sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk +==============================================================================+ | altree 1.3.2-2+b4 (amd64) Sat, 14 Sep 2024 17:29:31 +0000 | +==============================================================================+ Package: altree Version: 1.3.2-2+b4 Source Version: 1.3.2-2 Distribution: perl-5.40 Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.40-amd64-debomatic-13cc1f5f-f92a-44c1-bc07-fe5f76877af3' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup altree_1.3.2-2 perl-5.40 amd64 ----------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup altree_1.3.2-2 perl-5.40 amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/altree-f7qK1H/resolver-vVJGo4' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:2 http://deb.debian.org/debian unstable InRelease Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:3 http://localhost:3142/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/altree_1.3.2-2.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/altree-f7qK1H/altree-1.3.2' with '<>' I: NOTICE: Log filtering will replace 'build/altree-f7qK1H' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged 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, build-essential, fakeroot Filtered 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, libtest-deep-perl, fig2dev, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [845 B] Get:5 copy:/<>/apt_archive ./ Packages [864 B] Fetched 2318 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bash-completion bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot fig2dev file fontconfig-config fonts-lmodern fonts-urw-base35 gawk gettext gettext-base ghostscript groff-base intltool-debian latex-make libapache-pom-java libarchive-zip-perl libavahi-client3 libavahi-common-data libavahi-common3 libblas-dev libblas3 libbrotli1 libcairo2 libcom-err2 libcommons-logging-java libcommons-parent-java libcups2t64 libdbus-1-3 libdebhelper-perl libdeflate0 libelf1t64 libexpat1 libfakeroot libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 libfreetype6 libglib2.0-0t64 libgraphite2-3 libgs-common libgs10 libgs10-common libgsl-dev libgsl28 libgslcblas0 libgssapi-krb5-2 libharfbuzz0b libice6 libicu72 libidn12 libijs-0.35 libjbig0 libjbig2dec0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0 liblcms2-2 liblerc4 libmagic-mgc libmagic1t64 libmath-tamuanova-perl libmpfi0 libnetpbm11t64 libnsl2 libopenjp2-7 libpaper-utils libpaper1 libpdfbox-java libpipeline1 libpixman-1-0 libpng16-16t64 libpotrace0 libptexenc1 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libsharpyuv0 libsigsegv2 libsm6 libsynctex2 libtamuanova-0.2 libteckit0 libtest-deep-perl libtexlua53-5 libtiff6 libtirpc-common libtirpc3t64 libtool libuchardet0 libwebp7 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6t64 libzzip-0-13t64 m4 man-db media-types netbase netpbm po-debconf poppler-data preview-latex-style python3 python3-minimal python3.12 python3.12-minimal sensible-utils t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended texlive-lang-french texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures tzdata ucf x11-common xdg-utils xfonts-encodings xfonts-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make xfig fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gawk-doc gettext-doc libasprintf-dev libgettextpo-dev groff liblapack-doc libavalon-framework-java libexcalibur-logkit-java liblog4j1.2-java cups-common low-memory-monitor gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html krb5-doc krb5-user liblcms2-utils libmpfi-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl poppler-utils fonts-japanese-mincho | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-nanum python3-doc python3-tk python3-venv python3.12-venv python3.12-doc binfmt-support perl-tk xpdf | pdf-viewer xzdec texlive-binaries-sse2 hintview texlive-fonts-recommended-doc texlive-latex-base-doc wp2latex python3-pygments icc-profiles libfile-which-perl texlive-latex-extra-doc texlive-science texlive-latex-recommended-doc texlive-luatex texlive-pstricks dot2tex prerex texlive-pictures-doc vprerex Recommended packages: curl | wget | lynx inkscape dbus libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs fonts-droid-fallback krb5-locales libltdl-dev libmail-sendmail-perl ca-certificates lmodern dvisvgm tex-gyre tipa default-jre libspreadsheet-parseexcel-perl texlive-plain-generic ruby tk libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev bash-completion bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot fig2dev file fontconfig-config fonts-lmodern fonts-urw-base35 gawk gettext gettext-base ghostscript groff-base intltool-debian latex-make libapache-pom-java libarchive-zip-perl libavahi-client3 libavahi-common-data libavahi-common3 libblas-dev libblas3 libbrotli1 libcairo2 libcom-err2 libcommons-logging-java libcommons-parent-java libcups2t64 libdbus-1-3 libdebhelper-perl libdeflate0 libelf1t64 libexpat1 libfakeroot libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 libfreetype6 libglib2.0-0t64 libgraphite2-3 libgs-common libgs10 libgs10-common libgsl-dev libgsl28 libgslcblas0 libgssapi-krb5-2 libharfbuzz0b libice6 libicu72 libidn12 libijs-0.35 libjbig0 libjbig2dec0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0 liblcms2-2 liblerc4 libmagic-mgc libmagic1t64 libmath-tamuanova-perl libmpfi0 libnetpbm11t64 libnsl2 libopenjp2-7 libpaper-utils libpaper1 libpdfbox-java libpipeline1 libpixman-1-0 libpng16-16t64 libpotrace0 libptexenc1 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libsharpyuv0 libsigsegv2 libsm6 libsynctex2 libtamuanova-0.2 libteckit0 libtest-deep-perl libtexlua53-5 libtiff6 libtirpc-common libtirpc3t64 libtool libuchardet0 libwebp7 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6t64 libzzip-0-13t64 m4 man-db media-types netbase netpbm po-debconf poppler-data preview-latex-style python3 python3-minimal python3.12 python3.12-minimal sbuild-build-depends-main-dummy sensible-utils t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended texlive-lang-french texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures tzdata ucf x11-common xdg-utils xfonts-encodings xfonts-utils 0 upgraded, 149 newly installed, 0 to remove and 0 not upgraded. Need to get 252 MB/252 MB of archives. After this operation, 676 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [984 B] Get:2 file:/srv/reprepro perl-5.40/main amd64 libmath-tamuanova-perl amd64 1.0.2-4+b2 [13.9 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libsigsegv2 amd64 2.14-1+b1 [34.3 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 gawk amd64 1:5.2.1-2+b1 [674 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 libpython3.12-minimal amd64 3.12.6-1 [814 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.3-1 [105 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.6-1 [2168 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.5-1+b1 [27.0 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:17 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.6-1 [1963 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.6-1 [669 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.5-1+b1 [9884 B] Get:25 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.5-1+b1 [27.9 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 bash-completion all 1:2.14.0-1 [305 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-8 [97.3 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:49 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3+b1 [671 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libfakeroot amd64 1.36-1 [29.1 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 fakeroot amd64 1.36-1 [75.1 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1 [23.0 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get:67 http://deb.debian.org/debian unstable/main amd64 libgs-common all 10.03.1~dfsg-2 [148 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libgs10-common all 10.03.1~dfsg-2 [474 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-13+b2 [112 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-13+b2 [43.3 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.14.10-4+b1 [203 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-13+b2 [47.0 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.10-1 [249 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libidn12 amd64 1.42-2 [80.4 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libijs-0.35 amd64 0.35-15.1+b1 [15.1 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libjbig2dec0 amd64 0.20-1+b2 [64.3 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.0-2+b3 [190 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libpaper1 amd64 1.1.29+b1 [12.9 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.21-1 [47.3 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 libgs10 amd64 10.03.1~dfsg-2 [2543 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 ghostscript amd64 10.03.1~dfsg-2 [50.2 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 libnetpbm11t64 amd64 2:11.07.00-2 [182 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 netpbm amd64 2:11.07.00-2 [2061 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 fig2dev amd64 1:3.2.9-4 [444 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 tex-common all 6.18 [32.5 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 latex-make all 2.4.3-1 [1030 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 29-2 [5276 B] Get:106 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.0-3 [159 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2 [115 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2 [105 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get:113 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.2-1 [534 kB] Get:114 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get:115 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 libfontbox-java all 1:1.8.16-5 [211 kB] Get:117 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.82.0-1 [1498 kB] Get:118 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:119 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-3 [116 kB] Get:120 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-3 [994 kB] Get:121 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-3 [1223 kB] Get:122 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 9.0.0-1 [474 kB] Get:123 http://deb.debian.org/debian unstable/main amd64 libkpathsea6 amd64 2024.20240313.70630+ds-4 [157 kB] Get:124 http://deb.debian.org/debian unstable/main amd64 libtamuanova-0.2 amd64 0.2-5+b3 [9228 B] Get:125 http://deb.debian.org/debian unstable/main amd64 libmpfi0 amd64 1.5.4+ds-3 [35.1 kB] Get:126 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 1.1.29+b1 [9176 B] Get:127 http://deb.debian.org/debian unstable/main amd64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get:128 http://deb.debian.org/debian unstable/main amd64 libpotrace0 amd64 1.16-2+b1 [25.2 kB] Get:129 http://deb.debian.org/debian unstable/main amd64 libptexenc1 amd64 2024.20240313.70630+ds-4 [49.1 kB] Get:130 http://deb.debian.org/debian unstable/main amd64 libsynctex2 amd64 2024.20240313.70630+ds-4 [62.5 kB] Get:131 http://deb.debian.org/debian unstable/main amd64 libteckit0 amd64 2.5.12+ds1-1 [339 kB] Get:132 http://deb.debian.org/debian unstable/main amd64 libtest-deep-perl all 1.204-1 [52.9 kB] Get:133 http://deb.debian.org/debian unstable/main amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-4 [114 kB] Get:134 http://deb.debian.org/debian unstable/main amd64 libxmu6 amd64 2:1.1.3-3+b2 [58.7 kB] Get:135 http://deb.debian.org/debian unstable/main amd64 libxpm4 amd64 1:3.5.17-1+b1 [56.1 kB] Get:136 http://deb.debian.org/debian unstable/main amd64 libxaw7 amd64 2:1.0.14-1+b2 [199 kB] Get:137 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB] Get:138 http://deb.debian.org/debian unstable/main amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.3 [56.2 kB] Get:139 http://deb.debian.org/debian unstable/main amd64 preview-latex-style all 13.2-1 [350 kB] Get:140 http://deb.debian.org/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:141 http://deb.debian.org/debian unstable/main amd64 texlive-binaries amd64 2024.20240313.70630+ds-4 [8493 kB] Get:142 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:143 http://deb.debian.org/debian unstable/main amd64 texlive-base all 2024.20240829-2 [22.7 MB] Get:144 http://deb.debian.org/debian unstable/main amd64 texlive-fonts-recommended all 2024.20240829-2 [4990 kB] Get:145 http://deb.debian.org/debian unstable/main amd64 texlive-lang-french all 2024.20240829-1 [96.0 MB] Get:146 http://deb.debian.org/debian unstable/main amd64 texlive-latex-base all 2024.20240829-2 [1273 kB] Get:147 http://deb.debian.org/debian unstable/main amd64 texlive-latex-recommended all 2024.20240829-2 [8845 kB] Get:148 http://deb.debian.org/debian unstable/main amd64 texlive-pictures all 2024.20240829-2 [17.0 MB] Get:149 http://deb.debian.org/debian unstable/main amd64 texlive-latex-extra all 2024.20240829-1 [20.9 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 252 MB in 4s (63.5 MB/s) Selecting previously unselected package libsigsegv2:amd64. 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Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Sep 14 17:30:07 UTC 2024. Universal Time is now: Sat Sep 14 17:30:07 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.36-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up libfontenc1:amd64 (1:1.1.8-1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:amd64 (2.82.0-1) ... No schema files found: doing nothing. Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libjbig2dec0:amd64 (0.20-1+b2) ... Setting up libteckit0:amd64 (2.5.12+ds1-1) ... Setting up bash-completion (1:2.14.0-1) ... Setting up libapache-pom-java (29-2) ... Setting up libavahi-common-data:amd64 (0.8-13+b2) ... Setting up libdbus-1-3:amd64 (1.14.10-4+b1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up t1utils (1.41-4) ... Setting up libtexlua53-5:amd64 (2024.20240313.70630+ds-4) ... Setting up libpng16-16t64:amd64 (1.6.43-5) ... Setting up libidn12:amd64 (1.42-2) ... Setting up autopoint (0.22.5-2) ... Setting up libmpfi0:amd64 (1.5.4+ds-3) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libkpathsea6:amd64 (2024.20240313.70630+ds-4) ... Setting up autoconf (2.72-3) ... Setting up libwebp7:amd64 (1.4.0-0.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up fonts-lmodern (2.005-1) ... Setting up libopenjp2-7:amd64 (2.5.0-2+b3) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up netbase (6.4) ... Configuration file '/etc/protocols' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Configuration file '/etc/services' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libgsl28:amd64 (2.8+dfsg-3) ... Setting up libxml2:amd64 (2.12.7+dfsg-3+b1) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libblas-dev:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up libsynctex2:amd64 (2024.20240313.70630+ds-4) ... Setting up libpotrace0:amd64 (1.16-2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libice6:amd64 (2:1.0.10-1+b1) ... Setting up gettext (0.22.5-2) ... Setting up libgsl-dev (2.8+dfsg-3) ... Setting up libpdfbox-java (1:1.8.16-5) ... Setting up libxpm4:amd64 (1:3.5.17-1+b1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up libtool (2.4.7-7) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-13+b2) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libptexenc1:amd64 (2024.20240313.70630+ds-4) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up ucf (3.0043+nmu1) ... Setting up netpbm (2:11.07.00-2) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libtamuanova-0.2 (0.2-5+b3) ... Setting up groff-base (1.23.0-5) ... Setting up libharfbuzz0b:amd64 (9.0.0-1) ... Setting up libsm6:amd64 (2:1.2.3-1+b1) ... Setting up libavahi-client3:amd64 (0.8-13+b2) ... Setting up libpaper1:amd64 (1.1.29+b1) ... Creating config file /etc/papersize with new version Setting up libxi6:amd64 (2:1.8.1-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpaper-utils (1.1.29+b1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libmath-tamuanova-perl (1.0.2-4+b2) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2) ... Setting up libnsl2:amd64 (1.3.0-3+b2) ... Setting up libcups2t64:amd64 (2.4.10-1) ... Setting up libxmu6:amd64 (2:1.1.3-3+b2) ... Setting up libpython3.12-stdlib:amd64 (3.12.6-1) ... Setting up preview-latex-style (13.2-1) ... Setting up python3.12 (3.12.6-1) ... Setting up debhelper (13.20) ... Setting up libxaw7:amd64 (2:1.0.14-1+b2) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libpython3-stdlib:amd64 (3.12.5-1+b1) ... Setting up libgs10-common (10.03.1~dfsg-2) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up python3 (3.12.5-1+b1) ... Setting up latex-make (2.4.3-1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up libgs10:amd64 (10.03.1~dfsg-2) ... Setting up ghostscript (10.03.1~dfsg-2) ... Setting up fig2dev (1:3.2.9-4) ... Setting up libcairo2:amd64 (1.18.2-1) ... Setting up texlive-binaries (2024.20240313.70630+ds-4) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up texlive-base (2024.20240829-2) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up texlive-lang-french (2024.20240829-1) ... Setting up texlive-latex-base (2024.20240829-2) ... Setting up texlive-latex-recommended (2024.20240829-2) ... Setting up texlive-pictures (2024.20240829-2) ... Setting up texlive-fonts-recommended (2024.20240829-2) ... Setting up texlive-latex-extra (2024.20240829-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.40-2) ... Processing triggers for tex-common (6.18) ... 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. +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.9.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.9.7-1 (2024-06-27) amd64 (x86_64) Toolchain package versions: binutils_2.43.1-4 dpkg-dev_1.22.11 g++-13_13.3.0-6 g++-14_14.2.0-4 gcc-13_13.3.0-6 gcc-14_14.2.0-4 libc6-dev_2.40-2 libstdc++-13-dev_13.3.0-6 libstdc++-14-dev_14.2.0-4 libstdc++6_14.2.0-4 linux-libc-dev_6.10.9-1 Package versions: adduser_3.137 apt_2.9.8 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.5 base-passwd_3.6.4 bash_5.2.32-1+b1 bash-completion_1:2.14.0-1 binutils_2.43.1-4 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openssl-provider-legacy_3.3.2-1 passwd_1:4.16.0-4 patch_2.7.6-7 perl_5.40.0-5 perl-base_5.40.0-5 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0-5 pinentry-curses_1.2.1-4+b1 po-debconf_1.0.21+nmu1 poppler-data_0.4.12-1 preview-latex-style_13.2-1 python3_3.12.5-1+b1 python3-minimal_3.12.5-1+b1 python3.12_3.12.6-1 python3.12-minimal_3.12.6-1 readline-common_8.2-5 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 sysvinit-utils_3.10-2 t1utils_1.41-4 tar_1.35+dfsg-3 tex-common_6.18 texlive-base_2024.20240829-2 texlive-binaries_2024.20240313.70630+ds-4 texlive-fonts-recommended_2024.20240829-2 texlive-lang-french_2024.20240829-1 texlive-latex-base_2024.20240829-2 texlive-latex-extra_2024.20240829-1 texlive-latex-recommended_2024.20240829-2 texlive-pictures_2024.20240829-2 tzdata_2024a-4 ucf_3.0043+nmu1 usr-is-merged_39 util-linux_2.40.2-8 x11-common_1:7.7+23.1 xdg-utils_1.1.3-4.1 xfonts-encodings_1:1.0.4-2.2 xfonts-utils_1:7.7+6 xz-utils_5.6.2-2 zlib1g_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----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 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space for build Hack binNMU version ------------------- Created changelog entry for binNMU version 1.3.2-2+b4 +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network altree_1.3.2-2 perl-5.40 amd64 ----------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network altree_1.3.2-2 perl-5.40 amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SCHROOT_ALIAS_NAME=perl-5.40-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-13cc1f5f-f92a-44c1-bc07-fe5f76877af3 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -mDebian Perl autobuilder -B -rfakeroot -Zxz dpkg-buildpackage: info: source package altree dpkg-buildpackage: info: source version 1.3.2-2+b4 dpkg-buildpackage: info: source distribution perl-5.40 dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' /usr/bin/make -C Documentation distclean || true make[2]: Entering directory '/<>/Documentation' make[2]: Nothing to be done for 'distclean'. make[2]: Leaving directory '/<>/Documentation' dh_auto_clean make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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=/<>=. -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 override_dh_auto_build make[1]: Entering directory '/<>' /usr/bin/make -C Documentation pdf make[2]: Entering directory '/<>/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 '/<>/Documentation' make[3]: Nothing to be done for 'LU_WATCH_FILES_SAVE'. make[3]: Leaving directory '/<>/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 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 '/<>/Documentation' ======> building fig/option_b.subfig.mk <====== make[3]: Leaving directory '/<>/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 '/<>/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 '/<>/Documentation' ======> building manual.bbl <====== This is BibTeX, Version 0.99d (TeX Live 2025/dev/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 '/<>/Documentation' make[5]: Leaving directory '/<>/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. 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 '/<>/Documentation' make[5]: Leaving directory '/<>/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 '/<>/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 '/<>/Documentation' ======> building manual.bbl <====== This is BibTeX, Version 0.99d (TeX Live 2025/dev/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 '/<>/Documentation' make[7]: Leaving directory '/<>/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 '/<>/Documentation' make[7]: Leaving directory '/<>/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 '/<>/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 '/<>/Documentation' ======> building manual.bbl <====== This is BibTeX, Version 0.99d (TeX Live 2025/dev/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 '/<>/Documentation' make[9]: Leaving directory '/<>/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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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 '/<>/Documentation' make[9]: Leaving directory '/<>/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 '/<>/Documentation' *** Checking rebuild with rule 'latex' *** Checking rebuild with rule 'texdepends' /usr/bin/make LU_REC_LEVEL=5 manual.pdf make[10]: Entering directory '/<>/Documentation' make[10]: 'manual.pdf' is up to date. make[10]: Leaving directory '/<>/Documentation' make[9]: Leaving directory '/<>/Documentation' make[8]: Leaving directory '/<>/Documentation' make[7]: Leaving directory '/<>/Documentation' make[6]: Leaving directory '/<>/Documentation' make[5]: Leaving directory '/<>/Documentation' make[4]: Leaving directory '/<>/Documentation' make[3]: Leaving directory '/<>/Documentation' make[2]: Leaving directory '/<>/Documentation' dh_auto_build make -j2 make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/CUtils' cp ALTree/SitePerTree.pm blib/lib/ALTree/SitePerTree.pm cp ALTree/Foret.pm blib/lib/ALTree/Foret.pm cp ALTree/Sens.pm blib/lib/ALTree/Sens.pm cp ALTree/to_rewrite.pm blib/lib/ALTree/to_rewrite.pm cp ALTree/SiteSensPerTree.pm blib/lib/ALTree/SiteSensPerTree.pm cp ALTree/SiteCollection.pm blib/lib/ALTree/SiteCollection.pm cp ALTree/SiteSensPerForet.pm blib/lib/ALTree/SiteSensPerForet.pm cp ALTree/Input.pm blib/lib/ALTree/Input.pm cp ALTree/Chi2.pm blib/lib/ALTree/Chi2.pm cp ALTree/SiteSens.pm blib/lib/ALTree/SiteSens.pm cp ALTree/Node.pm blib/lib/ALTree/Node.pm cp ALTree/Utils.pm blib/lib/ALTree/Utils.pm cp ALTree/Import.pm blib/lib/ALTree/Import.pm cp ALTree/SitePerForet.pm blib/lib/ALTree/SitePerForet.pm cp ALTree/Base.pm blib/lib/ALTree/Base.pm cp ALTree/Site.pm blib/lib/ALTree/Site.pm cp ALTree/Nanova.pm blib/lib/ALTree/Nanova.pm cp ALTree/Tree.pm blib/lib/ALTree/Tree.pm make -C c_sources make[4]: Entering directory '/<>/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=/<>=. -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 cp lib/ALTree/CUtils.pm ../blib/lib/ALTree/CUtils.pm AutoSplitting ../blib/lib/ALTree/CUtils.pm (../blib/lib/auto/ALTree/CUtils) Running Mkbootstrap for CUtils () chmod 644 "CUtils.bs" "/usr/bin/perl" "/usr/share/perl/5.40.0/ExtUtils/xsubpp" -typemap '/usr/share/perl/5.40/ExtUtils/typemap' CUtils.xs > CUtils.xsc Please specify prototyping behavior for CUtils.xs (see perlxs manual) mv CUtils.xsc CUtils.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=/<>=. -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=/<>=. -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 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]; | ^~~ 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=/<>=. -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=/<>=. -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=/<>=. -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=/<>=. -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 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=/<>=. -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=/<>=. -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 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=/<>=. -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 z.c:12:13: warning: ‘sccsfid’ defined but not used [-Wunused-variable] 12 | static char sccsfid[] = "@(#) z.c 5.1 (|stat) 12/26/85"; | ^~~~~~~ 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 '/<>/CUtils/c_sources' make[4]: Entering directory '/<>/CUtils/c_sources' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/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=/<>=. -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[3]: Leaving directory '/<>/CUtils' cp progs/altree blib/script/altree cp progs/altree-add-S blib/script/altree-add-S "/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 cp progs/altree-convert blib/script/altree-convert "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/altree-convert Manifying 3 pod documents make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_auto_test -a make -j2 test TEST_VERBOSE=1 make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/CUtils' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CUtils.bs ../blib/arch/auto/ALTree/CUtils/CUtils.bs 644 make[3]: Entering directory '/<>/CUtils/c_sources' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/CUtils/c_sources' Manifying 1 pod document make[2]: Leaving directory '/<>/CUtils' make[2]: Entering directory '/<>/CUtils' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CUtils.bs ../blib/arch/auto/ALTree/CUtils/CUtils.bs 644 make[3]: Entering directory '/<>/CUtils/c_sources' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/CUtils/c_sources' make[3]: Entering directory '/<>/CUtils/c_sources' No tests defined for ALTree::CUtils extension. make[3]: Leaving directory '/<>/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 + 0.09 cusr 0.02 csys = 0.13 CPU) Result: PASS make[2]: Leaving directory '/<>/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 + 0.07 cusr 0.01 csys = 0.10 CPU) Result: PASS make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install -a make -j2 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/CUtils' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CUtils.bs ../blib/arch/auto/ALTree/CUtils/CUtils.bs 644 make[3]: Entering directory '/<>/CUtils/c_sources' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/CUtils/c_sources' Manifying 1 pod document make[2]: Leaving directory '/<>/CUtils' Manifying 3 pod documents Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing /<>/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/ALTree/CUtils/CUtils.so Installing /<>/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Sens.pm Installing /<>/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Input.pm Installing /<>/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Foret.pm Installing /<>/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Tree.pm Installing /<>/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteSensPerForet.pm Installing /<>/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Site.pm Installing /<>/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Node.pm Installing /<>/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SitePerForet.pm Installing /<>/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Import.pm Installing /<>/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Base.pm Installing /<>/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SitePerTree.pm Installing /<>/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteSens.pm Installing /<>/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/CUtils.pm Installing /<>/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteCollection.pm Installing /<>/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/to_rewrite.pm Installing /<>/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Chi2.pm Installing /<>/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteSensPerTree.pm Installing /<>/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Utils.pm Installing /<>/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Nanova.pm Installing /<>/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/ALTree/CUtils/autosplit.ix Installing /<>/debian/tmp/usr/share/man/man1/altree-add-S.1p Installing /<>/debian/tmp/usr/share/man/man1/altree-convert.1p Installing /<>/debian/tmp/usr/share/man/man1/altree.1p Installing /<>/debian/tmp/usr/share/man/man3/ALTree::CUtils.3pm Installing /<>/debian/tmp/usr/bin/altree Installing /<>/debian/tmp/usr/bin/altree-add-S Installing /<>/debian/tmp/usr/bin/altree-convert make[1]: Leaving directory '/<>' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a debian/rules override_dh_compress make[1]: Entering directory '/<>' dh_compress --exclude=.pdf make[1]: Leaving directory '/<>' dh_fixperms -a dh_missing -a 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 -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'altree-dbgsym' in '../altree-dbgsym_1.3.2-2+b4_amd64.deb'. dpkg-deb: building package 'altree' in '../altree_1.3.2-2+b4_amd64.deb'. dpkg-genbuildinfo --build=any -O../altree_1.3.2-2+b4_amd64.buildinfo dpkg-genchanges --build=any -mDebian Perl autobuilder -O../altree_1.3.2-2+b4_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-09-14T17:31:18Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ altree_1.3.2-2+b4_amd64.changes: -------------------------------- Format: 1.8 Date: Sat, 14 Sep 2024 17:31:06 +0000 Source: altree (1.3.2-2) Binary: altree altree-dbgsym Binary-Only: yes Architecture: amd64 Version: 1.3.2-2+b4 Distribution: perl-5.40 Urgency: low Maintainer: Debian Perl autobuilder Changed-By: Debian Perl autobuilder Description: altree - program to perform phylogeny-based association and localization a Changes: altree (1.3.2-2+b4) perl-5.40; urgency=low, binary-only=yes . * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild for Perl 5.40 Checksums-Sha1: 4f7c6d32c4bb7474a864e802810e84d3fd37dba5 350020 altree-dbgsym_1.3.2-2+b4_amd64.deb ef27b1ccbd2629ec7ff36713747d86c3b1bbafbf 9216 altree_1.3.2-2+b4_amd64.buildinfo 94f7d8799c60edbdb133e8fdd6bc54a812348356 345324 altree_1.3.2-2+b4_amd64.deb Checksums-Sha256: 3a7d44b4a60c6e8b1363f196148186dbaddaebaa664c657d224dc4d488621b6a 350020 altree-dbgsym_1.3.2-2+b4_amd64.deb b22430c93582272d70cd24f3b25891ffe19237990edca4a8c603157ade9c7ea8 9216 altree_1.3.2-2+b4_amd64.buildinfo 079169db9ec9e073b333e173b8db57f8d4225e7f51f5f36470471e0438abde42 345324 altree_1.3.2-2+b4_amd64.deb Files: 41ea6c7ed22217c975aec353f40ca5fe 350020 debug optional 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94f7d8799c60edbdb133e8fdd6bc54a812348356 345324 altree_1.3.2-2+b4_amd64.deb Checksums-Sha256: 3a7d44b4a60c6e8b1363f196148186dbaddaebaa664c657d224dc4d488621b6a 350020 altree-dbgsym_1.3.2-2+b4_amd64.deb 079169db9ec9e073b333e173b8db57f8d4225e7f51f5f36470471e0438abde42 345324 altree_1.3.2-2+b4_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sat, 14 Sep 2024 17:31:17 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3), automake (= 1:1.16.5-1.3), autopoint (= 0.22.5-2), autotools-dev (= 20220109.1), base-files (= 13.5), base-passwd (= 3.6.4), bash (= 5.2.32-1+b1), bash-completion (= 1:2.14.0-1), binutils (= 2.43.1-4), binutils-common (= 2.43.1-4), binutils-x86-64-linux-gnu (= 2.43.1-4), bsdextrautils (= 2.40.2-8), bsdutils (= 1:2.40.2-8), build-essential (= 12.10), bzip2 (= 1.0.8-6), coreutils (= 9.4-3.1), cpp (= 4:14.1.0-2), cpp-13 (= 13.3.0-6), cpp-13-x86-64-linux-gnu (= 13.3.0-6), 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1.5.3-7), libpaper-utils (= 1.1.29+b1), libpaper1 (= 1.1.29+b1), libpcre2-8-0 (= 10.42-4+b1), libpdfbox-java (= 1:1.8.16-5), libperl5.40 (= 5.40.0-5), libpipeline1 (= 1.5.8-1), libpixman-1-0 (= 0.42.2-1+b1), libpng16-16t64 (= 1.6.43-5), libpotrace0 (= 1.16-2+b1), libptexenc1 (= 2024.20240313.70630+ds-4), libpython3-stdlib (= 3.12.5-1+b1), libpython3.12-minimal (= 3.12.6-1), libpython3.12-stdlib (= 3.12.6-1), libquadmath0 (= 14.2.0-4), libreadline8t64 (= 8.2-5), libseccomp2 (= 2.5.5-1+b1), libselinux1 (= 3.7-3), libsframe1 (= 2.43.1-4), libsharpyuv0 (= 1.4.0-0.1), libsigsegv2 (= 2.14-1+b1), libsm6 (= 2:1.2.3-1+b1), libsmartcols1 (= 2.40.2-8), libsqlite3-0 (= 3.46.1-1), libssl3t64 (= 3.3.2-1), libstdc++-14-dev (= 14.2.0-4), libstdc++6 (= 14.2.0-4), libsynctex2 (= 2024.20240313.70630+ds-4), libsystemd0 (= 256.6-1), libtamuanova-0.2 (= 0.2-5+b3), libtasn1-6 (= 4.19.0-3+b2), libteckit0 (= 2.5.12+ds1-1), libtest-deep-perl (= 1.204-1), libtexlua53-5 (= 2024.20240313.70630+ds-4), libtiff6 (= 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openssl-provider-legacy (= 3.3.2-1), patch (= 2.7.6-7), perl (= 5.40.0-5), perl-base (= 5.40.0-5), perl-modules-5.40 (= 5.40.0-5), po-debconf (= 1.0.21+nmu1), poppler-data (= 0.4.12-1), preview-latex-style (= 13.2-1), python3 (= 3.12.5-1+b1), python3-minimal (= 3.12.5-1+b1), python3.12 (= 3.12.6-1), python3.12-minimal (= 3.12.6-1), readline-common (= 8.2-5), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.24), sysvinit-utils (= 3.10-2), t1utils (= 1.41-4), tar (= 1.35+dfsg-3), tex-common (= 6.18), texlive-base (= 2024.20240829-2), texlive-binaries (= 2024.20240313.70630+ds-4), texlive-fonts-recommended (= 2024.20240829-2), texlive-lang-french (= 2024.20240829-1), texlive-latex-base (= 2024.20240829-2), texlive-latex-extra (= 2024.20240829-1), texlive-latex-recommended (= 2024.20240829-2), texlive-pictures (= 2024.20240829-2), tzdata (= 2024a-4), ucf (= 3.0043+nmu1), usr-is-merged (= 39), util-linux (= 2.40.2-8), x11-common (= 1:7.7+23.1), xdg-utils (= 1.1.3-4.1), xfonts-encodings (= 1:1.0.4-2.2), xfonts-utils (= 1:7.7+6), xz-utils (= 5.6.2-2), zlib1g (= 1:1.3.dfsg+really1.3.1-1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1726335066" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ altree-dbgsym_1.3.2-2+b4_amd64.deb ---------------------------------- new Debian package, version 2.0. size 350020 bytes: control archive=540 bytes. 382 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: altree-dbgsym Source: altree (1.3.2-2) Version: 1.3.2-2+b4 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 358 Depends: altree (= 1.3.2-2+b4) Section: debug Priority: optional Description: debug symbols for altree Build-Ids: 4473ffcede6fdf316c6891d9816482f8509fbb63 drwxr-xr-x root/root 0 2024-09-14 17:31 ./ drwxr-xr-x root/root 0 2024-09-14 17:31 ./usr/ drwxr-xr-x root/root 0 2024-09-14 17:31 ./usr/lib/ drwxr-xr-x root/root 0 2024-09-14 17:31 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-09-14 17:31 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-09-14 17:31 ./usr/lib/debug/.build-id/44/ -rw-r--r-- root/root 355688 2024-09-14 17:31 ./usr/lib/debug/.build-id/44/73ffcede6fdf316c6891d9816482f8509fbb63.debug drwxr-xr-x root/root 0 2024-09-14 17:31 ./usr/share/ drwxr-xr-x root/root 0 2024-09-14 17:31 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-09-14 17:31 ./usr/share/doc/altree-dbgsym -> altree altree_1.3.2-2+b4_amd64.deb --------------------------- new Debian package, version 2.0. size 345324 bytes: control archive=1776 bytes. 872 bytes, 17 lines control 2882 bytes, 36 lines md5sums Package: altree Source: altree (1.3.2-2) Version: 1.3.2-2+b4 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 562 Depends: libblas3 | libblas.so.3, libc6 (>= 2.38), libgsl28 (>= 2.8+dfsg), perl (>= 5.40.0-5), perlapi-5.40.0, libmath-tamuanova-perl Recommends: libopenblas0 | libblis4 | libmkl-rt | libblas.so.3 Suggests: altree-examples Section: science Priority: optional Homepage: https://gitlab.inria.fr/NGS/ALTree Description: program to perform phylogeny-based association and localization analysis ALTree was designed to perform association detection and localization of susceptibility sites using haplotype phylogenetic trees: first, it allows the detection of an association between a candidate gene and a disease, and second, it enables to make hypothesis about the susceptibility loci. drwxr-xr-x root/root 0 2024-09-14 17:31 ./ drwxr-xr-x root/root 0 2024-09-14 17:31 ./usr/ drwxr-xr-x root/root 0 2024-09-14 17:31 ./usr/bin/ -rwxr-xr-x root/root 55855 2024-09-14 17:31 ./usr/bin/altree -rwxr-xr-x root/root 15365 2024-09-14 17:31 ./usr/bin/altree-add-S -rwxr-xr-x root/root 22801 2024-09-14 17:31 ./usr/bin/altree-convert drwxr-xr-x root/root 0 2024-09-14 17:31 ./usr/lib/ drwxr-xr-x root/root 0 2024-09-14 17:31 ./usr/lib/x86_64-linux-gnu/ drwxr-xr-x root/root 0 2024-09-14 17:31 ./usr/lib/x86_64-linux-gnu/perl5/ drwxr-xr-x root/root 0 2024-09-14 17:31 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ drwxr-xr-x root/root 0 2024-09-14 17:31 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/ -rw-r--r-- root/root 342 2021-09-17 14:32 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Base.pm -rw-r--r-- root/root 3081 2021-09-17 14:32 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/CUtils.pm -rw-r--r-- root/root 2897 2021-09-17 14:32 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Chi2.pm -rw-r--r-- root/root 2817 2021-09-17 14:32 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Foret.pm -rw-r--r-- root/root 2026 2021-09-17 14:32 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Import.pm -rw-r--r-- root/root 24521 2021-09-17 14:32 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Input.pm -rw-r--r-- root/root 2371 2021-09-17 14:32 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Nanova.pm -rw-r--r-- root/root 5965 2021-09-17 14:32 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Node.pm -rw-r--r-- root/root 1455 2021-09-17 14:32 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Sens.pm -rw-r--r-- root/root 1895 2021-09-17 14:32 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Site.pm -rw-r--r-- root/root 1044 2021-09-17 14:32 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteCollection.pm -rw-r--r-- root/root 3569 2021-09-17 14:32 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SitePerForet.pm -rw-r--r-- root/root 876 2021-09-17 14:32 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SitePerTree.pm -rw-r--r-- root/root 1287 2021-09-17 14:32 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteSens.pm -rw-r--r-- root/root 905 2021-09-17 14:32 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteSensPerForet.pm -rw-r--r-- root/root 2781 2021-09-17 14:32 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/SiteSensPerTree.pm -rw-r--r-- root/root 4804 2021-09-17 14:32 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Tree.pm -rw-r--r-- root/root 1467 2021-09-17 14:32 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/Utils.pm -rw-r--r-- root/root 9288 2021-09-17 14:32 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ALTree/to_rewrite.pm drwxr-xr-x root/root 0 2024-09-14 17:31 ./usr/lib/x86_64-linux-gnu/perl5/5.40/auto/ drwxr-xr-x root/root 0 2024-09-14 17:31 ./usr/lib/x86_64-linux-gnu/perl5/5.40/auto/ALTree/ drwxr-xr-x root/root 0 2024-09-14 17:31 ./usr/lib/x86_64-linux-gnu/perl5/5.40/auto/ALTree/CUtils/ -rw-r--r-- root/root 74200 2024-09-14 17:31 ./usr/lib/x86_64-linux-gnu/perl5/5.40/auto/ALTree/CUtils/CUtils.so -rw-r--r-- root/root 95 2024-09-14 17:31 ./usr/lib/x86_64-linux-gnu/perl5/5.40/auto/ALTree/CUtils/autosplit.ix drwxr-xr-x root/root 0 2024-09-14 17:31 ./usr/share/ drwxr-xr-x root/root 0 2024-09-14 17:31 ./usr/share/doc-base/ -rw-r--r-- root/root 513 2023-11-29 10:13 ./usr/share/doc-base/altree.altree drwxr-xr-x 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./usr/share/man/man1/altree.1p.gz drwxr-xr-x root/root 0 2024-09-14 17:31 ./usr/share/man/man3/ -rw-r--r-- root/root 1568 2024-09-14 17:31 ./usr/share/man/man3/ALTree::CUtils.3pm.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 17932 Build-Time: 12 Distribution: perl-5.40 Host Architecture: amd64 Install-Time: 85 Job: /srv/debomatic/incoming/altree_1.3.2-2.dsc Machine Architecture: amd64 Package: altree Package-Time: 107 Source-Version: 1.3.2-2 Space: 17932 Status: successful Version: 1.3.2-2+b4 -------------------------------------------------------------------------------- Finished at 2024-09-14T17:31:18Z Build needed 00:01:47, 17932k disk space