I: pbuilder: network access will be disabled during build
I: Current time: Wed Dec 11 19:41:18 +14 2024
I: pbuilder-time-stamp: 1733895678
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [clustalo_1.2.4-8.dsc]
I: copying [./clustalo_1.2.4.orig.tar.gz]
I: copying [./clustalo_1.2.4-8.debian.tar.xz]
I: Extracting source
gpgv: Signature made Wed Dec 6 21:28:55 2023
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./clustalo_1.2.4-8.dsc: no acceptable signature found
dpkg-source: info: extracting clustalo in clustalo-1.2.4
dpkg-source: info: unpacking clustalo_1.2.4.orig.tar.gz
dpkg-source: info: unpacking clustalo_1.2.4-8.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying clustalo-log-format-calls.patch
dpkg-source: info: applying array_out_of_bounds.patch
dpkg-source: info: applying memory_leak.patch
dpkg-source: info: applying fix_syntax.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/2185/tmp/hooks/D01_modify_environment starting
debug: Running on wbq0.
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 Dec 11 05:42 /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/2185/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/2185/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]="37" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf")
BASH_VERSION='5.2.37(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=unstable
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=arm
HOST_ARCH=armhf
IFS='
'
INVOCATION_ID=e3231cf247734bce8be8f6405e181db7
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=2185
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.tztRSk6d/pbuilderrc_sKmj --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.tztRSk6d/b2 --logfile b2/build.log clustalo_1.2.4-8.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 6.1.0-28-armmp #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/2185/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 <pbuilder-maint@lists.alioth.debian.org>
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), libargtable2-dev, doxygen, graphviz, sphinx-common
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19680 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 libargtable2-dev; however:
Package libargtable2-dev is not installed.
pbuilder-satisfydepends-dummy depends on doxygen; however:
Package doxygen is not installed.
pbuilder-satisfydepends-dummy depends on graphviz; however:
Package graphviz is not installed.
pbuilder-satisfydepends-dummy depends on sphinx-common; however:
Package sphinx-common 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} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} doxygen{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} graphviz{a} groff-base{a} intltool-debian{a} libabsl20230802{a} libaom3{a} libarchive-zip-perl{a} libargtable2-0{a} libargtable2-dev{a} libavif16{a} libbrotli1{a} libcairo2{a} libcdt5{a} libcgraph6{a} libclang-cpp19{a} libclang1-19{a} libdatrie1{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfmt10{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd3{a} libglib2.0-0t64{a} libgraphite2-3{a} libgts-0.7-5t64{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libice6{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} liblab-gamut1{a} liblerc4{a} libllvm19{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpathplan4{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libraqm0{a} librav1e0.7{a} libsharpyuv0{a} libsm6{a} libsvtav1enc2{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6t64{a} libyuv0{a} libz3-4{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} sphinx-common{a} x11-common{a}
The following packages are RECOMMENDED but will NOT be installed:
curl fonts-liberation javascript-common libarchive-cpio-perl libglib2.0-data libgts-bin libheif-plugin-aomenc libheif-plugin-x265 libjson-xs-perl libltdl-dev libmail-sendmail-perl lynx python3-sphinx shared-mime-info wget xdg-user-dirs
0 packages upgraded, 111 newly installed, 0 to remove and 0 not upgraded.
Need to get 91.5 MB of archives. After unpacking 356 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB]
Get: 4 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3+b1 [42.3 kB]
Get: 5 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.22.5-2 [195 kB]
Get: 6 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB]
Get: 7 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-6 [1091 kB]
Get: 8 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.2-12 [83.9 kB]
Get: 9 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB]
Get: 10 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB]
Get: 11 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB]
Get: 12 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian unstable/main armhf autopoint all 0.22.5-2 [723 kB]
Get: 16 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.20 [89.7 kB]
Get: 17 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-8 [517 kB]
Get: 18 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 21 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 22 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.192-4 [184 kB]
Get: 23 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB]
Get: 24 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-5+b1 [9088 kB]
Get: 25 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB]
Get: 26 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.22.5-2 [1485 kB]
Get: 27 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 28 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 29 http://deb.debian.org/debian unstable/main armhf debhelper all 13.20 [915 kB]
Get: 30 http://deb.debian.org/debian unstable/main armhf libedit2 armhf 3.1-20240808-1 [77.9 kB]
Get: 31 http://deb.debian.org/debian unstable/main armhf libz3-4 armhf 4.13.3-1 [7252 kB]
Get: 32 http://deb.debian.org/debian unstable/main armhf libllvm19 armhf 1:19.1.5-1 [23.8 MB]
Get: 33 http://deb.debian.org/debian unstable/main armhf libclang-cpp19 armhf 1:19.1.5-1 [11.6 MB]
Get: 34 http://deb.debian.org/debian unstable/main armhf libclang1-19 armhf 1:19.1.5-1 [6609 kB]
Get: 35 http://deb.debian.org/debian unstable/main armhf libfmt10 armhf 10.1.1+ds1-4 [118 kB]
Get: 36 http://deb.debian.org/debian unstable/main armhf doxygen armhf 1.9.8+ds-2+b3 [4499 kB]
Get: 37 http://deb.debian.org/debian unstable/main armhf libexpat1 armhf 2.6.4-1 [83.5 kB]
Get: 38 http://deb.debian.org/debian unstable/main armhf libbrotli1 armhf 1.1.0-2+b6 [282 kB]
Get: 39 http://deb.debian.org/debian unstable/main armhf libpng16-16t64 armhf 1.6.44-3 [263 kB]
Get: 40 http://deb.debian.org/debian unstable/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [385 kB]
Get: 41 http://deb.debian.org/debian unstable/main armhf fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 42 http://deb.debian.org/debian unstable/main armhf fonts-dejavu-core all 2.37-8 [840 kB]
Get: 43 http://deb.debian.org/debian unstable/main armhf fontconfig-config armhf 2.15.0-1.1+b1 [318 kB]
Get: 44 http://deb.debian.org/debian unstable/main armhf libfontconfig1 armhf 2.15.0-1.1+b1 [371 kB]
Get: 45 http://deb.debian.org/debian unstable/main armhf fontconfig armhf 2.15.0-1.1+b1 [461 kB]
Get: 46 http://deb.debian.org/debian unstable/main armhf libcdt5 armhf 2.42.4-2+b1 [37.9 kB]
Get: 47 http://deb.debian.org/debian unstable/main armhf libcgraph6 armhf 2.42.4-2+b1 [56.8 kB]
Get: 48 http://deb.debian.org/debian unstable/main armhf libaom3 armhf 3.11.0-1 [1599 kB]
Get: 49 http://deb.debian.org/debian unstable/main armhf libdav1d7 armhf 1.5.0-1+b1 [250 kB]
Get: 50 http://deb.debian.org/debian unstable/main armhf libabsl20230802 armhf 20230802.1-4 [432 kB]
Get: 51 http://deb.debian.org/debian unstable/main armhf libgav1-1 armhf 0.19.0-2+b2 [298 kB]
Get: 52 http://deb.debian.org/debian unstable/main armhf librav1e0.7 armhf 0.7.1-7+b2 [587 kB]
Get: 53 http://deb.debian.org/debian unstable/main armhf libsvtav1enc2 armhf 2.2.1+dfsg-2 [937 kB]
Get: 54 http://deb.debian.org/debian unstable/main armhf libjpeg62-turbo armhf 1:2.1.5-3+b1 [145 kB]
Get: 55 http://deb.debian.org/debian unstable/main armhf libyuv0 armhf 0.0.1898.20241125-1 [86.6 kB]
Get: 56 http://deb.debian.org/debian unstable/main armhf libavif16 armhf 1.1.1-1 [103 kB]
Get: 57 http://deb.debian.org/debian unstable/main armhf libsharpyuv0 armhf 1.4.0-0.1+b1 [111 kB]
Get: 58 http://deb.debian.org/debian unstable/main armhf libheif-plugin-dav1d armhf 1.19.3-1 [10.8 kB]
Get: 59 http://deb.debian.org/debian unstable/main armhf libde265-0 armhf 1.0.15-1+b2 [145 kB]
Get: 60 http://deb.debian.org/debian unstable/main armhf libheif-plugin-libde265 armhf 1.19.3-1 [13.9 kB]
Get: 61 http://deb.debian.org/debian unstable/main armhf libheif1 armhf 1.19.3-1 [410 kB]
Get: 62 http://deb.debian.org/debian unstable/main armhf libimagequant0 armhf 2.18.0-1+b2 [30.5 kB]
Get: 63 http://deb.debian.org/debian unstable/main armhf libfribidi0 armhf 1.0.16-1 [24.6 kB]
Get: 64 http://deb.debian.org/debian unstable/main armhf libglib2.0-0t64 armhf 2.82.3-2 [1327 kB]
Get: 65 http://deb.debian.org/debian unstable/main armhf libgraphite2-3 armhf 1.3.14-2+b1 [63.1 kB]
Get: 66 http://deb.debian.org/debian unstable/main armhf libharfbuzz0b armhf 10.1.0-1 [418 kB]
Get: 67 http://deb.debian.org/debian unstable/main armhf libraqm0 armhf 0.10.2-1 [11.6 kB]
Get: 68 http://deb.debian.org/debian unstable/main armhf libdeflate0 armhf 1.22-1 [36.3 kB]
Get: 69 http://deb.debian.org/debian unstable/main armhf libjbig0 armhf 2.1-6.1+b2 [27.3 kB]
Get: 70 http://deb.debian.org/debian unstable/main armhf liblerc4 armhf 4.0.0+ds-5 [146 kB]
Get: 71 http://deb.debian.org/debian unstable/main armhf libwebp7 armhf 1.4.0-0.1+b1 [266 kB]
Get: 72 http://deb.debian.org/debian unstable/main armhf libtiff6 armhf 4.5.1+git230720-5 [302 kB]
Get: 73 http://deb.debian.org/debian unstable/main armhf libxau6 armhf 1:1.0.11-1 [19.7 kB]
Get: 74 http://deb.debian.org/debian unstable/main armhf libxdmcp6 armhf 1:1.1.5-1 [26.4 kB]
Get: 75 http://deb.debian.org/debian unstable/main armhf libxcb1 armhf 1.17.0-2+b1 [140 kB]
Get: 76 http://deb.debian.org/debian unstable/main armhf libx11-data all 2:1.8.10-2 [337 kB]
Get: 77 http://deb.debian.org/debian unstable/main armhf libx11-6 armhf 2:1.8.10-2 [750 kB]
Get: 78 http://deb.debian.org/debian unstable/main armhf libxpm4 armhf 1:3.5.17-1+b2 [50.4 kB]
Get: 79 http://deb.debian.org/debian unstable/main armhf libgd3 armhf 2.3.3-12+b1 [105 kB]
Get: 80 http://deb.debian.org/debian unstable/main armhf libgts-0.7-5t64 armhf 0.7.6+darcs121130-5.2+b1 [133 kB]
Get: 81 http://deb.debian.org/debian unstable/main armhf libpixman-1-0 armhf 0.44.0-3 [164 kB]
Get: 82 http://deb.debian.org/debian unstable/main armhf libxcb-render0 armhf 1.17.0-2+b1 [114 kB]
Get: 83 http://deb.debian.org/debian unstable/main armhf libxcb-shm0 armhf 1.17.0-2+b1 [105 kB]
Get: 84 http://deb.debian.org/debian unstable/main armhf libxext6 armhf 2:1.3.4-1+b2 [45.2 kB]
Get: 85 http://deb.debian.org/debian unstable/main armhf libxrender1 armhf 1:0.9.10-1.1+b2 [25.0 kB]
Get: 86 http://deb.debian.org/debian unstable/main armhf libcairo2 armhf 1.18.2-2 [443 kB]
Get: 87 http://deb.debian.org/debian unstable/main armhf libltdl7 armhf 2.4.7-8 [390 kB]
Get: 88 http://deb.debian.org/debian unstable/main armhf libthai-data all 0.1.29-2 [168 kB]
Get: 89 http://deb.debian.org/debian unstable/main armhf libdatrie1 armhf 0.2.13-3+b1 [34.7 kB]
Get: 90 http://deb.debian.org/debian unstable/main armhf libthai0 armhf 0.1.29-2+b1 [46.0 kB]
Get: 91 http://deb.debian.org/debian unstable/main armhf libpango-1.0-0 armhf 1.55.0+ds-3 [200 kB]
Get: 92 http://deb.debian.org/debian unstable/main armhf libpangoft2-1.0-0 armhf 1.55.0+ds-3 [47.7 kB]
Get: 93 http://deb.debian.org/debian unstable/main armhf libpangocairo-1.0-0 armhf 1.55.0+ds-3 [31.3 kB]
Get: 94 http://deb.debian.org/debian unstable/main armhf libpathplan4 armhf 2.42.4-2+b1 [39.9 kB]
Get: 95 http://deb.debian.org/debian unstable/main armhf libgvc6 armhf 2.42.4-2+b1 [581 kB]
Get: 96 http://deb.debian.org/debian unstable/main armhf libgvpr2 armhf 2.42.4-2+b1 [168 kB]
Get: 97 http://deb.debian.org/debian unstable/main armhf liblab-gamut1 armhf 2.42.4-2+b1 [198 kB]
Get: 98 http://deb.debian.org/debian unstable/main armhf x11-common all 1:7.7+23.1 [216 kB]
Get: 99 http://deb.debian.org/debian unstable/main armhf libice6 armhf 2:1.1.1-1 [58.5 kB]
Get: 100 http://deb.debian.org/debian unstable/main armhf libsm6 armhf 2:1.2.4-1 [33.5 kB]
Get: 101 http://deb.debian.org/debian unstable/main armhf libxt6t64 armhf 1:1.2.1-1.2+b1 [160 kB]
Get: 102 http://deb.debian.org/debian unstable/main armhf libxmu6 armhf 2:1.1.3-3+b3 [51.2 kB]
Get: 103 http://deb.debian.org/debian unstable/main armhf libxaw7 armhf 2:1.0.16-1 [177 kB]
Get: 104 http://deb.debian.org/debian unstable/main armhf graphviz armhf 2.42.4-2+b1 [500 kB]
Get: 105 http://deb.debian.org/debian unstable/main armhf libargtable2-0 armhf 13-3 [15.8 kB]
Get: 106 http://deb.debian.org/debian unstable/main armhf libargtable2-dev armhf 13-3 [39.7 kB]
Get: 107 http://deb.debian.org/debian unstable/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 108 http://deb.debian.org/debian unstable/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 109 http://deb.debian.org/debian unstable/main armhf libjs-sphinxdoc all 7.4.7-4 [158 kB]
Get: 110 http://deb.debian.org/debian unstable/main armhf libjson-perl all 4.10000-1 [87.5 kB]
Get: 111 http://deb.debian.org/debian unstable/main armhf sphinx-common all 7.4.7-4 [731 kB]
Fetched 91.5 MB in 10s (9175 kB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sensible-utils.
(Reading database ...
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Not building database; man-db/auto-update is not 'true'.
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Processing triggers for libc-bin (2.40-4) ...
Reading package lists...
Building dependency tree...
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-> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/2185/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/2185/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/clustalo-1.2.4/ && 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 > ../clustalo_1.2.4-8_source.changes
dpkg-buildpackage: info: source package clustalo
dpkg-buildpackage: info: source version 1.2.4-8
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_clean
make[1]: Entering directory '/build/reproducible-path/clustalo-1.2.4'
if [ -e src/clustal-omega-config.h~ ] ; then \
mv src/clustal-omega-config.h~ src/clustal-omega-config.h ; \
fi
dh_clean
rm -f _configs.sed
rm -rf doc
make[1]: Leaving directory '/build/reproducible-path/clustalo-1.2.4'
debian/rules binary
dh binary
dh_update_autotools_config
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:287: warning: The macro 'AC_HEADER_STDC' is obsolete.
configure.ac:287: You should run autoupdate.
./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from...
configure.ac:287: the top level
configure.ac:133: installing './compile'
configure.ac:115: installing './missing'
src/Makefile.am: installing './depcomp'
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/reproducible-path/clustalo-1.2.4'
cp -a src/clustal-omega-config.h src/clustal-omega-config.h~
dh_auto_configure
./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
configure:
Welcome to Clustal Omega - version 1.2.4 (AndreaGiacomo)
+NMMMMMMMMMS=
MMMMM? :MMMMM8
IMMMMS MMMMM,
~MMMMN ,MMMMM
=MMMMM MMMMM
?MMMMM +MMMMM
MMMMMS MMMMM
MMMMM MMMMM:
MMMMM MMMMM+
MMMMM MMMMM~
MMMMM MMMMM
MMMMMZ MMMMM
MMMMM ,MMMMZ
MMMM8 MMMM+
MMMMS MMMM,
MMMMO MMMM
,N SMMM MMM8 +8
,M7 M+ M+ :M8
,MMMMMMMMMMMMI MMMMMMMMMMMM8
,MMMMMMMMMMMM8 MMMMMMMMMMMM8
,MMMMMMMMMMMMN MMMMMMMMMMMM8
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 whether make supports the include directive... yes (GNU style)
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 dependency style of gcc... none
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 wchar.h... yes
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking whether _XOPEN_SOURCE should be defined... no
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking whether make sets $(MAKE)... (cached) yes
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 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 for gcc... (cached) gcc
checking whether the compiler supports GNU C... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to enable C11 features... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) none
checking how to run the C preprocessor... gcc -E
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 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 how to run the C++ preprocessor... g++ -E
checking for egrep... (cached) /usr/bin/grep -E
checking for assert.h... yes
checking for ctype.h... yes
checking for float.h... yes
checking for limits.h... yes
checking for math.h... yes
checking for memory.h... yes
checking for stdarg.h... yes
checking for stdio.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking for inline... inline
checking for log in -lm... yes
checking for log2 in -lm... yes
checking for argtable2.h... yes
checking for arg_parse in -largtable2... yes
checking for OpenMP flag of C compiler... -fopenmp
checking whether byte ordering is bigendian... no
checking for ntohs... yes
checking for ntohl... yes
checking for ntons... no
checking for ntonl... no
checking size of unsigned short... 2
checking size of unsigned int... 4
checking size of unsigned long... 4
checking size of unsigned long long... 8
checking for stroul... no
checking for strtoull... yes
checking for ftello... yes
checking for fseeko... yes
checking for ftello64... yes
checking for fseeko64... yes
checking for ftell64... no
checking for fseek64... no
checking for off_t... yes
checking size of fpos_t... 16
checking if malloc debugging is wanted... no
checking whether to build with debug information... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating clustalo.pc
config.status: creating Doxyfile
config.status: creating src/clustal/Makefile
config.status: creating src/hhalign/Makefile
config.status: creating src/kmpp/Makefile
config.status: creating src/squid/Makefile
config.status: creating src/config.h
config.status: executing src/clustal-omega-config.h commands
config.status: creating src/clustal-omega-config.h - prefix CLUSTAL_OMEGA for src/config.h defines
config.status: executing depfiles commands
config.status: executing libtool commands
make[1]: Leaving directory '/build/reproducible-path/clustalo-1.2.4'
debian/rules override_dh_auto_build-indep
make[1]: Entering directory '/build/reproducible-path/clustalo-1.2.4'
# nothing to do here
make[1]: Leaving directory '/build/reproducible-path/clustalo-1.2.4'
dh_auto_build -Nlibclustalo-doc
make -j4
make[1]: Entering directory '/build/reproducible-path/clustalo-1.2.4'
Making all in src
make[2]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src'
make all-recursive
make[3]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src'
Making all in hhalign
make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/hhalign'
/bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o hhalign.lo hhalign.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c hhalign.cpp -fPIC -DPIC -o .libs/hhalign.o
In file included from hhalign.cpp:70:
hhhmm-C.h: In member function 'void HMM::UseSecStrucDependentGapPenalties()':
hhhmm-C.h:1748:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
1748 | iis[0]=iis[L]=0;
| ~~~~~~^~
hhhmm-C.h:1734:17: note: at offset [-2147483648, -1] into destination object 'iis' of size [0, 2147483647]
1734 | unsigned char iis[par.maxResLen]; // inside-integer array
| ^~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c hhalign.cpp -o hhalign.o >/dev/null 2>&1
/bin/sh ../../libtool --tag=CXX --mode=link g++ -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o libhhalign.la hhalign.lo -largtable2 -lm
libtool: link: ar cr .libs/libhhalign.a .libs/hhalign.o
libtool: link: ranlib .libs/libhhalign.a
libtool: link: ( cd ".libs" && rm -f "libhhalign.la" && ln -s "../libhhalign.la" "libhhalign.la" )
make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/hhalign'
Making all in squid
make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/squid'
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o a2m.lo a2m.c
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o aligneval.lo aligneval.c
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o alignio.lo alignio.c
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o clustal.lo clustal.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c aligneval.c -fPIC -DPIC -o .libs/aligneval.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c clustal.c -fPIC -DPIC -o .libs/clustal.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c a2m.c -fPIC -DPIC -o .libs/a2m.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c alignio.c -fPIC -DPIC -o .libs/alignio.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c a2m.c -o a2m.o >/dev/null 2>&1
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o cluster.lo cluster.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c aligneval.c -o aligneval.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c clustal.c -o clustal.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c cluster.c -fPIC -DPIC -o .libs/cluster.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c alignio.c -o alignio.o >/dev/null 2>&1
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o dayhoff.lo dayhoff.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c dayhoff.c -fPIC -DPIC -o .libs/dayhoff.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c cluster.c -o cluster.o >/dev/null 2>&1
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o eps.lo eps.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c eps.c -fPIC -DPIC -o .libs/eps.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c dayhoff.c -o dayhoff.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c eps.c -o eps.o >/dev/null 2>&1
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o file.lo file.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c file.c -fPIC -DPIC -o .libs/file.o
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o getopt.lo getopt.c
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o gki.lo gki.c
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o gsi.lo gsi.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c getopt.c -fPIC -DPIC -o .libs/getopt.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c gki.c -fPIC -DPIC -o .libs/gki.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c gsi.c -fPIC -DPIC -o .libs/gsi.o
file.c: In function 'EnvFileOpen':
file.c:243:26: warning: '%s' directive writing up to 1022 bytes into a region of size between 1 and 1023 [-Wformat-overflow=]
243 | sprintf(full, "%s%c%s", s, DIRSLASH, fname);
| ^~
In file included from /usr/include/stdio.h:970,
from file.c:24:
In function 'sprintf',
inlined from 'EnvFileOpen' at file.c:243:7:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 2 and 2046 bytes into a destination of size 1024
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c file.c -o file.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c getopt.c -o getopt.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c gki.c -o gki.o >/dev/null 2>&1
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o gsi64.lo gsi64.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c gsi64.c -fPIC -DPIC -o .libs/gsi64.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c gsi.c -o gsi.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c gsi64.c -o gsi64.o >/dev/null 2>&1
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o hsregex.lo hsregex.c
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o iupac.lo iupac.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c hsregex.c -fPIC -DPIC -o .libs/hsregex.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c iupac.c -fPIC -DPIC -o .libs/iupac.o
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o msa.lo msa.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c msa.c -fPIC -DPIC -o .libs/msa.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c iupac.c -o iupac.o >/dev/null 2>&1
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o msf.lo msf.c
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o phylip.lo phylip.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c msf.c -fPIC -DPIC -o .libs/msf.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c phylip.c -fPIC -DPIC -o .libs/phylip.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c phylip.c -o phylip.o >/dev/null 2>&1
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o revcomp.lo revcomp.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c msf.c -o msf.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c revcomp.c -fPIC -DPIC -o .libs/revcomp.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c revcomp.c -o revcomp.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c hsregex.c -o hsregex.o >/dev/null 2>&1
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o rk.lo rk.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c msa.c -o msa.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c rk.c -fPIC -DPIC -o .libs/rk.o
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o selex.lo selex.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c selex.c -fPIC -DPIC -o .libs/selex.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c rk.c -o rk.o >/dev/null 2>&1
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o seqencode.lo seqencode.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c seqencode.c -fPIC -DPIC -o .libs/seqencode.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c seqencode.c -o seqencode.o >/dev/null 2>&1
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o shuffle.lo shuffle.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c shuffle.c -fPIC -DPIC -o .libs/shuffle.o
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sqerror.lo sqerror.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sqerror.c -fPIC -DPIC -o .libs/sqerror.o
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sqio.lo sqio.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sqerror.c -o sqerror.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c selex.c -o selex.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sqio.c -fPIC -DPIC -o .libs/sqio.o
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o squidcore.lo squidcore.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c squidcore.c -fPIC -DPIC -o .libs/squidcore.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c squidcore.c -o squidcore.o >/dev/null 2>&1
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sre_ctype.lo sre_ctype.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c shuffle.c -o shuffle.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sre_ctype.c -fPIC -DPIC -o .libs/sre_ctype.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sre_ctype.c -o sre_ctype.o >/dev/null 2>&1
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sre_math.lo sre_math.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sre_math.c -fPIC -DPIC -o .libs/sre_math.o
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sre_random.lo sre_random.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sre_random.c -fPIC -DPIC -o .libs/sre_random.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sre_math.c -o sre_math.o >/dev/null 2>&1
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sre_string.lo sre_string.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sre_string.c -fPIC -DPIC -o .libs/sre_string.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sre_random.c -o sre_random.o >/dev/null 2>&1
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o ssi.lo ssi.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c ssi.c -fPIC -DPIC -o .libs/ssi.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sre_string.c -o sre_string.o >/dev/null 2>&1
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o stack.lo stack.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c stack.c -fPIC -DPIC -o .libs/stack.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sqio.c -o sqio.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c stack.c -o stack.o >/dev/null 2>&1
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o stockholm.lo stockholm.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c stockholm.c -fPIC -DPIC -o .libs/stockholm.o
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o stopwatch.lo stopwatch.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c stopwatch.c -fPIC -DPIC -o .libs/stopwatch.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c stopwatch.c -o stopwatch.o >/dev/null 2>&1
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o translate.lo translate.c
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c hhalign_wrapper.c -o hhalign_wrapper.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c pair_dist.c -o pair_dist.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c mbed.c -o mbed.o >/dev/null 2>&1
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o progress.lo progress.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c progress.c -fPIC -DPIC -o .libs/progress.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c progress.c -o progress.o >/dev/null 2>&1
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o seq.lo seq.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c seq.c -fPIC -DPIC -o .libs/seq.o
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o symmatrix.lo symmatrix.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c symmatrix.c -fPIC -DPIC -o .libs/symmatrix.o
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o tree.lo tree.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c tree.c -fPIC -DPIC -o .libs/tree.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c symmatrix.c -o symmatrix.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c tree.c -o tree.o >/dev/null 2>&1
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o util.lo util.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c util.c -fPIC -DPIC -o .libs/util.o
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o weights.lo weights.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c seq.c -o seq.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c weights.c -fPIC -DPIC -o .libs/weights.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c util.c -o util.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c weights.c -o weights.o >/dev/null 2>&1
/bin/sh ../../libtool --tag=CC --mode=link gcc -fopenmp -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o libclustal.la hhalign_wrapper.lo ktuple_pair.lo list.lo log.lo muscle_upgma.lo muscle_tree.lo mbed.lo pair_dist.lo progress.lo seq.lo symmatrix.lo tree.lo util.lo weights.lo -largtable2 -lm
libtool: link: ar cr .libs/libclustal.a .libs/hhalign_wrapper.o .libs/ktuple_pair.o .libs/list.o .libs/log.o .libs/muscle_upgma.o .libs/muscle_tree.o .libs/mbed.o .libs/pair_dist.o .libs/progress.o .libs/seq.o .libs/symmatrix.o .libs/tree.o .libs/util.o .libs/weights.o
libtool: link: ranlib .libs/libclustal.a
libtool: link: ( cd ".libs" && rm -f "libclustal.la" && ln -s "../libclustal.la" "libclustal.la" )
make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/clustal'
make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src'
g++ -DHAVE_CONFIG_H -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o main.o main.cpp
gcc -DHAVE_CONFIG_H -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o mymain.o mymain.c
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o clustal-omega.lo clustal-omega.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c clustal-omega.c -fPIC -DPIC -o .libs/clustal-omega.o
clustal-omega.c: In function 'PrintLongVersion':
clustal-omega.c:152:49: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
152 | PACKAGE_VERSION, PACKAGE_CODENAME, __DATE__);
| ^~~~~~~~
libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c clustal-omega.c -o clustal-omega.o >/dev/null 2>&1
/bin/sh ../libtool --tag=CC --mode=link gcc -O3 -fopenmp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -static -Wl,-z,relro -Wl,-z,now -o libclustalo.la -rpath /usr/lib/arm-linux-gnueabihf clustal-omega.lo clustal/libclustal.la hhalign/libhhalign.la squid/libsquid.la kmpp/libkmpp.la -largtable2 -lm
libtool: link: (cd .libs/libclustalo.lax/libclustal.a && ar x "/build/reproducible-path/clustalo-1.2.4/src/clustal/.libs/libclustal.a")
libtool: link: (cd .libs/libclustalo.lax/libhhalign.a && ar x "/build/reproducible-path/clustalo-1.2.4/src/hhalign/.libs/libhhalign.a")
libtool: link: (cd .libs/libclustalo.lax/libsquid.a && ar x "/build/reproducible-path/clustalo-1.2.4/src/squid/.libs/libsquid.a")
libtool: link: (cd .libs/libclustalo.lax/libkmpp.a && ar x "/build/reproducible-path/clustalo-1.2.4/src/kmpp/.libs/libkmpp.a")
libtool: link: ar cr .libs/libclustalo.a clustal-omega.o .libs/libclustalo.lax/libclustal.a/hhalign_wrapper.o .libs/libclustalo.lax/libclustal.a/ktuple_pair.o .libs/libclustalo.lax/libclustal.a/list.o .libs/libclustalo.lax/libclustal.a/log.o .libs/libclustalo.lax/libclustal.a/mbed.o .libs/libclustalo.lax/libclustal.a/muscle_tree.o .libs/libclustalo.lax/libclustal.a/muscle_upgma.o .libs/libclustalo.lax/libclustal.a/pair_dist.o .libs/libclustalo.lax/libclustal.a/progress.o .libs/libclustalo.lax/libclustal.a/seq.o .libs/libclustalo.lax/libclustal.a/symmatrix.o .libs/libclustalo.lax/libclustal.a/tree.o .libs/libclustalo.lax/libclustal.a/util.o .libs/libclustalo.lax/libclustal.a/weights.o .libs/libclustalo.lax/libhhalign.a/hhalign.o .libs/libclustalo.lax/libsquid.a/a2m.o .libs/libclustalo.lax/libsquid.a/aligneval.o .libs/libclustalo.lax/libsquid.a/alignio.o .libs/libclustalo.lax/libsquid.a/clustal.o .libs/libclustalo.lax/libsquid.a/cluster.o .libs/libclustalo.lax/libsquid.a/dayhoff.o .libs/libclustalo.lax/libsquid.a/eps.o .libs/libclustalo.lax/libsquid.a/file.o .libs/libclustalo.lax/libsquid.a/getopt.o .libs/libclustalo.lax/libsquid.a/gki.o .libs/libclustalo.lax/libsquid.a/gsi.o .libs/libclustalo.lax/libsquid.a/gsi64.o .libs/libclustalo.lax/libsquid.a/hsregex.o .libs/libclustalo.lax/libsquid.a/iupac.o .libs/libclustalo.lax/libsquid.a/msa.o .libs/libclustalo.lax/libsquid.a/msf.o .libs/libclustalo.lax/libsquid.a/phylip.o .libs/libclustalo.lax/libsquid.a/revcomp.o .libs/libclustalo.lax/libsquid.a/rk.o .libs/libclustalo.lax/libsquid.a/selex.o .libs/libclustalo.lax/libsquid.a/seqencode.o .libs/libclustalo.lax/libsquid.a/shuffle.o .libs/libclustalo.lax/libsquid.a/sqerror.o .libs/libclustalo.lax/libsquid.a/sqio.o .libs/libclustalo.lax/libsquid.a/squidcore.o .libs/libclustalo.lax/libsquid.a/sre_ctype.o .libs/libclustalo.lax/libsquid.a/sre_math.o .libs/libclustalo.lax/libsquid.a/sre_random.o .libs/libclustalo.lax/libsquid.a/sre_string.o .libs/libclustalo.lax/libsquid.a/ssi.o .libs/libclustalo.lax/libsquid.a/stack.o .libs/libclustalo.lax/libsquid.a/stockholm.o .libs/libclustalo.lax/libsquid.a/stopwatch.o .libs/libclustalo.lax/libsquid.a/translate.o .libs/libclustalo.lax/libsquid.a/types.o .libs/libclustalo.lax/libsquid.a/vectorops.o .libs/libclustalo.lax/libsquid.a/weight.o .libs/libclustalo.lax/libkmpp.a/KMeans.o .libs/libclustalo.lax/libkmpp.a/KmTree.o .libs/libclustalo.lax/libkmpp.a/KmUtils.o
libtool: link: ranlib .libs/libclustalo.a
libtool: link: rm -fr .libs/libclustalo.lax
libtool: link: ( cd ".libs" && rm -f "libclustalo.la" && ln -s "../libclustalo.la" "libclustalo.la" )
/bin/sh ../libtool --tag=CXX --mode=link g++ -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o clustalo main.o mymain.o libclustalo.la -largtable2 -lm
libtool: link: g++ -O3 -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/clustalo-1.2.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o clustalo main.o mymain.o ./.libs/libclustalo.a /usr/lib/arm-linux-gnueabihf/libargtable2.so -lm -fopenmp
/usr/bin/ld: ./.libs/libclustalo.a(clustal-omega.o): in function `AlnToHHMFile':
./src/clustal-omega.c:393:(.text+0x4e0): warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src'
make[3]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src'
make[2]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src'
make[2]: Entering directory '/build/reproducible-path/clustalo-1.2.4'
make[2]: Nothing to be done for 'all-am'.
make[2]: Leaving directory '/build/reproducible-path/clustalo-1.2.4'
make[1]: Leaving directory '/build/reproducible-path/clustalo-1.2.4'
debian/rules override_dh_auto_test-arch
make[1]: Entering directory '/build/reproducible-path/clustalo-1.2.4'
dh_auto_test -a
make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1
make[2]: Entering directory '/build/reproducible-path/clustalo-1.2.4'
Making check in src
make[3]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src'
Making check in hhalign
make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/hhalign'
make[4]: Nothing to be done for 'check'.
make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/hhalign'
Making check in squid
make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/squid'
make[4]: Nothing to be done for 'check'.
make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/squid'
Making check in kmpp
make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/kmpp'
make[4]: Nothing to be done for 'check'.
make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/kmpp'
Making check in clustal
make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/clustal'
make[4]: Nothing to be done for 'check'.
make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/clustal'
make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src'
make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src'
make[3]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src'
make[3]: Entering directory '/build/reproducible-path/clustalo-1.2.4'
make[3]: Nothing to be done for 'check-am'.
make[3]: Leaving directory '/build/reproducible-path/clustalo-1.2.4'
make[2]: Leaving directory '/build/reproducible-path/clustalo-1.2.4'
# Run additional test from python-biopython package to verify that
# this will work as well
src/clustalo -i debian/tests/biopython_testdata/f002 --guidetree-out temp_test.dnd -o temp_test.aln --outfmt clustal --force
rm temp_test.aln temp_test.dnd
make[1]: Leaving directory '/build/reproducible-path/clustalo-1.2.4'
debian/rules override_dh_auto_test-indep
make[1]: Entering directory '/build/reproducible-path/clustalo-1.2.4'
echo "Do not run build time test"
Do not run build time test
make[1]: Leaving directory '/build/reproducible-path/clustalo-1.2.4'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_installdirs
debian/rules override_dh_auto_install-arch
make[1]: Entering directory '/build/reproducible-path/clustalo-1.2.4'
dh_auto_install -a
make -j1 install DESTDIR=/build/reproducible-path/clustalo-1.2.4/debian/tmp AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/build/reproducible-path/clustalo-1.2.4'
Making install in src
make[3]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src'
Making install in hhalign
make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/hhalign'
make[5]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/hhalign'
make[5]: Nothing to be done for 'install-exec-am'.
/usr/bin/mkdir -p '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/include/clustalo/hhalign'
/usr/bin/install -c -m 644 general.h hhfunc.h '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/include/clustalo/hhalign'
make[5]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/hhalign'
make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/hhalign'
Making install in squid
make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/squid'
make[5]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/squid'
make[5]: Nothing to be done for 'install-exec-am'.
/usr/bin/mkdir -p '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/include/clustalo/squid'
/usr/bin/install -c -m 644 gki.h gsi64.h msa.h rk.h squid.h stopwatch.h sqfuncs.h sre_random.h ssi.h stockholm.h vectorops.h version.h '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/include/clustalo/squid'
make[5]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/squid'
make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/squid'
Making install in kmpp
make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/kmpp'
make[5]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/kmpp'
make[5]: Nothing to be done for 'install-exec-am'.
make[5]: Nothing to be done for 'install-data-am'.
make[5]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/kmpp'
make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/kmpp'
Making install in clustal
make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/clustal'
make[5]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src/clustal'
make[5]: Nothing to be done for 'install-exec-am'.
/usr/bin/mkdir -p '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/include/clustalo/clustal'
/usr/bin/install -c -m 644 hhalign_wrapper.h ktuple_pair.h log.h mbed.h muscle_tree.h pair_dist.h progress.h seq.h symmatrix.h tree.h util.h weights.h '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/include/clustalo/clustal'
make[5]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/clustal'
make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src/clustal'
make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src'
make[5]: Entering directory '/build/reproducible-path/clustalo-1.2.4/src'
/usr/bin/mkdir -p '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf'
/bin/sh ../libtool --mode=install /usr/bin/install -c libclustalo.la '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/libclustalo.lai /build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf/libclustalo.la
libtool: install: /usr/bin/install -c .libs/libclustalo.a /build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf/libclustalo.a
libtool: install: chmod 644 /build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf/libclustalo.a
libtool: install: ranlib /build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf/libclustalo.a
libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf'
/usr/bin/mkdir -p '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/bin'
/bin/sh ../libtool --mode=install /usr/bin/install -c clustalo '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/bin'
libtool: install: /usr/bin/install -c clustalo /build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/bin/clustalo
/usr/bin/mkdir -p '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/include/clustalo/'
/usr/bin/install -c -m 644 clustal-omega-config.h clustal-omega.h '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/include/clustalo/'
make[5]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src'
make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src'
make[3]: Leaving directory '/build/reproducible-path/clustalo-1.2.4/src'
make[3]: Entering directory '/build/reproducible-path/clustalo-1.2.4'
make[4]: Entering directory '/build/reproducible-path/clustalo-1.2.4'
make[4]: Nothing to be done for 'install-exec-am'.
/usr/bin/mkdir -p '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/share/doc/clustal-omega'
/usr/bin/install -c -m 644 README '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/share/doc/clustal-omega'
/usr/bin/mkdir -p '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig'
/usr/bin/install -c -m 644 clustalo.pc '/build/reproducible-path/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig'
make[4]: Leaving directory '/build/reproducible-path/clustalo-1.2.4'
make[3]: Leaving directory '/build/reproducible-path/clustalo-1.2.4'
make[2]: Leaving directory '/build/reproducible-path/clustalo-1.2.4'
rm -rf debian/tmp/usr/lib/pkgconfig
rm -f debian/tmp/usr/lib/*/libclustalo.la
mv debian/tmp/usr/include debian/libclustalo-dev/usr
mv debian/tmp/usr/lib debian/libclustalo-dev/usr
mv debian/tmp/usr/bin debian/clustalo/usr
make[1]: Leaving directory '/build/reproducible-path/clustalo-1.2.4'
debian/rules override_dh_auto_install-indep
make[1]: Entering directory '/build/reproducible-path/clustalo-1.2.4'
# Generate doxygen doc
mkdir -p doc
doxygen Doxyfile
warning: Tag 'SYMBOL_CACHE_SIZE' at line 289 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 473 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 744 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 799 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 1136 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 1142 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 1307 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 1320 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 1329 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 1353 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 1358 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 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: 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.
/build/reproducible-path/clustalo-1.2.4/src/clustal-omega.c:726: warning: argument 'pdSeqWeights_p' from the argument list of AlignmentOrder has multiple @param documentation sections
/build/reproducible-path/clustalo-1.2.4/src/clustal-omega.c:726: warning: The following parameters of AlignmentOrder(int **piOrderLR_p, double **pdSeqWeights_p, mseq_t *prMSeq, int iPairDistType, char *pcDistmatInfile, char *pcDistmatOutfile, int iClusteringType, int iClustersizes, char *pcGuidetreeInfile, char *pcGuidetreeOutfile, char *pcClusterFile, bool bUseMbed, bool bPercID) are not documented:
parameter 'iClustersizes'
parameter 'pcClusterFile'
parameter 'bPercID'
/build/reproducible-path/clustalo-1.2.4/src/clustal-omega.c:726: warning: argument 'pdSeqWeights_p' from the argument list of AlignmentOrder has multiple @param documentation sections
/build/reproducible-path/clustalo-1.2.4/src/clustal-omega.c:726: warning: The following parameters of AlignmentOrder(int **piOrderLR_p, double **pdSeqWeights_p, mseq_t *prMSeq, int iPairDistType, char *pcDistmatInfile, char *pcDistmatOutfile, int iClusteringType, int iClustersizes, char *pcGuidetreeInfile, char *pcGuidetreeOutfile, char *pcClusterFile, bool bUseMbed, bool bPercID) are not documented:
parameter 'iClustersizes'
parameter 'pcClusterFile'
parameter 'bPercID'
/build/reproducible-path/clustalo-1.2.4/src/clustal/mbed.c:646: warning: The following parameter of BisectingKmeans(bisecting_kmeans_result_t **prKMeansResult_p, const int iNObjs, const int iDim, double **ppdVectors, const int iMinRequiredObjsPerCluster, const int iMaxAllowedObjsPerCluster, char ***ppcClusterSplits_p) is not documented:
parameter 'ppcClusterSplits_p'
/build/reproducible-path/clustalo-1.2.4/src/clustal/mbed.c:1133: warning: The following parameters of Mbed(tree_t **prMbedTree_p, mseq_t *prMSeq, const int iPairDistType, const char *pcGuidetreeOut, int iClustersizes, const char *pcClusterFile) are not documented:
parameter 'iClustersizes'
parameter 'pcClusterFile'
/build/reproducible-path/clustalo-1.2.4/src/clustal/mbed.c:1133: warning: The following parameters of Mbed(tree_t **prMbedTree_p, mseq_t *prMSeq, const int iPairDistType, const char *pcGuidetreeOut, int iClustersizes, const char *pcClusterFile) are not documented:
parameter 'iClustersizes'
parameter 'pcClusterFile'
/build/reproducible-path/clustalo-1.2.4/src/clustal/pair_dist.c:264: warning: Unsupported xml/html tag <j> found
/build/reproducible-path/clustalo-1.2.4/src/clustal/pair_dist.c:270: warning: Unsupported xml/html tag <j> found
/build/reproducible-path/clustalo-1.2.4/src/clustal/pair_dist.c:249: warning: The following parameter of PairDistances(symmatrix_t **distmat, mseq_t *mseq, int pairdist_type, bool bPercID, int istart, const unsigned long int iend, int jstart, const unsigned long int jend, char *fdist_in, char *fdist_out) is not documented:
parameter 'bPercID'
/build/reproducible-path/clustalo-1.2.4/src/clustal/pair_dist.c:264: warning: Unsupported xml/html tag <j> found
/build/reproducible-path/clustalo-1.2.4/src/clustal/pair_dist.c:270: warning: Unsupported xml/html tag <j> found
/build/reproducible-path/clustalo-1.2.4/src/clustal/pair_dist.c:249: warning: The following parameter of PairDistances(symmatrix_t **distmat, mseq_t *mseq, int pairdist_type, bool bPercID, int istart, const unsigned long int iend, int jstart, const unsigned long int jend, char *fdist_in, char *fdist_out) is not documented:
parameter 'bPercID'
/build/reproducible-path/clustalo-1.2.4/src/clustal/seq.c:399: warning: The following parameters of ReadSequences(mseq_t *prMSeq, char *seqfile, int iSeqType, int iSeqFmt, bool bIsProfile, bool bDealignInputSeqs, int iMaxNumSeq, int iMaxSeqLen, char *pcHMMBatch) are not documented:
parameter 'iSeqFmt'
parameter 'bIsProfile'
parameter 'bDealignInputSeqs'
parameter 'pcHMMBatch'
/build/reproducible-path/clustalo-1.2.4/src/clustal/seq.c:1104: warning: The following parameters of SeqsAreAligned(mseq_t *prMSeq, bool bIsProfile, bool bDealignInputSeqs) are not documented:
parameter 'bIsProfile'
parameter 'bDealignInputSeqs'
/build/reproducible-path/clustalo-1.2.4/src/clustal/seq.c:867: warning: The following parameter of WriteAlignment(mseq_t *mseq, const char *pcAlnOutfile, int outfmt, int iWrap, bool bResno) is not documented:
parameter 'bResno'
/build/reproducible-path/clustalo-1.2.4/src/clustal/seq.c:399: warning: The following parameters of ReadSequences(mseq_t *prMSeq, char *seqfile, int iSeqType, int iSeqFmt, bool bIsProfile, bool bDealignInputSeqs, int iMaxNumSeq, int iMaxSeqLen, char *pcHMMBatch) are not documented:
parameter 'iSeqFmt'
parameter 'bIsProfile'
parameter 'bDealignInputSeqs'
parameter 'pcHMMBatch'
/build/reproducible-path/clustalo-1.2.4/src/clustal/seq.c:1104: warning: The following parameters of SeqsAreAligned(mseq_t *prMSeq, bool bIsProfile, bool bDealignInputSeqs) are not documented:
parameter 'bIsProfile'
parameter 'bDealignInputSeqs'
/build/reproducible-path/clustalo-1.2.4/src/clustal/seq.c:867: warning: The following parameter of WriteAlignment(mseq_t *mseq, const char *pcAlnOutfile, int outfmt, int iWrap, bool bResno) is not documented:
parameter 'bResno'
/build/reproducible-path/clustalo-1.2.4/src/clustal/symmatrix.c:231: warning: found documented return type for SymMatrixGetValueP that does not return anything
/build/reproducible-path/clustalo-1.2.4/src/clustal/symmatrix.c:307: warning: The following parameter of SymMatrixPrint(symmatrix_t *symmat, char **labels, const char *path, bool bPercID) is not documented:
parameter 'bPercID'
/build/reproducible-path/clustalo-1.2.4/src/clustal/symmatrix.c:231: warning: found documented return type for SymMatrixGetValueP that does not return anything
/build/reproducible-path/clustalo-1.2.4/src/clustal/symmatrix.c:307: warning: The following parameter of SymMatrixPrint(symmatrix_t *symmat, char **labels, const char *path, bool bPercID) is not documented:
parameter 'bPercID'
find doc -name "*.md5" -delete
make[1]: Leaving directory '/build/reproducible-path/clustalo-1.2.4'
dh_install
dh_installdocs
dh_installchangelogs
dh_installexamples
dh_installman
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-armhf.so.3
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged
dpkg-shlibdeps: warning: debian/clustalo/usr/bin/clustalo contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dh_installdeb
dh_gencontrol
dpkg-gencontrol: warning: Depends field of package libclustalo-dev: substitution variable ${shlibs:Depends} used, but is not defined
dpkg-gencontrol: warning: Depends field of package libclustalo-doc: substitution variable ${js:Depends} used, but is not defined
dh_md5sums
dh_builddeb
dpkg-deb: building package 'clustalo' in '../clustalo_1.2.4-8_armhf.deb'.
dpkg-deb: building package 'clustalo-dbgsym' in '../clustalo-dbgsym_1.2.4-8_armhf.deb'.
dpkg-deb: building package 'libclustalo-dev' in '../libclustalo-dev_1.2.4-8_armhf.deb'.
dpkg-deb: building package 'libclustalo-doc' in '../libclustalo-doc_1.2.4-8_all.deb'.
dpkg-genbuildinfo --build=binary -O../clustalo_1.2.4-8_armhf.buildinfo
dpkg-genchanges --build=binary -O../clustalo_1.2.4-8_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/2185/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/2185/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/2185 and its subdirectories
I: Current time: Wed Dec 11 19:54:00 +14 2024
I: pbuilder-time-stamp: 1733896440