I: pbuilder: network access will be disabled during build
I: Current time: Sun Jun 30 11:24:53 -12 2024
I: pbuilder-time-stamp: 1719789893
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-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-8.dsc]
I: copying [./hmmer2_2.3.2+dfsg.orig.tar.xz]
I: copying [./hmmer2_2.3.2+dfsg-8.debian.tar.xz]
I: Extracting source
gpgv: Signature made Sun Dec 11 04:03:58 2022 -12
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 ./hmmer2_2.3.2+dfsg-8.dsc: no acceptable signature found
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-8.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
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/1594052/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 '
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='ba2fdb77b44740abb9c8a349f7dad914'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='1594052'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.TZDV5VK3/pbuilderrc_XenV --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.TZDV5VK3/b1 --logfile b1/build.log hmmer2_2.3.2+dfsg-8.dsc'
SUDO_GID='111'
SUDO_UID='106'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://85.184.249.68:3128'
I: uname -a
Linux ionos15-amd64 6.1.0-0.deb11.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.20-2~bpo11+1 (2023-04-23) x86_64 GNU/Linux
I: ls -l /bin
total 5632
-rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2
-rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore
-rwxr-xr-x 1 root root 44016 Sep 20 2022 cat
-rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 72752 Sep 20 2022 chown
-rwxr-xr-x 1 root root 151152 Sep 20 2022 cp
-rwxr-xr-x 1 root root 125640 Jan 5 2023 dash
-rwxr-xr-x 1 root root 121904 Sep 20 2022 date
-rwxr-xr-x 1 root root 89240 Sep 20 2022 dd
-rwxr-xr-x 1 root root 102200 Sep 20 2022 df
-rwxr-xr-x 1 root root 151344 Sep 20 2022 dir
-rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg
lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname
-rwxr-xr-x 1 root root 43856 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 2023 egrep
-rwxr-xr-x 1 root root 35664 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep
-rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt
-rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount
-rwxr-xr-x 1 root root 203152 Jan 24 2023 grep
-rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe
-rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip
-rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname
-rwxr-xr-x 1 root root 72824 Sep 20 2022 ln
-rwxr-xr-x 1 root root 53024 Mar 23 2023 login
-rwxr-xr-x 1 root root 151344 Sep 20 2022 ls
-rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk
-rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 59712 Mar 22 2023 more
-rwsr-xr-x 1 root root 59704 Mar 22 2023 mount
-rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint
-rwxr-xr-x 1 root root 142968 Sep 20 2022 mv
lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash
-rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 72752 Sep 20 2022 rm
-rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts
-rwxr-xr-x 1 root root 126424 Jan 5 2023 sed
lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash
-rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 85008 Sep 20 2022 stty
-rwsr-xr-x 1 root root 72000 Mar 22 2023 su
-rwxr-xr-x 1 root root 39824 Sep 20 2022 sync
-rwxr-xr-x 1 root root 531984 Apr 6 2023 tar
-rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile
-rwxr-xr-x 1 root root 109616 Sep 20 2022 touch
-rwxr-xr-x 1 root root 35664 Sep 20 2022 true
-rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server
-rwsr-xr-x 1 root root 35128 Mar 22 2023 umount
-rwxr-xr-x 1 root root 43888 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
-rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl
lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 9 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 9 2022 znew
I: user script /srv/workspace/pbuilder/1594052/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <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, pkg-config, 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 ... 19591 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 pkg-config; however:
Package pkg-config 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} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libperl4-corelibs-perl{a} libpipeline1{a} libpkgconf3{a} libsquid-dev{a} libsquid1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkg-config{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, 39 newly installed, 0 to remove and 0 not upgraded.
Need to get 19.1 MB of archives. After unpacking 73.8 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 2 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB]
Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB]
Get: 4 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB]
Get: 5 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB]
Get: 6 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB]
Get: 7 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB]
Get: 8 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB]
Get: 9 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB]
Get: 10 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB]
Get: 11 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB]
Get: 12 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB]
Get: 13 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB]
Get: 16 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 17 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB]
Get: 18 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B]
Get: 21 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 22 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 23 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB]
Get: 24 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB]
Get: 25 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB]
Get: 26 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB]
Get: 27 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB]
Get: 28 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB]
Get: 31 http://deb.debian.org/debian bookworm/main amd64 dh-exec amd64 0.27 [27.8 kB]
Get: 32 http://deb.debian.org/debian bookworm/main amd64 libperl4-corelibs-perl all 0.004-3 [38.5 kB]
Get: 33 http://deb.debian.org/debian bookworm/main amd64 libpkgconf3 amd64 1.8.1-1 [36.1 kB]
Get: 34 http://deb.debian.org/debian bookworm/main amd64 libsquid1 amd64 1.9g+cvs20050121-12 [76.6 kB]
Get: 35 http://deb.debian.org/debian bookworm/main amd64 libsquid-dev amd64 1.9g+cvs20050121-12 [145 kB]
Get: 36 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB]
Get: 37 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB]
Get: 38 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB]
Get: 39 http://deb.debian.org/debian bookworm/main amd64 rename all 2.01-1 [21.0 kB]
Fetched 19.1 MB in 0s (85.2 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sensible-utils.
(Reading database ...
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(Reading database ... 10%
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19591 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ...
Unpacking sensible-utils (0.0.17+nmu1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_amd64.deb ...
Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:amd64.
Preparing to unpack .../02-libmagic1_1%3a5.44-3_amd64.deb ...
Unpacking libmagic1:amd64 (1:5.44-3) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.44-3_amd64.deb ...
Unpacking file (1:5.44-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.21-12_amd64.deb ...
Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:amd64.
Preparing to unpack .../05-libuchardet0_0.0.7-1_amd64.deb ...
Unpacking libuchardet0:amd64 (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.22.4-10_amd64.deb ...
Unpacking groff-base (1.22.4-10) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_amd64.deb ...
Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:amd64.
Preparing to unpack .../08-libpipeline1_1.5.7-1_amd64.deb ...
Unpacking libpipeline1:amd64 (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.11.2-2_amd64.deb ...
Unpacking man-db (2.11.2-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-3_amd64.deb ...
Unpacking m4 (1.4.19-3) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../11-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
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_0.21-12_all.deb ...
Unpacking autopoint (0.21-12) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ...
Unpacking libdebhelper-perl (13.11.4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../16-libtool_2.4.7-5_all.deb ...
Unpacking libtool (2.4.7-5) ...
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 libsub-override-perl.
Preparing to unpack .../19-libsub-override-perl_0.09-4_all.deb ...
Unpacking libsub-override-perl (0.09-4) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.13.1-1) ...
Selecting previously unselected package libelf1:amd64.
Preparing to unpack .../22-libelf1_0.188-2.1_amd64.deb ...
Unpacking libelf1:amd64 (0.188-2.1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../23-dwz_0.15-1_amd64.deb ...
Unpacking dwz (0.15-1) ...
Selecting previously unselected package libicu72:amd64.
Preparing to unpack .../24-libicu72_72.1-3_amd64.deb ...
Unpacking libicu72:amd64 (72.1-3) ...
Selecting previously unselected package libxml2:amd64.
Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.2_amd64.deb ...
Unpacking libxml2:amd64 (2.9.14+dfsg-1.2) ...
Selecting previously unselected package gettext.
Preparing to unpack .../26-gettext_0.21-12_amd64.deb ...
Unpacking gettext (0.21-12) ...
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_13.11.4_all.deb ...
Unpacking debhelper (13.11.4) ...
Selecting previously unselected package dh-exec.
Preparing to unpack .../30-dh-exec_0.27_amd64.deb ...
Unpacking dh-exec (0.27) ...
Selecting previously unselected package libperl4-corelibs-perl.
Preparing to unpack .../31-libperl4-corelibs-perl_0.004-3_all.deb ...
Unpacking libperl4-corelibs-perl (0.004-3) ...
Selecting previously unselected package libpkgconf3:amd64.
Preparing to unpack .../32-libpkgconf3_1.8.1-1_amd64.deb ...
Unpacking libpkgconf3:amd64 (1.8.1-1) ...
Selecting previously unselected package libsquid1.
Preparing to unpack .../33-libsquid1_1.9g+cvs20050121-12_amd64.deb ...
Unpacking libsquid1 (1.9g+cvs20050121-12) ...
Selecting previously unselected package libsquid-dev.
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Setting up libpipeline1:amd64 (1.5.7-1) ...
Setting up libicu72:amd64 (72.1-3) ...
Setting up bsdextrautils (2.38.1-5+b1) ...
Setting up libmagic-mgc (1:5.44-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.11.4) ...
Setting up libperl4-corelibs-perl (0.004-3) ...
Setting up libmagic1:amd64 (1:5.44-3) ...
Setting up gettext-base (0.21-12) ...
Setting up m4 (1.4.19-3) ...
Setting up rename (2.01-1) ...
update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode
Setting up file (1:5.44-3) ...
Setting up autotools-dev (20220109.1) ...
Setting up libpkgconf3:amd64 (1.8.1-1) ...
Setting up autopoint (0.21-12) ...
Setting up pkgconf-bin (1.8.1-1) ...
Setting up autoconf (2.71-3) ...
Setting up libsquid1 (1.9g+cvs20050121-12) ...
Setting up sensible-utils (0.0.17+nmu1) ...
Setting up libuchardet0:amd64 (0.0.7-1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libelf1:amd64 (0.188-2.1) ...
Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ...
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 (1.13.1-1) ...
Setting up gettext (0.21-12) ...
Setting up libtool (2.4.7-5) ...
Setting up libsquid-dev (1.9g+cvs20050121-12) ...
Setting up pkgconf:amd64 (1.8.1-1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up pkg-config:amd64 (1.8.1-1) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
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Not building database; man-db/auto-update is not 'true'.
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Setting up dh-exec (0.27) ...
Processing triggers for libc-bin (2.36-9) ...
Reading package lists...
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/hmmer2-2.3.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../hmmer2_2.3.2+dfsg-8_source.changes
dpkg-buildpackage: info: source package hmmer2
dpkg-buildpackage: info: source version 2.3.2+dfsg-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 amd64
debian/rules clean
dh clean
debian/rules override_dh_clean
make[1]: Entering directory '/build/hmmer2-2.3.2+dfsg'
if [ -e configure_not_used ] ; then mv configure_not_used configure; fi
rm -f configure.ac
make[1]: Leaving directory '/build/hmmer2-2.3.2+dfsg'
debian/rules binary
dh binary
dh_update_autotools_config
debian/rules override_dh_autoreconf
make[1]: Entering directory '/build/hmmer2-2.3.2+dfsg'
cp -a debian/missing-sources/configure.ac .
mv configure configure_not_used
dh_autoreconf
configure.ac:111: warning: underquoted definition of CHECK_GNU_MAKE
configure.ac:111: run info Automake 'Extending aclocal'
configure.ac:111: or see https://www.gnu.org/software/automake/manual/automake.html#Extending-aclocal
configure.ac:153: warning: The macro `AC_TRY_COMPILE' is obsolete.
configure.ac:153: You should run autoupdate.
./lib/autoconf/general.m4:2847: AC_TRY_COMPILE is expanded from...
configure.ac:153: the top level
configure.ac:479: warning: The macro `AC_LANG_C' is obsolete.
configure.ac:479: You should run autoupdate.
./lib/autoconf/c.m4:72: AC_LANG_C is expanded from...
configure.ac:281: ACX_PTHREAD is expanded from...
lib/m4sugar/m4sh.m4:699: AS_IF is expanded from...
./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from...
configure.ac:479: the top level
configure.ac:479: warning: The macro `AC_TRY_LINK' is obsolete.
configure.ac:479: You should run autoupdate.
./lib/autoconf/general.m4:2920: AC_TRY_LINK is expanded from...
configure.ac:281: ACX_PTHREAD is expanded from...
lib/m4sugar/m4sh.m4:699: AS_IF is expanded from...
./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from...
configure.ac:479: the top level
make[1]: Leaving directory '/build/hmmer2-2.3.2+dfsg'
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/hmmer2-2.3.2+dfsg'
dh_auto_configure -- --enable-threads --enable-lfs # --enable-pvm
./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-threads --enable-lfs
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 build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
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 the pthreads library -lpthreads... no
checking whether pthreads work without any flags... 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/hmmer2-2.3.2+dfsg'
dh_auto_build
make -j16
make[1]: Entering directory '/build/hmmer2-2.3.2+dfsg'
make[2]: Entering directory '/build/hmmer2-2.3.2+dfsg/src'
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmalign.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c alphabet.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c core_algorithms.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c debug.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c display.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c emit.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c emulation.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c fast_algorithms.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c histogram.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmio.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c mathsupport.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c masks.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c misc.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c modelmakers.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c plan7.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c plan9.c
mathsupport.c: In function 'Logp_cvec':
mathsupport.c:229:15: warning: implicit declaration of function 'Gammln' [-Wimplicit-function-declaration]
229 | lnp += Gammln(alpha[x] + cvec[x]);
| ^~~~~~
histogram.c: In function 'ExtremeValueSetHistogram':
histogram.c:725:23: warning: implicit declaration of function 'IncompleteGamma' [-Wimplicit-function-declaration]
725 | h->chip = (float) IncompleteGamma((double)(nbins-1-ndegrees)/2.,
| ^~~~~~~~~~~~~~~
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c postprob.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c prior.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c pvm.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c threads.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c tophits.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c trace.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmbuild.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmcalibrate.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmconvert.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmemit.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmfetch.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmindex.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmpfam.c
hmmcalibrate.c: In function 'workpool_start':
hmmcalibrate.c:646:3: warning: implicit declaration of function 'pthread_setconcurrency' [-Wimplicit-function-declaration]
646 | pthread_setconcurrency(num_threads+1);
| ^~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -c hmmsearch.c
hmmpfam.c: In function 'workpool_start':
hmmpfam.c:1032:3: warning: implicit declaration of function 'pthread_setconcurrency' [-Wimplicit-function-declaration]
1032 | pthread_setconcurrency(num_threads+1);
| ^~~~~~~~~~~~~~~~~~~~~~
hmmsearch.c: In function 'workpool_start':
hmmsearch.c:1021:3: warning: implicit declaration of function 'pthread_setconcurrency' [-Wimplicit-function-declaration]
1021 | pthread_setconcurrency(num_threads+1);
| ^~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -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 `pkg-config --libs libsquid` -lm
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -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 `pkg-config --libs libsquid` -lm
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -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 `pkg-config --libs libsquid` -lm
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -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 `pkg-config --libs libsquid` -lm
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -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 `pkg-config --libs libsquid` -lm
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -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 `pkg-config --libs libsquid` -lm
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -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 `pkg-config --libs libsquid` -lm
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -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 `pkg-config --libs libsquid` -lm
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -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 `pkg-config --libs libsquid` -lm
make[2]: Leaving directory '/build/hmmer2-2.3.2+dfsg/src'
make[2]: Entering directory '/build/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/hmmer2-2.3.2+dfsg/src'
make[2]: Entering directory '/build/hmmer2-2.3.2+dfsg/testsuite'
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c alignalign_test.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c evd_test.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c masks_test.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c parsingviterbi_test.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c tophits_test.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c trace_test.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c viterbi_exercise.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c weeviterbi_test.c
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o trace_test -L../src trace_test.o -lhmmer `pkg-config --libs libsquid` -lm
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o tophits_test -L../src tophits_test.o -lhmmer `pkg-config --libs libsquid` -lm
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o masks_test -L../src masks_test.o -lhmmer `pkg-config --libs libsquid` -lm
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o weeviterbi_test -L../src weeviterbi_test.o -lhmmer `pkg-config --libs libsquid` -lm
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o alignalign_test -L../src alignalign_test.o -lhmmer `pkg-config --libs libsquid` -lm
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o parsingviterbi_test -L../src parsingviterbi_test.o -lhmmer `pkg-config --libs libsquid` -lm
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o viterbi_exercise -L../src viterbi_exercise.o -lhmmer `pkg-config --libs libsquid` -lm
gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o evd_test -L../src evd_test.o -lhmmer `pkg-config --libs libsquid` -lm
make[2]: Leaving directory '/build/hmmer2-2.3.2+dfsg/testsuite'
make[1]: Leaving directory '/build/hmmer2-2.3.2+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/hmmer2-2.3.2+dfsg'
dh_auto_test
make -j16 check "TESTSUITEFLAGS=-j16 --verbose" VERBOSE=1
make[2]: Entering directory '/build/hmmer2-2.3.2+dfsg'
(cd testsuite; make check)
make[3]: Entering directory '/build/hmmer2-2.3.2+dfsg/testsuite'
make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
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:
Sun Jun 30 11:25:21 -12 2024
Linux ionos15-amd64 6.1.0-0.deb11.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.20-2~bpo11+1 (2023-04-23) x86_64 GNU/Linux
make[3]: Leaving directory '/build/hmmer2-2.3.2+dfsg/testsuite'
make[2]: Leaving directory '/build/hmmer2-2.3.2+dfsg'
rm -f testsuite/*.ssi
cd testsuite && make clean
make[2]: Entering directory '/build/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/hmmer2-2.3.2+dfsg/testsuite'
make[1]: Leaving directory '/build/hmmer2-2.3.2+dfsg'
create-stamp debian/debhelper-build-stamp
dh_prep
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/hmmer2-2.3.2+dfsg'
dh_auto_install -- prefix=/build/hmmer2-2.3.2+dfsg/debian/tmp
make -j16 install DESTDIR=/build/hmmer2-2.3.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/build/hmmer2-2.3.2\+dfsg/debian/tmp
make[2]: Entering directory '/build/hmmer2-2.3.2+dfsg'
mkdir -p /build/hmmer2-2.3.2+dfsg/debian/tmp/bin
mkdir -p /build/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/$file /build/hmmer2-2.3.2+dfsg/debian/tmp/bin/;\
done
for file in hmmer hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch; do\
cp documentation/man/$file.man /build/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/$file.1;\
done
make[2]: Leaving directory '/build/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/hmmer2-2.3.2+dfsg/debian/tmp/bin/*
cd /build/hmmer2-2.3.2+dfsg/debian/tmp/bin; rename 's/^hmm/hmm2/;' *
cd /build/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1; rename 's/^hmm/hmm2/;' *
mv /build/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/hmm2er.1 /build/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/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/*
make[1]: Leaving directory '/build/hmmer2-2.3.2+dfsg'
dh_install
dh_installdocs
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/build/hmmer2-2.3.2+dfsg'
dh_installchangelogs -k NOTES
make[1]: Leaving directory '/build/hmmer2-2.3.2+dfsg'
debian/rules override_dh_installexamples
make[1]: Entering directory '/build/hmmer2-2.3.2+dfsg'
dh_installexamples
mkdir -p /build/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples;
sed -i "s#hmm#hmm2#g" testsuite/exercises.sqc
cp -a testsuite/* /build/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/;
mkdir /build/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/tutorial;
cp -a tutorial/* /build/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/tutorial;
sed -i "s#../tut#./tut#g" /build/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/exercises.sqc
find /build/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples -name 'Makefile' | xargs sed -i "s^/build/hmmer2-2.3.2+dfsg^.^g"
make[1]: Leaving directory '/build/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
dh_installdeb
dh_gencontrol
dpkg-gencontrol: warning: Depends field of package hmmer2-doc: substitution variable ${shlibs:Depends} used, but is not defined
dpkg-gencontrol: warning: Depends field of package libhmmer2-dev: substitution variable ${shlibs:Depends} used, but is not defined
dh_md5sums
dh_builddeb
dpkg-deb: building package 'hmmer2' in '../hmmer2_2.3.2+dfsg-8_amd64.deb'.
dpkg-deb: building package 'hmmer2-doc' in '../hmmer2-doc_2.3.2+dfsg-8_all.deb'.
dpkg-deb: building package 'hmmer2-dbgsym' in '../hmmer2-dbgsym_2.3.2+dfsg-8_amd64.deb'.
dpkg-deb: building package 'libhmmer2-dev' in '../libhmmer2-dev_2.3.2+dfsg-8_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../hmmer2_2.3.2+dfsg-8_amd64.buildinfo
dpkg-genchanges --build=binary -O../hmmer2_2.3.2+dfsg-8_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: 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/1594052 and its subdirectories
I: Current time: Sun Jun 30 11:25:29 -12 2024
I: pbuilder-time-stamp: 1719789929