I: pbuilder: network access will be disabled during build
I: Current time: Thu Jan 16 18:31:30 +14 2025
I: pbuilder-time-stamp: 1737001890
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 [hmmer2_2.3.2+dfsg-12.dsc]
I: copying [./hmmer2_2.3.2+dfsg.orig.tar.xz]
I: copying [./hmmer2_2.3.2+dfsg-12.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./hmmer2_2.3.2+dfsg-12.dsc: unsupported subcommand
dpkg-source: info: extracting hmmer2 in hmmer2-2.3.2+dfsg
dpkg-source: info: unpacking hmmer2_2.3.2+dfsg.orig.tar.xz
dpkg-source: info: unpacking hmmer2_2.3.2+dfsg-12.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying version2-manpage
dpkg-source: info: applying userguidepdf
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying use_debian_packaged_biosquid.patch
dpkg-source: info: applying build_libhmmer.a_with-fPIC.patch
dpkg-source: info: applying add-runstatedir-option.patch
dpkg-source: info: applying fixup-implicit-function-declaration.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/20717/tmp/hooks/D01_modify_environment starting
debug: Running on virt64a.
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 Jan 16 04:31 /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/20717/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/20717/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=cfff7151dbe44b68a31ccd981e7845c5
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=20717
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.y4DlVTPn/pbuilderrc_Pcrx --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.y4DlVTPn/b2 --logfile b2/build.log hmmer2_2.3.2+dfsg-12.dsc'
SUDO_GID=114
SUDO_UID=108
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 6.1.0-30-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/20717/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), libperl4-corelibs-perl, libsquid-dev, pkgconf, dh-exec, rename
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19563 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 libperl4-corelibs-perl; however:
Package libperl4-corelibs-perl is not installed.
pbuilder-satisfydepends-dummy depends on libsquid-dev; however:
Package libsquid-dev is not installed.
pbuilder-satisfydepends-dummy depends on pkgconf; however:
Package pkgconf is not installed.
pbuilder-satisfydepends-dummy depends on dh-exec; however:
Package dh-exec is not installed.
pbuilder-satisfydepends-dummy depends on rename; however:
Package rename 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-exec{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libperl4-corelibs-perl{a} libpipeline1{a} libpkgconf3{a} libsquid-dev{a} libsquid1t64{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} rename{a} sensible-utils{a}
The following packages are RECOMMENDED but will NOT be installed:
curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 38 newly installed, 0 to remove and 0 not upgraded.
Need to get 20.1 MB of archives. After unpacking 75.4 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 0.23.1-1 [238 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 1.23.0-7 [1095 kB]
Get: 8 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.4-1 [84.6 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 1.4.19-5 [272 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 0.23.1-1 [770 kB]
Get: 16 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.23 [90.6 kB]
Get: 17 http://deb.debian.org/debian unstable/main armhf libtool all 2.5.4-2 [539 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 libunistring5 armhf 1.3-1 [444 kB]
Get: 25 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-6 [9086 kB]
Get: 26 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB]
Get: 27 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.23.1-1 [1560 kB]
Get: 28 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian unstable/main armhf debhelper all 13.23 [919 kB]
Get: 31 http://deb.debian.org/debian unstable/main armhf dh-exec armhf 0.30 [24.3 kB]
Get: 32 http://deb.debian.org/debian unstable/main armhf libperl4-corelibs-perl all 0.005-1 [39.0 kB]
Get: 33 http://deb.debian.org/debian unstable/main armhf libpkgconf3 armhf 1.8.1-4 [31.8 kB]
Get: 34 http://deb.debian.org/debian unstable/main armhf libsquid1t64 armhf 1.9g+cvs20050121-15.1+b2 [63.6 kB]
Get: 35 http://deb.debian.org/debian unstable/main armhf libsquid-dev armhf 1.9g+cvs20050121-15.1+b2 [132 kB]
Get: 36 http://deb.debian.org/debian unstable/main armhf pkgconf-bin armhf 1.8.1-4 [29.2 kB]
Get: 37 http://deb.debian.org/debian unstable/main armhf pkgconf armhf 1.8.1-4 [26.1 kB]
Get: 38 http://deb.debian.org/debian unstable/main armhf rename all 2.02-1 [21.8 kB]
Fetched 20.1 MB in 1s (29.0 MB/s)
Preconfiguring packages ...
Selecting previously unselected package sensible-utils.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19563 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_armhf.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:armhf.
Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_armhf.deb ...
Unpacking libmagic1t64:armhf (1:5.45-3+b1) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.45-3+b1_armhf.deb ...
Unpacking file (1:5.45-3+b1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.23.1-1_armhf.deb ...
Unpacking gettext-base (0.23.1-1) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.23.0-7_armhf.deb ...
Unpacking groff-base (1.23.0-7) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.40.4-1_armhf.deb ...
Unpacking bsdextrautils (2.40.4-1) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../08-libpipeline1_1.5.8-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.8-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.13.0-1_armhf.deb ...
Unpacking man-db (2.13.0-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-5_armhf.deb ...
Unpacking m4 (1.4.19-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../11-autoconf_2.72-3_all.deb ...
Unpacking autoconf (2.72-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ...
Unpacking autopoint (0.23.1-1) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../15-libdebhelper-perl_13.23_all.deb ...
Unpacking libdebhelper-perl (13.23) ...
Selecting previously unselected package libtool.
Preparing to unpack .../16-libtool_2.5.4-2_all.deb ...
Unpacking libtool (2.5.4-2) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../17-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.14.0-1) ...
Selecting previously unselected package libelf1t64:armhf.
Preparing to unpack .../21-libelf1t64_0.192-4_armhf.deb ...
Unpacking libelf1t64:armhf (0.192-4) ...
Selecting previously unselected package dwz.
Preparing to unpack .../22-dwz_0.15-1+b2_armhf.deb ...
Unpacking dwz (0.15-1+b2) ...
Selecting previously unselected package libunistring5:armhf.
Preparing to unpack .../23-libunistring5_1.3-1_armhf.deb ...
Unpacking libunistring5:armhf (1.3-1) ...
Selecting previously unselected package libicu72:armhf.
Preparing to unpack .../24-libicu72_72.1-6_armhf.deb ...
Unpacking libicu72:armhf (72.1-6) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_armhf.deb ...
Unpacking libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../26-gettext_0.23.1-1_armhf.deb ...
Unpacking gettext (0.23.1-1) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../29-debhelper_13.23_all.deb ...
Unpacking debhelper (13.23) ...
Selecting previously unselected package dh-exec.
Preparing to unpack .../30-dh-exec_0.30_armhf.deb ...
Unpacking dh-exec (0.30) ...
Selecting previously unselected package libperl4-corelibs-perl.
Preparing to unpack .../31-libperl4-corelibs-perl_0.005-1_all.deb ...
Unpacking libperl4-corelibs-perl (0.005-1) ...
Selecting previously unselected package libpkgconf3:armhf.
Preparing to unpack .../32-libpkgconf3_1.8.1-4_armhf.deb ...
Unpacking libpkgconf3:armhf (1.8.1-4) ...
Selecting previously unselected package libsquid1t64:armhf.
Preparing to unpack .../33-libsquid1t64_1.9g+cvs20050121-15.1+b2_armhf.deb ...
Unpacking libsquid1t64:armhf (1.9g+cvs20050121-15.1+b2) ...
Selecting previously unselected package libsquid-dev.
Preparing to unpack .../34-libsquid-dev_1.9g+cvs20050121-15.1+b2_armhf.deb ...
Unpacking libsquid-dev (1.9g+cvs20050121-15.1+b2) ...
Selecting previously unselected package pkgconf-bin.
Preparing to unpack .../35-pkgconf-bin_1.8.1-4_armhf.deb ...
Unpacking pkgconf-bin (1.8.1-4) ...
Selecting previously unselected package pkgconf:armhf.
Preparing to unpack .../36-pkgconf_1.8.1-4_armhf.deb ...
Unpacking pkgconf:armhf (1.8.1-4) ...
Selecting previously unselected package rename.
Preparing to unpack .../37-rename_2.02-1_all.deb ...
Unpacking rename (2.02-1) ...
Setting up libpipeline1:armhf (1.5.8-1) ...
Setting up libicu72:armhf (72.1-6) ...
Setting up bsdextrautils (2.40.4-1) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.23) ...
Setting up libperl4-corelibs-perl (0.005-1) ...
Setting up libmagic1t64:armhf (1:5.45-3+b1) ...
Setting up gettext-base (0.23.1-1) ...
Setting up m4 (1.4.19-5) ...
Setting up rename (2.02-1) ...
update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:armhf (0.192-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up libpkgconf3:armhf (1.8.1-4) ...
Setting up libunistring5:armhf (1.3-1) ...
Setting up autopoint (0.23.1-1) ...
Setting up pkgconf-bin (1.8.1-4) ...
Setting up autoconf (2.72-3) ...
Setting up dwz (0.15-1+b2) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:armhf (0.0.8-1+b2) ...
Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up libsquid1t64:armhf (1.9g+cvs20050121-15.1+b2) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.0-1) ...
Setting up gettext (0.23.1-1) ...
Setting up libtool (2.5.4-2) ...
Setting up libsquid-dev (1.9g+cvs20050121-15.1+b2) ...
Setting up pkgconf:armhf (1.8.1-4) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.14.0-1) ...
Setting up groff-base (1.23.0-7) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.23) ...
Setting up dh-exec (0.30) ...
Processing triggers for libc-bin (2.40-5) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/20717/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/20717/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/hmmer2-2.3.2+dfsg/ && 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 > ../hmmer2_2.3.2+dfsg-12_source.changes
dpkg-buildpackage: info: source package hmmer2
dpkg-buildpackage: info: source version 2.3.2+dfsg-12
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/hmmer2-2.3.2+dfsg'
dh_clean
if [ -e configure_not_used ] ; then mv configure_not_used configure; fi
rm -f configure.ac src/config.h
make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg'
debian/rules binary
dh binary
dh_update_autotools_config
debian/rules override_dh_autoreconf
make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg'
cp -a debian/missing-sources/configure.ac .
mv configure configure_not_used
dh_autoreconf
configure.ac:119: warning: underquoted definition of CHECK_GNU_MAKE
configure.ac:119: run info Automake 'Extending aclocal'
configure.ac:119: or see https://www.gnu.org/software/automake/manual/automake.html#Extending-aclocal
configure.ac:161: warning: The macro 'AC_TRY_COMPILE' is obsolete.
configure.ac:161: You should run autoupdate.
./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from...
configure.ac:161: the top level
configure.ac:487: warning: The macro 'AC_LANG_C' is obsolete.
configure.ac:487: You should run autoupdate.
./lib/autoconf/c.m4:72: AC_LANG_C is expanded from...
configure.ac:289: ACX_PTHREAD is expanded from...
lib/m4sugar/m4sh.m4:697: AS_IF is expanded from...
./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from...
configure.ac:487: the top level
configure.ac:487: warning: The macro 'AC_TRY_LINK' is obsolete.
configure.ac:487: You should run autoupdate.
./lib/autoconf/general.m4:2918: AC_TRY_LINK is expanded from...
configure.ac:289: ACX_PTHREAD is expanded from...
lib/m4sugar/m4sh.m4:697: AS_IF is expanded from...
./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from...
configure.ac:487: the top level
make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg'
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg'
dh_auto_configure -- --enable-threads --enable-lfs PTHREAD_CFLAGS="-D_XOPEN_SOURCE=500" # --enable-pvm
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-threads --enable-lfs PTHREAD_CFLAGS=-D_XOPEN_SOURCE=500
configure: configuring HMMER for your system.
configure: This is a full source distribution - using full config
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 for ranlib... ranlib
checking for ar... /usr/bin/ar
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking whether your make is GNU make... yes, it is.
configure: configured for optional LFS, large file support
configure: enabled POSIX multithreading support
checking for pthread_setconcurrency... yes
checking for pthread_attr_setscope... yes
checking for pthread_join in LIBS= with CFLAGS=-D_XOPEN_SOURCE=500... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for cc_r... gcc
checking for ntohs... yes
checking for ntohl... yes
checking for htons... yes
checking for htonl... yes
configure: creating ./config.status
config.status: creating src/Makefile
config.status: creating testsuite/Makefile
config.status: creating Makefile
config.status: WARNING: 'Makefile.in' seems to ignore the --datarootdir setting
config.status: creating src/config.h
# avoid duplicated definition of PACKAGE_NAME (basically conflicting with biosquid when used together)
sed -i -e '/^#define PACKAGE_NAME /i #ifndef PACKAGE_NAME' \
-e '/^#define PACKAGE_NAME /a #endif' \
-e '/^#define PACKAGE_VERSION /i #ifndef PACKAGE_VERSION' \
-e '/^#define PACKAGE_VERSION /a #endif' \
-e '/^#define _LARGEFILE_SOURCE /i #ifndef _LARGEFILE_SOURCE' \
-e '/^#define _LARGEFILE_SOURCE /a #endif' \
-e '/^#define _LARGEFILE64_SOURCE /i #ifndef _LARGEFILE64_SOURCE' \
-e '/^#define _LARGEFILE64_SOURCE /a #endif' \
-e '/^#define VERSION /i #ifndef VERSION' \
-e '/^#define VERSION /a #endif' \
src/config.h
make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg'
dh_auto_build
make -j4
make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg'
make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/src'
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmalign.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c alphabet.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c core_algorithms.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c debug.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c display.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c emit.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c emulation.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c fast_algorithms.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c histogram.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmio.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c mathsupport.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c masks.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c misc.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c modelmakers.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c plan7.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c plan9.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c postprob.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c prior.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c pvm.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c threads.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c tophits.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c trace.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmbuild.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmcalibrate.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmconvert.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmemit.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmfetch.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmindex.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmpfam.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -D_XOPEN_SOURCE=500 `/usr/bin/pkg-config --cflags libsquid` -c hmmsearch.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmalign hmmalign.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmcalibrate hmmcalibrate.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmconvert hmmconvert.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmemit hmmemit.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmfetch hmmfetch.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmindex hmmindex.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmbuild hmmbuild.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmpfam hmmpfam.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fPIC -D_XOPEN_SOURCE=500 -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmsearch hmmsearch.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `/usr/bin/pkg-config --libs libsquid` -lm
make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/src'
make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/src'
/usr/bin/ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o
a - alphabet.o
a - core_algorithms.o
a - debug.o
a - display.o
a - emit.o
a - emulation.o
a - fast_algorithms.o
a - histogram.o
a - hmmio.o
a - mathsupport.o
a - masks.o
a - misc.o
a - modelmakers.o
a - plan7.o
a - plan9.o
a - postprob.o
a - prior.o
a - pvm.o
a - threads.o
a - tophits.o
a - trace.o
ranlib libhmmer.a
chmod 644 libhmmer.a
make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/src'
make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite'
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_XOPEN_SOURCE=500 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c alignalign_test.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_XOPEN_SOURCE=500 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c evd_test.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_XOPEN_SOURCE=500 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c masks_test.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_XOPEN_SOURCE=500 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c parsingviterbi_test.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_XOPEN_SOURCE=500 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c tophits_test.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_XOPEN_SOURCE=500 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c trace_test.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_XOPEN_SOURCE=500 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c viterbi_exercise.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_XOPEN_SOURCE=500 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `/usr/bin/pkg-config --cflags libsquid` -I../src -c weeviterbi_test.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o alignalign_test -L../src alignalign_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o evd_test -L../src evd_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o masks_test -L../src masks_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o parsingviterbi_test -L../src parsingviterbi_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o tophits_test -L../src tophits_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o trace_test -L../src trace_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o viterbi_exercise -L../src viterbi_exercise.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_XOPEN_SOURCE=500 -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o weeviterbi_test -L../src weeviterbi_test.o -lhmmer `/usr/bin/pkg-config --libs libsquid` -lm
make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite'
make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg'
dh_auto_test
make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1
make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg'
(cd testsuite; make check)
make[3]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite'
Running test suite exercises.
Warning: some tests may take several minutes to complete.
./sqc 2 exercises.sqc . ../src
exercise 1 [ hmmalign] ... ok.
exercise 2 [ hmmalign/h] ... ok.
exercise 3 [ hmmalign/m] ... ok.
exercise 4 [ hmmalign/o] ... ok.
exercise 5 [ hmmalign/q] ... ok.
exercise 6 [ hmmalign/informat] ... ok.
exercise 7 [ hmmalign/selex] ... ok.
exercise 8 [ hmmalign/a2m] ... ok.
exercise 9 [ hmmalign/clustal] ... ok.
exercise 10 [ hmmalign/msf] ... ok.
exercise 11 [ hmmalign/phylip] ... ok.
exercise 12 [ hmmalign/oneline] ... ok.
exercise 13 [ hmmalign/withali] ... ok.
exercise 14 [ hmmalign/mapali] ... ok.
exercise 15 [ hmmbuild] ... ok.
exercise 16 [ hmmbuild/h] ... ok.
exercise 17 [ hmmbuild/F] ... ok.
exercise 18 [ hmmbuild/n] ... ok.
exercise 19 [ hmmbuild/o] ... ok.
exercise 20 [ hmmbuild/A] ... ok.
exercise 21 [ hmmbuild/f] ... ok.
exercise 22 [ hmmbuild/g] ... ok.
exercise 23 [ hmmbuild/s] ... ok.
exercise 24 [ hmmbuild/fast] ... ok.
exercise 25 [ hmmbuild/hand] ... ok.
exercise 26 [ hmmbuild/null] ... ok.
exercise 27 [ hmmbuild/pam] ... ok.
exercise 28 [ hmmbuild/prior] ... ok.
exercise 29 [ hmmbuild/wblosum] ... ok.
exercise 30 [ hmmbuild/wgsc] ... ok.
exercise 31 [ hmmbuild/wme] ... ok.
exercise 32 [ hmmbuild/wpb] ... ok.
exercise 33 [ hmmbuild/wvoronoi] ... ok.
exercise 34 [ hmmbuild/wnone] ... ok.
exercise 35 [ hmmbuild/noeff] ... ok.
exercise 36 [ hmmbuild/pbswitch] ... ok.
exercise 37 [ hmmbuild/amino] ... ok.
exercise 38 [ hmmbuild/nucleic] ... ok.
exercise 39 [ hmmbuild/archpri] ... ok.
exercise 40 [ hmmbuild/binary] ... ok.
exercise 41 [ hmmbuild/cfile] ... ok.
exercise 42 [ hmmbuild/gapmax] ... ok.
exercise 43 [ hmmbuild/idlevel] ... ok.
exercise 44 [ hmmbuild/informat] ... ok.
exercise 45 [ hmmbuild/pamwgt] ... ok.
exercise 46 [ hmmbuild/swentry] ... ok.
exercise 47 [ hmmbuild/swexit] ... ok.
exercise 48 [ hmmbuild/verbose] ... ok.
exercise 49 [ hmmcalibrate] ... ok.
exercise 50 [ hmmcalibrate/h] ... ok.
exercise 51 [ hmmcalibrate/fixed] ... ok.
exercise 52 [ hmmcalibrate/mean] ... ok.
exercise 53 [ hmmcalibrate/hist] ... ok.
exercise 54 [ hmmcalibrate/num] ... ok.
exercise 55 [ hmmcalibrate/sd] ... ok.
exercise 56 [ hmmcalibrate/seed] ... ok.
exercise 57 [ hmmconvert] ... ok.
exercise 58 [ hmmconvert/h] ... ok.
exercise 59 [ hmmconvert/F] ... ok.
exercise 60 [ hmmconvert/a] ... ok.
exercise 61 [ hmmconvert/A] ... ok.
exercise 62 [ hmmconvert/b] ... ok.
exercise 63 [ hmmconvert/p] ... ok.
exercise 64 [ hmmconvert/P] ... ok.
exercise 65 [ hmmemit] ... ok.
exercise 66 [ hmmemit/a] ... ok.
exercise 67 [ hmmemit/c] ... ok.
exercise 68 [ hmmemit/h] ... ok.
exercise 69 [ hmmemit/n] ... ok.
exercise 70 [ hmmemit/o] ... ok.
exercise 71 [ hmmemit/q] ... ok.
exercise 72 [ hmmemit/seed] ... ok.
exercise 73 [ hmmindex] ... ok.
exercise 74 [ hmmindex/h] ... ok.
exercise 75 [ hmmfetch] ... ok.
exercise 76 [ hmmfetch/h] ... ok.
exercise 77 [ hmmfetch/n] ... ok.
exercise 78 [ hmmpfam] ... ok.
exercise 79 [ hmmpfam/h] ... ok.
exercise 80 [ hmmpfam/n] ... ok.
exercise 81 [ hmmpfam/A] ... ok.
exercise 82 [ hmmpfam/E] ... ok.
exercise 83 [ hmmpfam/T] ... ok.
exercise 84 [ hmmpfam/Z] ... ok.
exercise 85 [ hmmpfam/acc] ... ok.
exercise 86 [ hmmpfam/compat] ... ok.
exercise 87 [ hmmpfam/cut_ga] ... ok.
exercise 88 [ hmmpfam/cut_nc] ... ok.
exercise 89 [ hmmpfam/cut_tc] ... ok.
exercise 90 [ hmmpfam/domE] ... ok.
exercise 91 [ hmmpfam/domT] ... ok.
exercise 92 [ hmmpfam/forward] ... ok.
exercise 93 [ hmmpfam/informat] ... ok.
exercise 94 [ hmmpfam/null2] ... ok.
exercise 95 [ hmmpfam/xnu] ... ok.
exercise 96 [ hmmsearch] ... ok.
exercise 97 [ hmmsearch/h] ... ok.
exercise 98 [ hmmsearch/A] ... ok.
exercise 99 [ hmmsearch/E] ... ok.
exercise 100 [ hmmsearch/T] ... ok.
exercise 101 [ hmmsearch/Z] ... ok.
exercise 102 [ hmmsearch/compat] ... ok.
exercise 103 [ hmmsearch/cut_ga] ... ok.
exercise 104 [ hmmsearch/cut_nc] ... ok.
exercise 105 [ hmmsearch/cut_tc] ... ok.
exercise 106 [ hmmsearch/domE] ... ok.
exercise 107 [ hmmsearch/domT] ... ok.
exercise 108 [ hmmsearch/forward] ... ok.
exercise 109 [ hmmsearch/informat] ... ok.
exercise 110 [ hmmsearch/null2] ... ok.
exercise 111 [ hmmsearch/xnu] ... ok.
exercise 112 [ align_align] ... ok.
exercise 113 [ evd] ... ok.
exercise 114 [ masks] ... ok.
exercise 115 [ parsingv] ... ok.
exercise 116 [ tophits] ... ok.
exercise 117 [ trace] ... ok.
exercise 118 [ viterbi] ... ok.
exercise 119 [ weeviterbi] ... ok.
exercise 120 [ test1/conversion] ... ok.
All 120 exercises at level <= 2 passed.
System information:
Thu Jan 16 04:34:19 2025
Linux i-capture-the-hostname 6.1.0-30-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux
make[3]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite'
make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg'
rm -f testsuite/*.ssi
cd testsuite && make clean
make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite'
rm -f *.o *~ Makefile.bak core alignalign_test evd_test masks_test parsingviterbi_test tophits_test trace_test viterbi_exercise weeviterbi_test TAGS gmon.out
make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite'
make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg'
create-stamp debian/debhelper-build-stamp
dh_prep
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg'
dh_auto_install -- prefix=/build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp
make -j4 install DESTDIR=/build/reproducible-path/hmmer2-2.3.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/build/reproducible-path/hmmer2-2.3.2\+dfsg/debian/tmp
make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg'
mkdir -p /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/bin
mkdir -p /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1
for file in hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch ; do\
cp src/$file /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/bin/;\
done
for file in hmmer hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch; do\
cp documentation/man/$file.man /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/$file.1;\
done
make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg'
# lkajan: rename binaries and man pages like this: s/hmm/hmm2/ - except hmmer.1, rename that to hmmer2.1:
rename 's/^hmm/hmm2/;' /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/bin/*
cd /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/bin; rename 's/^hmm/hmm2/;' *
cd /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1; rename 's/^hmm/hmm2/;' *
mv /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/hmm2er.1 /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/hmmer2.1
# lkajan: resolve man page hypen issue:
sed -i -e 's/--/\\-\\-/g;s/-\([[:alpha:]]\)\b/\\-\1/g;' /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/*
make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg'
debian/rules override_dh_install
make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg'
sed -e "s/@DEB_HOST_MULTIARCH@/arm-linux-gnueabihf/" \
-e "s/@VERSION@/2.3.2/" debian/pkgconfig/libhmmer2.pc.in > debian/pkgconfig/libhmmer2.pc
dh_install
rm -f debian/pkgconfig/libhmmer2.pc
make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg'
dh_installdocs
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg'
dh_installchangelogs -k NOTES
make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg'
debian/rules override_dh_installexamples
make[1]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg'
cd testsuite && make clean && cd ..
make[2]: Entering directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite'
rm -f *.o *~ Makefile.bak core alignalign_test evd_test masks_test parsingviterbi_test tophits_test trace_test viterbi_exercise weeviterbi_test TAGS gmon.out
make[2]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg/testsuite'
dh_installexamples
mkdir -p /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples;
cp -a testsuite/* /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/;
mkdir /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/tutorial;
cp -a tutorial/* /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/tutorial;
sed -i "s#hmm#hmm2#g" /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/exercises.sqc
sed -i "s#../tut#./tut#g" /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/exercises.sqc
find /build/reproducible-path/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples -name 'Makefile' | xargs sed -i "s^/build/reproducible-path/hmmer2-2.3.2+dfsg^.^g"
make[1]: Leaving directory '/build/reproducible-path/hmmer2-2.3.2+dfsg'
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
dh_installdeb
dh_gencontrol
dpkg-gencontrol: warning: Depends field of package libhmmer2-dev: substitution variable ${shlibs:Depends} used, but is not defined
dpkg-gencontrol: warning: Depends field of package hmmer2-doc: substitution variable ${shlibs:Depends} used, but is not defined
dh_md5sums
dh_builddeb
dpkg-deb: building package 'hmmer2-doc' in '../hmmer2-doc_2.3.2+dfsg-12_all.deb'.
dpkg-deb: building package 'libhmmer2-dev' in '../libhmmer2-dev_2.3.2+dfsg-12_armhf.deb'.
dpkg-deb: building package 'hmmer2-dbgsym' in '../hmmer2-dbgsym_2.3.2+dfsg-12_armhf.deb'.
dpkg-deb: building package 'hmmer2' in '../hmmer2_2.3.2+dfsg-12_armhf.deb'.
dpkg-genbuildinfo --build=binary -O../hmmer2_2.3.2+dfsg-12_armhf.buildinfo
dpkg-genchanges --build=binary -O../hmmer2_2.3.2+dfsg-12_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/20717/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/20717/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/20717 and its subdirectories
I: Current time: Thu Jan 16 18:34:46 +14 2025
I: pbuilder-time-stamp: 1737002086