise/usr/bin/scanwise_server install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/15 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/15/b71fd1f83f767f96ea1987c77a793d2ba0d27a.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/15/b71fd1f83f767f96ea1987c77a793d2ba0d27a.debug strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewisedb objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/15/b71fd1f83f767f96ea1987c77a793d2ba0d27a.debug debian/wise/usr/bin/genewisedb install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/8b objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/8b/9831f5876d3702924b10fd5d1372de0a1ad042.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/8b/9831f5876d3702924b10fd5d1372de0a1ad042.debug strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/8b/9831f5876d3702924b10fd5d1372de0a1ad042.debug debian/wise/usr/bin/scanwise install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/1e objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genomewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/1e/efbcf65b9772ce30ff9f9808a47aa77895baf4.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/1e/efbcf65b9772ce30ff9f9808a47aa77895baf4.debug strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genomewise objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/1e/efbcf65b9772ce30ff9f9808a47aa77895baf4.debug debian/wise/usr/bin/genomewise install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/55 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/pswdb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/55/28750be65971e7d0d85b4020e53f5894a2fcc7.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/55/28750be65971e7d0d85b4020e53f5894a2fcc7.debug strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/pswdb objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/55/28750be65971e7d0d85b4020e53f5894a2fcc7.debug debian/wise/usr/bin/pswdb install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/c2 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/promoterwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/c2/5172c15b5ed33b5715501e82078e0194cdea09.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/c2/5172c15b5ed33b5715501e82078e0194cdea09.debug strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/promoterwise objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/c2/5172c15b5ed33b5715501e82078e0194cdea09.debug debian/wise/usr/bin/promoterwise install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/de objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/de/77d8aa72b59fa4ec38975fb4eaf1551e9830ff.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/de/77d8aa72b59fa4ec38975fb4eaf1551e9830ff.debug strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwise objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/de/77d8aa72b59fa4ec38975fb4eaf1551e9830ff.debug debian/wise/usr/bin/estwise install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/wise/usr/lib/debug/.dwz/i386-linux-gnu debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/wise/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/wise/usr/lib/debug install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/share/doc ln -s wise debian/.debhelper/wise/dbgsym-root/usr/share/doc/wise-dbgsym install -m0755 -d debian/.debhelper/wise dh_makeshlibs -a rm -f debian/wise/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/wise/DEBIAN dpkg-shlibdeps -Tdebian/wise.substvars debian/wise/usr/bin/genewise debian/wise/usr/bin/estwisedb debian/wise/usr/bin/dba debian/wise/usr/bin/psw debian/wise/usr/bin/dnal debian/wise/usr/bin/scanwise_server debian/wise/usr/bin/genewisedb debian/wise/usr/bin/scanwise debian/wise/usr/bin/genomewise debian/wise/usr/bin/pswdb debian/wise/usr/bin/promoterwise debian/wise/usr/bin/estwise dh_installdeb install -m0755 -d debian/wise/DEBIAN install -m0755 -d debian/wise-doc/DEBIAN install -m0755 -d debian/wise-data/DEBIAN dh_gencontrol install -m0755 -d debian/wise/DEBIAN echo misc:Depends= >> debian/wise.substvars echo misc:Pre-Depends= >> debian/wise.substvars install -m0755 -d debian/.debhelper/wise/dbgsym-root/DEBIAN dpkg-gencontrol -pwise -ldebian/changelog -Tdebian/wise.substvars -cdebian/control -Pdebian/.debhelper/wise/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=wise-dbgsym "-DDepends=wise (= \${binary:Version})" "-DDescription=debug symbols for wise" "-DBuild-Ids=153d115572107bf39211a00d09943cb29d9dc405 15b71fd1f83f767f96ea1987c77a793d2ba0d27a 1eefbcf65b9772ce30ff9f9808a47aa77895baf4 5528750be65971e7d0d85b4020e53f5894a2fcc7 667657120013b02d53aae5dbeed4b615ab6e5356 8b9831f5876d3702924b10fd5d1372de0a1ad042 9e188079903d2ef30eec16461616818f33bf5d7f b2b81f4514d6d515a18485d64ce60a46680832cd be428782ad2b76c9582c768d4a0bde250ce94ebc c25172c15b5ed33b5715501e82078e0194cdea09 d45847b600ab5a6a8f6adeec8545789ab1b3434e de77d8aa72b59fa4ec38975fb4eaf1551e9830ff" -DSection=debug -UMulti-Arch -UReplaces -UBreaks install -m0755 -d debian/wise-data/DEBIAN echo misc:Depends= >> debian/wise-data.substvars echo misc:Pre-Depends= >> debian/wise-data.substvars dpkg-gencontrol -pwise-data -ldebian/changelog -Tdebian/wise-data.substvars -cdebian/control -Pdebian/wise-data install -m0755 -d debian/wise-doc/DEBIAN echo misc:Depends= >> debian/wise-doc.substvars echo misc:Pre-Depends= >> debian/wise-doc.substvars dpkg-gencontrol -pwise-doc -ldebian/changelog -Tdebian/wise-doc.substvars -cdebian/control -Pdebian/wise-doc chmod 0644 -- debian/wise-doc/DEBIAN/control chmod 0644 -- debian/wise-data/DEBIAN/control chmod 0644 -- debian/.debhelper/wise/dbgsym-root/DEBIAN/control dpkg-gencontrol -pwise -ldebian/changelog -Tdebian/wise.substvars -cdebian/control -Pdebian/wise chmod 0644 -- debian/wise/DEBIAN/control dh_md5sums install -m0755 -d debian/wise/DEBIAN install -m0755 -d debian/wise-data/DEBIAN cd debian/wise-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/wise >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums install -m0755 -d debian/wise-doc/DEBIAN cd debian/wise-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/wise/DEBIAN/md5sums install -m0755 -d debian/.debhelper/wise/dbgsym-root/DEBIAN cd debian/.debhelper/wise/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/wise-data/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/wise/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/wise-doc/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/wise .. dpkg-deb --root-owner-group --build debian/wise-doc .. dpkg-deb: building package 'wise' in '../wise_2.4.1-25_i386.deb'. dpkg-deb: building package 'wise-doc' in '../wise-doc_2.4.1-25_all.deb'. dpkg-deb --root-owner-group --build debian/wise-data .. dpkg-deb --root-owner-group --build debian/.debhelper/wise/dbgsym-root .. dpkg-deb: building package 'wise-data' in '../wise-data_2.4.1-25_all.deb'. dpkg-deb: building package 'wise-dbgsym' in '../wise-dbgsym_2.4.1-25_i386.deb'. dpkg-genbuildinfo --build=binary -O../wise_2.4.1-25_i386.buildinfo dpkg-genchanges --build=binary -O../wise_2.4.1-25_i386.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/28329 and its subdirectories I: Current time: Thu Aug 15 06:30:49 -12 2024 I: pbuilder-time-stamp: 1723746649 Thu Aug 15 18:30:51 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom08-i386.debian.net. Thu Aug 15 18:30:51 UTC 2024 I: Preparing to do remote build '2' on infom08-i386.debian.net. Thu Aug 15 18:33:07 UTC 2024 I: Deleting $TMPDIR on infom08-i386.debian.net. Thu Aug 15 18:33:08 UTC 2024 I: wise_2.4.1-25_i386.changes: Format: 1.8 Date: Thu, 15 Aug 2024 12:15:41 +0200 Source: wise Binary: wise wise-data wise-dbgsym wise-doc Architecture: all i386 Version: 2.4.1-25 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: wise - comparison of biopolymers, like DNA and protein sequences wise-data - data files for the wise package wise-doc - documentation for the wise package Closes: 1075638 Changes: wise (2.4.1-25) unstable; urgency=medium . * Team upload. * gcc-14.patch: fix multiple build failures with gcc 14. Note that the patch alone is not sufficient as such as motifmatrix.c is still affected by a case of assignment to integer from pointer without a cast which feels like a compiler bug. See #1075638. * d/control: build depends on the libfl-dev. Apparently the missing libl.a went below the radar for building dyc. * d/rules: build and provide the dyc compiler to the rest of the build. * d/rules: work around weird compiler behavior. (Closes: #1075638) * d/control: declare compliance to standards version 4.7.0. Checksums-Sha1: 2788d34754cb5d92633f5322993d776fd036672a 76128 wise-data_2.4.1-25_all.deb 9b1037006e94e44c0785512e4f43a60be1f37675 6789740 wise-dbgsym_2.4.1-25_i386.deb a2b6dedf6d2ed469ecf8b20e1401780a5ae5b2e5 827360 wise-doc_2.4.1-25_all.deb f0d8ec90ad0d5fb41b24eb654b59b4add56cf2ac 10481 wise_2.4.1-25_i386.buildinfo 09fa3ba3446e7ef7e549dc38396b82c739b459e8 1119964 wise_2.4.1-25_i386.deb Checksums-Sha256: 7c1cb88bded495690f2263bd098baeae9da340585c888f6d418f8c39cda2ba35 76128 wise-data_2.4.1-25_all.deb b3757c83cf856946c32d3ad77055af7b0415326aeaa28a5ac3633c468f3f0bff 6789740 wise-dbgsym_2.4.1-25_i386.deb 199592ee8b83facf55930fb00954a9c6bb5cafe89cd1061003a13c552e82870c 827360 wise-doc_2.4.1-25_all.deb 9ff65ab0b37fd5730757636f786da82321e1fa942190a826b2e69e8368054820 10481 wise_2.4.1-25_i386.buildinfo b7f3c7a6ccf68a254bbe1786a7ace77c171d35417a0203bf6366d135fa504544 1119964 wise_2.4.1-25_i386.deb Files: 528f9491d9a5f692417a26aa6582f118 76128 doc optional wise-data_2.4.1-25_all.deb c645e4786ca3ad8c5253275ef974c4c3 6789740 debug optional wise-dbgsym_2.4.1-25_i386.deb 9bf799b36d426a0dba58210299d60610 827360 doc optional wise-doc_2.4.1-25_all.deb 51e9b3dc30179b07f8fe9b50d3e18714 10481 science optional wise_2.4.1-25_i386.buildinfo 7f38d2c8fdfa034874ffdb1e561b4b01 1119964 science optional wise_2.4.1-25_i386.deb Thu Aug 15 18:33:09 UTC 2024 I: diffoscope 274 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_15-32721.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.arrGDNNn/wise_2.4.1-25.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.arrGDNNn/wise_2.4.1-25.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.arrGDNNn/wise_2.4.1-25.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.arrGDNNn/b1/wise_2.4.1-25_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.arrGDNNn/b2/wise_2.4.1-25_i386.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: 0.485s) 0.485s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.111s) 0.111s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 851ms CPU time consumed: 853ms Thu Aug 15 18:33:11 UTC 2024 I: diffoscope 274 found no differences in the changes files, and a .buildinfo file also exists. Thu Aug 15 18:33:11 UTC 2024 I: wise from unstable built successfully and reproducibly on i386. Thu Aug 15 18:33:12 UTC 2024 I: Submitting .buildinfo files to external archives: Thu Aug 15 18:33:12 UTC 2024 I: Submitting 12K b1/wise_2.4.1-25_i386.buildinfo.asc Thu Aug 15 18:33:13 UTC 2024 I: Submitting 12K b2/wise_2.4.1-25_i386.buildinfo.asc Thu Aug 15 18:33:14 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Aug 15 18:33:14 UTC 2024 I: Done submitting .buildinfo files. Thu Aug 15 18:33:14 UTC 2024 I: Removing signed wise_2.4.1-25_i386.buildinfo.asc files: removed './b1/wise_2.4.1-25_i386.buildinfo.asc' removed './b2/wise_2.4.1-25_i386.buildinfo.asc'