I: pbuilder: network access will be disabled during build I: Current time: Fri May 30 16:44:33 +14 2025 I: pbuilder-time-stamp: 1748573073 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: Copying source file I: copying [librostlab-blast_1.0.1-14.dsc] I: copying [./librostlab-blast_1.0.1.orig.tar.gz] I: copying [./librostlab-blast_1.0.1-14.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Apr 24 11:20:29 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./librostlab-blast_1.0.1-14.dsc: no acceptable signature found dpkg-source: info: extracting librostlab-blast in librostlab-blast-1.0.1 dpkg-source: info: unpacking librostlab-blast_1.0.1.orig.tar.gz dpkg-source: info: unpacking librostlab-blast_1.0.1-14.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying reproducible.patch dpkg-source: info: applying modernize_c++.patch dpkg-source: info: applying gcc-12.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2818887/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 30 02:44 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2818887/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2818887/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=3dc8903f52b64e50a645f7d5146b7bcc LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2818887 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.jJekeUBB/pbuilderrc_6JUs --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.jJekeUBB/b2 --logfile b2/build.log librostlab-blast_1.0.1-14.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 27 17:46 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2818887/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), d-shlibs, bison, doxygen, flex, graphviz, texlive-latex-recommended, librostlab-dev, texlive-fonts-recommended, texlive-latex-extra dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19722 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on bison; however: Package bison is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on flex; however: Package flex is not installed. pbuilder-satisfydepends-dummy depends on graphviz; however: Package graphviz is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-recommended; however: Package texlive-latex-recommended is not installed. pbuilder-satisfydepends-dummy depends on librostlab-dev; however: Package librostlab-dev is not installed. pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however: Package texlive-fonts-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however: Package texlive-latex-extra 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} bison{a} bsdextrautils{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} doxygen{a} dwz{a} file{a} flex{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lmodern{a} gettext{a} gettext-base{a} graphviz{a} groff-base{a} intltool-debian{a} libabsl20230802{a} libann0{a} libaom3{a} libapache-pom-java{a} libarchive-zip-perl{a} libavif16{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcdt5{a} libcgraph6{a} libclang-cpp16{a} libclang1-16{a} libcom-err2{a} libcommons-logging-java{a} libcommons-parent-java{a} libdatrie1{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfmt9{a} libfontbox-java{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd3{a} libglib2.0-0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgts-0.7-5{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libice6{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblab-gamut1{a} liblerc4{a} libllvm16{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libnsl2{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpathplan4{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} librav1e0{a} libreadline8t64{a} librostlab3-dev{a} librostlab3t64{a} libsharpyuv0{a} libsm6{a} libsub-override-perl{a} libsvtav1enc1d1{a} libsynctex2{a} libteckit0{a} libtexlua53-5{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{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} libyuv0{a} libz3-4{a} libzzip-0-13t64{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{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-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} tzdata{a} ucf{a} x11-common{a} xdg-utils{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl default-jre dvisvgm fonts-liberation2 krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libfl-dev libglib2.0-data libgts-bin libheif-plugin-aomenc libheif-plugin-x265 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, 159 newly installed, 0 to remove and 0 not upgraded. Need to get 197 MB of archives. After unpacking 760 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 flex amd64 2.6.4-8.2+b2 [426 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.8-1 [817 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.8-1 [2037 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.6-1 [26.2 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-3 [255 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.20.1-5+b1 [33.2 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.0-2.4 [20.2 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.20.1-5+b1 [80.0 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 14 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.20.1-5+b1 [333 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.20.1-5+b1 [135 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.8-1 [1825 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.8-1 [597 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.6-1 [9224 B] Get: 24 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.6-1 [26.2 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-2+b1 [314 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libmagic1 amd64 1:5.45-2+b1 [105 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-2+b1 [43.1 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-3+b1 [1180 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.39.3-6 [89.4 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.0-3 [1401 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 bison amd64 2:3.8.2+dfsg-1+b1 [1175 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 d-shlibs all 0.106 [10.9 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 49 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b2 [692 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20230828-1 [93.1 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libllvm16 amd64 1:16.0.6-20 [23.1 MB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libclang-cpp16 amd64 1:16.0.6-20 [11.5 MB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libclang1-16 amd64 1:16.0.6-20 [6588 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libfmt9 amd64 9.1.0+ds1-2 [113 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 doxygen amd64 1.9.8+ds-2 [4910 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libann0 amd64 1.1.2+doc-9+b1 [25.1 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libcdt5 amd64 2.42.2-8 [39.4 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libcgraph6 amd64 2.42.2-8 [63.2 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libaom3 amd64 3.8.2-2 [1869 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libdav1d7 amd64 1.4.1-1 [547 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libabsl20230802 amd64 20230802.1-4 [464 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libgav1-1 amd64 0.19.0-2 [350 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 librav1e0 amd64 0.7.1-2 [900 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.3.2-0.4+b1 [108 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libsvtav1enc1d1 amd64 1.7.0+dfsg-2+b1 [2169 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libyuv0 amd64 0.0~git202401110.af6ac82-1 [169 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libavif16 amd64 1.0.4-1 [105 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-dav1d amd64 1.17.6-1 [9592 B] Get: 88 http://deb.debian.org/debian trixie/main amd64 libde265-0 amd64 1.0.15-1 [187 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-libde265 amd64 1.17.6-1 [12.9 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libheif1 amd64 1.17.6-1 [284 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.3.2-0.4+b1 [308 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1 [802 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libxpm4 amd64 1:3.5.17-1+b1 [56.1 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libgd3 amd64 2.3.3-9+b3 [125 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0 amd64 2.78.4-1 [1452 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libgts-0.7-5 amd64 0.7.6+darcs121130-5+b1 [160 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.0-1+b1 [531 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libltdl7 amd64 2.4.7-7 [393 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 8.3.0-2 [2213 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.52.0+ds-1 [216 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.52.0+ds-1 [48.0 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.52.0+ds-1 [35.0 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libpathplan4 amd64 2.42.2-8 [41.8 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libgvc6 amd64 2.42.2-8 [683 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libgvpr2 amd64 2.42.2-8 [189 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 liblab-gamut1 amd64 2.42.2-8 [198 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libxmu6 amd64 2:1.1.3-3+b2 [58.7 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libxaw7 amd64 2:1.0.14-1+b2 [199 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 graphviz amd64 2.42.2-8 [614 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libapache-pom-java all 29-2 [5276 B] Get: 133 http://deb.debian.org/debian trixie/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libkpathsea6 amd64 2023.20230311.66589-9+b2 [154 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libpaper1 amd64 1.1.29 [12.5 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 1.1.29 [8868 B] Get: 139 http://deb.debian.org/debian trixie/main amd64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libpotrace0 amd64 1.16-2+b1 [25.2 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libptexenc1 amd64 2023.20230311.66589-9+b2 [47.2 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 librostlab3t64 amd64 1.0.20-13.1 [5036 B] Get: 143 http://deb.debian.org/debian trixie/main amd64 librostlab3-dev amd64 1.0.20-13.1 [12.5 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libsynctex2 amd64 2023.20230311.66589-9+b2 [62.2 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libteckit0 amd64 2.5.12+ds1-1 [339 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libtexlua53-5 amd64 2023.20230311.66589-9+b2 [113 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.2+b1 [56.2 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 tex-common all 6.18 [32.5 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 preview-latex-style all 13.2-1 [350 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 texlive-binaries amd64 2023.20230311.66589-9+b2 [8495 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 texlive-base all 2023.20240207-1 [22.0 MB] Get: 155 http://deb.debian.org/debian trixie/main amd64 texlive-fonts-recommended all 2023.20240207-1 [4990 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 texlive-latex-base all 2023.20240207-1 [1255 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 texlive-latex-recommended all 2023.20240207-1 [8843 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 texlive-pictures all 2023.20240207-1 [16.7 MB] Get: 159 http://deb.debian.org/debian trixie/main amd64 texlive-latex-extra all 2023.20240207-1 [19.7 MB] Fetched 197 MB in 5s (36.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package m4. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19722 files and directories currently installed.) Preparing to unpack .../archives/m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package flex. Preparing to unpack .../flex_2.6.4-8.2+b2_amd64.deb ... Unpacking flex (2.6.4-8.2+b2) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.8-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.8-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.8-1_amd64.deb ... Unpacking python3.11-minimal (3.11.8-1) ... Setting up libpython3.11-minimal:amd64 (3.11.8-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.8-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 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Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. 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Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../003-libmagic1_1%3a5.45-2+b1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.45-2+b1_amd64.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../006-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../007-groff-base_1.23.0-3+b1_amd64.deb ... Unpacking groff-base (1.23.0-3+b1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../008-bsdextrautils_2.39.3-6_amd64.deb ... Unpacking bsdextrautils (2.39.3-6) ... 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Setting up texlive-binaries (2023.20230311.66589-9+b2) ... 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 (2023.20240207-1) ... 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 libpython3-stdlib:amd64 (3.11.6-1) ... Setting up python3.11 (3.11.8-1) ... Setting up python3 (3.11.6-1) ... Setting up texlive-latex-base (2023.20240207-1) ... Setting up texlive-latex-recommended (2023.20240207-1) ... Setting up texlive-pictures (2023.20240207-1) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2818887/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2818887/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/librostlab-blast-1.0.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../librostlab-blast_1.0.1-14_source.changes dpkg-buildpackage: info: source package librostlab-blast dpkg-buildpackage: info: source version 1.0.1-14 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/librostlab-blast-1.0.1' dh_auto_clean rm -f lib/librostlab-blast.tag make[1]: Leaving directory '/build/reproducible-path/librostlab-blast-1.0.1' dh_clean debian/rules binary dh binary dh_update_autotools_config cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:9: warning: The macro `AC_PROG_LIBTOOL' is obsolete. configure.ac:9: You should run autoupdate. m4/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.ac:9: the top level configure.ac:11: warning: AC_PROG_LEX without either yywrap or noyywrap is obsolete ./lib/autoconf/programs.m4:716: _AC_PROG_LEX is expanded from... ./lib/autoconf/programs.m4:709: AC_PROG_LEX is expanded from... configure.ac:11: the top level configure.ac:7: installing './compile' configure.ac:5: installing './missing' lib/Makefile.am: installing './depcomp' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/librostlab-blast-1.0.1' dh_auto_configure -- --enable-doxygen-dot --enable-doxygen-pdf=No ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-doxygen-dot --enable-doxygen-pdf=No checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for bison... bison -y checking for flex... flex checking for lex output file root... lex.yy checking for lex library... none needed checking for library containing yywrap... no checking whether yytext is a pointer... yes checking for rostlab/aux_functions.h... yes checking for rostlab/rostlab_stdexcept.h... yes checking for doxygen... /usr/bin/doxygen checking for perl... /usr/bin/perl checking for dot... /usr/bin/dot checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating lib/Makefile config.status: creating lib/Doxyfile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands make[1]: Leaving directory '/build/reproducible-path/librostlab-blast-1.0.1' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/librostlab-blast-1.0.1' dh_auto_build make -j42 make[2]: Entering directory '/build/reproducible-path/librostlab-blast-1.0.1' make all-recursive make[3]: Entering directory '/build/reproducible-path/librostlab-blast-1.0.1' Making all in lib make[4]: Entering directory '/build/reproducible-path/librostlab-blast-1.0.1/lib' mkdir -p rostlab /bin/sh ../ylwrap blast-parser-scanner.lpp lex.yy.c blast-parser-scanner.cpp -- flex /bin/sh ../ylwrap blast-parser-parser.ypp y.tab.c blast-parser-parser.cpp y.tab.h rostlab/blast-parser-parser.h y.output blast-parser-parser.output stack.hh rostlab/blast-parser-stack.h location.hh rostlab/blast-parser-location.h position.hh rostlab/blast-parser-position.h -- bison -y /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:1.1-9: warning: POSIX Yacc does not support %skeleton [-Wyacc] 1 | %skeleton "lalr1.cc" | ^~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:1.11-20: warning: POSIX Yacc does not support string literals [-Wyacc] 1 | %skeleton "lalr1.cc" | ^~~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:20.1-8: warning: POSIX Yacc does not support %require [-Wyacc] 20 | %require "2.4.1" | ^~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:20.10-16: warning: POSIX Yacc does not support string literals [-Wyacc] 20 | %require "2.4.1" | ^~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:21.1-8: warning: POSIX Yacc does not support %defines [-Wyacc] 21 | %defines | ^~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:22.1-7: warning: POSIX Yacc does not support %define [-Wyacc] 22 | %define namespace "rostlab::blast" | ^~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:22.19-34: warning: POSIX Yacc does not support string literals [-Wyacc] 22 | %define namespace "rostlab::blast" | ^~~~~~~~~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:22.1-34: warning: deprecated directive: '%define namespace "rostlab::blast"', use '%define api.namespace {rostlab::blast}' [-Wdeprecated] 22 | %define namespace "rostlab::blast" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | %define api.namespace {rostlab::blast} /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:24.1-5: warning: POSIX Yacc does not support %code [-Wyacc] 24 | %code requires { | ^~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:37.1-14: warning: POSIX Yacc does not support %error-verbose [-Wyacc] 37 | %error-verbose | ^~~~~~~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:37.1-14: warning: deprecated directive: '%error-verbose', use '%define parse.error verbose' [-Wdeprecated] 37 | %error-verbose | ^~~~~~~~~~~~~~ | %define parse.error verbose /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:39.1-15: warning: POSIX Yacc does not support %initial-action [-Wyacc] 39 | %initial-action | ^~~~~~~~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:53.1-5: warning: POSIX Yacc does not support %code [-Wyacc] 53 | %code { | ^~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:59.29-41: warning: POSIX Yacc does not support string literals [-Wyacc] 59 | %token END 0 "end of file" | ^~~~~~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:72.29-36: warning: POSIX Yacc does not support string literals [-Wyacc] 72 | %token QUERYEQ "Query=" | ^~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:73.29-39: warning: POSIX Yacc does not support string literals [-Wyacc] 73 | %token DATABASECOLON "Database:" | ^~~~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:74.29-48: warning: POSIX Yacc does not support string literals [-Wyacc] 74 | %token RESFROMROUND "Results from round" | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:75.29-37: warning: POSIX Yacc does not support string literals [-Wyacc] 75 | %token SCOREEQ "Score =" | ^~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:76.29-38: warning: POSIX Yacc does not support string literals [-Wyacc] 76 | %token EXPECTEQ "Expect =" | ^~~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:77.29-37: warning: POSIX Yacc does not support string literals [-Wyacc] 77 | %token METHODCOLON "Method:" | ^~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:78.29-42: warning: POSIX Yacc does not support string literals [-Wyacc] 78 | %token IDENTITIESEQ "Identities =" | ^~~~~~~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:79.29-41: warning: POSIX Yacc does not support string literals [-Wyacc] 79 | %token POSITIVESEQ "Positives =" | ^~~~~~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:80.29-36: warning: POSIX Yacc does not support string literals [-Wyacc] 80 | %token GAPSEQ "Gaps =" | ^~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:81.29-38: warning: POSIX Yacc does not support string literals [-Wyacc] 81 | %token STRANDEQ "Strand =" | ^~~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:82.29-37: warning: POSIX Yacc does not support string literals [-Wyacc] 82 | %token FRAMEEQ "Frame =" | ^~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:83.29-36: warning: POSIX Yacc does not support string literals [-Wyacc] 83 | %token QUERYCOLON "Query:" | ^~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:84.29-36: warning: POSIX Yacc does not support string literals [-Wyacc] 84 | %token SBJCTCOLON "Sbjct:" | ^~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:88.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc] 88 | %destructor { delete $$; } | ^~~~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:90.1-8: warning: POSIX Yacc does not support %printer [-Wyacc] 90 | %printer { debug_stream () << *$$; } | ^~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:91.1-8: warning: POSIX Yacc does not support %printer [-Wyacc] 91 | %printer { debug_stream () << $$; } | ^~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:109.9-16: warning: POSIX Yacc does not support string literals [-Wyacc] 109 | query: "Query=" STRING INT | ^~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:122.11-21: warning: POSIX Yacc does not support string literals [-Wyacc] 122 | database: "Database:" STRING INT INT | ^~~~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:137.15-34: warning: POSIX Yacc does not support string literals [-Wyacc] 137 | | "Results from round" INT | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:201.19-27: warning: POSIX Yacc does not support string literals [-Wyacc] 201 | hsp_headerfield: "Score =" num INT | ^~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:203.19-28: warning: POSIX Yacc does not support string literals [-Wyacc] 203 | | "Expect =" num | ^~~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:205.19-27: warning: POSIX Yacc does not support string literals [-Wyacc] 205 | | "Method:" STRING | ^~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:207.19-32: warning: POSIX Yacc does not support string literals [-Wyacc] 207 | | "Identities =" INT | ^~~~~~~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:209.19-31: warning: POSIX Yacc does not support string literals [-Wyacc] 209 | | "Positives =" INT | ^~~~~~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:211.19-26: warning: POSIX Yacc does not support string literals [-Wyacc] 211 | | "Gaps =" INT | ^~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:213.19-28: warning: POSIX Yacc does not support string literals [-Wyacc] 213 | | "Strand =" STRING '/' STRING | ^~~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:215.19-27: warning: POSIX Yacc does not support string literals [-Wyacc] 215 | | "Frame =" INT '/' INT | ^~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:217.19-27: warning: POSIX Yacc does not support string literals [-Wyacc] 217 | | "Frame =" INT | ^~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:224.15-22: warning: POSIX Yacc does not support string literals [-Wyacc] 224 | alitriple: "Query:" INT STRING INT STRING "Sbjct:" INT STRING INT | ^~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:224.46-53: warning: POSIX Yacc does not support string literals [-Wyacc] 224 | alitriple: "Query:" INT STRING INT STRING "Sbjct:" INT STRING INT | ^~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:247.15-22: warning: POSIX Yacc does not support string literals [-Wyacc] 247 | | "Query:" '0' /* bug as far as I can tell */ | ^~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:22.1-34: warning: %define variable 'api.namespace' requires '{...}' values [-Wdeprecated] 22 | %define namespace "rostlab::blast" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp: warning: fix-its can be applied. Rerun with option '--update'. [-Wother] updating rostlab/blast-parser-location.h updating rostlab/blast-parser-position.h updating rostlab/blast-parser-stack.h updating rostlab/blast-parser-parser.h sed -i -e 's,\by.tab.h\b,rostlab/blast-parser-parser.h,g' blast-parser-parser.cpp sed -i -e 's,\bstack.hh\b,rostlab/blast-parser-stack.h,g;s,\blocation.hh\b,rostlab/blast-parser-location.h,g;' rostlab/blast-parser-parser.h sed -i -e 's,\bposition.hh\b,rostlab/blast-parser-position.h,g;' rostlab/blast-parser-location.h make all-am make[5]: Entering directory '/build/reproducible-path/librostlab-blast-1.0.1/lib' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/librostlab-blast-1.0.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o librostlab_blast_la-blast-parser-driver.lo `test -f 'blast-parser-driver.cpp' || echo './'`blast-parser-driver.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/librostlab-blast-1.0.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o librostlab_blast_la-blast-parser-parser.lo `test -f 'blast-parser-parser.cpp' || echo './'`blast-parser-parser.cpp \ \ /bin/sh ../ylwrap `test -f 'blast-parser-scanner.lpp' || echo './'`blast-parser-scanner.lpp lex.yy.c librostlab_blast_la-blast-parser-scanner.cpp -- flex -Cfe libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/librostlab-blast-1.0.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c blast-parser-driver.cpp -fPIC -DPIC -o .libs/librostlab_blast_la-blast-parser-driver.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/librostlab-blast-1.0.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c blast-parser-parser.cpp -fPIC -DPIC -o .libs/librostlab_blast_la-blast-parser-parser.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/librostlab-blast-1.0.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o librostlab_blast_la-librostlab_blast_la-blast-parser-scanner.lo `test -f 'librostlab_blast_la-blast-parser-scanner.cpp' || echo './'`librostlab_blast_la-blast-parser-scanner.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/librostlab-blast-1.0.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c librostlab_blast_la-blast-parser-scanner.cpp -fPIC -DPIC -o .libs/librostlab_blast_la-librostlab_blast_la-blast-parser-scanner.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/librostlab-blast-1.0.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c blast-parser-driver.cpp -o librostlab_blast_la-blast-parser-driver.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/librostlab-blast-1.0.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c blast-parser-parser.cpp -o librostlab_blast_la-blast-parser-parser.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/librostlab-blast-1.0.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c librostlab_blast_la-blast-parser-scanner.cpp -o librostlab_blast_la-librostlab_blast_la-blast-parser-scanner.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/librostlab-blast-1.0.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -version-info 0:0:0 -Wall -Wl,-z,relro -Wl,-z,now -o librostlab-blast.la -rpath /usr/lib/x86_64-linux-gnu librostlab_blast_la-blast-parser-driver.lo librostlab_blast_la-blast-parser-parser.lo librostlab_blast_la-librostlab_blast_la-blast-parser-scanner.lo libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o .libs/librostlab_blast_la-blast-parser-driver.o .libs/librostlab_blast_la-blast-parser-parser.o .libs/librostlab_blast_la-librostlab_blast_la-blast-parser-scanner.o -L/usr/lib/gcc/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/13/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,librostlab-blast.so.0 -o .libs/librostlab-blast.so.0.0.0 libtool: link: (cd ".libs" && rm -f "librostlab-blast.so.0" && ln -s "librostlab-blast.so.0.0.0" "librostlab-blast.so.0") libtool: link: (cd ".libs" && rm -f "librostlab-blast.so" && ln -s "librostlab-blast.so.0.0.0" "librostlab-blast.so") libtool: link: ar cr .libs/librostlab-blast.a librostlab_blast_la-blast-parser-driver.o librostlab_blast_la-blast-parser-parser.o librostlab_blast_la-librostlab_blast_la-blast-parser-scanner.o libtool: link: ranlib .libs/librostlab-blast.a libtool: link: ( cd ".libs" && rm -f "librostlab-blast.la" && ln -s "../librostlab-blast.la" "librostlab-blast.la" ) make[5]: Leaving directory '/build/reproducible-path/librostlab-blast-1.0.1/lib' make[4]: Leaving directory '/build/reproducible-path/librostlab-blast-1.0.1/lib' make[4]: Entering directory '/build/reproducible-path/librostlab-blast-1.0.1' make[4]: Leaving directory '/build/reproducible-path/librostlab-blast-1.0.1' make[3]: Leaving directory '/build/reproducible-path/librostlab-blast-1.0.1' make[2]: Leaving directory '/build/reproducible-path/librostlab-blast-1.0.1' /usr/bin/make -C lib doxygen-doc make[2]: Entering directory '/build/reproducible-path/librostlab-blast-1.0.1/lib' rm -rf ../doxygen-doc SRCDIR='.' PROJECT='librostlab-blast' DOCDIR='../doxygen-doc' VERSION='1.0.1' PERL_PATH='/usr/bin/perl' HAVE_DOT='YES' DOT_PATH='/usr/bin' GENERATE_MAN='NO' GENERATE_RTF='NO' GENERATE_XML='NO' GENERATE_HTMLHELP='NO' GENERATE_CHI='NO' GENERATE_HTML='YES' GENERATE_LATEX='NO' /usr/bin/doxygen ./Doxyfile warning: Tag 'SYMBOL_CACHE_SIZE' at line 290 of file './Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'SHOW_DIRECTORIES' at line 490 of file './Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'COLS_IN_ALPHA_INDEX' at line 761 of file './Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'HTML_TIMESTAMP' at line 841 of file './Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'HTML_ALIGN_MEMBERS' at line 847 of file './Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'USE_INLINE_TREES' at line 1032 of file './Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'FORMULA_TRANSPARENT' at line 1059 of file './Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'LATEX_SOURCE_CODE' at line 1165 of file './Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'XML_SCHEMA' at line 1257 of file './Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'XML_DTD' at line 1263 of file './Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'PERL_PATH' at line 1428 of file './Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'CLASS_DIAGRAMS' at line 1441 of file './Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'MSCGEN_PATH' at line 1450 of file './Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'DOT_FONTNAME' at line 1482 of file './Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'DOT_FONTSIZE' at line 1487 of file './Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'DOT_TRANSPARENT' at line 1611 of file './Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: argument 'a4wide' for option PAPER_TYPE is not a valid enum value Using the default: a4! warning: doxygen no longer ships with the FreeSans font. You may want to clear or change DOT_FONTNAME. Otherwise you run the risk that the wrong font is being used for dot generated graphs. error: Tag file '/usr/share/doc/librostlab-doc/librostlab.tag' does not exist or is not a file. Skipping it... /build/reproducible-path/librostlab-blast-1.0.1/lib/rostlab/blast-parser-location.h:34: warning: the name 'location.hh' supplied as the argument in the \file statement is not an input file /build/reproducible-path/librostlab-blast-1.0.1/lib/rostlab/blast-parser-parser.h:35: warning: the name 'y.tab.h' supplied as the argument in the \file statement is not an input file Doxygen version used: 1.9.8 Notice: Output directory '../doxygen-doc' does not exist. I have created it for you. Searching for include files... Searching for example files... Searching for files in directory /build/reproducible-path/librostlab-blast-1.0.1/examples Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching INPUT for files to process... Searching for files in directory /build/reproducible-path/librostlab-blast-1.0.1/lib/rostlab Reading and parsing tag files Parsing files Preprocessing /build/reproducible-path/librostlab-blast-1.0.1/lib/rostlab/blast-parser-driver.h... Parsing file /build/reproducible-path/librostlab-blast-1.0.1/lib/rostlab/blast-parser-driver.h... Preprocessing /build/reproducible-path/librostlab-blast-1.0.1/lib/rostlab/blast-parser-location.h... Parsing file /build/reproducible-path/librostlab-blast-1.0.1/lib/rostlab/blast-parser-location.h... Preprocessing /build/reproducible-path/librostlab-blast-1.0.1/lib/rostlab/blast-parser-parser.h... Parsing file /build/reproducible-path/librostlab-blast-1.0.1/lib/rostlab/blast-parser-parser.h... Preprocessing /build/reproducible-path/librostlab-blast-1.0.1/lib/rostlab/blast-parser-position.h... Parsing file /build/reproducible-path/librostlab-blast-1.0.1/lib/rostlab/blast-parser-position.h... Preprocessing /build/reproducible-path/librostlab-blast-1.0.1/lib/rostlab/blast-parser-stack.h... Parsing file /build/reproducible-path/librostlab-blast-1.0.1/lib/rostlab/blast-parser-stack.h... Preprocessing /build/reproducible-path/librostlab-blast-1.0.1/lib/rostlab/blast-result.h... Parsing file /build/reproducible-path/librostlab-blast-1.0.1/lib/rostlab/blast-result.h... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Building concept list... Computing nesting relations for classes... Associating documentation with classes... Associating documentation with concepts... Associating documentation with modules... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Computing module relations... Sorting lists... Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Setting anonymous enum type... Computing dependencies between directories... Generating citations page... Counting members... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Correcting members for VHDL... Computing tooltip texts... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file rostlab/blast-parser-driver.h... Generating code for file rostlab/blast-parser-location.h... Generating code for file rostlab/blast-parser-parser.h... Generating code for file rostlab/blast-parser-position.h... Generating code for file rostlab/blast-parser-stack.h... Generating code for file rostlab/blast-result.h... Generating file documentation... Generating docs for file rostlab/blast-parser-driver.h... Generating docs for file rostlab/blast-parser-location.h... Generating docs for file rostlab/blast-parser-parser.h... Generating docs for file rostlab/blast-parser-position.h... Generating docs for file rostlab/blast-parser-stack.h... Generating docs for file rostlab/blast-result.h... Generating page documentation... Generating group documentation... Generating class documentation... Generating concept documentation... Generating module documentation... Generating namespace documentation... Generating docs for namespace rostlab Generating docs for namespace rostlab::blast Generating docs for compound rostlab::blast::hit... Generating docs for compound rostlab::blast::hsp... Generating docs for compound rostlab::blast::location... Generating docs for compound rostlab::blast::oneline... Generating docs for compound rostlab::blast::parser... Generating docs for nested compound rostlab::blast::parser::basic_symbol... Generating docs for nested compound rostlab::blast::parser::by_kind... Generating docs for nested compound rostlab::blast::parser::context... Generating docs for nested compound rostlab::blast::parser::stack::slice... Generating docs for nested compound rostlab::blast::parser::symbol_kind... Generating docs for nested compound rostlab::blast::parser::symbol_type... Generating docs for nested compound rostlab::blast::parser::syntax_error... Generating docs for nested compound rostlab::blast::parser::token... Generating docs for nested compound rostlab::blast::parser::value_type... Generating docs for compound rostlab::blast::parser_driver... Generating docs for compound rostlab::blast::parser_error... Generating docs for compound rostlab::blast::position... Generating docs for compound rostlab::blast::result... Generating docs for compound rostlab::blast::round... Generating graph info page... Generating directory documentation... Generating index page... Generating page index... Generating topic index... Generating module index... Generating module member index... Generating namespace index... Generating namespace member index... Generating concept index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating graphical class hierarchy... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Running plantuml with JAVA... Running dot... Generating dot graphs using 43 parallel threads... Running dot for graph 1/56 Running dot for graph 2/56 Running dot for graph 3/56 Running dot for graph 4/56 Running dot for graph 5/56 Running dot for graph 6/56 Running dot for graph 7/56 Running dot for graph 8/56 Running dot for graph 9/56 Running dot for graph 10/56 Running dot for graph 11/56 Running dot for graph 12/56 Running dot for graph 13/56 Running dot for graph 14/56 Running dot for graph 15/56 Running dot for graph 16/56 Running dot for graph 17/56 Running dot for graph 18/56 Running dot for graph 19/56 Running dot for graph 20/56 Running dot for graph 21/56 Running dot for graph 22/56 Running dot for graph 23/56 Running dot for graph 24/56 Running dot for graph 25/56 Running dot for graph 26/56 Running dot for graph 27/56 Running dot for graph 28/56 Running dot for graph 29/56 Running dot for graph 30/56 Running dot for graph 31/56 Running dot for graph 32/56 Running dot for graph 33/56 Running dot for graph 34/56 Running dot for graph 35/56 Running dot for graph 36/56 Running dot for graph 37/56 Running dot for graph 38/56 Running dot for graph 39/56 Running dot for graph 40/56 Running dot for graph 41/56 Running dot for graph 42/56 Running dot for graph 43/56 Running dot for graph 44/56 Running dot for graph 45/56 Running dot for graph 46/56 Running dot for graph 47/56 Running dot for graph 48/56 Running dot for graph 49/56 Running dot for graph 50/56 Running dot for graph 51/56 Running dot for graph 52/56 Running dot for graph 53/56 Running dot for graph 54/56 Running dot for graph 55/56 Running dot for graph 56/56 Patching output file 1/23 Patching output file 2/23 Patching output file 3/23 Patching output file 4/23 Patching output file 5/23 Patching output file 6/23 Patching output file 7/23 Patching output file 8/23 Patching output file 9/23 Patching output file 10/23 Patching output file 11/23 Patching output file 12/23 Patching output file 13/23 Patching output file 14/23 Patching output file 15/23 Patching output file 16/23 Patching output file 17/23 Patching output file 18/23 Patching output file 19/23 Patching output file 20/23 Patching output file 21/23 Patching output file 22/23 Patching output file 23/23 type lookup cache used 573/65536 hits=1135 misses=666 symbol lookup cache used 476/65536 hits=2431 misses=476 finished... make[2]: Leaving directory '/build/reproducible-path/librostlab-blast-1.0.1/lib' make[1]: Leaving directory '/build/reproducible-path/librostlab-blast-1.0.1' dh_auto_test make -j42 check "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/librostlab-blast-1.0.1' Making check in lib make[2]: Entering directory '/build/reproducible-path/librostlab-blast-1.0.1/lib' make check-am make[3]: Entering directory '/build/reproducible-path/librostlab-blast-1.0.1/lib' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/reproducible-path/librostlab-blast-1.0.1/lib' make[2]: Leaving directory '/build/reproducible-path/librostlab-blast-1.0.1/lib' make[2]: Entering directory '/build/reproducible-path/librostlab-blast-1.0.1' make[2]: Leaving directory '/build/reproducible-path/librostlab-blast-1.0.1' make[1]: Leaving directory '/build/reproducible-path/librostlab-blast-1.0.1' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j1 install DESTDIR=/build/reproducible-path/librostlab-blast-1.0.1/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/librostlab-blast-1.0.1' Making install in lib make[2]: Entering directory '/build/reproducible-path/librostlab-blast-1.0.1/lib' make install-am make[3]: Entering directory '/build/reproducible-path/librostlab-blast-1.0.1/lib' make[4]: Entering directory '/build/reproducible-path/librostlab-blast-1.0.1/lib' /usr/bin/mkdir -p '/build/reproducible-path/librostlab-blast-1.0.1/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/sh ../libtool --mode=install /usr/bin/install -c librostlab-blast.la '/build/reproducible-path/librostlab-blast-1.0.1/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/librostlab-blast.so.0.0.0 /build/reproducible-path/librostlab-blast-1.0.1/debian/tmp/usr/lib/x86_64-linux-gnu/librostlab-blast.so.0.0.0 libtool: install: (cd /build/reproducible-path/librostlab-blast-1.0.1/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f librostlab-blast.so.0.0.0 librostlab-blast.so.0 || { rm -f librostlab-blast.so.0 && ln -s librostlab-blast.so.0.0.0 librostlab-blast.so.0; }; }) libtool: install: (cd /build/reproducible-path/librostlab-blast-1.0.1/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f librostlab-blast.so.0.0.0 librostlab-blast.so || { rm -f librostlab-blast.so && ln -s librostlab-blast.so.0.0.0 librostlab-blast.so; }; }) libtool: install: /usr/bin/install -c .libs/librostlab-blast.lai /build/reproducible-path/librostlab-blast-1.0.1/debian/tmp/usr/lib/x86_64-linux-gnu/librostlab-blast.la libtool: install: /usr/bin/install -c .libs/librostlab-blast.a /build/reproducible-path/librostlab-blast-1.0.1/debian/tmp/usr/lib/x86_64-linux-gnu/librostlab-blast.a libtool: install: chmod 644 /build/reproducible-path/librostlab-blast-1.0.1/debian/tmp/usr/lib/x86_64-linux-gnu/librostlab-blast.a libtool: install: ranlib /build/reproducible-path/librostlab-blast-1.0.1/debian/tmp/usr/lib/x86_64-linux-gnu/librostlab-blast.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /usr/bin/mkdir -p '/build/reproducible-path/librostlab-blast-1.0.1/debian/tmp/usr/include/rostlab' /usr/bin/install -c -m 644 rostlab/blast-parser-driver.h rostlab/blast-result.h '/build/reproducible-path/librostlab-blast-1.0.1/debian/tmp/usr/include/rostlab' /usr/bin/mkdir -p '/build/reproducible-path/librostlab-blast-1.0.1/debian/tmp/usr/include/rostlab' /usr/bin/install -c -m 644 rostlab/blast-parser-location.h rostlab/blast-parser-parser.h rostlab/blast-parser-position.h rostlab/blast-parser-stack.h '/build/reproducible-path/librostlab-blast-1.0.1/debian/tmp/usr/include/rostlab' make[4]: Leaving directory '/build/reproducible-path/librostlab-blast-1.0.1/lib' make[3]: Leaving directory '/build/reproducible-path/librostlab-blast-1.0.1/lib' make[2]: Leaving directory '/build/reproducible-path/librostlab-blast-1.0.1/lib' make[2]: Entering directory '/build/reproducible-path/librostlab-blast-1.0.1' make[3]: Entering directory '/build/reproducible-path/librostlab-blast-1.0.1' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/librostlab-blast-1.0.1/debian/tmp/usr/share/doc/librostlab-blast/examples' /usr/bin/install -c -m 644 examples/converged.ali examples/parseblast.cpp '/build/reproducible-path/librostlab-blast-1.0.1/debian/tmp/usr/share/doc/librostlab-blast/examples' make[3]: Leaving directory '/build/reproducible-path/librostlab-blast-1.0.1' make[2]: Leaving directory '/build/reproducible-path/librostlab-blast-1.0.1' make[1]: Leaving directory '/build/reproducible-path/librostlab-blast-1.0.1' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/librostlab-blast-1.0.1' d-shlibmove --commit \ --multiarch \ --exclude-la \ --v5 \ --movedev debian/tmp/usr/include/* usr/include \ debian/tmp/usr/lib/*/*.so Library package automatic movement utility set -e install -d -m 755 debian/librostlab-blast0-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/librostlab-blast0v5/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/librostlab-blast.a debian/librostlab-blast0-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/librostlab-blast.so debian/librostlab-blast0-dev/usr/lib/x86_64-linux-gnu mv /build/reproducible-path/librostlab-blast-1.0.1/debian/tmp/usr/lib/x86_64-linux-gnu/librostlab-blast.so.0 debian/librostlab-blast0v5/usr/lib/x86_64-linux-gnu mv /build/reproducible-path/librostlab-blast-1.0.1/debian/tmp/usr/lib/x86_64-linux-gnu/librostlab-blast.so.0.0.0 debian/librostlab-blast0v5/usr/lib/x86_64-linux-gnu PKGDEV=librostlab-blast0-dev PKGSHL=librostlab-blast0v5 install -d -m 755 debian/librostlab-blast0-dev/usr/include mv debian/tmp/usr/include/rostlab debian/librostlab-blast0-dev/usr/include find debian -name "lib*.la" -delete make[1]: Leaving directory '/build/reproducible-path/librostlab-blast-1.0.1' debian/rules override_dh_installdocs-indep make[1]: Entering directory '/build/reproducible-path/librostlab-blast-1.0.1' dh_installdocs dh_installdocs: warning: Cannot auto-detect main package for librostlab-blast-doc. If the default is wrong, please use --doc-main-package find debian -name "*.md5" -delete sed -i 's@/.*/lib/rostlab/@/fakebuildpath/lib/rostlab/@' \ debian/librostlab-blast-doc/usr/share/doc/librostlab-blast-doc/librostlab-blast.tag make[1]: Leaving directory '/build/reproducible-path/librostlab-blast-1.0.1' dh_installdocs -Nlibrostlab-blast-doc dh_installchangelogs dh_installexamples dh_perl debian/rules override_dh_link make[1]: Entering directory '/build/reproducible-path/librostlab-blast-1.0.1' find debian -name jquery.js -delete dh_link make[1]: Leaving directory '/build/reproducible-path/librostlab-blast-1.0.1' dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/reproducible-path/librostlab-blast-1.0.1' dh_compress -Xlibrostlab-blast.tag make[1]: Leaving directory '/build/reproducible-path/librostlab-blast-1.0.1' dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package librostlab-blast-doc: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'librostlab-blast0v5' in '../librostlab-blast0v5_1.0.1-14_amd64.deb'. dpkg-deb: building package 'librostlab-blast0v5-dbgsym' in '../librostlab-blast0v5-dbgsym_1.0.1-14_amd64.deb'. dpkg-deb: building package 'librostlab-blast0-dev' in '../librostlab-blast0-dev_1.0.1-14_amd64.deb'. dpkg-deb: building package 'librostlab-blast-doc' in '../librostlab-blast-doc_1.0.1-14_all.deb'. dpkg-genbuildinfo --build=binary -O../librostlab-blast_1.0.1-14_amd64.buildinfo dpkg-genchanges --build=binary -O../librostlab-blast_1.0.1-14_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2818887/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2818887/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2818887 and its subdirectories I: Current time: Fri May 30 16:47:16 +14 2025 I: pbuilder-time-stamp: 1748573236