Sun Apr 28 15:44:49 UTC 2024 I: starting to build altree/trixie/i386 on jenkins on '2024-04-28 15:44' Sun Apr 28 15:44:49 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_12/9543/console.log Sun Apr 28 15:44:49 UTC 2024 I: Downloading source for trixie/altree=1.3.2-2 --2024-04-28 15:44:49-- http://deb.debian.org/debian/pool/main/a/altree/altree_1.3.2-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2304 (2.2K) [text/prs.lines.tag] Saving to: ‘altree_1.3.2-2.dsc’ 0K .. 100% 219M=0s 2024-04-28 15:44:49 (219 MB/s) - ‘altree_1.3.2-2.dsc’ saved [2304/2304] Sun Apr 28 15:44:49 UTC 2024 I: altree_1.3.2-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: altree Binary: altree, altree-examples Architecture: any all Version: 1.3.2-2 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Vincent Danjean , Andreas Tille Homepage: https://gitlab.inria.fr/NGS/ALTree Standards-Version: 4.6.2 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), 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 7aa27b7775707a6660381ef03fb78757f33929b2 7196 altree_1.3.2-2.debian.tar.xz Checksums-Sha256: f9d5beda91aaab219e1397b4c19e0649788a871c8c29fa1e8343a53c5f710b8e 610823 altree_1.3.2.orig.tar.gz 1747f795ec12019cdb81c42b9205d0cbdedd8a735df8a653d52ebf0a1f1cec29 7196 altree_1.3.2-2.debian.tar.xz Files: fd17066d7f6bc07baacf526ff3ee1c3b 610823 altree_1.3.2.orig.tar.gz 9812f8181ed7dc8647d1ae8d78a7f09a 7196 altree_1.3.2-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJCBAEBCgAsFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmVnNiUOHHRpbGxlYUBy a2kuZGUACgkQV4oElNHGRtFWPg/+PO/ZSp79mrNF/Z9N/k4uXb33LVCruKePa6cf tJJzoEeauulp5hvuwvLUENnN8MUk6N1epGdr0GoRnNWhZcSbn+dyJN5JVZTqVcfV T96GUjOa7mcvpbeH2F/vIUflB7tEo4lI8AS8QwaImBlX8XOdG5HKjmVjKIYztdPl mV8LOkMKwtae/H24ILvtry/wc3D4sCBmuWHRh+DsyesZ5ECCM5I+7oB5eOVxGDrY xkMi/mkefJ2/r4AituMM7IUkI6noXu5NgK20LK7ArIT7rhhDl+iQi08qClFFca34 cvvqUiZgRCndg4nmdRUGUhCLUTsScY9ScID7ihfGO4br02t3xTNoEYTsO0CQ5TYH R/7pDlqBBc2pJ+GBmoJmi8SWXzu5y7Z0pod0jsFkh4VDDLG41yMVYhikjsg2FeFb 7snxJ1hChv9PCczc0hWVUqqT5hAHtO6T8Ll4Pk/kKjVkEVH6RlP17+Sok27xbuq9 flAsWYVo7ADdgxnVt+AChyJWJd4UgxLorxqjOSUE1phQTuCg/vwzh3k6oefYm3Xg 1OUIC7DolbklrcGFoLNo0qTeSr+oPFgX4y2hjzNhlIdAd7q6Md5iM7XzzeJwm3Rm V4CgNMJPwVcp1SpFKE0idJcRQ1NKQdF/lwtSle9iyx339WtgUG0xigFsYqaEU8VB 3ikw5Aw= =rtwp -----END PGP SIGNATURE----- Sun Apr 28 15:44:49 UTC 2024 I: Checking whether the package is not for us Sun Apr 28 15:44:49 UTC 2024 I: Starting 1st build on remote node ionos12-i386.debian.net. Sun Apr 28 15:44:49 UTC 2024 I: Preparing to do remote build '1' on ionos12-i386.debian.net. Sun Apr 28 15:49:26 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Apr 28 03:44:51 -12 2024 I: pbuilder-time-stamp: 1714319091 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [altree_1.3.2-2.dsc] I: copying [./altree_1.3.2.orig.tar.gz] I: copying [./altree_1.3.2-2.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Nov 29 13:01:25 2023 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./altree_1.3.2-2.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_1.3.2-2.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/60875/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='6fc9b99030fd46239390a8d8c9b72213' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='60875' 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.o6GP6DgI/pbuilderrc_uTsk --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.o6GP6DgI/b1 --logfile b1/build.log altree_1.3.2-2.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos12-i386 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 21 07:12 /bin -> usr/bin I: user script /srv/workspace/pbuilder/60875/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: bash-completion, debhelper-compat (= 13), 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 ... 19884 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 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} libbsd0{a} libcairo2{a} libcommons-logging-java{a} libcommons-parent-java{a} libcups2{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontbox-java{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libglib2.0-0t64{a} libgraphite2-3{a} libgs-common{a} libgs10{a} libgs10-common{a} libgsl-dev{a} libgsl27{a} libgslcblas0{a} libharfbuzz0b{a} libice6{a} libicu72{a} libidn12{a} libijs-0.35{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libkpathsea6{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1{a} libmath-tamuanova-perl{a} libnetpbm11{a} libopenjp2-7{a} libpaper-utils{a} libpaper1{a} libpdfbox-java{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpotrace0{a} libptexenc1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} libsharpyuv0{a} libsigsegv2{a} libsm6{a} libsub-override-perl{a} libsynctex2{a} libtamuanova-0.2{a} libteckit0{a} libtest-deep-perl{a} libtexlua53-5{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{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} python3{a} python3-minimal{a} python3.11{a} python3.11-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 libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libltdl-dev libmail-sendmail-perl libnet-dbus-perl libspreadsheet-parseexcel-perl libx11-protocol-perl lmodern lynx ruby shared-mime-info tex-gyre texlive-plain-generic tipa tk wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 140 newly installed, 0 to remove and 0 not upgraded. Need to get 246 MB of archives. After unpacking 658 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-4 [69.3 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-4 [171 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 libsigsegv2 i386 2.14-1+b1 [34.6 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 gawk i386 1:5.2.1-2+b1 [680 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 poppler-data all 0.4.12-1 [1601 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 libpython3.11-minimal i386 3.11.8-1 [817 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.2-1 [107 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 python3.11-minimal i386 3.11.8-1 [2087 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.11.6-1 [26.2 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 tzdata all 2024a-3 [255 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 libpython3.11-stdlib i386 3.11.8-1 [1821 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 python3.11 i386 3.11.8-1 [597 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.11.6-1 [9224 B] Get: 16 http://deb.debian.org/debian trixie/main i386 python3 i386 3.11.6-1 [26.2 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 bash-completion all 1:2.11-8 [224 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-2+b1 [314 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libmagic1 i386 1:5.45-2+b1 [114 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-2+b1 [43.0 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-3+b1 [1195 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.39.3-6 [93.3 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 man-db i386 2.12.0-3 [1413 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 ucf all 3.0043+nmu1 [55.2 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 autoconf all 2.71-3 [332 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 autopoint all 0.21-14 [496 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 41 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.191-1+b1 [194 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.9.14+dfsg-1.3+b3 [727 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 debhelper all 13.15.3 [901 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 libfontenc1 i386 1:1.1.8-1 [23.1 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b3 [314 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 libpng16-16t64 i386 1.6.43-5 [286 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 libfreetype6 i386 2.13.2+dfsg-1+b4 [449 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 x11-common all 1:7.7+23 [252 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 xfonts-utils i386 1:7.7+6 [95.2 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 57 http://deb.debian.org/debian trixie/main i386 libgs-common all 10.02.1~dfsg-3 [147 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 libgs10-common all 10.02.1~dfsg-3 [474 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 libavahi-common-data i386 0.8-13+b1 [111 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 libavahi-common3 i386 0.8-13+b1 [45.3 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 libdbus-1-3 i386 1.14.10-4+b1 [217 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 libavahi-client3 i386 0.8-13+b1 [49.2 kB] Get: 63 http://deb.debian.org/debian trixie/main i386 libcups2 i386 2.4.7-1+b1 [263 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 fontconfig-config i386 2.15.0-1.1 [317 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 libfontconfig1 i386 2.15.0-1.1 [401 kB] Get: 66 http://deb.debian.org/debian trixie/main i386 libidn12 i386 1.42-2 [81.3 kB] Get: 67 http://deb.debian.org/debian trixie/main i386 libijs-0.35 i386 0.35-15.1+b1 [15.7 kB] Get: 68 http://deb.debian.org/debian trixie/main i386 libjbig2dec0 i386 0.20-1+b2 [66.5 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo i386 1:2.1.5-2+b2 [169 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 liblcms2-2 i386 2.14-2+b1 [165 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 libopenjp2-7 i386 2.5.0-2+b3 [197 kB] Get: 72 http://deb.debian.org/debian trixie/main i386 libpaper1 i386 1.1.29+b1 [13.0 kB] Get: 73 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.20-1 [46.9 kB] Get: 74 http://deb.debian.org/debian trixie/main i386 libjbig0 i386 2.1-6.1+b1 [31.8 kB] Get: 75 http://deb.debian.org/debian trixie/main i386 liblerc4 i386 4.0.0+ds-4+b1 [180 kB] Get: 76 http://deb.debian.org/debian trixie/main i386 libsharpyuv0 i386 1.3.2-0.4+b1 [107 kB] Get: 77 http://deb.debian.org/debian trixie/main i386 libwebp7 i386 1.3.2-0.4+b1 [314 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 libtiff6 i386 4.5.1+git230720-4 [338 kB] Get: 79 http://deb.debian.org/debian trixie/main i386 libxau6 i386 1:1.0.9-1+b1 [18.5 kB] Get: 80 http://deb.debian.org/debian trixie/main i386 libbsd0 i386 0.12.2-1 [134 kB] Get: 81 http://deb.debian.org/debian trixie/main i386 libxdmcp6 i386 1:1.1.2-3+b1 [24.8 kB] Get: 82 http://deb.debian.org/debian trixie/main i386 libxcb1 i386 1.15-1 [148 kB] Get: 83 http://deb.debian.org/debian trixie/main i386 libx11-data all 2:1.8.7-1 [328 kB] Get: 84 http://deb.debian.org/debian trixie/main i386 libx11-6 i386 2:1.8.7-1+b1 [822 kB] Get: 85 http://deb.debian.org/debian trixie/main i386 libice6 i386 2:1.0.10-1+b1 [58.6 kB] Get: 86 http://deb.debian.org/debian trixie/main i386 libsm6 i386 2:1.2.3-1+b1 [33.9 kB] Get: 87 http://deb.debian.org/debian trixie/main i386 libxt6t64 i386 1:1.2.1-1.2 [193 kB] Get: 88 http://deb.debian.org/debian trixie/main i386 libgs10 i386 10.02.1~dfsg-3 [2639 kB] Get: 89 http://deb.debian.org/debian trixie/main i386 ghostscript i386 10.02.1~dfsg-3 [49.9 kB] Get: 90 http://deb.debian.org/debian trixie/main i386 libnetpbm11 i386 2:11.05.02-1 [186 kB] Get: 91 http://deb.debian.org/debian trixie/main i386 netpbm i386 2:11.05.02-1 [2067 kB] Get: 92 http://deb.debian.org/debian trixie/main i386 fig2dev i386 1:3.2.9-3 [433 kB] Get: 93 http://deb.debian.org/debian trixie/main i386 fonts-lmodern all 2.005-1 [4540 kB] Get: 94 http://deb.debian.org/debian trixie/main i386 tex-common all 6.18 [32.5 kB] Get: 95 http://deb.debian.org/debian trixie/main i386 latex-make all 2.4.3-1 [1030 kB] Get: 96 http://deb.debian.org/debian trixie/main i386 libapache-pom-java all 29-2 [5276 B] Get: 97 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.0-3 [140 kB] Get: 98 http://deb.debian.org/debian trixie/main i386 libblas-dev i386 3.12.0-3 [152 kB] Get: 99 http://deb.debian.org/debian trixie/main i386 libpixman-1-0 i386 0.42.2-1+b1 [555 kB] Get: 100 http://deb.debian.org/debian trixie/main i386 libxcb-render0 i386 1.15-1 [116 kB] Get: 101 http://deb.debian.org/debian trixie/main i386 libxcb-shm0 i386 1.15-1 [106 kB] Get: 102 http://deb.debian.org/debian trixie/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 103 http://deb.debian.org/debian trixie/main i386 libxrender1 i386 1:0.9.10-1.1+b1 [28.8 kB] Get: 104 http://deb.debian.org/debian trixie/main i386 libcairo2 i386 1.18.0-1+b1 [587 kB] Get: 105 http://deb.debian.org/debian trixie/main i386 libcommons-parent-java all 56-1 [10.8 kB] Get: 106 http://deb.debian.org/debian trixie/main i386 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 107 http://deb.debian.org/debian trixie/main i386 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 108 http://deb.debian.org/debian trixie/main i386 libglib2.0-0t64 i386 2.78.4-7 [1522 kB] Get: 109 http://deb.debian.org/debian trixie/main i386 libgraphite2-3 i386 1.3.14-2 [77.7 kB] Get: 110 http://deb.debian.org/debian trixie/main i386 libgslcblas0 i386 2.7.1+dfsg-6+b1 [97.7 kB] Get: 111 http://deb.debian.org/debian trixie/main i386 libgsl27 i386 2.7.1+dfsg-6+b1 [920 kB] Get: 112 http://deb.debian.org/debian trixie/main i386 libgsl-dev i386 2.7.1+dfsg-6+b1 [1169 kB] Get: 113 http://deb.debian.org/debian trixie/main i386 libharfbuzz0b i386 8.3.0-2+b1 [2234 kB] Get: 114 http://deb.debian.org/debian trixie/main i386 libkpathsea6 i386 2023.20230311.66589-9+b2 [157 kB] Get: 115 http://deb.debian.org/debian trixie/main i386 libtamuanova-0.2 i386 0.2-5+b2 [8716 B] Get: 116 http://deb.debian.org/debian trixie/main i386 libmath-tamuanova-perl i386 1.0.2-3+b2 [13.7 kB] Get: 117 http://deb.debian.org/debian trixie/main i386 libpaper-utils i386 1.1.29+b1 [9280 B] Get: 118 http://deb.debian.org/debian trixie/main i386 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 119 http://deb.debian.org/debian trixie/main i386 libpotrace0 i386 1.16-2+b1 [24.2 kB] Get: 120 http://deb.debian.org/debian trixie/main i386 libptexenc1 i386 2023.20230311.66589-9+b2 [48.3 kB] Get: 121 http://deb.debian.org/debian trixie/main i386 libsynctex2 i386 2023.20230311.66589-9+b2 [64.9 kB] Get: 122 http://deb.debian.org/debian trixie/main i386 libteckit0 i386 2.5.12+ds1-1 [284 kB] Get: 123 http://deb.debian.org/debian trixie/main i386 libtest-deep-perl all 1.204-1 [52.9 kB] Get: 124 http://deb.debian.org/debian trixie/main i386 libtexlua53-5 i386 2023.20230311.66589-9+b2 [128 kB] Get: 125 http://deb.debian.org/debian trixie/main i386 libxmu6 i386 2:1.1.3-3+b2 [60.5 kB] Get: 126 http://deb.debian.org/debian trixie/main i386 libxpm4 i386 1:3.5.17-1+b1 [57.8 kB] Get: 127 http://deb.debian.org/debian trixie/main i386 libxaw7 i386 2:1.0.14-1+b2 [208 kB] Get: 128 http://deb.debian.org/debian trixie/main i386 libxi6 i386 2:1.8.1-1 [81.0 kB] Get: 129 http://deb.debian.org/debian trixie/main i386 libzzip-0-13t64 i386 0.13.72+dfsg.1-1.2+b1 [58.1 kB] Get: 130 http://deb.debian.org/debian trixie/main i386 preview-latex-style all 13.2-1 [350 kB] Get: 131 http://deb.debian.org/debian trixie/main i386 t1utils i386 1.41-4 [62.3 kB] Get: 132 http://deb.debian.org/debian trixie/main i386 texlive-binaries i386 2023.20230311.66589-9+b2 [8273 kB] Get: 133 http://deb.debian.org/debian trixie/main i386 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 134 http://deb.debian.org/debian trixie/main i386 texlive-base all 2023.20240207-1 [22.0 MB] Get: 135 http://deb.debian.org/debian trixie/main i386 texlive-fonts-recommended all 2023.20240207-1 [4990 kB] Get: 136 http://deb.debian.org/debian trixie/main i386 texlive-lang-french all 2023.20240207-1 [91.4 MB] Get: 137 http://deb.debian.org/debian trixie/main i386 texlive-latex-base all 2023.20240207-1 [1255 kB] Get: 138 http://deb.debian.org/debian trixie/main i386 texlive-latex-recommended all 2023.20240207-1 [8843 kB] Get: 139 http://deb.debian.org/debian trixie/main i386 texlive-pictures all 2023.20240207-1 [16.7 MB] Get: 140 http://deb.debian.org/debian trixie/main i386 texlive-latex-extra all 2023.20240207-1 [19.7 MB] Fetched 246 MB in 4s (56.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19884 files and directories currently installed.) Preparing to unpack .../readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:i386. Preparing to unpack .../libreadline8t64_8.2-4_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-4) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../libsigsegv2_2.14-1+b1_i386.deb ... Unpacking libsigsegv2:i386 (2.14-1+b1) ... Setting up readline-common (8.2-4) ... Setting up libreadline8t64:i386 (8.2-4) ... Setting up libsigsegv2:i386 (2.14-1+b1) ... 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 ... 19926 files and directories currently installed.) Preparing to unpack .../gawk_1%3a5.2.1-2+b1_i386.deb ... Unpacking gawk (1:5.2.1-2+b1) ... 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 libpython3.11-minimal:i386. Preparing to unpack .../libpython3.11-minimal_3.11.8-1_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.8-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.2-1_i386.deb ... Unpacking libexpat1:i386 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.8-1_i386.deb ... Unpacking python3.11-minimal (3.11.8-1) ... Setting up libpython3.11-minimal:i386 (3.11.8-1) ... Setting up libexpat1:i386 (2.6.2-1) ... Setting up python3.11-minimal (3.11.8-1) ... 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 ... 20965 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.6-1_i386.deb ... Unpacking python3-minimal (3.11.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-3_all.deb ... Unpacking tzdata (2024a-3) ... Selecting previously unselected package libpython3.11-stdlib:i386. Preparing to unpack .../4-libpython3.11-stdlib_3.11.8-1_i386.deb ... Unpacking libpython3.11-stdlib:i386 (3.11.8-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.8-1_i386.deb ... Unpacking python3.11 (3.11.8-1) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../6-libpython3-stdlib_3.11.6-1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.11.6-1) ... Setting up python3-minimal (3.11.6-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21927 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.6-1_i386.deb ... Unpacking python3 (3.11.6-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package bash-completion. Preparing to unpack .../002-bash-completion_1%3a2.11-8_all.deb ... Unpacking bash-completion (1:2.11-8) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../003-libmagic-mgc_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../004-libmagic1_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic1:i386 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.45-2+b1_i386.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.21-14+b1_i386.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../007-libuchardet0_0.0.8-1+b1_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../008-groff-base_1.23.0-3+b1_i386.deb ... Unpacking groff-base (1.23.0-3+b1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../009-bsdextrautils_2.39.3-6_i386.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../010-libpipeline1_1.5.7-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../011-man-db_2.12.0-3_i386.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package ucf. Preparing to unpack .../012-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package m4. Preparing to unpack .../013-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../014-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../015-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../016-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../017-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../018-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../019-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../020-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../021-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../022-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../023-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../024-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:i386. Preparing to unpack .../025-libelf1t64_0.191-1+b1_i386.deb ... Unpacking libelf1t64:i386 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../026-dwz_0.15-1+b1_i386.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../027-libicu72_72.1-4+b1_i386.deb ... Unpacking libicu72:i386 (72.1-4+b1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../028-libxml2_2.9.14+dfsg-1.3+b3_i386.deb ... Unpacking libxml2:i386 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../029-gettext_0.21-14+b1_i386.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../030-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../031-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../032-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package libfontenc1:i386. Preparing to unpack .../033-libfontenc1_1%3a1.1.8-1_i386.deb ... Unpacking libfontenc1:i386 (1:1.1.8-1) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../034-libbrotli1_1.1.0-2+b3_i386.deb ... Unpacking libbrotli1:i386 (1.1.0-2+b3) ... Selecting previously unselected package libpng16-16t64:i386. Preparing to unpack .../035-libpng16-16t64_1.6.43-5_i386.deb ... Unpacking libpng16-16t64:i386 (1.6.43-5) ... Selecting previously unselected package libfreetype6:i386. Preparing to unpack .../036-libfreetype6_2.13.2+dfsg-1+b4_i386.deb ... Unpacking libfreetype6:i386 (2.13.2+dfsg-1+b4) ... Selecting previously unselected package x11-common. Preparing to unpack .../037-x11-common_1%3a7.7+23_all.deb ... Unpacking x11-common (1:7.7+23) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../038-xfonts-encodings_1%3a1.0.4-2.2_all.deb ... Unpacking xfonts-encodings (1:1.0.4-2.2) ... 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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_1.3.2-2_source.changes dpkg-buildpackage: info: source package altree dpkg-buildpackage: info: source version 1.3.2-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean debian/rules override_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' dh_auto_clean 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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -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 override_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. Package texdepends Warning: Figure 'fig/option_b_2.fig' needed (texdepends) Skipping it this time (the last one however) (texdepends) on input line 853. Overfull \hbox (9.75981pt 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. 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- Package texdepends Warning: No 'fig/create_file_paup.pdftex' file (texdepends) using 1 for graphic dimensions on input line 1009. Package texdepends Warning: Figure 'fig/create_file_paup.pdftex_t' needed (texdepends) Skipping it this time (the last one however) (texdepends) on input line 1009. 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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 Package texdepends Warning: No 'fig/localisation_paup.pdftex' file (texdepends) using 1 for graphic dimensions on input line 1130. Package texdepends Warning: Figure 'fig/localisation_paup.pdftex_t' needed (texdepends) Skipping it this time (the last one however) (texdepends) on input line 1130. Package texdepends Warning: No 'fig/association_phylip.pdftex' file (texdepends) using 1 for graphic dimensions on input line 1168. Package texdepends Warning: Figure 'fig/association_phylip.pdftex_t' needed (texdepends) Skipping it this time (the last one however) (texdepends) on input line 1168. Package natbib Warning: Citation `Guindon03' on page 28 undefined on input line 1181. 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 2023/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. 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 Package natbib Warning: Citation `Guindon03' on page 26 undefined on input line 1181. 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. 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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...') 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 2023/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. 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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 2023/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' dh_auto_build make -j11 make[2]: Entering directory '/build/reproducible-path/altree-1.3.2' make[3]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils' make -C c_sources make[4]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' i686-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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/i386-linux-gnu/perl/5.38/CORE" chisq.c i686-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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/i386-linux-gnu/perl/5.38/CORE" double_permutation.c Running Mkbootstrap for CUtils () i686-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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/i386-linux-gnu/perl/5.38/CORE" fisher.c i686-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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/i386-linux-gnu/perl/5.38/CORE" mt19937ar.c cp lib/ALTree/CUtils.pm ../blib/lib/ALTree/CUtils.pm AutoSplitting ../blib/lib/ALTree/CUtils.pm (../blib/lib/auto/ALTree/CUtils) chmod 644 "CUtils.bs" i686-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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/i386-linux-gnu/perl/5.38/CORE" myrand.c "/usr/bin/perl" "/usr/share/perl/5.38.2/ExtUtils/xsubpp" -typemap '/usr/share/perl/5.38/ExtUtils/typemap' CUtils.xs > CUtils.xsc cp ALTree/SiteSensPerForet.pm blib/lib/ALTree/SiteSensPerForet.pm cp ALTree/to_rewrite.pm blib/lib/ALTree/to_rewrite.pm cp ALTree/Input.pm blib/lib/ALTree/Input.pm cp ALTree/SitePerTree.pm blib/lib/ALTree/SitePerTree.pm cp ALTree/Nanova.pm blib/lib/ALTree/Nanova.pm cp ALTree/SitePerForet.pm blib/lib/ALTree/SitePerForet.pm cp ALTree/SiteCollection.pm blib/lib/ALTree/SiteCollection.pm cp ALTree/Base.pm blib/lib/ALTree/Base.pm cp ALTree/Import.pm blib/lib/ALTree/Import.pm cp ALTree/Node.pm blib/lib/ALTree/Node.pm cp ALTree/SiteSens.pm blib/lib/ALTree/SiteSens.pm cp ALTree/Foret.pm blib/lib/ALTree/Foret.pm cp ALTree/SiteSensPerTree.pm blib/lib/ALTree/SiteSensPerTree.pm cp ALTree/Utils.pm blib/lib/ALTree/Utils.pm cp ALTree/Chi2.pm blib/lib/ALTree/Chi2.pm cp ALTree/Site.pm blib/lib/ALTree/Site.pm cp ALTree/Sens.pm blib/lib/ALTree/Sens.pm cp ALTree/Tree.pm blib/lib/ALTree/Tree.pm i686-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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/i386-linux-gnu/perl/5.38/CORE" resampling.c i686-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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/i386-linux-gnu/perl/5.38/CORE" rhyper.c i686-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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/i386-linux-gnu/perl/5.38/CORE" stats.c "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CUtils.bs ../blib/arch/auto/ALTree/CUtils/CUtils.bs 644 i686-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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/i386-linux-gnu/perl/5.38/CORE" z.c 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 i686-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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"1.1\" -DXS_VERSION=\"1.1\" -fPIC "-I/usr/lib/i386-linux-gnu/perl/5.38/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[4]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' make[4]: Entering directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/altree-1.3.2/CUtils/c_sources' rm -f ../blib/arch/auto/ALTree/CUtils/CUtils.so i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/altree-1.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -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[3]: 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[2]: Leaving directory '/build/reproducible-path/altree-1.3.2' make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' dh_auto_test make -j11 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 + 0.24 cusr 0.04 csys = 0.30 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 0.02 sys + 0.18 cusr 0.00 csys = 0.22 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 -j11 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/i386-linux-gnu/perl5/5.38/auto/ALTree/CUtils/CUtils.so Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/i386-linux-gnu/perl5/5.38/auto/ALTree/CUtils/autosplit.ix Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/i386-linux-gnu/perl5/5.38/ALTree/Tree.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/i386-linux-gnu/perl5/5.38/ALTree/Import.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/i386-linux-gnu/perl5/5.38/ALTree/Nanova.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/i386-linux-gnu/perl5/5.38/ALTree/SitePerForet.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/i386-linux-gnu/perl5/5.38/ALTree/SiteCollection.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/i386-linux-gnu/perl5/5.38/ALTree/to_rewrite.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/i386-linux-gnu/perl5/5.38/ALTree/Input.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/i386-linux-gnu/perl5/5.38/ALTree/SiteSensPerTree.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/i386-linux-gnu/perl5/5.38/ALTree/SiteSensPerForet.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/i386-linux-gnu/perl5/5.38/ALTree/Chi2.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/i386-linux-gnu/perl5/5.38/ALTree/Site.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/i386-linux-gnu/perl5/5.38/ALTree/Sens.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/i386-linux-gnu/perl5/5.38/ALTree/Utils.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/i386-linux-gnu/perl5/5.38/ALTree/SitePerTree.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/i386-linux-gnu/perl5/5.38/ALTree/Node.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/i386-linux-gnu/perl5/5.38/ALTree/SiteSens.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/i386-linux-gnu/perl5/5.38/ALTree/Base.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/i386-linux-gnu/perl5/5.38/ALTree/CUtils.pm Installing /build/reproducible-path/altree-1.3.2/debian/tmp/usr/lib/i386-linux-gnu/perl5/5.38/ALTree/Foret.pm 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-convert.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-add-S 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 make[1]: Leaving directory '/build/reproducible-path/altree-1.3.2' dh_install 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: package could avoid a useless dependency if debian/altree/usr/lib/i386-linux-gnu/perl5/5.38/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_1.3.2-2_i386.deb'. dpkg-deb: building package 'altree-examples' in '../altree-examples_1.3.2-2_all.deb'. dpkg-deb: building package 'altree-dbgsym' in '../altree-dbgsym_1.3.2-2_i386.deb'. dpkg-genbuildinfo --build=binary -O../altree_1.3.2-2_i386.buildinfo dpkg-genchanges --build=binary -O../altree_1.3.2-2_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/60875 and its subdirectories I: Current time: Sun Apr 28 03:49:25 -12 2024 I: pbuilder-time-stamp: 1714319365 Sun Apr 28 15:49:27 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos16-i386.debian.net. Sun Apr 28 15:49:27 UTC 2024 I: Preparing to do remote build '2' on ionos16-i386.debian.net. Sun Apr 28 15:57:31 UTC 2024 I: Deleting $TMPDIR on ionos16-i386.debian.net. Sun Apr 28 15:57:32 UTC 2024 I: altree_1.3.2-2_i386.changes: Format: 1.8 Date: Wed, 29 Nov 2023 11:13:27 +0100 Source: altree Binary: altree altree-dbgsym altree-examples Architecture: i386 all Version: 1.3.2-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: altree - program to perform phylogeny-based association and localization a altree-examples - example files for ALTree Changes: altree (1.3.2-2) unstable; urgency=medium . * Alternative to libblas-dev | libblas.so * Drop libatlas3-base from Recommends * Standards-Version: 4.6.2 (routine-update) * Set upstream metadata fields: Repository-Browse. Checksums-Sha1: 706d76b704a679338b9f709707f0abbc62b1f058 339220 altree-dbgsym_1.3.2-2_i386.deb d8ef261c5c5244f41d4edbc4a9a10516609e358a 330144 altree-examples_1.3.2-2_all.deb 61c7d86035fdd195bca6d55eb660d46ce98cf4b3 9259 altree_1.3.2-2_i386.buildinfo 77ff18ac875b29ee05d1a439386d7dcfb634cf4a 344840 altree_1.3.2-2_i386.deb Checksums-Sha256: fde24fd5eba116741d1b19bca2756969519f83010daa2d647278b2ba42588518 339220 altree-dbgsym_1.3.2-2_i386.deb d7c02ae87376cfd2c8be28a7343ec6efe90802c2069e7e7b520e4d77623e498b 330144 altree-examples_1.3.2-2_all.deb ecf16266a8d341d8a97c3d15c6c50a390c454a209b9c2924ebfa14cbcd24aa48 9259 altree_1.3.2-2_i386.buildinfo db0e548f4f52738ec731eaf393030470aab78796ef12e7b759352e66971141af 344840 altree_1.3.2-2_i386.deb Files: 2ff063c9d2b73524ce9ec0397a9c1845 339220 debug optional altree-dbgsym_1.3.2-2_i386.deb 39224446815f821214e22bf2cc288331 330144 science optional altree-examples_1.3.2-2_all.deb 59234535be690947297148ec4a471614 9259 science optional altree_1.3.2-2_i386.buildinfo 42104e08e761934969d94ac5e5e8c997 344840 science optional altree_1.3.2-2_i386.deb Sun Apr 28 15:57:33 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_12-9543.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.o6GP6DgI/altree_1.3.2-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.o6GP6DgI/altree_1.3.2-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.o6GP6DgI/altree_1.3.2-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.o6GP6DgI/b1/altree_1.3.2-2_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.o6GP6DgI/b2/altree_1.3.2-2_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.326s) 0.326s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.026s) 0.026s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 623ms CPU time consumed: 623ms Sun Apr 28 15:57:34 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Sun Apr 28 15:57:34 UTC 2024 I: altree from trixie built successfully and reproducibly on i386. Sun Apr 28 15:57:35 UTC 2024 I: Submitting .buildinfo files to external archives: Sun Apr 28 15:57:35 UTC 2024 I: Submitting 12K b1/altree_1.3.2-2_i386.buildinfo.asc Sun Apr 28 15:57:37 UTC 2024 I: Submitting 12K b2/altree_1.3.2-2_i386.buildinfo.asc Sun Apr 28 15:57:38 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Apr 28 15:57:38 UTC 2024 I: Done submitting .buildinfo files. Sun Apr 28 15:57:38 UTC 2024 I: Removing signed altree_1.3.2-2_i386.buildinfo.asc files: removed './b1/altree_1.3.2-2_i386.buildinfo.asc' removed './b2/altree_1.3.2-2_i386.buildinfo.asc'