I: pbuilder: network access will be disabled during build I: Current time: Fri Apr 26 19:46:29 +14 2024 I: pbuilder-time-stamp: 1714110389 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/13228/tmp/hooks/D01_modify_environment starting debug: Running on virt64c. 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 Apr 26 05:46 /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/13228/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/13228/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]="arm-unknown-linux-gnueabihf") 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=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=e1a419b277c04a03b25117ee043a4617 LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf 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=13228 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.rhYedMuT/pbuilderrc_Jxek --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.rhYedMuT/b2 --logfile b2/build.log librostlab-blast_1.0.1-14.dsc' SUDO_GID=113 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 6.1.0-20-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 25 11:27 /bin -> usr/bin I: user script /srv/workspace/pbuilder/13228/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: armhf 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 ... 19468 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} 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} libpng16-16{a} libpotrace0{a} libptexenc1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} librav1e0{a} libreadline8{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} libtirpc3{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} libxt6{a} libyuv0{a} libz3-4{a} libzzip-0-13{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, 158 newly installed, 0 to remove and 0 not upgraded. Need to get 183 MB of archives. After unpacking 685 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf flex armhf 2.6.4-8.2+b2 [406 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf libpython3.11-minimal armhf 3.11.8-1 [802 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.6.2-1 [83.5 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf python3.11-minimal armhf 3.11.8-1 [1707 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf python3-minimal armhf 3.11.6-1 [26.2 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf tzdata all 2024a-3 [255 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf libkrb5support0 armhf 1.20.1-5+b1 [30.4 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf libcom-err2 armhf 1.47.0-2.4 [19.5 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf libk5crypto3 armhf 1.20.1-5+b1 [75.4 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf libkeyutils1 armhf 1.6.3-3 [7908 B] Get: 14 http://deb.debian.org/debian trixie/main armhf libkrb5-3 armhf 1.20.1-5+b1 [289 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf libgssapi-krb5-2 armhf 1.20.1-5+b1 [112 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libtirpc3 armhf 1.3.4+ds-1 [70.0 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf libnsl2 armhf 1.3.0-3 [33.7 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf readline-common all 8.2-4 [69.3 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf libreadline8 armhf 8.2-3+b1 [144 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libpython3.11-stdlib armhf 3.11.8-1 [1709 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf python3.11 armhf 3.11.8-1 [597 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf libpython3-stdlib armhf 3.11.6-1 [9224 B] Get: 24 http://deb.debian.org/debian trixie/main armhf python3 armhf 3.11.6-1 [26.2 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-2+b1 [314 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf libmagic1 armhf 1:5.45-2+b1 [97.9 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-2+b1 [42.2 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-3 [1088 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.39.3-6 [81.2 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.0-3 [1367 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf ucf all 3.0043+nmu1 [55.2 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf bison armhf 2:3.8.2+dfsg-1+b1 [1142 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf d-shlibs all 0.106 [10.9 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 49 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.191-1+b1 [183 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b2 [599 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf libbsd0 armhf 0.12.2-1 [127 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf libedit2 armhf 3.1-20230828-1 [76.8 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf libz3-4 armhf 4.8.12-3.1+b2 [6324 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf libllvm16 armhf 1:16.0.6-20 [20.6 MB] Get: 61 http://deb.debian.org/debian trixie/main armhf libclang-cpp16 armhf 1:16.0.6-20 [9875 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf libclang1-16 armhf 1:16.0.6-20 [5545 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf libfmt9 armhf 9.1.0+ds1-2 [105 kB] Get: 64 http://deb.debian.org/debian trixie/main armhf doxygen armhf 1.9.8+ds-2 [4458 kB] Get: 65 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b3 [284 kB] Get: 66 http://deb.debian.org/debian trixie/main armhf libpng16-16 armhf 1.6.43-1 [262 kB] Get: 67 http://deb.debian.org/debian trixie/main armhf libfreetype6 armhf 2.13.2+dfsg-1+b1 [371 kB] Get: 68 http://deb.debian.org/debian trixie/main armhf fonts-dejavu-mono all 2.37-8 [489 kB] Get: 69 http://deb.debian.org/debian trixie/main armhf fonts-dejavu-core all 2.37-8 [840 kB] Get: 70 http://deb.debian.org/debian trixie/main armhf fontconfig-config armhf 2.15.0-1.1 [317 kB] Get: 71 http://deb.debian.org/debian trixie/main armhf libfontconfig1 armhf 2.15.0-1.1 [370 kB] Get: 72 http://deb.debian.org/debian trixie/main armhf fontconfig armhf 2.15.0-1.1 [461 kB] Get: 73 http://deb.debian.org/debian trixie/main armhf fonts-lmodern all 2.005-1 [4540 kB] Get: 74 http://deb.debian.org/debian trixie/main armhf libcdt5 armhf 2.42.2-8 [37.0 kB] Get: 75 http://deb.debian.org/debian trixie/main armhf libcgraph6 armhf 2.42.2-8 [56.0 kB] Get: 76 http://deb.debian.org/debian trixie/main armhf libaom3 armhf 3.8.2-2 [1526 kB] Get: 77 http://deb.debian.org/debian trixie/main armhf libdav1d7 armhf 1.4.1-1 [262 kB] Get: 78 http://deb.debian.org/debian trixie/main armhf libabsl20230802 armhf 20230802.1-4 [432 kB] Get: 79 http://deb.debian.org/debian trixie/main armhf libgav1-1 armhf 0.19.0-2 [298 kB] Get: 80 http://deb.debian.org/debian trixie/main armhf librav1e0 armhf 0.7.1-2 [546 kB] Get: 81 http://deb.debian.org/debian trixie/main armhf libsharpyuv0 armhf 1.3.2-0.4+b1 [106 kB] Get: 82 http://deb.debian.org/debian trixie/main armhf libsvtav1enc1d1 armhf 1.7.0+dfsg-2+b1 [936 kB] Get: 83 http://deb.debian.org/debian trixie/main armhf libjpeg62-turbo armhf 1:2.1.5-2+b2 [143 kB] Get: 84 http://deb.debian.org/debian trixie/main armhf libyuv0 armhf 0.0~git202401110.af6ac82-1 [85.1 kB] Get: 85 http://deb.debian.org/debian trixie/main armhf libavif16 armhf 1.0.4-1 [95.0 kB] Get: 86 http://deb.debian.org/debian trixie/main armhf libheif-plugin-dav1d armhf 1.17.6-1 [9252 B] Get: 87 http://deb.debian.org/debian trixie/main armhf libde265-0 armhf 1.0.15-1 [145 kB] Get: 88 http://deb.debian.org/debian trixie/main armhf libheif-plugin-libde265 armhf 1.17.6-1 [12.0 kB] Get: 89 http://deb.debian.org/debian trixie/main armhf libheif1 armhf 1.17.6-1 [242 kB] Get: 90 http://deb.debian.org/debian trixie/main armhf libdeflate0 armhf 1.20-1 [35.9 kB] Get: 91 http://deb.debian.org/debian trixie/main armhf libjbig0 armhf 2.1-6.1+b1 [27.3 kB] Get: 92 http://deb.debian.org/debian trixie/main armhf liblerc4 armhf 4.0.0+ds-4+b1 [137 kB] Get: 93 http://deb.debian.org/debian trixie/main armhf libwebp7 armhf 1.3.2-0.4+b1 [262 kB] Get: 94 http://deb.debian.org/debian trixie/main armhf libtiff6 armhf 4.5.1+git230720-4 [301 kB] Get: 95 http://deb.debian.org/debian trixie/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB] Get: 96 http://deb.debian.org/debian trixie/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 97 http://deb.debian.org/debian trixie/main armhf libxcb1 armhf 1.15-1 [140 kB] Get: 98 http://deb.debian.org/debian trixie/main armhf libx11-data all 2:1.8.7-1 [328 kB] Get: 99 http://deb.debian.org/debian trixie/main armhf libx11-6 armhf 2:1.8.7-1 [735 kB] Get: 100 http://deb.debian.org/debian trixie/main armhf libxpm4 armhf 1:3.5.17-1+b1 [50.0 kB] Get: 101 http://deb.debian.org/debian trixie/main armhf libgd3 armhf 2.3.3-9+b1 [103 kB] Get: 102 http://deb.debian.org/debian trixie/main armhf libglib2.0-0 armhf 2.78.4-1 [1281 kB] Get: 103 http://deb.debian.org/debian trixie/main armhf libgts-0.7-5 armhf 0.7.6+darcs121130-5+b1 [137 kB] Get: 104 http://deb.debian.org/debian trixie/main armhf libpixman-1-0 armhf 0.42.2-1+b1 [476 kB] Get: 105 http://deb.debian.org/debian trixie/main armhf libxcb-render0 armhf 1.15-1 [114 kB] Get: 106 http://deb.debian.org/debian trixie/main armhf libxcb-shm0 armhf 1.15-1 [106 kB] Get: 107 http://deb.debian.org/debian trixie/main armhf libxext6 armhf 2:1.3.4-1+b1 [47.8 kB] Get: 108 http://deb.debian.org/debian trixie/main armhf libxrender1 armhf 1:0.9.10-1.1 [30.1 kB] Get: 109 http://deb.debian.org/debian trixie/main armhf libcairo2 armhf 1.18.0-1+b1 [441 kB] Get: 110 http://deb.debian.org/debian trixie/main armhf libltdl7 armhf 2.4.7-7 [390 kB] Get: 111 http://deb.debian.org/debian trixie/main armhf libfribidi0 armhf 1.0.13-3+b1 [69.4 kB] Get: 112 http://deb.debian.org/debian trixie/main armhf libgraphite2-3 armhf 1.3.14-2 [63.2 kB] Get: 113 http://deb.debian.org/debian trixie/main armhf libharfbuzz0b armhf 8.3.0-2 [2155 kB] Get: 114 http://deb.debian.org/debian trixie/main armhf libthai-data all 0.1.29-2 [168 kB] Get: 115 http://deb.debian.org/debian trixie/main armhf libdatrie1 armhf 0.2.13-3 [34.4 kB] Get: 116 http://deb.debian.org/debian trixie/main armhf libthai0 armhf 0.1.29-2 [45.8 kB] Get: 117 http://deb.debian.org/debian trixie/main armhf libpango-1.0-0 armhf 1.52.0+ds-1 [192 kB] Get: 118 http://deb.debian.org/debian trixie/main armhf libpangoft2-1.0-0 armhf 1.52.0+ds-1 [41.8 kB] Get: 119 http://deb.debian.org/debian trixie/main armhf libpangocairo-1.0-0 armhf 1.52.0+ds-1 [31.2 kB] Get: 120 http://deb.debian.org/debian trixie/main armhf libpathplan4 armhf 2.42.2-8 [39.3 kB] Get: 121 http://deb.debian.org/debian trixie/main armhf libgvc6 armhf 2.42.2-8 [578 kB] Get: 122 http://deb.debian.org/debian trixie/main armhf libgvpr2 armhf 2.42.2-8 [164 kB] Get: 123 http://deb.debian.org/debian trixie/main armhf liblab-gamut1 armhf 2.42.2-8 [198 kB] Get: 124 http://deb.debian.org/debian trixie/main armhf x11-common all 1:7.7+23 [252 kB] Get: 125 http://deb.debian.org/debian trixie/main armhf libice6 armhf 2:1.0.10-1 [51.9 kB] Get: 126 http://deb.debian.org/debian trixie/main armhf libsm6 armhf 2:1.2.3-1 [33.0 kB] Get: 127 http://deb.debian.org/debian trixie/main armhf libxt6 armhf 1:1.2.1-1.1 [157 kB] Get: 128 http://deb.debian.org/debian trixie/main armhf libxmu6 armhf 2:1.1.3-3 [52.6 kB] Get: 129 http://deb.debian.org/debian trixie/main armhf libxaw7 armhf 2:1.0.14-1 [167 kB] Get: 130 http://deb.debian.org/debian trixie/main armhf graphviz armhf 2.42.2-8 [497 kB] Get: 131 http://deb.debian.org/debian trixie/main armhf libapache-pom-java all 29-2 [5276 B] Get: 132 http://deb.debian.org/debian trixie/main armhf libcommons-parent-java all 56-1 [10.8 kB] Get: 133 http://deb.debian.org/debian trixie/main armhf libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 134 http://deb.debian.org/debian trixie/main armhf libfontbox-java all 1:1.8.16-5 [211 kB] Get: 135 http://deb.debian.org/debian trixie/main armhf libkpathsea6 armhf 2023.20230311.66589-9 [144 kB] Get: 136 http://deb.debian.org/debian trixie/main armhf libpaper1 armhf 1.1.29 [11.9 kB] Get: 137 http://deb.debian.org/debian trixie/main armhf libpaper-utils armhf 1.1.29 [8400 B] Get: 138 http://deb.debian.org/debian trixie/main armhf libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 139 http://deb.debian.org/debian trixie/main armhf libpotrace0 armhf 1.16-2+b1 [22.6 kB] Get: 140 http://deb.debian.org/debian trixie/main armhf libptexenc1 armhf 2023.20230311.66589-9 [42.8 kB] Get: 141 http://deb.debian.org/debian trixie/main armhf librostlab3t64 armhf 1.0.20-13.1 [5080 B] Get: 142 http://deb.debian.org/debian trixie/main armhf librostlab3-dev armhf 1.0.20-13.1 [12.6 kB] Get: 143 http://deb.debian.org/debian trixie/main armhf libsynctex2 armhf 2023.20230311.66589-9 [48.5 kB] Get: 144 http://deb.debian.org/debian trixie/main armhf libteckit0 armhf 2.5.12+ds1-1 [259 kB] Get: 145 http://deb.debian.org/debian trixie/main armhf libtexlua53-5 armhf 2023.20230311.66589-9 [82.2 kB] Get: 146 http://deb.debian.org/debian trixie/main armhf libxi6 armhf 2:1.8.1-1 [73.8 kB] Get: 147 http://deb.debian.org/debian trixie/main armhf libzzip-0-13 armhf 0.13.72+dfsg.1-1.1+b1 [52.3 kB] Get: 148 http://deb.debian.org/debian trixie/main armhf tex-common all 6.18 [32.5 kB] Get: 149 http://deb.debian.org/debian trixie/main armhf preview-latex-style all 13.2-1 [350 kB] Get: 150 http://deb.debian.org/debian trixie/main armhf t1utils armhf 1.41-4 [54.7 kB] Get: 151 http://deb.debian.org/debian trixie/main armhf texlive-binaries armhf 2023.20230311.66589-9 [6071 kB] Get: 152 http://deb.debian.org/debian trixie/main armhf xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 153 http://deb.debian.org/debian trixie/main armhf texlive-base all 2023.20240207-1 [22.0 MB] Get: 154 http://deb.debian.org/debian trixie/main armhf texlive-fonts-recommended all 2023.20240207-1 [4990 kB] Get: 155 http://deb.debian.org/debian trixie/main armhf texlive-latex-base all 2023.20240207-1 [1255 kB] Get: 156 http://deb.debian.org/debian trixie/main armhf texlive-latex-recommended all 2023.20240207-1 [8843 kB] Get: 157 http://deb.debian.org/debian trixie/main armhf texlive-pictures all 2023.20240207-1 [16.7 MB] Get: 158 http://deb.debian.org/debian trixie/main armhf texlive-latex-extra all 2023.20240207-1 [19.7 MB] Fetched 183 MB in 4s (47.4 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 ... 19468 files and directories currently installed.) Preparing to unpack .../archives/m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package flex. Preparing to unpack .../flex_2.6.4-8.2+b2_armhf.deb ... Unpacking flex (2.6.4-8.2+b2) ... Selecting previously unselected package libpython3.11-minimal:armhf. Preparing to unpack .../libpython3.11-minimal_3.11.8-1_armhf.deb ... Unpacking libpython3.11-minimal:armhf (3.11.8-1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.6.2-1_armhf.deb ... Unpacking libexpat1:armhf (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.8-1_armhf.deb ... Unpacking python3.11-minimal (3.11.8-1) ... Setting up libpython3.11-minimal:armhf (3.11.8-1) ... Setting up libexpat1:armhf (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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(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 ... 21020 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.6-1_armhf.deb ... Unpacking python3 (3.11.6-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.45-2+b1_armhf.deb ... 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Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../022-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../023-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../024-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../025-libelf1t64_0.191-1+b1_armhf.deb ... Unpacking libelf1t64:armhf (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../026-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../027-libicu72_72.1-4+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-4+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../028-libxml2_2.9.14+dfsg-1.3+b2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../029-gettext_0.21-14+b1_armhf.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../030-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../031-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../032-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package libbsd0:armhf. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/13228/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/13228/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 armhf 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=arm-linux-gnueabihf --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/arm-linux-gnueabihf --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... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf 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 arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop checking how to convert arm-unknown-linux-gnueabihf 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) 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 checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) 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) 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 -j4 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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -c blast-parser-parser.cpp -fPIC -DPIC -o .libs/librostlab_blast_la-blast-parser-parser.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -c blast-parser-driver.cpp -fPIC -DPIC -o .libs/librostlab_blast_la-blast-parser-driver.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -c librostlab_blast_la-blast-parser-scanner.cpp -fPIC -DPIC -o .libs/librostlab_blast_la-librostlab_blast_la-blast-parser-scanner.o In file included from /usr/include/c++/13/vector:65, from ./rostlab/blast-result.h:24, from blast-parser-parser.ypp:26, from rostlab/blast-parser-driver.h:26, from blast-parser-driver.cpp:19: /usr/include/c++/13/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = rostlab::blast::hsp*]': /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = rostlab::blast::hsp*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = rostlab::blast::hsp*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = rostlab::blast::hsp*; _Tp = rostlab::blast::hsp]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = rostlab::blast::hsp; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1619:35, inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = rostlab::blast::hsp; _Alloc = std::allocator]' at /usr/include/c++/13/bits/vector.tcc:238:44: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = rostlab::blast::hsp*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = rostlab::blast::hsp*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = rostlab::blast::hsp*; _Tp = rostlab::blast::hsp]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = rostlab::blast::hsp; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from 'rostlab::blast::hit::hit(const rostlab::blast::hit&)' at ./rostlab/blast-result.h:140:8, inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = rostlab::blast::hit; _Args = {const rostlab::blast::hit&}]' at /usr/include/c++/13/bits/stl_construct.h:119:7, inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = rostlab::blast::hit*]' at /usr/include/c++/13/bits/stl_uninitialized.h:120:21, inlined from 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = rostlab::blast::hit*; bool _TrivialValueTypes = false]' at /usr/include/c++/13/bits/stl_uninitialized.h:137:32, inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = rostlab::blast::hit*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = rostlab::blast::hit*; _Tp = rostlab::blast::hit]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = rostlab::blast::hit; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1619:35, inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = rostlab::blast::hit; _Alloc = std::allocator]' at /usr/include/c++/13/bits/vector.tcc:238:44, inlined from 'rostlab::blast::result& rostlab::blast::result::operator=(const rostlab::blast::result&)' at ./rostlab/blast-result.h:164:8, inlined from 'const rostlab::blast::parser_driver::result_type& rostlab::blast::parser_driver::parse(bool, bool)' at blast-parser-driver.cpp:29:25: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = rostlab::blast::hsp*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = rostlab::blast::hsp*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = rostlab::blast::hsp*; _Tp = rostlab::blast::hsp]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = rostlab::blast::hsp; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:603:31, inlined from 'rostlab::blast::hit::hit(const rostlab::blast::hit&)' at ./rostlab/blast-result.h:140:8, inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = rostlab::blast::hit; _Args = {rostlab::blast::hit&}]' at /usr/include/c++/13/bits/stl_construct.h:119:7, inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = rostlab::blast::hit*; _ForwardIterator = rostlab::blast::hit*]' at /usr/include/c++/13/bits/stl_uninitialized.h:120:21, inlined from 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = rostlab::blast::hit*; _ForwardIterator = rostlab::blast::hit*; bool _TrivialValueTypes = false]' at /usr/include/c++/13/bits/stl_uninitialized.h:137:32, inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = rostlab::blast::hit*; _ForwardIterator = rostlab::blast::hit*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = rostlab::blast::hit*; _ForwardIterator = rostlab::blast::hit*; _Tp = rostlab::blast::hit]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = rostlab::blast::hit; _Alloc = std::allocator]' at /usr/include/c++/13/bits/vector.tcc:257:35, inlined from 'rostlab::blast::result& rostlab::blast::result::operator=(const rostlab::blast::result&)' at ./rostlab/blast-result.h:164:8, inlined from 'const rostlab::blast::parser_driver::result_type& rostlab::blast::parser_driver::parse(bool, bool)' at blast-parser-driver.cpp:29:25: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from ./rostlab/blast-result.h:24, from blast-parser-parser.ypp:26, from blast-parser-parser.cpp:41: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const rostlab::blast::oneline&}; _Tp = rostlab::blast::oneline; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {rostlab::blast::hsp}; _Tp = rostlab::blast::hsp; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/13/vector:65: /usr/include/c++/13/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = move_iterator; _ForwardIterator = rostlab::blast::parser::stack_symbol_type*]': /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {rostlab::blast::parser::stack_symbol_type}; _Tp = rostlab::blast::parser::stack_symbol_type; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = rostlab::blast::parser::stack_symbol_type*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = move_iterator; _ForwardIterator = rostlab::blast::parser::stack_symbol_type*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = move_iterator; _ForwardIterator = rostlab::blast::parser::stack_symbol_type*; _Tp = rostlab::blast::parser::stack_symbol_type]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = rostlab::blast::parser::stack_symbol_type*; _ForwardIterator = rostlab::blast::parser::stack_symbol_type*; _Allocator = allocator]' at /usr/include/c++/13/bits/stl_uninitialized.h:399:2, inlined from 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {rostlab::blast::parser::stack_symbol_type}; _Tp = rostlab::blast::parser::stack_symbol_type; _Alloc = std::allocator]' at /usr/include/c++/13/bits/vector.tcc:493:3: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = rostlab::blast::parser::stack_symbol_type*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = move_iterator; _ForwardIterator = rostlab::blast::parser::stack_symbol_type*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = move_iterator; _ForwardIterator = rostlab::blast::parser::stack_symbol_type*; _Tp = rostlab::blast::parser::stack_symbol_type]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = rostlab::blast::parser::stack_symbol_type*; _ForwardIterator = rostlab::blast::parser::stack_symbol_type*; _Allocator = allocator]' at /usr/include/c++/13/bits/stl_uninitialized.h:399:2, inlined from 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {rostlab::blast::parser::stack_symbol_type}; _Tp = rostlab::blast::parser::stack_symbol_type; _Alloc = std::allocator]' at /usr/include/c++/13/bits/vector.tcc:500:3: /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {rostlab::blast::parser::stack_symbol_type}; _Tp = rostlab::blast::parser::stack_symbol_type; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = rostlab::blast::parser::stack_symbol_type; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void rostlab::blast::parser::stack::push(T&&) [with T = rostlab::blast::parser::stack_symbol_type; S = std::vector >]' at rostlab/blast-parser-parser.h:761:24, inlined from 'void rostlab::blast::parser::yypush_(const char*, stack_symbol_type&&)' at blast-parser-parser.cpp:443:19: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -c blast-parser-driver.cpp -o librostlab_blast_la-blast-parser-driver.o >/dev/null 2>&1 In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = rostlab::blast::oneline; _Alloc = std::allocator]', inlined from 'virtual int rostlab::blast::parser::parse()' at blast-parser-parser.ypp:160:33: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {rostlab::blast::hsp}; _Tp = rostlab::blast::hsp; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = rostlab::blast::hsp; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'virtual int rostlab::blast::parser::parse()' at blast-parser-parser.ypp:202:69: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -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 -version-info 0:0:0 -Wall -Wl,-z,relro -Wl,-z,now -o librostlab-blast.la -rpath /usr/lib/arm-linux-gnueabihf 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/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/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/arm-linux-gnueabihf/13 -L/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/13/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/13/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/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 5 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 -j4 check "TESTSUITEFLAGS=-j4 --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/arm-linux-gnueabihf' /bin/sh ../libtool --mode=install /usr/bin/install -c librostlab-blast.la '/build/reproducible-path/librostlab-blast-1.0.1/debian/tmp/usr/lib/arm-linux-gnueabihf' 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/arm-linux-gnueabihf/librostlab-blast.so.0.0.0 libtool: install: (cd /build/reproducible-path/librostlab-blast-1.0.1/debian/tmp/usr/lib/arm-linux-gnueabihf && { 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/arm-linux-gnueabihf && { 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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/librostlab-blast.a libtool: install: chmod 644 /build/reproducible-path/librostlab-blast-1.0.1/debian/tmp/usr/lib/arm-linux-gnueabihf/librostlab-blast.a libtool: install: ranlib /build/reproducible-path/librostlab-blast-1.0.1/debian/tmp/usr/lib/arm-linux-gnueabihf/librostlab-blast.a libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf' /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/arm-linux-gnueabihf install -d -m 755 debian/librostlab-blast0v5/usr/lib/arm-linux-gnueabihf mv debian/tmp/usr/lib/arm-linux-gnueabihf/librostlab-blast.a debian/librostlab-blast0-dev/usr/lib/arm-linux-gnueabihf mv debian/tmp/usr/lib/arm-linux-gnueabihf/librostlab-blast.so debian/librostlab-blast0-dev/usr/lib/arm-linux-gnueabihf mv /build/reproducible-path/librostlab-blast-1.0.1/debian/tmp/usr/lib/arm-linux-gnueabihf/librostlab-blast.so.0 debian/librostlab-blast0v5/usr/lib/arm-linux-gnueabihf mv /build/reproducible-path/librostlab-blast-1.0.1/debian/tmp/usr/lib/arm-linux-gnueabihf/librostlab-blast.so.0.0.0 debian/librostlab-blast0v5/usr/lib/arm-linux-gnueabihf 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_armhf.deb'. dpkg-deb: building package 'librostlab-blast0v5-dbgsym' in '../librostlab-blast0v5-dbgsym_1.0.1-14_armhf.deb'. dpkg-deb: building package 'librostlab-blast0-dev' in '../librostlab-blast0-dev_1.0.1-14_armhf.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_armhf.buildinfo dpkg-genchanges --build=binary -O../librostlab-blast_1.0.1-14_armhf.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/13228/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/13228/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/13228 and its subdirectories I: Current time: Fri Apr 26 20:00:12 +14 2024 I: pbuilder-time-stamp: 1714111212