Running as unit: rb-build-amd64_36-80962.service; invocation ID: 1e04a1d86ef4402ab18badcd3a96a5dd ==================================================================================== Thu Sep 18 01:11:49 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_36) on jenkins, called using "infom02-amd64 infom01-amd64" as arguments. Thu Sep 18 01:11:49 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-IYHRrHMK" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Sep 18 01:11:49 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom02-amd64.debian.net is marked as down. Thu Sep 18 01:11:49 UTC 2025 - checking via ssh if infom02-amd64.debian.net is up. removed '/tmp/read-only-fs-test-4Iegjl' Thu Sep 18 01:11:50 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom01-amd64.debian.net is marked as down. Thu Sep 18 01:11:50 UTC 2025 - checking via ssh if infom01-amd64.debian.net is up. removed '/tmp/read-only-fs-test-cTpvoP' ok, let's check if altree is building anywhere yet… ok, altree is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of altree in unstable on amd64 on jenkins now. 1st build will be done on infom02-amd64.debian.net. 2nd build will be done on infom01-amd64.debian.net. ============================================================================= Thu Sep 18 01:11:52 UTC 2025 I: starting to build altree/unstable/amd64 on jenkins on '2025-09-18 01:11' Thu Sep 18 01:11:52 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_36/80962/console.log 1758157912 amd64 unstable altree Thu Sep 18 01:11:52 UTC 2025 I: Downloading source for unstable/altree=1.3.2-4 --2025-09-18 01:11:52-- http://deb.debian.org/debian/pool/main/a/altree/altree_1.3.2-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2535 (2.5K) [text/prs.lines.tag] Saving to: ‘altree_1.3.2-4.dsc’ 0K .. 100% 29.1M=0s 2025-09-18 01:11:52 (29.1 MB/s) - ‘altree_1.3.2-4.dsc’ saved [2535/2535] --2025-09-18 01:11:52-- http://deb.debian.org/debian/pool/main/a/altree/altree_1.3.2-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2535 (2.5K) [text/prs.lines.tag] Saving to: ‘altree_1.3.2-4.dsc’ 0K .. 100% 29.1M=0s 2025-09-18 01:11:52 (29.1 MB/s) - ‘altree_1.3.2-4.dsc’ saved [2535/2535] Thu Sep 18 01:11:52 UTC 2025 I: altree_1.3.2-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: altree Binary: altree, altree-examples Architecture: any all Version: 1.3.2-4 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Vincent Danjean , Andreas Tille Homepage: https://gitlab.inria.fr/NGS/ALTree Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/altree Vcs-Git: https://salsa.debian.org/med-team/altree.git Testsuite: autopkgtest Build-Depends: bash-completion, debhelper-compat (= 13), perl:native, perl-xs-dev, latex-make , ghostscript , texlive-lang-french , texlive-latex-extra , texlive-latex-recommended , texlive-fonts-recommended , libmath-tamuanova-perl , libgsl-dev, libblas-dev | libblas.so, libtest-deep-perl , fig2dev Package-List: altree deb science optional arch=any altree-examples deb science optional arch=all Checksums-Sha1: 095d136e5ffbeeb2f0e0da550a8a06e8ff5ca7f0 610823 altree_1.3.2.orig.tar.gz 9eea3bc6fd990154c1114fcc4152f8433a928ba9 8600 altree_1.3.2-4.debian.tar.xz Checksums-Sha256: f9d5beda91aaab219e1397b4c19e0649788a871c8c29fa1e8343a53c5f710b8e 610823 altree_1.3.2.orig.tar.gz 7a5fbcde62b2fcf6574d0e8a7f93d251052a7e8e7d28f2d40306df95d6c33cdf 8600 altree_1.3.2-4.debian.tar.xz Files: fd17066d7f6bc07baacf526ff3ee1c3b 610823 altree_1.3.2.orig.tar.gz 6a0c58fdbbec7352b2c4191fab69612a 8600 altree_1.3.2-4.debian.tar.xz Dgit: d47aaa76f33b223dbc6ef2dcac903f2235815635 debian archive/debian/1.3.2-4 https://git.dgit.debian.org/altree -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmjLBX8UHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdo+2w/5AdN4l/fz/jwYIyC/Y2yK0q8SxfAg pieIP0NbTmhZ3/p+xMX+oG7FuhvmM4YOwJzp4Cm9gaXVj5pRLwto1P9YASB/cmz/ xObBRRVlxXgqApcCDPknamep92XxJ+yip4601VvG65n6rDR9vNG2lBeSlPgipNO3 v8+xqv2YzUxTvBWEgnBs1uFhhCZauxAFDpEejXk+VUOpAPicGW/v0vtznLp9ds+E IHDfMyBeKPP5WO8p7Td6YQIuM0C7aya0/s89csonbrdD3EwQpnXm+nn6mbEfpKlG dqLKGbUnBF33U4jG6x3sU0sW8uR9M7eYQIlXHOpNruL/qzltaFb8eWO+DgCFvcNB ebUxJcSY3CL+ck/61DJbF3FsMB8TUye0jVLDlNOjWMQ0WumoWlyp1xwdMFI9uXCZ DyIPvGxZVEIk4XGsOpB2XZTuDOND9+1+u/ehNOvDdEb0CUt4SdQGN+TzoxVSPGdj yRrEuImUfOUUr0Z/VkRrUEUnldPahpd6u8SMM5ps09cQLlBeG2i3RNP2FWnQ6lLF x5rrQl8/Wh1jmHExVaVh0oocu3nnZXF0q4YsmxaqdrwYCPdqmror9CuPwT79RS8L sTIBDDvUTTiqq0g9T+093NvjmPqOqwrc7G76Gw+aJ3vkCVSskcCDWt/l2slc/cc0 urzG6Ztw5JgshQ0= =fRO8 -----END PGP SIGNATURE----- Thu Sep 18 01:11:52 UTC 2025 I: Checking whether the package is not for us Thu Sep 18 01:11:52 UTC 2025 I: Starting 1st build on remote node infom02-amd64.debian.net. Thu Sep 18 01:11:52 UTC 2025 I: Preparing to do remote build '1' on infom02-amd64.debian.net. Thu Sep 18 01:11:52 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom02-amd64.debian.net is marked as down. Thu Sep 18 01:11:52 UTC 2025 - checking via ssh if infom02-amd64.debian.net is up. removed '/tmp/read-only-fs-test-jOhBIa' ==================================================================================== Wed Oct 21 07:34:53 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on infom02-amd64, called using "1 altree unstable /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm 1.3.2-4" as arguments. Wed Oct 21 07:34:53 UTC 2026 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-u6L3LLLi" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Oct 21 07:34:53 UTC 2026 I: Downloading source for unstable/altree=1.3.2-4 Reading package lists... NOTICE: 'altree' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/altree.git Please use: git clone https://salsa.debian.org/med-team/altree.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 622 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main altree 1.3.2-4 (dsc) [2535 B] Get:2 http://deb.debian.org/debian unstable/main altree 1.3.2-4 (tar) [611 kB] Get:3 http://deb.debian.org/debian unstable/main altree 1.3.2-4 (diff) [8600 B] Fetched 622 kB in 0s (3652 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'altree' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/altree.git Please use: git clone https://salsa.debian.org/med-team/altree.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 622 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main altree 1.3.2-4 (dsc) [2535 B] Get:2 http://deb.debian.org/debian unstable/main altree 1.3.2-4 (tar) [611 kB] Get:3 http://deb.debian.org/debian unstable/main altree 1.3.2-4 (diff) [8600 B] Fetched 622 kB in 0s (3652 kB/s) Download complete and in download only mode ============================================================================= Building altree in unstable on amd64 on infom02-amd64 now. Date: Wed Oct 21 07:34:54 UTC 2026 Date UTC: Wed Oct 21 07:34:54 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Tue Oct 20 19:34:54 -12 2026 I: pbuilder-time-stamp: 1792568094 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: Copying source file I: copying [altree_1.3.2-4.dsc] I: copying [./altree_1.3.2.orig.tar.gz] I: copying [./altree_1.3.2-4.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./altree_1.3.2-4.dsc: no acceptable signature found dpkg-source: info: extracting altree in altree-1.3.2 dpkg-source: info: unpacking altree_1.3.2.orig.tar.gz dpkg-source: info: unpacking altree_1.3.2-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc-15.patch dpkg-source: info: applying typo.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1210918/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='0431957afced46ecb2038fbd6b63d63b' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1210918' 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.2NH9R5Xm/pbuilderrc_Tq6n --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.2NH9R5Xm/b1 --logfile b1/build.log altree_1.3.2-4.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' 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 infom02-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1210918/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: bash-completion, debhelper-compat (= 13), perl:native, perl-xs-dev, latex-make, ghostscript, texlive-lang-french, texlive-latex-extra, texlive-latex-recommended, texlive-fonts-recommended, libmath-tamuanova-perl, libgsl-dev, libblas-dev | libblas.so, libtest-deep-perl, fig2dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 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 bash-completion; however: Package bash-completion is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on perl:native. pbuilder-satisfydepends-dummy depends on perl-xs-dev; however: Package perl-xs-dev is not installed. pbuilder-satisfydepends-dummy depends on latex-make; however: Package latex-make is not installed. pbuilder-satisfydepends-dummy depends on ghostscript; however: Package ghostscript is not installed. pbuilder-satisfydepends-dummy depends on texlive-lang-french; however: Package texlive-lang-french is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however: Package texlive-latex-extra is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-recommended; however: Package texlive-latex-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however: Package texlive-fonts-recommended is not installed. pbuilder-satisfydepends-dummy depends on libmath-tamuanova-perl; however: Package libmath-tamuanova-perl is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev | libblas.so; however: Package libblas-dev is not installed. Package libblas.so is not installed. pbuilder-satisfydepends-dummy depends on libtest-deep-perl; however: Package libtest-deep-perl is not installed. pbuilder-satisfydepends-dummy depends on fig2dev; however: Package fig2dev 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} bash-completion{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} fig2dev{a} file{a} fontconfig-config{a} fonts-lmodern{a} fonts-urw-base35{a} gawk{a} gettext{a} gettext-base{a} ghostscript{a} groff-base{a} intltool-debian{a} latex-make{a} libapache-pom-java{a} libarchive-zip-perl{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libblas-dev{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcommons-logging-java{a} libcommons-parent-java{a} libcups2t64{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontbox-java{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libglib2.0-0t64{a} libgnutls30t64{a} libgraphite2-3{a} libgs-common{a} libgs10{a} libgs10-common{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libice6{a} libicu76{a} libidn12{a} libidn2-0{a} libijs-0.35{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libmath-tamuanova-perl{a} libmpfi0{a} libnetpbm11t64{a} libopenjp2-7{a} libp11-kit0{a} libpaper-utils{a} libpaper2{a} libpdfbox-java{a} libperl-dev{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpotrace0{a} libproc2-0{a} libptexenc1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libsharpyuv0{a} libsm6{a} libsynctex2{a} libtamuanova-0.2{a} libtasn1-6{a} libteckit0{a} libtest-deep-perl{a} libtexlua53-5{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libtiff6{a} libtool{a} libuchardet0{a} libunistring5{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} libxml2-16{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6t64{a} libzzip-0-13t64{a} m4{a} man-db{a} media-types{a} netbase{a} netpbm{a} po-debconf{a} poppler-data{a} preview-latex-style{a} procps{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} t1utils{a} tex-common{a} texlive-base{a} texlive-binaries{a} texlive-fonts-recommended{a} texlive-lang-french{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} tzdata{a} ucf{a} x11-common{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl dbus default-jre dvisvgm fonts-droid-fallback inkscape krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libltdl-dev libmail-sendmail-perl libnet-dbus-perl libspreadsheet-parseexcel-perl libx11-protocol-perl linux-sysctl-defaults lmodern lynx psmisc ruby shared-mime-info tex-gyre texlive-plain-generic tipa tk wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 155 newly installed, 0 to remove and 0 not upgraded. Need to get 322 MB of archives. After unpacking 809 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 gawk amd64 1:5.3.2-1 [772 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.2-1 [111 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 poppler-data all 0.4.12-1 [1601 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-5 [260 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 bash-completion all 1:2.16.0-7 [319 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B] Get: 31 http://deb.debian.org/debian unstable/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get: 32 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0052 [43.3 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 44 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.50-1 [282 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+25 [217 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libgs-common all 10.05.1~dfsg-3 [149 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libgs10-common all 10.05.1~dfsg-3 [479 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-17 [112 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-17 [47.3 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.16.2-2 [178 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-17 [52.1 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 74 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.10-4 [267 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2.4 [318 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2.4 [401 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libidn12 amd64 1.43-2 [48.3 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libijs-0.35 amd64 0.35-16 [16.0 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libjbig2dec0 amd64 0.20-1+b3 [65.1 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [204 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libpaper2 amd64 2.2.5-0.3+b2 [16.7 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.7.0-5 [364 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.6-1 [37.3 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [208 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libgs10 amd64 10.05.1~dfsg-3 [2732 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 ghostscript amd64 10.05.1~dfsg-3 [50.5 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libnetpbm11t64 amd64 2:11.11.01-1 [194 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 netpbm amd64 2:11.11.01-1 [2140 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 fig2dev amd64 1:3.2.9a-4 [449 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 tex-common all 6.19 [29.4 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 latex-make all 2.4.3-1 [1030 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 33-2 [5852 B] Get: 109 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.1-7 [229 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.3.0-2 [68.6 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.84.4-3 [1518 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-7 [76.3 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5.1 [137 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5.1 [1068 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-5.1 [1336 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 11.4.5-1 [505 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libicu76 amd64 76.1-4 [9722 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libkpathsea6 amd64 2025.20250727.75242+ds-4 [154 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libtamuanova-0.2 amd64 0.2-5+b3 [9228 B] Get: 129 http://deb.debian.org/debian unstable/main amd64 libmath-tamuanova-perl amd64 1.0.2-4+b2 [13.9 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libmpfi0 amd64 1.5.4+ds-4 [35.5 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 2.2.5-0.3+b2 [16.5 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libperl-dev amd64 5.40.1-6 [1109 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libpotrace0 amd64 1.16-2+b2 [25.6 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libptexenc1 amd64 2025.20250727.75242+ds-4 [50.5 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libsynctex2 amd64 2025.20250727.75242+ds-4 [58.2 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libteckit0 amd64 2.5.12+ds1-1+b1 [341 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libtest-deep-perl all 1.205-1 [52.3 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libtexlua53-5 amd64 2025.20250727.75242+ds-4 [99.4 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libxmu6 amd64 2:1.1.3-3+b4 [59.0 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libxpm4 amd64 1:3.5.17-1+b3 [56.2 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libxaw7 amd64 2:1.0.16-1 [212 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libzzip-0-13t64 amd64 0.13.78+dfsg.1-0.1 [59.0 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 preview-latex-style all 13.2-1.1 [350 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 texlive-binaries amd64 2025.20250727.75242+ds-4 [7261 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 texlive-base all 2025.20250727-3 [23.1 MB] Get: 150 http://deb.debian.org/debian unstable/main amd64 texlive-fonts-recommended all 2025.20250727-3 [4991 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 texlive-lang-french all 2025.20250727-3 [149 MB] Get: 152 http://deb.debian.org/debian unstable/main amd64 texlive-latex-base all 2025.20250727-3 [1318 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 texlive-latex-recommended all 2025.20250727-3 [8454 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 texlive-pictures all 2025.20250727-3 [22.1 MB] Get: 155 http://deb.debian.org/debian unstable/main amd64 texlive-latex-extra all 2025.20250727-3 [27.4 MB] Fetched 322 MB in 4s (74.3 MB/s) Preconfiguring packages ... Selecting previously unselected package readline-common. (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 ... 19917 files and directories currently installed.) Preparing to unpack .../readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../libreadline8t64_8.3-3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Setting up readline-common (8.3-3) ... Setting up libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package gawk. (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 ... 19949 files and directories currently installed.) Preparing to unpack .../gawk_1%3a5.3.2-1_amd64.deb ... Unpacking gawk (1:5.3.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.7.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.2-1) ... Selecting previously unselected package poppler-data. Preparing to unpack .../poppler-data_0.4.12-1_all.deb ... Unpacking poppler-data (0.4.12-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.7-1_amd64.deb ... Unpacking python3.13-minimal (3.13.7-1) ... Setting up libpython3.13-minimal:amd64 (3.13.7-1) ... Setting up libexpat1:amd64 (2.7.2-1) ... Setting up python3.13-minimal (3.13.7-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21010 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_amd64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... 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(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 ... 21993 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.7-1_amd64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-9_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-9) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-9_amd64.deb ... Unpacking procps (2:4.0.4-9) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/altree-1.3.2/ && 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 > ../altree_1.3.2-4_source.changes dpkg-buildpackage: info: source package altree dpkg-buildpackage: info: source version 1.3.2-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules execute_before_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/altree-1.3.2' /usr/bin/make -C Documentation distclean || true make[2]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[2]: Nothing to be done for 'distclean'. make[2]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro" Checking if your kit is complete... Warning: the following files are missing in your kit: CUtils/c_sources/MYMETA.json CUtils/MYMETA.json MYMETA.json Please inform the author. MakeMaker (v7.70) Warning (non-fatal): Target 'dynamic' depends on targets in skipped section 'dynamic_lib' Warning (non-fatal): Target 'static' depends on targets in skipped section 'static_lib' Generating a Unix-style Makefile Writing Makefile for ALTree::CUtils Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for ALTree::CUtils Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for altree Writing MYMETA.yml and MYMETA.json debian/rules execute_before_dh_auto_build make[1]: Entering directory '/build/reproducible-path/altree-1.3.2' /usr/bin/make -C Documentation pdf make[2]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_SAVE make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[3]: Nothing to be done for 'LU_WATCH_FILES_SAVE'. make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' ======> building manual.pdf <====== Running: 'pdflatex' '--interaction' 'errorstopmode' '--jobname' 'manual' '\RequirePackage[extension=.pdf]{texdepends}\input{manual.tex}' Package texdepends Warning: graphicspath already redefined. Skipping it. on input line 36. Package texdepends Warning: Diverting empty macro 'Ginclude@eps' (texdepends) Probably a bug in texdepends.sty. Package texdepends Warning: Gin@getbase already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@pdf already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@pdf already redefined. Skipping it. on input line 87. Chapter 1. LaTeX Warning: Reference `fig:altree' on page 2 undefined on input line 121. Package texdepends Warning: No 'fig/overview.pdftex' file (texdepends) using 1 for graphic dimensions on input line 124. Package texdepends Warning: Figure 'fig/overview.pdftex_t' needed (texdepends) Skipping it this time (the last one however) (texdepends) on input line 124. LaTeX Warning: Reference `fig:nesting_algo' on page 2 undefined on input line 143. Package natbib Warning: Citation `Bardel05' on page 2 undefined on input line 143. Package natbib Warning: Citation `Ge03' on page 2 undefined on input line 146. Package natbib Warning: Citation `Becker04' on page 2 undefined on input line 146. Package texdepends Warning: No 'fig/altree-q.pdftex' file (texdepends) using 1 for graphic dimensions on input line 150. Package texdepends Warning: Figure 'fig/altree-q.pdftex_t' needed (texdepends) Skipping it this time (the last one however) (texdepends) on input line 150. LaTeX Warning: `h' float specifier changed to `ht'. Package natbib Warning: Citation `Bardel05' on page 4 undefined on input line 180. Package natbib Warning: Citation `Stephens01' on page 5 undefined on input line 197. Package natbib Warning: Citation `Stephens03' on page 5 undefined on input line 197. Package natbib Warning: Citation `Becker04' on page 5 undefined on input line 198. Package natbib Warning: Citation `Swofford02' on page 5 undefined on input line 199. Package natbib Warning: Citation `Felsenstein04' on page 5 undefined on input line 200. Package natbib Warning: Citation `YangPAML' on page 5 undefined on input line 200. Underfull \hbox (badness 1454) in paragraph at lines 196--201 []\T1/ptm/m/n/10.95 Currently, \T1/pcr/m/n/10.95 ALTree-convert \T1/ptm/m/n/10. Chapter 2. Package natbib Warning: Citation `Swofford02' on page 7 undefined on input line 278. Package natbib Warning: Citation `Felsenstein04' on page 7 undefined on input line 281. Underfull \hbox (badness 1142) in paragraph at lines 281--284 []\T1/pcr/m/n/10.95 phylip \T1/ptm/b/n/10.95 ?\T1/ptm/m/n/10.95 : freely avail- Package natbib Warning: Citation `YangPAML' on page 7 undefined on input line 284. Package natbib Warning: Citation `Guindon03' on page 7 undefined on input line 288. Underfull \hbox (badness 2486) in paragraph at lines 284--290 []\T1/pcr/m/n/10.95 paml \T1/ptm/b/n/10.95 ?\T1/ptm/m/n/10.95 : freely avail-ab Underfull \hbox (badness 10000) in paragraph at lines 314--315 Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 369--369 []|\T1/ptm/m/n/10.95 Output con-tain-ing the num-ber of Overfull \hbox (2.0805pt too wide) in paragraph at lines 355--370 [] Underfull \hbox (badness 10000) in paragraph at lines 396--397 Underfull \hbox (badness 10000) in paragraph at lines 400--401 Underfull \hbox (badness 10000) in paragraph at lines 416--417 Underfull \hbox (badness 1112) in paragraph at lines 505--507 []\T1/ptm/m/n/10.95 Other ex-am-ples may be found in the test di-rec-tory. Thes Chapter 4. Overfull \hbox (2.0805pt too wide) in paragraph at lines 537--553 [] LaTeX Warning: Reference `help' on page 13 undefined on input line 564. Overfull \hbox (8.63097pt too wide) in paragraph at lines 584--605 \T1/ptm/m/n/10.95 Examples: $[]$ $[]$ LaTeX Warning: Reference `description_etiquette' on page 14 undefined on input line 632. LaTeX Warning: Reference `description_etiquette' on page 14 undefined on input line 633. Package natbib Warning: Citation `Bardel05' on page 14 undefined on input line 634. LaTeX Warning: Reference `description_etiquette' on page 15 undefined on input line 649. LaTeX Warning: Reference `description_etiquette' on page 15 undefined on input line 649. Chapter 5. Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --data-qual|-q Underfull \hbox (badness 1281) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 remove the out-group se-quence for the Underfull \hbox (badness 5681) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 ancestral se-quence (only use-ful with Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --tree-building-program|-p Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --s-site-characters Underfull \hbox (badness 1565) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 print the tree with the char-ac-ter state Overfull \hbox (2.0805pt too wide) in paragraph at lines 664--698 [] LaTeX Warning: Reference `help' on page 16 undefined on input line 701. Underfull \hbox (badness 10000) in paragraph at lines 735--738 Underfull \hbox (badness 1622) in paragraph at lines 747--755 \T1/ptm/m/n/10.95 Example of such files are given in the test di-rec-tory. Thes Package natbib Warning: Citation `Ge03' on page 19 undefined on input line 830. Package natbib Warning: Citation `Becker04' on page 19 undefined on input line 830. LaTeX Warning: Reference `fig:option_b' on page 19 undefined on input line 846. LaTeX Warning: File `option_b.fig' not found on input line 852. Package texdepends Warning: No 'fig/option_b_1.pdftex' file (texdepends) using 1 for graphic dimensions on input line 852. Package texdepends Warning: Figure 'fig/option_b_1.fig' needed (texdepends) Skipping it this time (the last one however) (texdepends) on input line 852. LaTeX Warning: File `option_b.fig' not found on input line 853. Package texdepends Warning: No 'fig/option_b_2.pdftex' file (texdepends) using 1 for graphic dimensions on input line 853. 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Underfull \hbox (badness 2662) in paragraph at lines 1188--1195 \T1/ptm/m/n/10.95 The files nec-es-sary for the phy-lo-ge-netic re-con-struc-ti Package texdepends Warning: No 'fig/association_paml.pdftex' file (texdepends) using 1 for graphic dimensions on input line 1217. Package texdepends Warning: Figure 'fig/association_paml.pdftex_t' needed (texdepends) Skipping it this time (the last one however) (texdepends) on input line 1217. Underfull \hbox (badness 10000) in paragraph at lines 1247--1249 []\T1/ptm/m/n/10.95 a bash script con-tain-ing the three com-mand lines to run Package texdepends Warning: No 'fig/localisation_paml.pdftex' file (texdepends) using 1 for graphic dimensions on input line 1252. Package texdepends Warning: Figure 'fig/localisation_paml.pdftex_t' needed (texdepends) Skipping it this time (the last one however) (texdepends) on input line 1252. Chapter 7. Package texdepends Warning: Figure(s) missing. Check dependencies again. 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(rerunfilecheck) Rerun to get outlines right /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_RESTORE make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' ======> building fig/option_b.subfig.mk <====== make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" manual.pdf_NEED_REBUILD make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' *** Checking rebuild with rule 'latex' *** Checking rebuild with rule 'texdepends' ******************************************** *********** New build needed *************** ******************************************** New manual.aux file LU_rebuild_latex: new run needed (LaTeX message 'Rerun to get...') 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Rerun needed /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_SAVE make[5]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[5]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' ======> building manual.pdf <====== removed 'manual.pdf_NEED_REBUILD' removed 'manual.pdf.mk' Running: 'pdflatex' '--interaction' 'errorstopmode' '--jobname' 'manual' '\RequirePackage[extension=.pdf]{texdepends}\input{manual.tex}' Package texdepends Warning: graphicspath already redefined. Skipping it. on input line 36. Package texdepends Warning: Diverting empty macro 'Ginclude@eps' (texdepends) Probably a bug in texdepends.sty. Package texdepends Warning: Gin@getbase already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@pdf already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@pdf already redefined. Skipping it. on input line 87. Chapter 1. Package natbib Warning: Citation `Bardel05' on page 3 undefined on input line 143. Package natbib Warning: Citation `Ge03' on page 3 undefined on input line 146. Package natbib Warning: Citation `Becker04' on page 3 undefined on input line 146. LaTeX Warning: `h' float specifier changed to `ht'. Package natbib Warning: Citation `Bardel05' on page 4 undefined on input line 180. Package natbib Warning: Citation `Stephens01' on page 4 undefined on input line 197. Package natbib Warning: Citation `Stephens03' on page 4 undefined on input line 197. Package natbib Warning: Citation `Becker04' on page 4 undefined on input line 198. Package natbib Warning: Citation `Swofford02' on page 4 undefined on input line 199. Package natbib Warning: Citation `Felsenstein04' on page 4 undefined on input line 200. Package natbib Warning: Citation `YangPAML' on page 4 undefined on input line 200. Underfull \hbox (badness 1454) in paragraph at lines 196--201 []\T1/ptm/m/n/10.95 Currently, \T1/pcr/m/n/10.95 ALTree-convert \T1/ptm/m/n/10. Chapter 2. Package natbib Warning: Citation `Swofford02' on page 7 undefined on input line 278. Package natbib Warning: Citation `Felsenstein04' on page 7 undefined on input line 281. Underfull \hbox (badness 1142) in paragraph at lines 281--284 []\T1/pcr/m/n/10.95 phylip \T1/ptm/b/n/10.95 ?\T1/ptm/m/n/10.95 : freely avail- Package natbib Warning: Citation `YangPAML' on page 7 undefined on input line 284. Package natbib Warning: Citation `Guindon03' on page 7 undefined on input line 288. Underfull \hbox (badness 2486) in paragraph at lines 284--290 []\T1/pcr/m/n/10.95 paml \T1/ptm/b/n/10.95 ?\T1/ptm/m/n/10.95 : freely avail-ab Underfull \hbox (badness 10000) in paragraph at lines 314--315 Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 369--369 []|\T1/ptm/m/n/10.95 Output con-tain-ing the num-ber of Overfull \hbox (2.0805pt too wide) in paragraph at lines 355--370 [] Underfull \hbox (badness 10000) in paragraph at lines 396--397 Underfull \hbox (badness 10000) in paragraph at lines 400--401 Underfull \hbox (badness 10000) in paragraph at lines 416--417 Underfull \hbox (badness 1112) in paragraph at lines 505--507 []\T1/ptm/m/n/10.95 Other ex-am-ples may be found in the test di-rec-tory. Thes Chapter 4. Overfull \hbox (2.0805pt too wide) in paragraph at lines 537--553 [] Overfull \hbox (8.63097pt too wide) in paragraph at lines 584--605 \T1/ptm/m/n/10.95 Examples: $[]$ $[]$ Package natbib Warning: Citation `Bardel05' on page 14 undefined on input line 634. Chapter 5. Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --data-qual|-q Underfull \hbox (badness 1281) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 remove the out-group se-quence for the Underfull \hbox (badness 5681) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 ancestral se-quence (only use-ful with Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --tree-building-program|-p Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --s-site-characters Underfull \hbox (badness 1565) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 print the tree with the char-ac-ter state Overfull \hbox (2.0805pt too wide) in paragraph at lines 664--698 [] Underfull \hbox (badness 10000) in paragraph at lines 735--738 Underfull \hbox (badness 1622) in paragraph at lines 747--755 \T1/ptm/m/n/10.95 Example of such files are given in the test di-rec-tory. Thes Package natbib Warning: Citation `Ge03' on page 19 undefined on input line 830. Package natbib Warning: Citation `Becker04' on page 19 undefined on input line 830. Package texdepends Warning: No 'fig/option_b_1.pdftex' file (texdepends) using 1 for graphic dimensions on input line 852. Package texdepends Warning: Figure 'fig/option_b_1.pdftex_t' needed (texdepends) Skipping it this time (the last one however) (texdepends) on input line 852. Package texdepends Warning: No 'fig/option_b_2.pdftex' file (texdepends) using 1 for graphic dimensions on input line 853. Package texdepends Warning: Figure 'fig/option_b_2.pdftex_t' needed (texdepends) Skipping it this time (the last one however) (texdepends) on input line 853. Overfull \hbox (15.23479pt too wide) in paragraph at lines 850--865 [][] Package natbib Warning: Citation `Bardel05' on page 21 undefined on input line 921. Package natbib Warning: Citation `Bardel05' on page 21 undefined on input line 941. Chapter 6. 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(natbib) Rerun to get citations correct. /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_RESTORE make[5]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[5]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" manual.pdf_NEED_REBUILD make[5]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' *** Checking rebuild with rule 'latex' *** Checking rebuild with rule 'texdepends' ******************************************** *********** New build needed *************** ******************************************** New manual.aux file LU_rebuild_latex: new run needed (LaTeX message 'Rerun to get...') 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Rerun needed /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_SAVE make[7]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[7]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' ======> building manual.pdf <====== removed 'manual.pdf_NEED_REBUILD' removed 'manual.pdf.mk' Running: 'pdflatex' '--interaction' 'errorstopmode' '--jobname' 'manual' '\RequirePackage[extension=.pdf]{texdepends}\input{manual.tex}' Package texdepends Warning: graphicspath already redefined. Skipping it. on input line 36. Package texdepends Warning: Diverting empty macro 'Ginclude@eps' (texdepends) Probably a bug in texdepends.sty. Package texdepends Warning: Gin@getbase already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@pdf already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@pdf already redefined. Skipping it. on input line 87. Chapter 1. LaTeX Warning: `h' float specifier changed to `ht'. Underfull \hbox (badness 1454) in paragraph at lines 196--201 []\T1/ptm/m/n/10.95 Currently, \T1/pcr/m/n/10.95 ALTree-convert \T1/ptm/m/n/10. Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 314--315 Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 369--369 []|\T1/ptm/m/n/10.95 Output con-tain-ing the num-ber of Overfull \hbox (2.0805pt too wide) in paragraph at lines 355--370 [] Underfull \hbox (badness 10000) in paragraph at lines 396--397 Underfull \hbox (badness 10000) in paragraph at lines 400--401 Underfull \hbox (badness 10000) in paragraph at lines 416--417 Underfull \hbox (badness 1112) in paragraph at lines 505--507 []\T1/ptm/m/n/10.95 Other ex-am-ples may be found in the test di-rec-tory. Thes Chapter 4. Overfull \hbox (2.0805pt too wide) in paragraph at lines 537--553 [] Overfull \hbox (8.63097pt too wide) in paragraph at lines 584--605 \T1/ptm/m/n/10.95 Examples: $[]$ $[]$ Chapter 5. Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --data-qual|-q Underfull \hbox (badness 1281) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 remove the out-group se-quence for the Underfull \hbox (badness 5681) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 ancestral se-quence (only use-ful with Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --tree-building-program|-p Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --s-site-characters Underfull \hbox (badness 1565) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 print the tree with the char-ac-ter state Overfull \hbox (2.0805pt too wide) in paragraph at lines 664--698 [] Underfull \hbox (badness 10000) in paragraph at lines 735--738 Underfull \hbox (badness 1622) in paragraph at lines 747--755 \T1/ptm/m/n/10.95 Example of such files are given in the test di-rec-tory. Thes Overfull \hbox (15.23479pt too wide) in paragraph at lines 850--865 [][] Chapter 6. Underfull \hbox (badness 5519) in paragraph at lines 968--971 []\T1/ptm/b/n/10.95 create_file \T1/ptm/m/n/10.95 which con-tains files and in- Underfull \hbox (badness 10000) in paragraph at lines 1024--1026 []\T1/ptm/m/n/10.95 the two \T1/pcr/m/n/10.95 FamHap \T1/ptm/m/n/10.95 out-put Underfull \hbox (badness 10000) in paragraph at lines 1125--1127 []\T1/ptm/m/n/10.95 a bash script con-tain-ing the three com-mand lines to run Underfull \hbox (badness 2662) in paragraph at lines 1188--1195 \T1/ptm/m/n/10.95 The files nec-es-sary for the phy-lo-ge-netic re-con-struc-ti Underfull \hbox (badness 10000) in paragraph at lines 1247--1249 []\T1/ptm/m/n/10.95 a bash script con-tain-ing the three com-mand lines to run Chapter 7. Underfull \hbox (badness 10000) in paragraph at lines 58--61 []\T1/ptm/m/n/10.95 Z Yang. Phy-lo-ge-netic anal-y-sis by max-i-mum like-li-ho /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_RESTORE make[7]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[7]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" manual.pdf_NEED_REBUILD make[7]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' *** Checking rebuild with rule 'latex' *** Checking rebuild with rule 'texdepends' ******************************************** *********** New build needed *************** ******************************************** New manual.aux file LU_rebuild_latex: new run needed (LaTeX message 'Rerun to get...') ******************************************** /usr/bin/make LU_REC_LEVEL=4 manual.pdf make[8]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' ======> building manual.bbl <====== This is BibTeX, Version 0.99d (TeX Live 2025/Debian) The top-level auxiliary file: manual.aux The style file: plainnat.bst Database file #1: stage.bib Warning--empty year in YangPAML (There was 1 warning) Previous compilation failed. Rerun needed /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_SAVE make[9]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[9]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' ======> building manual.pdf <====== removed 'manual.pdf_NEED_REBUILD' removed 'manual.pdf.mk' Running: 'pdflatex' '--interaction' 'errorstopmode' '--jobname' 'manual' '\RequirePackage[extension=.pdf]{texdepends}\input{manual.tex}' Package texdepends Warning: graphicspath already redefined. Skipping it. on input line 36. Package texdepends Warning: Diverting empty macro 'Ginclude@eps' (texdepends) Probably a bug in texdepends.sty. Package texdepends Warning: Gin@getbase already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@pdf already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@pdf already redefined. Skipping it. on input line 87. Chapter 1. LaTeX Warning: `h' float specifier changed to `ht'. Underfull \hbox (badness 1454) in paragraph at lines 196--201 []\T1/ptm/m/n/10.95 Currently, \T1/pcr/m/n/10.95 ALTree-convert \T1/ptm/m/n/10. Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 314--315 Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 369--369 []|\T1/ptm/m/n/10.95 Output con-tain-ing the num-ber of Overfull \hbox (2.0805pt too wide) in paragraph at lines 355--370 [] Underfull \hbox (badness 10000) in paragraph at lines 396--397 Underfull \hbox (badness 10000) in paragraph at lines 400--401 Underfull \hbox (badness 10000) in paragraph at lines 416--417 Underfull \hbox (badness 1112) in paragraph at lines 505--507 []\T1/ptm/m/n/10.95 Other ex-am-ples may be found in the test di-rec-tory. Thes Chapter 4. Overfull \hbox (2.0805pt too wide) in paragraph at lines 537--553 [] Overfull \hbox (8.63097pt too wide) in paragraph at lines 584--605 \T1/ptm/m/n/10.95 Examples: $[]$ $[]$ Chapter 5. Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --data-qual|-q Underfull \hbox (badness 1281) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 remove the out-group se-quence for the Underfull \hbox (badness 5681) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 ancestral se-quence (only use-ful with Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --tree-building-program|-p Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --s-site-characters Underfull \hbox (badness 1565) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 print the tree with the char-ac-ter state Overfull \hbox (2.0805pt too wide) in paragraph at lines 664--698 [] Underfull \hbox (badness 10000) in paragraph at lines 735--738 Underfull \hbox (badness 1622) in paragraph at lines 747--755 \T1/ptm/m/n/10.95 Example of such files are given in the test di-rec-tory. Thes Overfull \hbox (15.23479pt too wide) in paragraph at lines 850--865 [][] Chapter 6. Underfull \hbox (badness 5519) in paragraph at lines 968--971 []\T1/ptm/b/n/10.95 create_file \T1/ptm/m/n/10.95 which con-tains files and in- Underfull \hbox (badness 10000) in paragraph at lines 1024--1026 []\T1/ptm/m/n/10.95 the two \T1/pcr/m/n/10.95 FamHap \T1/ptm/m/n/10.95 out-put Underfull \hbox (badness 10000) in paragraph at lines 1125--1127 []\T1/ptm/m/n/10.95 a bash script con-tain-ing the three com-mand lines to run Underfull \hbox (badness 2662) in paragraph at lines 1188--1195 \T1/ptm/m/n/10.95 The files nec-es-sary for the phy-lo-ge-netic re-con-struc-ti Underfull \hbox (badness 10000) in paragraph at lines 1247--1249 []\T1/ptm/m/n/10.95 a bash script con-tain-ing the three com-mand lines to run Chapter 7. Underfull \hbox (badness 10000) in paragraph at lines 58--61 /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_RESTORE make[9]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[9]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" manual.pdf_NEED_REBUILD make[9]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' *** Checking rebuild with rule 'latex' *** Checking rebuild with rule 'texdepends' /usr/bin/make LU_REC_LEVEL=5 manual.pdf make[10]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[10]: 'manual.pdf' is up to date. make[10]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[9]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[8]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[7]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[6]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[5]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[4]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[2]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' dh_auto_build make -j16 make[1]: Entering directory '/build/reproducible-path/altree-1.3.2' make[2]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils' make -C c_sources Running Mkbootstrap for CUtils () "/usr/bin/perl" "/usr/share/perl/5.40.1/ExtUtils/xsubpp" -typemap '/usr/share/perl/5.40/ExtUtils/typemap' CUtils.xs > CUtils.xsc make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" chisq.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" double_permutation.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" fisher.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" mt19937ar.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" myrand.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" resampling.c cp ALTree/Nanova.pm blib/lib/ALTree/Nanova.pm cp ALTree/Foret.pm blib/lib/ALTree/Foret.pm cp ALTree/Import.pm blib/lib/ALTree/Import.pm cp ALTree/to_rewrite.pm blib/lib/ALTree/to_rewrite.pm cp ALTree/Input.pm blib/lib/ALTree/Input.pm cp ALTree/SitePerForet.pm blib/lib/ALTree/SitePerForet.pm cp ALTree/SiteSensPerForet.pm blib/lib/ALTree/SiteSensPerForet.pm cp ALTree/Tree.pm blib/lib/ALTree/Tree.pm cp ALTree/Site.pm blib/lib/ALTree/Site.pm cp ALTree/Chi2.pm blib/lib/ALTree/Chi2.pm cp ALTree/SiteCollection.pm blib/lib/ALTree/SiteCollection.pm cp ALTree/Utils.pm blib/lib/ALTree/Utils.pm cp ALTree/Node.pm blib/lib/ALTree/Node.pm cp ALTree/Sens.pm blib/lib/ALTree/Sens.pm cp ALTree/SitePerTree.pm blib/lib/ALTree/SitePerTree.pm cp ALTree/SiteSensPerTree.pm blib/lib/ALTree/SiteSensPerTree.pm cp ALTree/Base.pm blib/lib/ALTree/Base.pm cp ALTree/SiteSens.pm blib/lib/ALTree/SiteSens.pm x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" rhyper.c chmod 644 "CUtils.bs" x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" stats.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" z.c "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CUtils.bs ../blib/arch/auto/ALTree/CUtils/CUtils.bs 644 chisq.c: In function 'pochisq': chisq.c:77:1: warning: old-style function definition [-Wold-style-definition] 77 | pochisq (x, df) | ^~~~~~~ chisq.c: In function 'critchi': chisq.c:129:1: warning: old-style function definition [-Wold-style-definition] 129 | critchi (p, df) | ^~~~~~~ cp lib/ALTree/CUtils.pm ../blib/lib/ALTree/CUtils.pm AutoSplitting ../blib/lib/ALTree/CUtils.pm (../blib/lib/auto/ALTree/CUtils) z.c: In function 'poz': z.c:44:1: warning: old-style function definition [-Wold-style-definition] 44 | poz (z) | ^~~ z.c: In function 'critz': z.c:91:1: warning: old-style function definition [-Wold-style-definition] 91 | critz (p) | ^~~~~ z.c: At top level: z.c:12:13: warning: 'sccsfid' defined but not used [-Wunused-variable] 12 | static char sccsfid[] = "@(#) z.c 5.1 (|stat) 12/26/85"; | ^~~~~~~ Please specify prototyping behavior for CUtils.xs (see perlxs manual) mv CUtils.xsc CUtils.c x86_64-linux-gnu-gcc -c -ggdb3 -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"1.1\" -DXS_VERSION=\"1.1\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" CUtils.c In function 'pval_min', inlined from 'double_permutation' at double_permutation.c:182:19: double_permutation.c:125:20: warning: '*(datatype_t *)local' may be used uninitialized [-Wmaybe-uninitialized] 125 | datatype_t ret=rep[0]; | ^~~ ar cr libaltree-cutils.a chisq.o double_permutation.o fisher.o mt19937ar.o myrand.o resampling.o rhyper.o stats.o z.o : libaltree-cutils.a make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' rm -f ../blib/arch/auto/ALTree/CUtils/CUtils.so x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -shared -L/usr/local/lib -fstack-protector-strong CUtils.o -o ../blib/arch/auto/ALTree/CUtils/CUtils.so c_sources/libaltree-cutils.a \ -lm -lpthread -lgsl -lblas \ chmod 755 ../blib/arch/auto/ALTree/CUtils/CUtils.so Manifying 1 pod document make[2]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils' cp progs/altree blib/script/altree cp progs/altree-add-S blib/script/altree-add-S cp progs/altree-convert blib/script/altree-convert "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/altree "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/altree-add-S "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/altree-convert Manifying 3 pod documents make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' dh_auto_test make -j16 test TEST_VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/altree-1.3.2' make[2]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CUtils.bs ../blib/arch/auto/ALTree/CUtils/CUtils.bs 644 make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' Manifying 1 pod document make[2]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils' make[2]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CUtils.bs ../blib/arch/auto/ALTree/CUtils/CUtils.bs 644 make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' No tests defined for ALTree::CUtils extension. make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, '../blib/lib', '../blib/arch')" t/*.t t/ALTree-CUtils.t ....... 1..1 ok 1 - use ALTree::CUtils; ok t/double_permutation.t .. 1..3 ok 1 - use ALTree::CUtils; ok 2 - undef when bad args ok 3 - double_permutation ok All tests successful. Files=2, Tests=4, 1 wallclock secs ( 0.01 usr 0.01 sys + 0.12 cusr 0.03 csys = 0.17 CPU) Result: PASS make[2]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils' PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t t/ALTree.t .. 1..1 ok 1 - use ALTree::Import; ok All tests successful. Files=1, Tests=1, 0 wallclock secs ( 0.02 usr 0.00 sys + 0.12 cusr 0.02 csys = 0.16 CPU) Result: PASS make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j16 install DESTDIR=/build/reproducible-path/altree-1.3.2/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/reproducible-path/altree-1.3.2' make[2]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CUtils.bs ../blib/arch/auto/ALTree/CUtils/CUtils.bs 644 make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' Manifying 1 pod document make[2]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils' Manifying 3 pod documents Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/ALTree/CUtils/CUtils.so Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Foret.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SitePerForet.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Tree.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Node.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SitePerTree.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteSensPerTree.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteCollection.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Base.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Site.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Utils.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Chi2.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Sens.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/to_rewrite.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Input.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Import.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/CUtils.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteSensPerForet.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Nanova.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteSens.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/ALTree/CUtils/autosplit.ix Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/share/man/man1/altree-convert.1p Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/share/man/man1/altree.1p Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/share/man/man1/altree-add-S.1p Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/share/man/man3/ALTree::CUtils.3pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/bin/altree Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/bin/altree-add-S Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/bin/altree-convert make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' dh_install debian/rules execute_after_dh_install-arch make[1]: Entering directory '/build/reproducible-path/altree-1.3.2' set -e \ ; cd debian/altree/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/ \ ; for file in Chi2.pm Import.pm Input.pm Node.pm SitePerForet.pm SiteSensPerTree.pm Tree.pm to_rewrite.pm \ ; do iconv -f ISO-8859-1 -t UTF-8 < "${file}" > "${file}.conv" \ ; mv -vf "${file}.conv" "${file}" \ ; done renamed 'Chi2.pm.conv' -> 'Chi2.pm' renamed 'Import.pm.conv' -> 'Import.pm' renamed 'Input.pm.conv' -> 'Input.pm' renamed 'Node.pm.conv' -> 'Node.pm' renamed 'SitePerForet.pm.conv' -> 'SitePerForet.pm' renamed 'SiteSensPerTree.pm.conv' -> 'SiteSensPerTree.pm' renamed 'Tree.pm.conv' -> 'Tree.pm' renamed 'to_rewrite.pm.conv' -> 'to_rewrite.pm' make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/reproducible-path/altree-1.3.2' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/altree/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/ALTree/CUtils/CUtils.so was not linked against libblas.so.3 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'altree-examples' in '../altree-examples_1.3.2-4_all.deb'. dpkg-deb: building package 'altree-dbgsym' in '../altree-dbgsym_1.3.2-4_amd64.deb'. dpkg-deb: building package 'altree' in '../altree_1.3.2-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../altree_1.3.2-4_amd64.buildinfo dpkg-genchanges --build=binary -O../altree_1.3.2-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1210918 and its subdirectories I: Current time: Tue Oct 20 19:40:37 -12 2026 I: pbuilder-time-stamp: 1792568437 Wed Oct 21 07:40:37 UTC 2026 I: Signing ./b1/altree_1.3.2-4_amd64.buildinfo as altree_1.3.2-4_amd64.buildinfo.asc Wed Oct 21 07:40:37 UTC 2026 I: Signed ./b1/altree_1.3.2-4_amd64.buildinfo as ./b1/altree_1.3.2-4_amd64.buildinfo.asc Wed Oct 21 07:40:37 UTC 2026 - build #1 for altree/unstable/amd64 on infom02-amd64 done. Starting cleanup. All cleanup done. Wed Oct 21 07:40:37 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-u6L3LLLi, removing. /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm: total 16 -rw-rw-r-- 1 jenkins jenkins 2535 Sep 17 19:14 altree_1.3.2-4.dsc drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 01:17 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 01:11 b2 -rw------- 1 jenkins jenkins 3631 Sep 18 01:11 rbuildlog.fnTyxL8 /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm/b1: total 1172 -rw-r--r-- 1 jenkins jenkins 353168 Sep 18 01:17 altree-dbgsym_1.3.2-4_amd64.deb -rw-r--r-- 1 jenkins jenkins 330628 Sep 18 01:17 altree-examples_1.3.2-4_all.deb -rw-r--r-- 1 jenkins jenkins 8600 Sep 18 01:17 altree_1.3.2-4.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2535 Sep 18 01:17 altree_1.3.2-4.dsc -rw-r--r-- 1 jenkins jenkins 8989 Sep 18 01:17 altree_1.3.2-4_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 9871 Sep 18 01:17 altree_1.3.2-4_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1869 Sep 18 01:17 altree_1.3.2-4_amd64.changes -rw-r--r-- 1 jenkins jenkins 341364 Sep 18 01:17 altree_1.3.2-4_amd64.deb -rw-r--r-- 1 jenkins jenkins 1371 Sep 18 01:17 altree_1.3.2-4_source.changes -rw-r--r-- 1 jenkins jenkins 116359 Sep 18 01:17 build.log /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm/b2: total 0 Thu Sep 18 01:17:38 UTC 2025 I: Deleting $TMPDIR on infom02-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Oct 20 19:34:54 -12 2026 I: pbuilder-time-stamp: 1792568094 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: Copying source file I: copying [altree_1.3.2-4.dsc] I: copying [./altree_1.3.2.orig.tar.gz] I: copying [./altree_1.3.2-4.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./altree_1.3.2-4.dsc: no acceptable signature found dpkg-source: info: extracting altree in altree-1.3.2 dpkg-source: info: unpacking altree_1.3.2.orig.tar.gz dpkg-source: info: unpacking altree_1.3.2-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc-15.patch dpkg-source: info: applying typo.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1210918/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='0431957afced46ecb2038fbd6b63d63b' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1210918' 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.2NH9R5Xm/pbuilderrc_Tq6n --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.2NH9R5Xm/b1 --logfile b1/build.log altree_1.3.2-4.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' 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 infom02-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1210918/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: bash-completion, debhelper-compat (= 13), perl:native, perl-xs-dev, latex-make, ghostscript, texlive-lang-french, texlive-latex-extra, texlive-latex-recommended, texlive-fonts-recommended, libmath-tamuanova-perl, libgsl-dev, libblas-dev | libblas.so, libtest-deep-perl, fig2dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 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 bash-completion; however: Package bash-completion is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on perl:native. pbuilder-satisfydepends-dummy depends on perl-xs-dev; however: Package perl-xs-dev is not installed. pbuilder-satisfydepends-dummy depends on latex-make; however: Package latex-make is not installed. pbuilder-satisfydepends-dummy depends on ghostscript; however: Package ghostscript is not installed. pbuilder-satisfydepends-dummy depends on texlive-lang-french; however: Package texlive-lang-french is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however: Package texlive-latex-extra is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-recommended; however: Package texlive-latex-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however: Package texlive-fonts-recommended is not installed. pbuilder-satisfydepends-dummy depends on libmath-tamuanova-perl; however: Package libmath-tamuanova-perl is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev | libblas.so; however: Package libblas-dev is not installed. Package libblas.so is not installed. pbuilder-satisfydepends-dummy depends on libtest-deep-perl; however: Package libtest-deep-perl is not installed. pbuilder-satisfydepends-dummy depends on fig2dev; however: Package fig2dev 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} bash-completion{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} fig2dev{a} file{a} fontconfig-config{a} fonts-lmodern{a} fonts-urw-base35{a} gawk{a} gettext{a} gettext-base{a} ghostscript{a} groff-base{a} intltool-debian{a} latex-make{a} libapache-pom-java{a} libarchive-zip-perl{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libblas-dev{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcommons-logging-java{a} libcommons-parent-java{a} libcups2t64{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontbox-java{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libglib2.0-0t64{a} libgnutls30t64{a} libgraphite2-3{a} libgs-common{a} libgs10{a} libgs10-common{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libice6{a} libicu76{a} libidn12{a} libidn2-0{a} libijs-0.35{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libmath-tamuanova-perl{a} libmpfi0{a} libnetpbm11t64{a} libopenjp2-7{a} libp11-kit0{a} libpaper-utils{a} libpaper2{a} libpdfbox-java{a} libperl-dev{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpotrace0{a} libproc2-0{a} libptexenc1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libsharpyuv0{a} libsm6{a} libsynctex2{a} libtamuanova-0.2{a} libtasn1-6{a} libteckit0{a} libtest-deep-perl{a} libtexlua53-5{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libtiff6{a} libtool{a} libuchardet0{a} libunistring5{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} libxml2-16{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6t64{a} libzzip-0-13t64{a} m4{a} man-db{a} media-types{a} netbase{a} netpbm{a} po-debconf{a} poppler-data{a} preview-latex-style{a} procps{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} t1utils{a} tex-common{a} texlive-base{a} texlive-binaries{a} texlive-fonts-recommended{a} texlive-lang-french{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} tzdata{a} ucf{a} x11-common{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl dbus default-jre dvisvgm fonts-droid-fallback inkscape krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libltdl-dev libmail-sendmail-perl libnet-dbus-perl libspreadsheet-parseexcel-perl libx11-protocol-perl linux-sysctl-defaults lmodern lynx psmisc ruby shared-mime-info tex-gyre texlive-plain-generic tipa tk wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 155 newly installed, 0 to remove and 0 not upgraded. Need to get 322 MB of archives. After unpacking 809 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 gawk amd64 1:5.3.2-1 [772 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.2-1 [111 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 poppler-data all 0.4.12-1 [1601 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-5 [260 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 bash-completion all 1:2.16.0-7 [319 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B] Get: 31 http://deb.debian.org/debian unstable/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get: 32 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0052 [43.3 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 44 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.50-1 [282 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+25 [217 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libgs-common all 10.05.1~dfsg-3 [149 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libgs10-common all 10.05.1~dfsg-3 [479 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-17 [112 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-17 [47.3 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.16.2-2 [178 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-17 [52.1 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 74 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.10-4 [267 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2.4 [318 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2.4 [401 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libidn12 amd64 1.43-2 [48.3 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libijs-0.35 amd64 0.35-16 [16.0 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libjbig2dec0 amd64 0.20-1+b3 [65.1 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [204 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libpaper2 amd64 2.2.5-0.3+b2 [16.7 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.7.0-5 [364 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.6-1 [37.3 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [208 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libgs10 amd64 10.05.1~dfsg-3 [2732 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 ghostscript amd64 10.05.1~dfsg-3 [50.5 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libnetpbm11t64 amd64 2:11.11.01-1 [194 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 netpbm amd64 2:11.11.01-1 [2140 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 fig2dev amd64 1:3.2.9a-4 [449 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 tex-common all 6.19 [29.4 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 latex-make all 2.4.3-1 [1030 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 33-2 [5852 B] Get: 109 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.1-7 [229 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.3.0-2 [68.6 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.84.4-3 [1518 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-7 [76.3 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5.1 [137 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5.1 [1068 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-5.1 [1336 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 11.4.5-1 [505 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libicu76 amd64 76.1-4 [9722 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libkpathsea6 amd64 2025.20250727.75242+ds-4 [154 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libtamuanova-0.2 amd64 0.2-5+b3 [9228 B] Get: 129 http://deb.debian.org/debian unstable/main amd64 libmath-tamuanova-perl amd64 1.0.2-4+b2 [13.9 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libmpfi0 amd64 1.5.4+ds-4 [35.5 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 2.2.5-0.3+b2 [16.5 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libperl-dev amd64 5.40.1-6 [1109 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libpotrace0 amd64 1.16-2+b2 [25.6 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libptexenc1 amd64 2025.20250727.75242+ds-4 [50.5 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libsynctex2 amd64 2025.20250727.75242+ds-4 [58.2 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libteckit0 amd64 2.5.12+ds1-1+b1 [341 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libtest-deep-perl all 1.205-1 [52.3 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libtexlua53-5 amd64 2025.20250727.75242+ds-4 [99.4 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libxmu6 amd64 2:1.1.3-3+b4 [59.0 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libxpm4 amd64 1:3.5.17-1+b3 [56.2 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libxaw7 amd64 2:1.0.16-1 [212 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libzzip-0-13t64 amd64 0.13.78+dfsg.1-0.1 [59.0 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 preview-latex-style all 13.2-1.1 [350 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 texlive-binaries amd64 2025.20250727.75242+ds-4 [7261 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 texlive-base all 2025.20250727-3 [23.1 MB] Get: 150 http://deb.debian.org/debian unstable/main amd64 texlive-fonts-recommended all 2025.20250727-3 [4991 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 texlive-lang-french all 2025.20250727-3 [149 MB] Get: 152 http://deb.debian.org/debian unstable/main amd64 texlive-latex-base all 2025.20250727-3 [1318 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 texlive-latex-recommended all 2025.20250727-3 [8454 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 texlive-pictures all 2025.20250727-3 [22.1 MB] Get: 155 http://deb.debian.org/debian unstable/main amd64 texlive-latex-extra all 2025.20250727-3 [27.4 MB] Fetched 322 MB in 4s (74.3 MB/s) Preconfiguring packages ... Selecting previously unselected package readline-common. (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 ... 19917 files and directories currently installed.) Preparing to unpack .../readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../libreadline8t64_8.3-3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Setting up readline-common (8.3-3) ... Setting up libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package gawk. (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 ... 19949 files and directories currently installed.) Preparing to unpack .../gawk_1%3a5.3.2-1_amd64.deb ... Unpacking gawk (1:5.3.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.7.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.2-1) ... Selecting previously unselected package poppler-data. Preparing to unpack .../poppler-data_0.4.12-1_all.deb ... Unpacking poppler-data (0.4.12-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.7-1_amd64.deb ... Unpacking python3.13-minimal (3.13.7-1) ... Setting up libpython3.13-minimal:amd64 (3.13.7-1) ... Setting up libexpat1:amd64 (2.7.2-1) ... Setting up python3.13-minimal (3.13.7-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21010 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_amd64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/altree-1.3.2/ && 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 > ../altree_1.3.2-4_source.changes dpkg-buildpackage: info: source package altree dpkg-buildpackage: info: source version 1.3.2-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules execute_before_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/altree-1.3.2' /usr/bin/make -C Documentation distclean || true make[2]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[2]: Nothing to be done for 'distclean'. make[2]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro" Checking if your kit is complete... Warning: the following files are missing in your kit: CUtils/c_sources/MYMETA.json CUtils/MYMETA.json MYMETA.json Please inform the author. MakeMaker (v7.70) Warning (non-fatal): Target 'dynamic' depends on targets in skipped section 'dynamic_lib' Warning (non-fatal): Target 'static' depends on targets in skipped section 'static_lib' Generating a Unix-style Makefile Writing Makefile for ALTree::CUtils Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for ALTree::CUtils Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for altree Writing MYMETA.yml and MYMETA.json debian/rules execute_before_dh_auto_build make[1]: Entering directory '/build/reproducible-path/altree-1.3.2' /usr/bin/make -C Documentation pdf make[2]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_SAVE make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[3]: Nothing to be done for 'LU_WATCH_FILES_SAVE'. make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' ======> building manual.pdf <====== Running: 'pdflatex' '--interaction' 'errorstopmode' '--jobname' 'manual' '\RequirePackage[extension=.pdf]{texdepends}\input{manual.tex}' Package texdepends Warning: graphicspath already redefined. Skipping it. on input line 36. Package texdepends Warning: Diverting empty macro 'Ginclude@eps' (texdepends) Probably a bug in texdepends.sty. Package texdepends Warning: Gin@getbase already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@pdf already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@pdf already redefined. Skipping it. on input line 87. Chapter 1. LaTeX Warning: Reference `fig:altree' on page 2 undefined on input line 121. Package texdepends Warning: No 'fig/overview.pdftex' file (texdepends) using 1 for graphic dimensions on input line 124. Package texdepends Warning: Figure 'fig/overview.pdftex_t' needed (texdepends) Skipping it this time (the last one however) (texdepends) on input line 124. LaTeX Warning: Reference `fig:nesting_algo' on page 2 undefined on input line 143. Package natbib Warning: Citation `Bardel05' on page 2 undefined on input line 143. Package natbib Warning: Citation `Ge03' on page 2 undefined on input line 146. Package natbib Warning: Citation `Becker04' on page 2 undefined on input line 146. Package texdepends Warning: No 'fig/altree-q.pdftex' file (texdepends) using 1 for graphic dimensions on input line 150. Package texdepends Warning: Figure 'fig/altree-q.pdftex_t' needed (texdepends) Skipping it this time (the last one however) (texdepends) on input line 150. LaTeX Warning: `h' float specifier changed to `ht'. Package natbib Warning: Citation `Bardel05' on page 4 undefined on input line 180. Package natbib Warning: Citation `Stephens01' on page 5 undefined on input line 197. Package natbib Warning: Citation `Stephens03' on page 5 undefined on input line 197. Package natbib Warning: Citation `Becker04' on page 5 undefined on input line 198. Package natbib Warning: Citation `Swofford02' on page 5 undefined on input line 199. Package natbib Warning: Citation `Felsenstein04' on page 5 undefined on input line 200. Package natbib Warning: Citation `YangPAML' on page 5 undefined on input line 200. Underfull \hbox (badness 1454) in paragraph at lines 196--201 []\T1/ptm/m/n/10.95 Currently, \T1/pcr/m/n/10.95 ALTree-convert \T1/ptm/m/n/10. Chapter 2. Package natbib Warning: Citation `Swofford02' on page 7 undefined on input line 278. Package natbib Warning: Citation `Felsenstein04' on page 7 undefined on input line 281. Underfull \hbox (badness 1142) in paragraph at lines 281--284 []\T1/pcr/m/n/10.95 phylip \T1/ptm/b/n/10.95 ?\T1/ptm/m/n/10.95 : freely avail- Package natbib Warning: Citation `YangPAML' on page 7 undefined on input line 284. Package natbib Warning: Citation `Guindon03' on page 7 undefined on input line 288. Underfull \hbox (badness 2486) in paragraph at lines 284--290 []\T1/pcr/m/n/10.95 paml \T1/ptm/b/n/10.95 ?\T1/ptm/m/n/10.95 : freely avail-ab Underfull \hbox (badness 10000) in paragraph at lines 314--315 Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 369--369 []|\T1/ptm/m/n/10.95 Output con-tain-ing the num-ber of Overfull \hbox (2.0805pt too wide) in paragraph at lines 355--370 [] Underfull \hbox (badness 10000) in paragraph at lines 396--397 Underfull \hbox (badness 10000) in paragraph at lines 400--401 Underfull \hbox (badness 10000) in paragraph at lines 416--417 Underfull \hbox (badness 1112) in paragraph at lines 505--507 []\T1/ptm/m/n/10.95 Other ex-am-ples may be found in the test di-rec-tory. Thes Chapter 4. Overfull \hbox (2.0805pt too wide) in paragraph at lines 537--553 [] LaTeX Warning: Reference `help' on page 13 undefined on input line 564. Overfull \hbox (8.63097pt too wide) in paragraph at lines 584--605 \T1/ptm/m/n/10.95 Examples: $[]$ $[]$ LaTeX Warning: Reference `description_etiquette' on page 14 undefined on input line 632. LaTeX Warning: Reference `description_etiquette' on page 14 undefined on input line 633. Package natbib Warning: Citation `Bardel05' on page 14 undefined on input line 634. LaTeX Warning: Reference `description_etiquette' on page 15 undefined on input line 649. LaTeX Warning: Reference `description_etiquette' on page 15 undefined on input line 649. Chapter 5. 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(rerunfilecheck) Rerun to get outlines right /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_RESTORE make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' ======> building fig/option_b.subfig.mk <====== make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" manual.pdf_NEED_REBUILD make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' *** Checking rebuild with rule 'latex' *** Checking rebuild with rule 'texdepends' ******************************************** *********** New build needed *************** ******************************************** New manual.aux file LU_rebuild_latex: new run needed (LaTeX message 'Rerun to get...') 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Rerun needed /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_SAVE make[5]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[5]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' ======> building manual.pdf <====== removed 'manual.pdf_NEED_REBUILD' removed 'manual.pdf.mk' Running: 'pdflatex' '--interaction' 'errorstopmode' '--jobname' 'manual' '\RequirePackage[extension=.pdf]{texdepends}\input{manual.tex}' Package texdepends Warning: graphicspath already redefined. Skipping it. on input line 36. Package texdepends Warning: Diverting empty macro 'Ginclude@eps' (texdepends) Probably a bug in texdepends.sty. Package texdepends Warning: Gin@getbase already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@pdf already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@pdf already redefined. Skipping it. on input line 87. Chapter 1. Package natbib Warning: Citation `Bardel05' on page 3 undefined on input line 143. Package natbib Warning: Citation `Ge03' on page 3 undefined on input line 146. Package natbib Warning: Citation `Becker04' on page 3 undefined on input line 146. LaTeX Warning: `h' float specifier changed to `ht'. Package natbib Warning: Citation `Bardel05' on page 4 undefined on input line 180. Package natbib Warning: Citation `Stephens01' on page 4 undefined on input line 197. Package natbib Warning: Citation `Stephens03' on page 4 undefined on input line 197. Package natbib Warning: Citation `Becker04' on page 4 undefined on input line 198. Package natbib Warning: Citation `Swofford02' on page 4 undefined on input line 199. Package natbib Warning: Citation `Felsenstein04' on page 4 undefined on input line 200. Package natbib Warning: Citation `YangPAML' on page 4 undefined on input line 200. Underfull \hbox (badness 1454) in paragraph at lines 196--201 []\T1/ptm/m/n/10.95 Currently, \T1/pcr/m/n/10.95 ALTree-convert \T1/ptm/m/n/10. Chapter 2. Package natbib Warning: Citation `Swofford02' on page 7 undefined on input line 278. Package natbib Warning: Citation `Felsenstein04' on page 7 undefined on input line 281. Underfull \hbox (badness 1142) in paragraph at lines 281--284 []\T1/pcr/m/n/10.95 phylip \T1/ptm/b/n/10.95 ?\T1/ptm/m/n/10.95 : freely avail- Package natbib Warning: Citation `YangPAML' on page 7 undefined on input line 284. Package natbib Warning: Citation `Guindon03' on page 7 undefined on input line 288. Underfull \hbox (badness 2486) in paragraph at lines 284--290 []\T1/pcr/m/n/10.95 paml \T1/ptm/b/n/10.95 ?\T1/ptm/m/n/10.95 : freely avail-ab Underfull \hbox (badness 10000) in paragraph at lines 314--315 Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 369--369 []|\T1/ptm/m/n/10.95 Output con-tain-ing the num-ber of Overfull \hbox (2.0805pt too wide) in paragraph at lines 355--370 [] Underfull \hbox (badness 10000) in paragraph at lines 396--397 Underfull \hbox (badness 10000) in paragraph at lines 400--401 Underfull \hbox (badness 10000) in paragraph at lines 416--417 Underfull \hbox (badness 1112) in paragraph at lines 505--507 []\T1/ptm/m/n/10.95 Other ex-am-ples may be found in the test di-rec-tory. Thes Chapter 4. Overfull \hbox (2.0805pt too wide) in paragraph at lines 537--553 [] Overfull \hbox (8.63097pt too wide) in paragraph at lines 584--605 \T1/ptm/m/n/10.95 Examples: $[]$ $[]$ Package natbib Warning: Citation `Bardel05' on page 14 undefined on input line 634. Chapter 5. Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --data-qual|-q Underfull \hbox (badness 1281) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 remove the out-group se-quence for the Underfull \hbox (badness 5681) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 ancestral se-quence (only use-ful with Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --tree-building-program|-p Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --s-site-characters Underfull \hbox (badness 1565) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 print the tree with the char-ac-ter state Overfull \hbox (2.0805pt too wide) in paragraph at lines 664--698 [] Underfull \hbox (badness 10000) in paragraph at lines 735--738 Underfull \hbox (badness 1622) in paragraph at lines 747--755 \T1/ptm/m/n/10.95 Example of such files are given in the test di-rec-tory. Thes Package natbib Warning: Citation `Ge03' on page 19 undefined on input line 830. Package natbib Warning: Citation `Becker04' on page 19 undefined on input line 830. Package texdepends Warning: No 'fig/option_b_1.pdftex' file (texdepends) using 1 for graphic dimensions on input line 852. Package texdepends Warning: Figure 'fig/option_b_1.pdftex_t' needed (texdepends) Skipping it this time (the last one however) (texdepends) on input line 852. Package texdepends Warning: No 'fig/option_b_2.pdftex' file (texdepends) using 1 for graphic dimensions on input line 853. Package texdepends Warning: Figure 'fig/option_b_2.pdftex_t' needed (texdepends) Skipping it this time (the last one however) (texdepends) on input line 853. Overfull \hbox (15.23479pt too wide) in paragraph at lines 850--865 [][] Package natbib Warning: Citation `Bardel05' on page 21 undefined on input line 921. Package natbib Warning: Citation `Bardel05' on page 21 undefined on input line 941. Chapter 6. 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(natbib) Rerun to get citations correct. /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_RESTORE make[5]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[5]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" manual.pdf_NEED_REBUILD make[5]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' *** Checking rebuild with rule 'latex' *** Checking rebuild with rule 'texdepends' ******************************************** *********** New build needed *************** ******************************************** New manual.aux file LU_rebuild_latex: new run needed (LaTeX message 'Rerun to get...') 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Rerun needed /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_SAVE make[7]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[7]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' ======> building manual.pdf <====== removed 'manual.pdf_NEED_REBUILD' removed 'manual.pdf.mk' Running: 'pdflatex' '--interaction' 'errorstopmode' '--jobname' 'manual' '\RequirePackage[extension=.pdf]{texdepends}\input{manual.tex}' Package texdepends Warning: graphicspath already redefined. Skipping it. on input line 36. Package texdepends Warning: Diverting empty macro 'Ginclude@eps' (texdepends) Probably a bug in texdepends.sty. Package texdepends Warning: Gin@getbase already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@pdf already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@pdf already redefined. Skipping it. on input line 87. Chapter 1. LaTeX Warning: `h' float specifier changed to `ht'. Underfull \hbox (badness 1454) in paragraph at lines 196--201 []\T1/ptm/m/n/10.95 Currently, \T1/pcr/m/n/10.95 ALTree-convert \T1/ptm/m/n/10. Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 314--315 Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 369--369 []|\T1/ptm/m/n/10.95 Output con-tain-ing the num-ber of Overfull \hbox (2.0805pt too wide) in paragraph at lines 355--370 [] Underfull \hbox (badness 10000) in paragraph at lines 396--397 Underfull \hbox (badness 10000) in paragraph at lines 400--401 Underfull \hbox (badness 10000) in paragraph at lines 416--417 Underfull \hbox (badness 1112) in paragraph at lines 505--507 []\T1/ptm/m/n/10.95 Other ex-am-ples may be found in the test di-rec-tory. Thes Chapter 4. Overfull \hbox (2.0805pt too wide) in paragraph at lines 537--553 [] Overfull \hbox (8.63097pt too wide) in paragraph at lines 584--605 \T1/ptm/m/n/10.95 Examples: $[]$ $[]$ Chapter 5. Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --data-qual|-q Underfull \hbox (badness 1281) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 remove the out-group se-quence for the Underfull \hbox (badness 5681) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 ancestral se-quence (only use-ful with Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --tree-building-program|-p Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --s-site-characters Underfull \hbox (badness 1565) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 print the tree with the char-ac-ter state Overfull \hbox (2.0805pt too wide) in paragraph at lines 664--698 [] Underfull \hbox (badness 10000) in paragraph at lines 735--738 Underfull \hbox (badness 1622) in paragraph at lines 747--755 \T1/ptm/m/n/10.95 Example of such files are given in the test di-rec-tory. Thes Overfull \hbox (15.23479pt too wide) in paragraph at lines 850--865 [][] Chapter 6. Underfull \hbox (badness 5519) in paragraph at lines 968--971 []\T1/ptm/b/n/10.95 create_file \T1/ptm/m/n/10.95 which con-tains files and in- Underfull \hbox (badness 10000) in paragraph at lines 1024--1026 []\T1/ptm/m/n/10.95 the two \T1/pcr/m/n/10.95 FamHap \T1/ptm/m/n/10.95 out-put Underfull \hbox (badness 10000) in paragraph at lines 1125--1127 []\T1/ptm/m/n/10.95 a bash script con-tain-ing the three com-mand lines to run Underfull \hbox (badness 2662) in paragraph at lines 1188--1195 \T1/ptm/m/n/10.95 The files nec-es-sary for the phy-lo-ge-netic re-con-struc-ti Underfull \hbox (badness 10000) in paragraph at lines 1247--1249 []\T1/ptm/m/n/10.95 a bash script con-tain-ing the three com-mand lines to run Chapter 7. Underfull \hbox (badness 10000) in paragraph at lines 58--61 []\T1/ptm/m/n/10.95 Z Yang. Phy-lo-ge-netic anal-y-sis by max-i-mum like-li-ho /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_RESTORE make[7]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[7]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" manual.pdf_NEED_REBUILD make[7]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' *** Checking rebuild with rule 'latex' *** Checking rebuild with rule 'texdepends' ******************************************** *********** New build needed *************** ******************************************** New manual.aux file LU_rebuild_latex: new run needed (LaTeX message 'Rerun to get...') ******************************************** /usr/bin/make LU_REC_LEVEL=4 manual.pdf make[8]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' ======> building manual.bbl <====== This is BibTeX, Version 0.99d (TeX Live 2025/Debian) The top-level auxiliary file: manual.aux The style file: plainnat.bst Database file #1: stage.bib Warning--empty year in YangPAML (There was 1 warning) Previous compilation failed. Rerun needed /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_SAVE make[9]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[9]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' ======> building manual.pdf <====== removed 'manual.pdf_NEED_REBUILD' removed 'manual.pdf.mk' Running: 'pdflatex' '--interaction' 'errorstopmode' '--jobname' 'manual' '\RequirePackage[extension=.pdf]{texdepends}\input{manual.tex}' Package texdepends Warning: graphicspath already redefined. Skipping it. on input line 36. Package texdepends Warning: Diverting empty macro 'Ginclude@eps' (texdepends) Probably a bug in texdepends.sty. Package texdepends Warning: Gin@getbase already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@pdf already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@pdf already redefined. Skipping it. on input line 87. Chapter 1. LaTeX Warning: `h' float specifier changed to `ht'. Underfull \hbox (badness 1454) in paragraph at lines 196--201 []\T1/ptm/m/n/10.95 Currently, \T1/pcr/m/n/10.95 ALTree-convert \T1/ptm/m/n/10. Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 314--315 Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 369--369 []|\T1/ptm/m/n/10.95 Output con-tain-ing the num-ber of Overfull \hbox (2.0805pt too wide) in paragraph at lines 355--370 [] Underfull \hbox (badness 10000) in paragraph at lines 396--397 Underfull \hbox (badness 10000) in paragraph at lines 400--401 Underfull \hbox (badness 10000) in paragraph at lines 416--417 Underfull \hbox (badness 1112) in paragraph at lines 505--507 []\T1/ptm/m/n/10.95 Other ex-am-ples may be found in the test di-rec-tory. Thes Chapter 4. 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Underfull \hbox (badness 10000) in paragraph at lines 58--61 /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_RESTORE make[9]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[9]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" manual.pdf_NEED_REBUILD make[9]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' *** Checking rebuild with rule 'latex' *** Checking rebuild with rule 'texdepends' /usr/bin/make LU_REC_LEVEL=5 manual.pdf make[10]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[10]: 'manual.pdf' is up to date. make[10]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[9]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[8]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[7]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[6]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[5]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[4]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[2]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' dh_auto_build make -j16 make[1]: Entering directory '/build/reproducible-path/altree-1.3.2' make[2]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils' make -C c_sources Running Mkbootstrap for CUtils () "/usr/bin/perl" "/usr/share/perl/5.40.1/ExtUtils/xsubpp" -typemap '/usr/share/perl/5.40/ExtUtils/typemap' CUtils.xs > CUtils.xsc make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" chisq.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" double_permutation.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" fisher.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" mt19937ar.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" myrand.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" resampling.c cp ALTree/Nanova.pm blib/lib/ALTree/Nanova.pm cp ALTree/Foret.pm blib/lib/ALTree/Foret.pm cp ALTree/Import.pm blib/lib/ALTree/Import.pm cp ALTree/to_rewrite.pm blib/lib/ALTree/to_rewrite.pm cp ALTree/Input.pm blib/lib/ALTree/Input.pm cp ALTree/SitePerForet.pm blib/lib/ALTree/SitePerForet.pm cp ALTree/SiteSensPerForet.pm blib/lib/ALTree/SiteSensPerForet.pm cp ALTree/Tree.pm blib/lib/ALTree/Tree.pm cp ALTree/Site.pm blib/lib/ALTree/Site.pm cp ALTree/Chi2.pm blib/lib/ALTree/Chi2.pm cp ALTree/SiteCollection.pm blib/lib/ALTree/SiteCollection.pm cp ALTree/Utils.pm blib/lib/ALTree/Utils.pm cp ALTree/Node.pm blib/lib/ALTree/Node.pm cp ALTree/Sens.pm blib/lib/ALTree/Sens.pm cp ALTree/SitePerTree.pm blib/lib/ALTree/SitePerTree.pm cp ALTree/SiteSensPerTree.pm blib/lib/ALTree/SiteSensPerTree.pm cp ALTree/Base.pm blib/lib/ALTree/Base.pm cp ALTree/SiteSens.pm blib/lib/ALTree/SiteSens.pm x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" rhyper.c chmod 644 "CUtils.bs" x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" stats.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" z.c "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CUtils.bs ../blib/arch/auto/ALTree/CUtils/CUtils.bs 644 chisq.c: In function 'pochisq': chisq.c:77:1: warning: old-style function definition [-Wold-style-definition] 77 | pochisq (x, df) | ^~~~~~~ chisq.c: In function 'critchi': chisq.c:129:1: warning: old-style function definition [-Wold-style-definition] 129 | critchi (p, df) | ^~~~~~~ cp lib/ALTree/CUtils.pm ../blib/lib/ALTree/CUtils.pm AutoSplitting ../blib/lib/ALTree/CUtils.pm (../blib/lib/auto/ALTree/CUtils) z.c: In function 'poz': z.c:44:1: warning: old-style function definition [-Wold-style-definition] 44 | poz (z) | ^~~ z.c: In function 'critz': z.c:91:1: warning: old-style function definition [-Wold-style-definition] 91 | critz (p) | ^~~~~ z.c: At top level: z.c:12:13: warning: 'sccsfid' defined but not used [-Wunused-variable] 12 | static char sccsfid[] = "@(#) z.c 5.1 (|stat) 12/26/85"; | ^~~~~~~ Please specify prototyping behavior for CUtils.xs (see perlxs manual) mv CUtils.xsc CUtils.c x86_64-linux-gnu-gcc -c -ggdb3 -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"1.1\" -DXS_VERSION=\"1.1\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" CUtils.c In function 'pval_min', inlined from 'double_permutation' at double_permutation.c:182:19: double_permutation.c:125:20: warning: '*(datatype_t *)local' may be used uninitialized [-Wmaybe-uninitialized] 125 | datatype_t ret=rep[0]; | ^~~ ar cr libaltree-cutils.a chisq.o double_permutation.o fisher.o mt19937ar.o myrand.o resampling.o rhyper.o stats.o z.o : libaltree-cutils.a make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' rm -f ../blib/arch/auto/ALTree/CUtils/CUtils.so x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -shared -L/usr/local/lib -fstack-protector-strong CUtils.o -o ../blib/arch/auto/ALTree/CUtils/CUtils.so c_sources/libaltree-cutils.a \ -lm -lpthread -lgsl -lblas \ chmod 755 ../blib/arch/auto/ALTree/CUtils/CUtils.so Manifying 1 pod document make[2]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils' cp progs/altree blib/script/altree cp progs/altree-add-S blib/script/altree-add-S cp progs/altree-convert blib/script/altree-convert "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/altree "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/altree-add-S "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/altree-convert Manifying 3 pod documents make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' dh_auto_test make -j16 test TEST_VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/altree-1.3.2' make[2]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CUtils.bs ../blib/arch/auto/ALTree/CUtils/CUtils.bs 644 make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' Manifying 1 pod document make[2]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils' make[2]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CUtils.bs ../blib/arch/auto/ALTree/CUtils/CUtils.bs 644 make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' No tests defined for ALTree::CUtils extension. make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, '../blib/lib', '../blib/arch')" t/*.t t/ALTree-CUtils.t ....... 1..1 ok 1 - use ALTree::CUtils; ok t/double_permutation.t .. 1..3 ok 1 - use ALTree::CUtils; ok 2 - undef when bad args ok 3 - double_permutation ok All tests successful. Files=2, Tests=4, 1 wallclock secs ( 0.01 usr 0.01 sys + 0.12 cusr 0.03 csys = 0.17 CPU) Result: PASS make[2]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils' PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t t/ALTree.t .. 1..1 ok 1 - use ALTree::Import; ok All tests successful. Files=1, Tests=1, 0 wallclock secs ( 0.02 usr 0.00 sys + 0.12 cusr 0.02 csys = 0.16 CPU) Result: PASS make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j16 install DESTDIR=/build/reproducible-path/altree-1.3.2/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/reproducible-path/altree-1.3.2' make[2]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CUtils.bs ../blib/arch/auto/ALTree/CUtils/CUtils.bs 644 make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' Manifying 1 pod document make[2]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils' Manifying 3 pod documents Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/ALTree/CUtils/CUtils.so Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Foret.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SitePerForet.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Tree.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Node.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SitePerTree.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteSensPerTree.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteCollection.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Base.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Site.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Utils.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Chi2.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Sens.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/to_rewrite.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Input.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Import.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/CUtils.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteSensPerForet.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Nanova.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteSens.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/ALTree/CUtils/autosplit.ix Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/share/man/man1/altree-convert.1p Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/share/man/man1/altree.1p Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/share/man/man1/altree-add-S.1p Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/share/man/man3/ALTree::CUtils.3pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/bin/altree Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/bin/altree-add-S Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/bin/altree-convert make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' dh_install debian/rules execute_after_dh_install-arch make[1]: Entering directory '/build/reproducible-path/altree-1.3.2' set -e \ ; cd debian/altree/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/ \ ; for file in Chi2.pm Import.pm Input.pm Node.pm SitePerForet.pm SiteSensPerTree.pm Tree.pm to_rewrite.pm \ ; do iconv -f ISO-8859-1 -t UTF-8 < "${file}" > "${file}.conv" \ ; mv -vf "${file}.conv" "${file}" \ ; done renamed 'Chi2.pm.conv' -> 'Chi2.pm' renamed 'Import.pm.conv' -> 'Import.pm' renamed 'Input.pm.conv' -> 'Input.pm' renamed 'Node.pm.conv' -> 'Node.pm' renamed 'SitePerForet.pm.conv' -> 'SitePerForet.pm' renamed 'SiteSensPerTree.pm.conv' -> 'SiteSensPerTree.pm' renamed 'Tree.pm.conv' -> 'Tree.pm' renamed 'to_rewrite.pm.conv' -> 'to_rewrite.pm' make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/reproducible-path/altree-1.3.2' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/altree/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/ALTree/CUtils/CUtils.so was not linked against libblas.so.3 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'altree-examples' in '../altree-examples_1.3.2-4_all.deb'. dpkg-deb: building package 'altree-dbgsym' in '../altree-dbgsym_1.3.2-4_amd64.deb'. dpkg-deb: building package 'altree' in '../altree_1.3.2-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../altree_1.3.2-4_amd64.buildinfo dpkg-genchanges --build=binary -O../altree_1.3.2-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1210918 and its subdirectories I: Current time: Tue Oct 20 19:40:37 -12 2026 I: pbuilder-time-stamp: 1792568437 Thu Sep 18 01:17:38 UTC 2025 I: 1st build successful. Starting 2nd build on remote node infom01-amd64.debian.net. Thu Sep 18 01:17:38 UTC 2025 I: Preparing to do remote build '2' on infom01-amd64.debian.net. Thu Sep 18 01:17:38 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom01-amd64.debian.net is marked as down. Thu Sep 18 01:17:38 UTC 2025 - checking via ssh if infom01-amd64.debian.net is up. removed '/tmp/read-only-fs-test-1EzzLS' ==================================================================================== Thu Sep 18 01:17:39 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on infom01-amd64, called using "2 altree unstable /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm 1.3.2-4" as arguments. Thu Sep 18 01:17:39 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-qHrjK0es" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Sep 18 01:17:39 UTC 2025 I: Downloading source for unstable/altree=1.3.2-4 Reading package lists... NOTICE: 'altree' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/altree.git Please use: git clone https://salsa.debian.org/med-team/altree.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 622 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main altree 1.3.2-4 (dsc) [2535 B] Get:2 http://deb.debian.org/debian unstable/main altree 1.3.2-4 (tar) [611 kB] Get:3 http://deb.debian.org/debian unstable/main altree 1.3.2-4 (diff) [8600 B] Fetched 622 kB in 0s (2549 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'altree' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/altree.git Please use: git clone https://salsa.debian.org/med-team/altree.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 622 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main altree 1.3.2-4 (dsc) [2535 B] Get:2 http://deb.debian.org/debian unstable/main altree 1.3.2-4 (tar) [611 kB] Get:3 http://deb.debian.org/debian unstable/main altree 1.3.2-4 (diff) [8600 B] Fetched 622 kB in 0s (2549 kB/s) Download complete and in download only mode ============================================================================= Re-Building altree in unstable on amd64 on infom01-amd64 now. Date: Thu Sep 18 01:17:39 UTC 2025 Date UTC: Thu Sep 18 01:17:39 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm/pbuilderrc_H5KR + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' altree = debian-installer -o altree = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' altree = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm/pbuilderrc_H5KR --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm/b2 --logfile b2/build.log altree_1.3.2-4.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Sep 18 15:17:40 +14 2025 I: pbuilder-time-stamp: 1758158260 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: Copying source file I: copying [altree_1.3.2-4.dsc] I: copying [./altree_1.3.2.orig.tar.gz] I: copying [./altree_1.3.2-4.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./altree_1.3.2-4.dsc: no acceptable signature found dpkg-source: info: extracting altree in altree-1.3.2 dpkg-source: info: unpacking altree_1.3.2.orig.tar.gz dpkg-source: info: unpacking altree_1.3.2-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc-15.patch dpkg-source: info: applying typo.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3005726/tmp/hooks/D01_modify_environment starting debug: Running on infom01-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Sep 18 01:17 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3005726/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3005726/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.3.3(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=fd225833945f4deeab11261e297212e2 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3005726 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm/pbuilderrc_H5KR --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm/b2 --logfile b2/build.log altree_1.3.2-4.dsc' SUDO_GID=109 SUDO_HOME=/var/lib/jenkins SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' I: uname -a Linux i-capture-the-hostname 6.12.43+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3005726/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: bash-completion, debhelper-compat (= 13), perl:native, perl-xs-dev, latex-make, ghostscript, texlive-lang-french, texlive-latex-extra, texlive-latex-recommended, texlive-fonts-recommended, libmath-tamuanova-perl, libgsl-dev, libblas-dev | libblas.so, libtest-deep-perl, fig2dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 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 bash-completion; however: Package bash-completion is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on perl:native. pbuilder-satisfydepends-dummy depends on perl-xs-dev; however: Package perl-xs-dev is not installed. pbuilder-satisfydepends-dummy depends on latex-make; however: Package latex-make is not installed. pbuilder-satisfydepends-dummy depends on ghostscript; however: Package ghostscript is not installed. pbuilder-satisfydepends-dummy depends on texlive-lang-french; however: Package texlive-lang-french is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however: Package texlive-latex-extra is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-recommended; however: Package texlive-latex-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however: Package texlive-fonts-recommended is not installed. pbuilder-satisfydepends-dummy depends on libmath-tamuanova-perl; however: Package libmath-tamuanova-perl is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev | libblas.so; however: Package libblas-dev is not installed. Package libblas.so is not installed. pbuilder-satisfydepends-dummy depends on libtest-deep-perl; however: Package libtest-deep-perl is not installed. pbuilder-satisfydepends-dummy depends on fig2dev; however: Package fig2dev 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} bash-completion{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} fig2dev{a} file{a} fontconfig-config{a} fonts-lmodern{a} fonts-urw-base35{a} gawk{a} gettext{a} gettext-base{a} ghostscript{a} groff-base{a} intltool-debian{a} latex-make{a} libapache-pom-java{a} libarchive-zip-perl{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libblas-dev{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcommons-logging-java{a} libcommons-parent-java{a} libcups2t64{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontbox-java{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libglib2.0-0t64{a} libgnutls30t64{a} libgraphite2-3{a} libgs-common{a} libgs10{a} libgs10-common{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libice6{a} libicu76{a} libidn12{a} libidn2-0{a} libijs-0.35{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libmath-tamuanova-perl{a} libmpfi0{a} libnetpbm11t64{a} libopenjp2-7{a} libp11-kit0{a} libpaper-utils{a} libpaper2{a} libpdfbox-java{a} libperl-dev{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpotrace0{a} libproc2-0{a} libptexenc1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libsharpyuv0{a} libsm6{a} libsynctex2{a} libtamuanova-0.2{a} libtasn1-6{a} libteckit0{a} libtest-deep-perl{a} libtexlua53-5{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libtiff6{a} libtool{a} libuchardet0{a} libunistring5{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} libxml2-16{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6t64{a} libzzip-0-13t64{a} m4{a} man-db{a} media-types{a} netbase{a} netpbm{a} po-debconf{a} poppler-data{a} preview-latex-style{a} procps{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} t1utils{a} tex-common{a} texlive-base{a} texlive-binaries{a} texlive-fonts-recommended{a} texlive-lang-french{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} tzdata{a} ucf{a} x11-common{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl dbus default-jre dvisvgm fonts-droid-fallback inkscape krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libltdl-dev libmail-sendmail-perl libnet-dbus-perl libspreadsheet-parseexcel-perl libx11-protocol-perl linux-sysctl-defaults lmodern lynx psmisc ruby shared-mime-info tex-gyre texlive-plain-generic tipa tk wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 155 newly installed, 0 to remove and 0 not upgraded. Need to get 322 MB of archives. After unpacking 809 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 gawk amd64 1:5.3.2-1 [772 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.2-1 [111 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 poppler-data all 0.4.12-1 [1601 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-5 [260 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 bash-completion all 1:2.16.0-7 [319 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B] Get: 31 http://deb.debian.org/debian unstable/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get: 32 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0052 [43.3 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 44 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.50-1 [282 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+25 [217 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libgs-common all 10.05.1~dfsg-3 [149 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libgs10-common all 10.05.1~dfsg-3 [479 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-17 [112 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-17 [47.3 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.16.2-2 [178 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-17 [52.1 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 74 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.10-4 [267 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2.4 [318 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2.4 [401 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libidn12 amd64 1.43-2 [48.3 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libijs-0.35 amd64 0.35-16 [16.0 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libjbig2dec0 amd64 0.20-1+b3 [65.1 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [204 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libpaper2 amd64 2.2.5-0.3+b2 [16.7 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.7.0-5 [364 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.6-1 [37.3 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [208 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libgs10 amd64 10.05.1~dfsg-3 [2732 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 ghostscript amd64 10.05.1~dfsg-3 [50.5 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libnetpbm11t64 amd64 2:11.11.01-1 [194 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 netpbm amd64 2:11.11.01-1 [2140 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 fig2dev amd64 1:3.2.9a-4 [449 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 tex-common all 6.19 [29.4 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 latex-make all 2.4.3-1 [1030 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 33-2 [5852 B] Get: 109 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.1-7 [229 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.3.0-2 [68.6 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.84.4-3 [1518 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-7 [76.3 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5.1 [137 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5.1 [1068 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-5.1 [1336 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 11.4.5-1 [505 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libicu76 amd64 76.1-4 [9722 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libkpathsea6 amd64 2025.20250727.75242+ds-4 [154 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libtamuanova-0.2 amd64 0.2-5+b3 [9228 B] Get: 129 http://deb.debian.org/debian unstable/main amd64 libmath-tamuanova-perl amd64 1.0.2-4+b2 [13.9 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libmpfi0 amd64 1.5.4+ds-4 [35.5 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 2.2.5-0.3+b2 [16.5 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libperl-dev amd64 5.40.1-6 [1109 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libpotrace0 amd64 1.16-2+b2 [25.6 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libptexenc1 amd64 2025.20250727.75242+ds-4 [50.5 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libsynctex2 amd64 2025.20250727.75242+ds-4 [58.2 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libteckit0 amd64 2.5.12+ds1-1+b1 [341 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libtest-deep-perl all 1.205-1 [52.3 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libtexlua53-5 amd64 2025.20250727.75242+ds-4 [99.4 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libxmu6 amd64 2:1.1.3-3+b4 [59.0 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libxpm4 amd64 1:3.5.17-1+b3 [56.2 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libxaw7 amd64 2:1.0.16-1 [212 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libzzip-0-13t64 amd64 0.13.78+dfsg.1-0.1 [59.0 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 preview-latex-style all 13.2-1.1 [350 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 texlive-binaries amd64 2025.20250727.75242+ds-4 [7261 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 texlive-base all 2025.20250727-3 [23.1 MB] Get: 150 http://deb.debian.org/debian unstable/main amd64 texlive-fonts-recommended all 2025.20250727-3 [4991 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 texlive-lang-french all 2025.20250727-3 [149 MB] Get: 152 http://deb.debian.org/debian unstable/main amd64 texlive-latex-base all 2025.20250727-3 [1318 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 texlive-latex-recommended all 2025.20250727-3 [8454 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 texlive-pictures all 2025.20250727-3 [22.1 MB] Get: 155 http://deb.debian.org/debian unstable/main amd64 texlive-latex-extra all 2025.20250727-3 [27.4 MB] Fetched 322 MB in 7s (48.9 MB/s) Preconfiguring packages ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Setting up readline-common (8.3-3) ... Setting up libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package gawk. (Reading database ... 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Processing triggers for libc-bin (2.41-12) ... Processing triggers for tex-common (6.19) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/3005726/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/3005726/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/altree-1.3.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../altree_1.3.2-4_source.changes dpkg-buildpackage: info: source package altree dpkg-buildpackage: info: source version 1.3.2-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules execute_before_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/altree-1.3.2' /usr/bin/make -C Documentation distclean || true make[2]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[2]: Nothing to be done for 'distclean'. make[2]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro" Checking if your kit is complete... Warning: the following files are missing in your kit: CUtils/c_sources/MYMETA.json CUtils/MYMETA.json MYMETA.json Please inform the author. MakeMaker (v7.70) Warning (non-fatal): Target 'dynamic' depends on targets in skipped section 'dynamic_lib' Warning (non-fatal): Target 'static' depends on targets in skipped section 'static_lib' Generating a Unix-style Makefile Writing Makefile for ALTree::CUtils Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for ALTree::CUtils Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for altree Writing MYMETA.yml and MYMETA.json debian/rules execute_before_dh_auto_build make[1]: Entering directory '/build/reproducible-path/altree-1.3.2' /usr/bin/make -C Documentation pdf make[2]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_SAVE make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[3]: Nothing to be done for 'LU_WATCH_FILES_SAVE'. make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' ======> building manual.pdf <====== Running: 'pdflatex' '--interaction' 'errorstopmode' '--jobname' 'manual' '\RequirePackage[extension=.pdf]{texdepends}\input{manual.tex}' Package texdepends Warning: graphicspath already redefined. Skipping it. on input line 36. Package texdepends Warning: Diverting empty macro 'Ginclude@eps' (texdepends) Probably a bug in texdepends.sty. Package texdepends Warning: Gin@getbase already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@pdf already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@pdf already redefined. Skipping it. on input line 87. Chapter 1. LaTeX Warning: Reference `fig:altree' on page 2 undefined on input line 121. Package texdepends Warning: No 'fig/overview.pdftex' file (texdepends) using 1 for graphic dimensions on input line 124. Package texdepends Warning: Figure 'fig/overview.pdftex_t' needed (texdepends) Skipping it this time (the last one however) (texdepends) on input line 124. 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Underfull \hbox (badness 2486) in paragraph at lines 284--290 []\T1/pcr/m/n/10.95 paml \T1/ptm/b/n/10.95 ?\T1/ptm/m/n/10.95 : freely avail-ab Underfull \hbox (badness 10000) in paragraph at lines 314--315 Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 369--369 []|\T1/ptm/m/n/10.95 Output con-tain-ing the num-ber of Overfull \hbox (2.0805pt too wide) in paragraph at lines 355--370 [] Underfull \hbox (badness 10000) in paragraph at lines 396--397 Underfull \hbox (badness 10000) in paragraph at lines 400--401 Underfull \hbox (badness 10000) in paragraph at lines 416--417 Underfull \hbox (badness 1112) in paragraph at lines 505--507 []\T1/ptm/m/n/10.95 Other ex-am-ples may be found in the test di-rec-tory. Thes Chapter 4. Overfull \hbox (2.0805pt too wide) in paragraph at lines 537--553 [] LaTeX Warning: Reference `help' on page 13 undefined on input line 564. Overfull \hbox (8.63097pt too wide) in paragraph at lines 584--605 \T1/ptm/m/n/10.95 Examples: $[]$ $[]$ LaTeX Warning: Reference `description_etiquette' on page 14 undefined on input line 632. LaTeX Warning: Reference `description_etiquette' on page 14 undefined on input line 633. Package natbib Warning: Citation `Bardel05' on page 14 undefined on input line 634. LaTeX Warning: Reference `description_etiquette' on page 15 undefined on input line 649. LaTeX Warning: Reference `description_etiquette' on page 15 undefined on input line 649. Chapter 5. Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --data-qual|-q Underfull \hbox (badness 1281) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 remove the out-group se-quence for the Underfull \hbox (badness 5681) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 ancestral se-quence (only use-ful with Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --tree-building-program|-p Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --s-site-characters Underfull \hbox (badness 1565) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 print the tree with the char-ac-ter state Overfull \hbox (2.0805pt too wide) in paragraph at lines 664--698 [] LaTeX Warning: Reference `help' on page 16 undefined on input line 701. 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Underfull \hbox (badness 2662) in paragraph at lines 1188--1195 \T1/ptm/m/n/10.95 The files nec-es-sary for the phy-lo-ge-netic re-con-struc-ti Package texdepends Warning: No 'fig/association_paml.pdftex' file (texdepends) using 1 for graphic dimensions on input line 1217. Package texdepends Warning: Figure 'fig/association_paml.pdftex_t' needed (texdepends) Skipping it this time (the last one however) (texdepends) on input line 1217. Underfull \hbox (badness 10000) in paragraph at lines 1247--1249 []\T1/ptm/m/n/10.95 a bash script con-tain-ing the three com-mand lines to run Package texdepends Warning: No 'fig/localisation_paml.pdftex' file (texdepends) using 1 for graphic dimensions on input line 1252. Package texdepends Warning: Figure 'fig/localisation_paml.pdftex_t' needed (texdepends) Skipping it this time (the last one however) (texdepends) on input line 1252. Chapter 7. Package texdepends Warning: Figure(s) missing. Check dependencies again. Package natbib Warning: There were undefined citations. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `manual.out' has changed. (rerunfilecheck) Rerun to get outlines right /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_RESTORE make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' ======> building fig/option_b.subfig.mk <====== make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" manual.pdf_NEED_REBUILD make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' *** Checking rebuild with rule 'latex' *** Checking rebuild with rule 'texdepends' ******************************************** *********** New build needed *************** ******************************************** New manual.aux file LU_rebuild_latex: new run needed (LaTeX message 'Rerun to get...') LU_rebuild_texdepends: new depends required ******************************************** /usr/bin/make LU_REC_LEVEL=2 manual.pdf make[4]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' ======> building manual.bbl <====== This is BibTeX, Version 0.99d (TeX Live 2025/Debian) The top-level auxiliary file: manual.aux The style file: plainnat.bst Database file #1: stage.bib Warning--empty year in YangPAML (There was 1 warning) ======> building fig/overview.pdftex <====== ======> building fig/overview.pdftex_t <====== ======> building fig/altree-q.pdftex <====== ======> building fig/altree-q.pdftex_t <====== ======> building fig/option_b_1.fig <====== ======> building fig/option_b_2.fig <====== ======> building fig/create_file_paup.pdftex <====== ======> building fig/create_file_paup.pdftex_t <====== ======> building fig/create_file_phy.pdftex <====== ======> building fig/create_file_phy.pdftex_t <====== ======> building fig/association_paup.pdftex <====== ======> building fig/association_paup.pdftex_t <====== ======> building fig/localisation_paup.pdftex <====== ======> building fig/localisation_paup.pdftex_t <====== ======> building fig/association_phylip.pdftex <====== ======> building fig/association_phylip.pdftex_t <====== ======> building fig/association_paml.pdftex <====== ======> building fig/association_paml.pdftex_t <====== ======> building fig/localisation_paml.pdftex <====== ======> building fig/localisation_paml.pdftex_t <====== Previous compilation failed. Rerun needed /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_SAVE make[5]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[5]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' ======> building manual.pdf <====== removed 'manual.pdf_NEED_REBUILD' removed 'manual.pdf.mk' Running: 'pdflatex' '--interaction' 'errorstopmode' '--jobname' 'manual' '\RequirePackage[extension=.pdf]{texdepends}\input{manual.tex}' Package texdepends Warning: graphicspath already redefined. Skipping it. on input line 36. Package texdepends Warning: Diverting empty macro 'Ginclude@eps' (texdepends) Probably a bug in texdepends.sty. Package texdepends Warning: Gin@getbase already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@pdf already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@pdf already redefined. Skipping it. on input line 87. Chapter 1. Package natbib Warning: Citation `Bardel05' on page 3 undefined on input line 143. Package natbib Warning: Citation `Ge03' on page 3 undefined on input line 146. Package natbib Warning: Citation `Becker04' on page 3 undefined on input line 146. LaTeX Warning: `h' float specifier changed to `ht'. Package natbib Warning: Citation `Bardel05' on page 4 undefined on input line 180. Package natbib Warning: Citation `Stephens01' on page 4 undefined on input line 197. Package natbib Warning: Citation `Stephens03' on page 4 undefined on input line 197. Package natbib Warning: Citation `Becker04' on page 4 undefined on input line 198. Package natbib Warning: Citation `Swofford02' on page 4 undefined on input line 199. Package natbib Warning: Citation `Felsenstein04' on page 4 undefined on input line 200. Package natbib Warning: Citation `YangPAML' on page 4 undefined on input line 200. Underfull \hbox (badness 1454) in paragraph at lines 196--201 []\T1/ptm/m/n/10.95 Currently, \T1/pcr/m/n/10.95 ALTree-convert \T1/ptm/m/n/10. Chapter 2. Package natbib Warning: Citation `Swofford02' on page 7 undefined on input line 278. Package natbib Warning: Citation `Felsenstein04' on page 7 undefined on input line 281. Underfull \hbox (badness 1142) in paragraph at lines 281--284 []\T1/pcr/m/n/10.95 phylip \T1/ptm/b/n/10.95 ?\T1/ptm/m/n/10.95 : freely avail- Package natbib Warning: Citation `YangPAML' on page 7 undefined on input line 284. Package natbib Warning: Citation `Guindon03' on page 7 undefined on input line 288. Underfull \hbox (badness 2486) in paragraph at lines 284--290 []\T1/pcr/m/n/10.95 paml \T1/ptm/b/n/10.95 ?\T1/ptm/m/n/10.95 : freely avail-ab Underfull \hbox (badness 10000) in paragraph at lines 314--315 Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 369--369 []|\T1/ptm/m/n/10.95 Output con-tain-ing the num-ber of Overfull \hbox (2.0805pt too wide) in paragraph at lines 355--370 [] Underfull \hbox (badness 10000) in paragraph at lines 396--397 Underfull \hbox (badness 10000) in paragraph at lines 400--401 Underfull \hbox (badness 10000) in paragraph at lines 416--417 Underfull \hbox (badness 1112) in paragraph at lines 505--507 []\T1/ptm/m/n/10.95 Other ex-am-ples may be found in the test di-rec-tory. Thes Chapter 4. Overfull \hbox (2.0805pt too wide) in paragraph at lines 537--553 [] Overfull \hbox (8.63097pt too wide) in paragraph at lines 584--605 \T1/ptm/m/n/10.95 Examples: $[]$ $[]$ Package natbib Warning: Citation `Bardel05' on page 14 undefined on input line 634. Chapter 5. Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --data-qual|-q Underfull \hbox (badness 1281) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 remove the out-group se-quence for the Underfull \hbox (badness 5681) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 ancestral se-quence (only use-ful with Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --tree-building-program|-p Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --s-site-characters Underfull \hbox (badness 1565) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 print the tree with the char-ac-ter state Overfull \hbox (2.0805pt too wide) in paragraph at lines 664--698 [] Underfull \hbox (badness 10000) in paragraph at lines 735--738 Underfull \hbox (badness 1622) in paragraph at lines 747--755 \T1/ptm/m/n/10.95 Example of such files are given in the test di-rec-tory. Thes Package natbib Warning: Citation `Ge03' on page 19 undefined on input line 830. Package natbib Warning: Citation `Becker04' on page 19 undefined on input line 830. Package texdepends Warning: No 'fig/option_b_1.pdftex' file (texdepends) using 1 for graphic dimensions on input line 852. Package texdepends Warning: Figure 'fig/option_b_1.pdftex_t' needed (texdepends) Skipping it this time (the last one however) (texdepends) on input line 852. Package texdepends Warning: No 'fig/option_b_2.pdftex' file (texdepends) using 1 for graphic dimensions on input line 853. Package texdepends Warning: Figure 'fig/option_b_2.pdftex_t' needed (texdepends) Skipping it this time (the last one however) (texdepends) on input line 853. Overfull \hbox (15.23479pt too wide) in paragraph at lines 850--865 [][] Package natbib Warning: Citation `Bardel05' on page 21 undefined on input line 921. Package natbib Warning: Citation `Bardel05' on page 21 undefined on input line 941. Chapter 6. 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Phy-lo-ge-netic anal-y-sis by max-i-mum like-li-ho Package texdepends Warning: Figure(s) missing. Check dependencies again. Package natbib Warning: There were undefined citations. Package natbib Warning: Citation(s) may have changed. (natbib) Rerun to get citations correct. /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_RESTORE make[5]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[5]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" manual.pdf_NEED_REBUILD make[5]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' *** Checking rebuild with rule 'latex' *** Checking rebuild with rule 'texdepends' ******************************************** *********** New build needed *************** ******************************************** New manual.aux file LU_rebuild_latex: new run needed (LaTeX message 'Rerun to get...') LU_rebuild_texdepends: new depends required ******************************************** /usr/bin/make LU_REC_LEVEL=3 manual.pdf make[6]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' ======> building manual.bbl <====== This is BibTeX, Version 0.99d (TeX Live 2025/Debian) The top-level auxiliary file: manual.aux The style file: plainnat.bst Database file #1: stage.bib Warning--empty year in YangPAML (There was 1 warning) ======> building fig/option_b_1.pdftex <====== ======> building fig/option_b_1.pdftex_t <====== ======> building fig/option_b_2.pdftex <====== ======> building fig/option_b_2.pdftex_t <====== Previous compilation failed. Rerun needed /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_SAVE make[7]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[7]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' ======> building manual.pdf <====== removed 'manual.pdf_NEED_REBUILD' removed 'manual.pdf.mk' Running: 'pdflatex' '--interaction' 'errorstopmode' '--jobname' 'manual' '\RequirePackage[extension=.pdf]{texdepends}\input{manual.tex}' Package texdepends Warning: graphicspath already redefined. Skipping it. on input line 36. Package texdepends Warning: Diverting empty macro 'Ginclude@eps' (texdepends) Probably a bug in texdepends.sty. Package texdepends Warning: Gin@getbase already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@pdf already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@pdf already redefined. Skipping it. on input line 87. Chapter 1. LaTeX Warning: `h' float specifier changed to `ht'. Underfull \hbox (badness 1454) in paragraph at lines 196--201 []\T1/ptm/m/n/10.95 Currently, \T1/pcr/m/n/10.95 ALTree-convert \T1/ptm/m/n/10. Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 314--315 Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 369--369 []|\T1/ptm/m/n/10.95 Output con-tain-ing the num-ber of Overfull \hbox (2.0805pt too wide) in paragraph at lines 355--370 [] Underfull \hbox (badness 10000) in paragraph at lines 396--397 Underfull \hbox (badness 10000) in paragraph at lines 400--401 Underfull \hbox (badness 10000) in paragraph at lines 416--417 Underfull \hbox (badness 1112) in paragraph at lines 505--507 []\T1/ptm/m/n/10.95 Other ex-am-ples may be found in the test di-rec-tory. Thes Chapter 4. Overfull \hbox (2.0805pt too wide) in paragraph at lines 537--553 [] Overfull \hbox (8.63097pt too wide) in paragraph at lines 584--605 \T1/ptm/m/n/10.95 Examples: $[]$ $[]$ Chapter 5. Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --data-qual|-q Underfull \hbox (badness 1281) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 remove the out-group se-quence for the Underfull \hbox (badness 5681) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 ancestral se-quence (only use-ful with Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --tree-building-program|-p Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --s-site-characters Underfull \hbox (badness 1565) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 print the tree with the char-ac-ter state Overfull \hbox (2.0805pt too wide) in paragraph at lines 664--698 [] Underfull \hbox (badness 10000) in paragraph at lines 735--738 Underfull \hbox (badness 1622) in paragraph at lines 747--755 \T1/ptm/m/n/10.95 Example of such files are given in the test di-rec-tory. Thes Overfull \hbox (15.23479pt too wide) in paragraph at lines 850--865 [][] Chapter 6. Underfull \hbox (badness 5519) in paragraph at lines 968--971 []\T1/ptm/b/n/10.95 create_file \T1/ptm/m/n/10.95 which con-tains files and in- Underfull \hbox (badness 10000) in paragraph at lines 1024--1026 []\T1/ptm/m/n/10.95 the two \T1/pcr/m/n/10.95 FamHap \T1/ptm/m/n/10.95 out-put Underfull \hbox (badness 10000) in paragraph at lines 1125--1127 []\T1/ptm/m/n/10.95 a bash script con-tain-ing the three com-mand lines to run Underfull \hbox (badness 2662) in paragraph at lines 1188--1195 \T1/ptm/m/n/10.95 The files nec-es-sary for the phy-lo-ge-netic re-con-struc-ti Underfull \hbox (badness 10000) in paragraph at lines 1247--1249 []\T1/ptm/m/n/10.95 a bash script con-tain-ing the three com-mand lines to run Chapter 7. Underfull \hbox (badness 10000) in paragraph at lines 58--61 []\T1/ptm/m/n/10.95 Z Yang. Phy-lo-ge-netic anal-y-sis by max-i-mum like-li-ho /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_RESTORE make[7]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[7]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" manual.pdf_NEED_REBUILD make[7]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' *** Checking rebuild with rule 'latex' *** Checking rebuild with rule 'texdepends' ******************************************** *********** New build needed *************** ******************************************** New manual.aux file LU_rebuild_latex: new run needed (LaTeX message 'Rerun to get...') ******************************************** /usr/bin/make LU_REC_LEVEL=4 manual.pdf make[8]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' ======> building manual.bbl <====== This is BibTeX, Version 0.99d (TeX Live 2025/Debian) The top-level auxiliary file: manual.aux The style file: plainnat.bst Database file #1: stage.bib Warning--empty year in YangPAML (There was 1 warning) Previous compilation failed. Rerun needed /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_SAVE make[9]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[9]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' ======> building manual.pdf <====== removed 'manual.pdf_NEED_REBUILD' removed 'manual.pdf.mk' Running: 'pdflatex' '--interaction' 'errorstopmode' '--jobname' 'manual' '\RequirePackage[extension=.pdf]{texdepends}\input{manual.tex}' Package texdepends Warning: graphicspath already redefined. Skipping it. on input line 36. Package texdepends Warning: Diverting empty macro 'Ginclude@eps' (texdepends) Probably a bug in texdepends.sty. Package texdepends Warning: Gin@getbase already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@pdf already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@pdf already redefined. Skipping it. on input line 87. Chapter 1. LaTeX Warning: `h' float specifier changed to `ht'. Underfull \hbox (badness 1454) in paragraph at lines 196--201 []\T1/ptm/m/n/10.95 Currently, \T1/pcr/m/n/10.95 ALTree-convert \T1/ptm/m/n/10. Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 314--315 Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 369--369 []|\T1/ptm/m/n/10.95 Output con-tain-ing the num-ber of Overfull \hbox (2.0805pt too wide) in paragraph at lines 355--370 [] Underfull \hbox (badness 10000) in paragraph at lines 396--397 Underfull \hbox (badness 10000) in paragraph at lines 400--401 Underfull \hbox (badness 10000) in paragraph at lines 416--417 Underfull \hbox (badness 1112) in paragraph at lines 505--507 []\T1/ptm/m/n/10.95 Other ex-am-ples may be found in the test di-rec-tory. Thes Chapter 4. Overfull \hbox (2.0805pt too wide) in paragraph at lines 537--553 [] Overfull \hbox (8.63097pt too wide) in paragraph at lines 584--605 \T1/ptm/m/n/10.95 Examples: $[]$ $[]$ Chapter 5. Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --data-qual|-q Underfull \hbox (badness 1281) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 remove the out-group se-quence for the Underfull \hbox (badness 5681) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 ancestral se-quence (only use-ful with Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --tree-building-program|-p Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --s-site-characters Underfull \hbox (badness 1565) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 print the tree with the char-ac-ter state Overfull \hbox (2.0805pt too wide) in paragraph at lines 664--698 [] Underfull \hbox (badness 10000) in paragraph at lines 735--738 Underfull \hbox (badness 1622) in paragraph at lines 747--755 \T1/ptm/m/n/10.95 Example of such files are given in the test di-rec-tory. Thes Overfull \hbox (15.23479pt too wide) in paragraph at lines 850--865 [][] Chapter 6. Underfull \hbox (badness 5519) in paragraph at lines 968--971 []\T1/ptm/b/n/10.95 create_file \T1/ptm/m/n/10.95 which con-tains files and in- Underfull \hbox (badness 10000) in paragraph at lines 1024--1026 []\T1/ptm/m/n/10.95 the two \T1/pcr/m/n/10.95 FamHap \T1/ptm/m/n/10.95 out-put Underfull \hbox (badness 10000) in paragraph at lines 1125--1127 []\T1/ptm/m/n/10.95 a bash script con-tain-ing the three com-mand lines to run Underfull \hbox (badness 2662) in paragraph at lines 1188--1195 \T1/ptm/m/n/10.95 The files nec-es-sary for the phy-lo-ge-netic re-con-struc-ti Underfull \hbox (badness 10000) in paragraph at lines 1247--1249 []\T1/ptm/m/n/10.95 a bash script con-tain-ing the three com-mand lines to run Chapter 7. Underfull \hbox (badness 10000) in paragraph at lines 58--61 /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_RESTORE make[9]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[9]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" manual.pdf_NEED_REBUILD make[9]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' *** Checking rebuild with rule 'latex' *** Checking rebuild with rule 'texdepends' /usr/bin/make LU_REC_LEVEL=5 manual.pdf make[10]: Entering directory '/build/reproducible-path/altree-1.3.2/Documentation' make[10]: 'manual.pdf' is up to date. make[10]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[9]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[8]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[7]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[6]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[5]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[4]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[2]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/altree-1.3.2' make[2]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils' make -C c_sources make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" chisq.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" double_permutation.c Running Mkbootstrap for CUtils () "/usr/bin/perl" "/usr/share/perl/5.40.1/ExtUtils/xsubpp" -typemap '/usr/share/perl/5.40/ExtUtils/typemap' CUtils.xs > CUtils.xsc x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" fisher.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" mt19937ar.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" myrand.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" resampling.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" rhyper.c cp ALTree/Sens.pm blib/lib/ALTree/Sens.pm cp ALTree/SiteCollection.pm blib/lib/ALTree/SiteCollection.pm cp ALTree/Tree.pm blib/lib/ALTree/Tree.pm cp ALTree/SiteSensPerTree.pm blib/lib/ALTree/SiteSensPerTree.pm cp ALTree/Base.pm blib/lib/ALTree/Base.pm cp ALTree/Nanova.pm blib/lib/ALTree/Nanova.pm cp ALTree/SiteSens.pm blib/lib/ALTree/SiteSens.pm cp ALTree/Chi2.pm blib/lib/ALTree/Chi2.pm cp ALTree/to_rewrite.pm blib/lib/ALTree/to_rewrite.pm cp ALTree/Import.pm blib/lib/ALTree/Import.pm cp ALTree/SiteSensPerForet.pm blib/lib/ALTree/SiteSensPerForet.pm cp ALTree/SitePerForet.pm blib/lib/ALTree/SitePerForet.pm cp ALTree/Site.pm blib/lib/ALTree/Site.pm cp ALTree/SitePerTree.pm blib/lib/ALTree/SitePerTree.pm cp ALTree/Node.pm blib/lib/ALTree/Node.pm cp ALTree/Utils.pm blib/lib/ALTree/Utils.pm cp ALTree/Input.pm blib/lib/ALTree/Input.pm cp ALTree/Foret.pm blib/lib/ALTree/Foret.pm x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" stats.c chmod 644 "CUtils.bs" x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" z.c chisq.c: In function 'pochisq': chisq.c:77:1: warning: old-style function definition [-Wold-style-definition] 77 | pochisq (x, df) | ^~~~~~~ "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CUtils.bs ../blib/arch/auto/ALTree/CUtils/CUtils.bs 644 chisq.c: In function 'critchi': chisq.c:129:1: warning: old-style function definition [-Wold-style-definition] 129 | critchi (p, df) | ^~~~~~~ cp lib/ALTree/CUtils.pm ../blib/lib/ALTree/CUtils.pm AutoSplitting ../blib/lib/ALTree/CUtils.pm (../blib/lib/auto/ALTree/CUtils) z.c: In function 'poz': z.c:44:1: warning: old-style function definition [-Wold-style-definition] 44 | poz (z) | ^~~ z.c: In function 'critz': z.c:91:1: warning: old-style function definition [-Wold-style-definition] 91 | critz (p) | ^~~~~ z.c: At top level: z.c:12:13: warning: 'sccsfid' defined but not used [-Wunused-variable] 12 | static char sccsfid[] = "@(#) z.c 5.1 (|stat) 12/26/85"; | ^~~~~~~ Please specify prototyping behavior for CUtils.xs (see perlxs manual) mv CUtils.xsc CUtils.c x86_64-linux-gnu-gcc -c -ggdb3 -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"1.1\" -DXS_VERSION=\"1.1\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" CUtils.c In function 'pval_min', inlined from 'double_permutation' at double_permutation.c:182:19: double_permutation.c:125:20: warning: '*(datatype_t *)local' may be used uninitialized [-Wmaybe-uninitialized] 125 | datatype_t ret=rep[0]; | ^~~ ar cr libaltree-cutils.a chisq.o double_permutation.o fisher.o mt19937ar.o myrand.o resampling.o rhyper.o stats.o z.o : libaltree-cutils.a make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' rm -f ../blib/arch/auto/ALTree/CUtils/CUtils.so x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -shared -L/usr/local/lib -fstack-protector-strong CUtils.o -o ../blib/arch/auto/ALTree/CUtils/CUtils.so c_sources/libaltree-cutils.a \ -lm -lpthread -lgsl -lblas \ chmod 755 ../blib/arch/auto/ALTree/CUtils/CUtils.so Manifying 1 pod document make[2]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils' cp progs/altree blib/script/altree cp progs/altree-add-S blib/script/altree-add-S cp progs/altree-convert blib/script/altree-convert "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/altree "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/altree-add-S "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/altree-convert Manifying 3 pod documents make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' dh_auto_test make -j12 test TEST_VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/altree-1.3.2' make[2]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CUtils.bs ../blib/arch/auto/ALTree/CUtils/CUtils.bs 644 make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' Manifying 1 pod document make[2]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils' make[2]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CUtils.bs ../blib/arch/auto/ALTree/CUtils/CUtils.bs 644 make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' No tests defined for ALTree::CUtils extension. make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, '../blib/lib', '../blib/arch')" t/*.t t/ALTree-CUtils.t ....... 1..1 ok 1 - use ALTree::CUtils; ok t/double_permutation.t .. 1..3 ok 1 - use ALTree::CUtils; ok 2 - undef when bad args ok 3 - double_permutation ok All tests successful. Files=2, Tests=4, 0 wallclock secs ( 0.02 usr 0.00 sys + 0.07 cusr 0.03 csys = 0.12 CPU) Result: PASS make[2]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils' PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t t/ALTree.t .. 1..1 ok 1 - use ALTree::Import; ok All tests successful. Files=1, Tests=1, 1 wallclock secs ( 0.02 usr 0.00 sys + 0.06 cusr 0.02 csys = 0.10 CPU) Result: PASS make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j12 install DESTDIR=/build/reproducible-path/altree-1.3.2/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/reproducible-path/altree-1.3.2' make[2]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CUtils.bs ../blib/arch/auto/ALTree/CUtils/CUtils.bs 644 make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' Manifying 1 pod document make[2]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils' Manifying 3 pod documents Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/ALTree/CUtils/CUtils.so Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/ALTree/CUtils/autosplit.ix Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteCollection.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Tree.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Nanova.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteSensPerForet.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Chi2.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SitePerTree.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteSensPerTree.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/CUtils.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Input.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Base.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/to_rewrite.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Import.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteSens.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Node.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SitePerForet.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Sens.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Site.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Foret.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Utils.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/share/man/man1/altree-convert.1p Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/share/man/man1/altree.1p Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/share/man/man1/altree-add-S.1p Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/share/man/man3/ALTree::CUtils.3pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/bin/altree Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/bin/altree-convert Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/bin/altree-add-S make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' dh_install debian/rules execute_after_dh_install-arch make[1]: Entering directory '/build/reproducible-path/altree-1.3.2' set -e \ ; cd debian/altree/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/ \ ; for file in Chi2.pm Import.pm Input.pm Node.pm SitePerForet.pm SiteSensPerTree.pm Tree.pm to_rewrite.pm \ ; do iconv -f ISO-8859-1 -t UTF-8 < "${file}" > "${file}.conv" \ ; mv -vf "${file}.conv" "${file}" \ ; done renamed 'Chi2.pm.conv' -> 'Chi2.pm' renamed 'Import.pm.conv' -> 'Import.pm' renamed 'Input.pm.conv' -> 'Input.pm' renamed 'Node.pm.conv' -> 'Node.pm' renamed 'SitePerForet.pm.conv' -> 'SitePerForet.pm' renamed 'SiteSensPerTree.pm.conv' -> 'SiteSensPerTree.pm' renamed 'Tree.pm.conv' -> 'Tree.pm' renamed 'to_rewrite.pm.conv' -> 'to_rewrite.pm' make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/reproducible-path/altree-1.3.2' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/altree/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/ALTree/CUtils/CUtils.so was not linked against libblas.so.3 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'altree' in '../altree_1.3.2-4_amd64.deb'. dpkg-deb: building package 'altree-dbgsym' in '../altree-dbgsym_1.3.2-4_amd64.deb'. dpkg-deb: building package 'altree-examples' in '../altree-examples_1.3.2-4_all.deb'. dpkg-genbuildinfo --build=binary -O../altree_1.3.2-4_amd64.buildinfo dpkg-genchanges --build=binary -O../altree_1.3.2-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3005726/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3005726/tmp/hooks/B01_cleanup finished 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/3005726 and its subdirectories I: Current time: Thu Sep 18 15:22:21 +14 2025 I: pbuilder-time-stamp: 1758158541 + false + set +x Thu Sep 18 01:22:21 UTC 2025 I: Signing ./b2/altree_1.3.2-4_amd64.buildinfo as altree_1.3.2-4_amd64.buildinfo.asc Thu Sep 18 01:22:21 UTC 2025 I: Signed ./b2/altree_1.3.2-4_amd64.buildinfo as ./b2/altree_1.3.2-4_amd64.buildinfo.asc Thu Sep 18 01:22:21 UTC 2025 - build #2 for altree/unstable/amd64 on infom01-amd64 done. Starting cleanup. All cleanup done. Thu Sep 18 01:22:21 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-qHrjK0es, removing. /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm: total 136 -rw-rw-r-- 1 jenkins jenkins 2535 Sep 17 19:14 altree_1.3.2-4.dsc drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 01:17 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 01:22 b2 -rw------- 1 jenkins jenkins 120279 Sep 18 01:17 rbuildlog.fnTyxL8 /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm/b1: total 1188 -rw-r--r-- 1 jenkins jenkins 353168 Sep 18 01:17 altree-dbgsym_1.3.2-4_amd64.deb -rw-r--r-- 1 jenkins jenkins 330628 Sep 18 01:17 altree-examples_1.3.2-4_all.deb -rw-r--r-- 1 jenkins jenkins 8600 Sep 18 01:17 altree_1.3.2-4.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2535 Sep 18 01:17 altree_1.3.2-4.dsc -rw-r--r-- 1 jenkins jenkins 8989 Sep 18 01:17 altree_1.3.2-4_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 9871 Sep 18 01:17 altree_1.3.2-4_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1869 Sep 18 01:17 altree_1.3.2-4_amd64.changes -rw-r--r-- 1 jenkins jenkins 341364 Sep 18 01:17 altree_1.3.2-4_amd64.deb -rw-r--r-- 1 jenkins jenkins 1371 Sep 18 01:17 altree_1.3.2-4_source.changes -rw-r--r-- 1 jenkins jenkins 116359 Sep 18 01:17 build.log /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm/b2: total 1172 -rw-r--r-- 1 jenkins jenkins 353168 Sep 18 01:22 altree-dbgsym_1.3.2-4_amd64.deb -rw-r--r-- 1 jenkins jenkins 330628 Sep 18 01:22 altree-examples_1.3.2-4_all.deb -rw-r--r-- 1 jenkins jenkins 8600 Sep 18 01:22 altree_1.3.2-4.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2535 Sep 18 01:22 altree_1.3.2-4.dsc -rw-rw-r-- 1 jenkins jenkins 8995 Sep 18 01:22 altree_1.3.2-4_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 9877 Sep 18 01:22 altree_1.3.2-4_amd64.buildinfo.asc -rw-rw-r-- 1 jenkins jenkins 1869 Sep 18 01:22 altree_1.3.2-4_amd64.changes -rw-r--r-- 1 jenkins jenkins 341364 Sep 18 01:22 altree_1.3.2-4_amd64.deb -rw-rw-r-- 1 jenkins jenkins 1371 Sep 18 01:22 altree_1.3.2-4_source.changes -rw-rw-r-- 1 jenkins jenkins 118295 Sep 18 01:22 build.log Thu Sep 18 01:22:21 UTC 2025 I: Deleting $TMPDIR on infom01-amd64.debian.net. Thu Sep 18 01:22:22 UTC 2025 I: altree_1.3.2-4_amd64.changes: Format: 1.8 Date: Wed, 17 Sep 2025 20:17:16 +0200 Source: altree Binary: altree altree-dbgsym altree-examples Architecture: amd64 all Version: 1.3.2-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: altree - program to perform phylogeny-based association and localization a altree-examples - example files for ALTree Closes: 1115489 Changes: altree (1.3.2-4) unstable; urgency=medium . * Team upload. . [ Santiago Vila ] * d/rules: fix ftbfs on architecture: all builds. The change also prevents mv from prompting. Signed-off-by: Étienne Mollier (Closes: #1115489) Checksums-Sha1: 5e290dae62845fc62127c97250880620376da810 353168 altree-dbgsym_1.3.2-4_amd64.deb fe5eebc2bdf05f965e290b697feb001130815df2 330628 altree-examples_1.3.2-4_all.deb cfbc02119fdf5fb42c0013f6f5dc614f45c90992 8989 altree_1.3.2-4_amd64.buildinfo b72ffa7ab098f359d5c4ddc4021d235e43a534bf 341364 altree_1.3.2-4_amd64.deb Checksums-Sha256: e7ae465c33d903ae9183795328da86c26508db72ac31727069624b10f3db52b0 353168 altree-dbgsym_1.3.2-4_amd64.deb e0152ce5a3898ab356a8622053713ff7844bc5c2424f9dfa9e8b9f88e5ce0884 330628 altree-examples_1.3.2-4_all.deb 554c7e92aef0d1f59d61e4bbf51a7c8255b3d8666f0c6cbcbcb136e66c57ffda 8989 altree_1.3.2-4_amd64.buildinfo c2fe5b23c316af1014a8f7729868f93eecd113bde79bc6b88297bebe2b2286de 341364 altree_1.3.2-4_amd64.deb Files: 6bfdfb691790e7d935da83482b6d0571 353168 debug optional altree-dbgsym_1.3.2-4_amd64.deb ada88dd80fde0d048f9fc45b9315d089 330628 science optional altree-examples_1.3.2-4_all.deb 933c4c70e1a46f3916af8325834c2365 8989 science optional altree_1.3.2-4_amd64.buildinfo c51412a33743a58000cb446ad765a44e 341364 science optional altree_1.3.2-4_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/altree_1.3.2-3.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/altree_1.3.2-3.rbuild.log.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-09-18 01:17:38.279797799 +0000 +++ b2/build.log 2025-09-18 01:22:21.684154243 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Oct 20 19:34:54 -12 2026 -I: pbuilder-time-stamp: 1792568094 +I: Current time: Thu Sep 18 15:17:40 +14 2025 +I: pbuilder-time-stamp: 1758158260 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -25,52 +25,84 @@ dpkg-source: info: applying typo.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1210918/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3005726/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 18 01:17 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3005726/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3005726/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='0431957afced46ecb2038fbd6b63d63b' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1210918' - PS1='# ' - PS2='> ' + INVOCATION_ID=fd225833945f4deeab11261e297212e2 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3005726 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.2NH9R5Xm/pbuilderrc_Tq6n --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.2NH9R5Xm/b1 --logfile b1/build.log altree_1.3.2-4.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm/pbuilderrc_H5KR --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm/b2 --logfile b2/build.log altree_1.3.2-4.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1210918/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3005726/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -289,7 +321,7 @@ Get: 153 http://deb.debian.org/debian unstable/main amd64 texlive-latex-recommended all 2025.20250727-3 [8454 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 texlive-pictures all 2025.20250727-3 [22.1 MB] Get: 155 http://deb.debian.org/debian unstable/main amd64 texlive-latex-extra all 2025.20250727-3 [27.4 MB] -Fetched 322 MB in 4s (74.3 MB/s) +Fetched 322 MB in 7s (48.9 MB/s) Preconfiguring packages ... Selecting previously unselected package readline-common. (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 ... 19917 files and directories currently installed.) @@ -816,8 +848,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Oct 21 07:38:01 UTC 2026. -Universal Time is now: Wed Oct 21 07:38:01 UTC 2026. +Local time is now: Thu Sep 18 01:20:19 UTC 2025. +Universal Time is now: Thu Sep 18 01:20:19 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:amd64 (1:1.1.8-1+b2) ... @@ -956,7 +988,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/altree-1.3.2/ && 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 > ../altree_1.3.2-4_source.changes +I: user script /srv/workspace/pbuilder/3005726/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3005726/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/altree-1.3.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../altree_1.3.2-4_source.changes dpkg-buildpackage: info: source package altree dpkg-buildpackage: info: source version 1.3.2-4 dpkg-buildpackage: info: source distribution unstable @@ -1548,46 +1584,46 @@ make[2]: Leaving directory '/build/reproducible-path/altree-1.3.2/Documentation' make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' dh_auto_build - make -j16 + make -j12 make[1]: Entering directory '/build/reproducible-path/altree-1.3.2' make[2]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils' make -C c_sources -Running Mkbootstrap for CUtils () -"/usr/bin/perl" "/usr/share/perl/5.40.1/ExtUtils/xsubpp" -typemap '/usr/share/perl/5.40/ExtUtils/typemap' CUtils.xs > CUtils.xsc make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" chisq.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" double_permutation.c +Running Mkbootstrap for CUtils () +"/usr/bin/perl" "/usr/share/perl/5.40.1/ExtUtils/xsubpp" -typemap '/usr/share/perl/5.40/ExtUtils/typemap' CUtils.xs > CUtils.xsc x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" fisher.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" mt19937ar.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" myrand.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" resampling.c +x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" rhyper.c +cp ALTree/Sens.pm blib/lib/ALTree/Sens.pm +cp ALTree/SiteCollection.pm blib/lib/ALTree/SiteCollection.pm +cp ALTree/Tree.pm blib/lib/ALTree/Tree.pm +cp ALTree/SiteSensPerTree.pm blib/lib/ALTree/SiteSensPerTree.pm +cp ALTree/Base.pm blib/lib/ALTree/Base.pm cp ALTree/Nanova.pm blib/lib/ALTree/Nanova.pm -cp ALTree/Foret.pm blib/lib/ALTree/Foret.pm -cp ALTree/Import.pm blib/lib/ALTree/Import.pm +cp ALTree/SiteSens.pm blib/lib/ALTree/SiteSens.pm +cp ALTree/Chi2.pm blib/lib/ALTree/Chi2.pm cp ALTree/to_rewrite.pm blib/lib/ALTree/to_rewrite.pm -cp ALTree/Input.pm blib/lib/ALTree/Input.pm -cp ALTree/SitePerForet.pm blib/lib/ALTree/SitePerForet.pm +cp ALTree/Import.pm blib/lib/ALTree/Import.pm cp ALTree/SiteSensPerForet.pm blib/lib/ALTree/SiteSensPerForet.pm -cp ALTree/Tree.pm blib/lib/ALTree/Tree.pm +cp ALTree/SitePerForet.pm blib/lib/ALTree/SitePerForet.pm cp ALTree/Site.pm blib/lib/ALTree/Site.pm -cp ALTree/Chi2.pm blib/lib/ALTree/Chi2.pm -cp ALTree/SiteCollection.pm blib/lib/ALTree/SiteCollection.pm -cp ALTree/Utils.pm blib/lib/ALTree/Utils.pm -cp ALTree/Node.pm blib/lib/ALTree/Node.pm -cp ALTree/Sens.pm blib/lib/ALTree/Sens.pm cp ALTree/SitePerTree.pm blib/lib/ALTree/SitePerTree.pm -cp ALTree/SiteSensPerTree.pm blib/lib/ALTree/SiteSensPerTree.pm -cp ALTree/Base.pm blib/lib/ALTree/Base.pm -cp ALTree/SiteSens.pm blib/lib/ALTree/SiteSens.pm -x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" rhyper.c -chmod 644 "CUtils.bs" +cp ALTree/Node.pm blib/lib/ALTree/Node.pm +cp ALTree/Utils.pm blib/lib/ALTree/Utils.pm +cp ALTree/Input.pm blib/lib/ALTree/Input.pm +cp ALTree/Foret.pm blib/lib/ALTree/Foret.pm x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" stats.c +chmod 644 "CUtils.bs" x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE" z.c -"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CUtils.bs ../blib/arch/auto/ALTree/CUtils/CUtils.bs 644 chisq.c: In function 'pochisq': chisq.c:77:1: warning: old-style function definition [-Wold-style-definition] 77 | pochisq (x, df) | ^~~~~~~ +"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CUtils.bs ../blib/arch/auto/ALTree/CUtils/CUtils.bs 644 chisq.c: In function 'critchi': chisq.c:129:1: warning: old-style function definition [-Wold-style-definition] 129 | critchi (p, df) @@ -1636,7 +1672,7 @@ Manifying 3 pod documents make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' dh_auto_test - make -j16 test TEST_VERBOSE=1 + make -j12 test TEST_VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/altree-1.3.2' make[2]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CUtils.bs ../blib/arch/auto/ALTree/CUtils/CUtils.bs 644 @@ -1665,7 +1701,7 @@ ok 3 - double_permutation ok All tests successful. -Files=2, Tests=4, 1 wallclock secs ( 0.01 usr 0.01 sys + 0.12 cusr 0.03 csys = 0.17 CPU) +Files=2, Tests=4, 0 wallclock secs ( 0.02 usr 0.00 sys + 0.07 cusr 0.03 csys = 0.12 CPU) Result: PASS make[2]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils' PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t @@ -1674,13 +1710,13 @@ ok 1 - use ALTree::Import; ok All tests successful. -Files=1, Tests=1, 0 wallclock secs ( 0.02 usr 0.00 sys + 0.12 cusr 0.02 csys = 0.16 CPU) +Files=1, Tests=1, 1 wallclock secs ( 0.02 usr 0.00 sys + 0.06 cusr 0.02 csys = 0.10 CPU) Result: PASS make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j16 install DESTDIR=/build/reproducible-path/altree-1.3.2/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr + make -j12 install DESTDIR=/build/reproducible-path/altree-1.3.2/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/reproducible-path/altree-1.3.2' make[2]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CUtils.bs ../blib/arch/auto/ALTree/CUtils/CUtils.bs 644 @@ -1692,33 +1728,33 @@ Manifying 3 pod documents Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/ALTree/CUtils/CUtils.so -Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Foret.pm -Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SitePerForet.pm +Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/ALTree/CUtils/autosplit.ix +Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteCollection.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Tree.pm -Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Node.pm +Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Nanova.pm +Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteSensPerForet.pm +Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Chi2.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SitePerTree.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteSensPerTree.pm -Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteCollection.pm +Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/CUtils.pm +Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Input.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Base.pm -Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Site.pm -Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Utils.pm -Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Chi2.pm -Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Sens.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/to_rewrite.pm -Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Input.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Import.pm -Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/CUtils.pm -Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteSensPerForet.pm -Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Nanova.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteSens.pm -Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/ALTree/CUtils/autosplit.ix +Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Node.pm +Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SitePerForet.pm +Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Sens.pm +Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Site.pm +Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Foret.pm +Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Utils.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/share/man/man1/altree-convert.1p Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/share/man/man1/altree.1p Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/share/man/man1/altree-add-S.1p Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/share/man/man3/ALTree::CUtils.3pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/bin/altree -Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/bin/altree-add-S Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/bin/altree-convert +Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/bin/altree-add-S make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' dh_install debian/rules execute_after_dh_install-arch @@ -1763,9 +1799,9 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'altree-examples' in '../altree-examples_1.3.2-4_all.deb'. -dpkg-deb: building package 'altree-dbgsym' in '../altree-dbgsym_1.3.2-4_amd64.deb'. dpkg-deb: building package 'altree' in '../altree_1.3.2-4_amd64.deb'. +dpkg-deb: building package 'altree-dbgsym' in '../altree-dbgsym_1.3.2-4_amd64.deb'. +dpkg-deb: building package 'altree-examples' in '../altree-examples_1.3.2-4_all.deb'. dpkg-genbuildinfo --build=binary -O../altree_1.3.2-4_amd64.buildinfo dpkg-genchanges --build=binary -O../altree_1.3.2-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1773,12 +1809,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3005726/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3005726/tmp/hooks/B01_cleanup finished 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/1210918 and its subdirectories -I: Current time: Tue Oct 20 19:40:37 -12 2026 -I: pbuilder-time-stamp: 1792568437 +I: removing directory /srv/workspace/pbuilder/3005726 and its subdirectories +I: Current time: Thu Sep 18 15:22:21 +14 2025 +I: pbuilder-time-stamp: 1758158541 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/altree_1.3.2-4.diff: 79.9% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/altree_1.3.2-4.diff.gz b2/build.log: 84.5% -- replaced with stdout Compressing the 1st log... b1/build.log: 84.9% -- replaced with stdout Thu Sep 18 01:22:22 UTC 2025 I: diffoscope 306 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_altree_unstable_amd64_1758158542 + touch /var/log/reproducible-builds/diffoscope_stamp_altree_unstable_amd64_1758158542 + RESULT=0 + systemd-run '--description=diffoscope on altree/1.3.2-4 in unstable/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_36-80962 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm --run-session -c jenkins-reproducible-unstable-diffoscope-adbcdbd8-c198-49ba-85d8-9c9add58d9ff -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm/dbd-tmp-W3BX6wn ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm/altree_1.3.2-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm/altree_1.3.2-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm/altree_1.3.2-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm/b1/altree_1.3.2-4_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm/b2/altree_1.3.2-4_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_36-80962.service; invocation ID: cc99bd8b19474ce693be069016961b85 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm/altree_1.3.2-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm/altree_1.3.2-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm/altree_1.3.2-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm/b1/altree_1.3.2-4_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.2NH9R5Xm/b2/altree_1.3.2-4_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 195ms CPU time consumed: 167ms Memory peak: 17.7M (swap: 0B) _ _ __ _| | |_ _ __ ___ ___ / _` | | __| '__/ _ \/ _ \ | (_| | | |_| | | __/ __/ \__,_|_|\__|_| \___|\___| Thu Sep 18 01:22:23 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Thu Sep 18 01:22:23 UTC 2025 I: altree from unstable built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-09-18 01:22:23] INFO: Starting at 2025-09-18 01:22:23.615278 [2025-09-18 01:22:23] INFO: Generating the pages of 1 package(s) [2025-09-18 01:22:23] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/altree didn't produce a buildlog, even though it has been built. [2025-09-18 01:22:23] CRITICAL: https://tests.reproducible-builds.org/debian/forky/arm64/altree didn't produce a buildlog, even though it has been built. [2025-09-18 01:22:23] INFO: Finished at 2025-09-18 01:22:23.888713, took: 0:00:00.273438 Thu Sep 18 01:22:23 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/altree.html Thu Sep 18 01:22:23 UTC 2025 I: Removing signed altree_1.3.2-4_amd64.buildinfo.asc files: removed './b1/altree_1.3.2-4_amd64.buildinfo.asc' removed './b2/altree_1.3.2-4_amd64.buildinfo.asc' 1758158543 amd64 unstable altree Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/altree_1.3.2-4.rbuild.log: 83.1% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/altree_1.3.2-4.rbuild.log.gz [2025-09-18 01:22:24] INFO: Starting at 2025-09-18 01:22:24.214691 [2025-09-18 01:22:24] INFO: Generating the pages of 1 package(s) [2025-09-18 01:22:24] CRITICAL: https://tests.reproducible-builds.org/debian/forky/arm64/altree didn't produce a buildlog, even though it has been built. [2025-09-18 01:22:24] INFO: Finished at 2025-09-18 01:22:24.489152, took: 0:00:00.274464 All cleanup done. Thu Sep 18 01:22:24 UTC 2025 - total duration: 0h 10m 34s. Thu Sep 18 01:22:24 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-IYHRrHMK, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 10min 34.729s CPU time consumed: 3.211s Memory peak: 42.9M (swap: 0B)