I: pbuilder: network access will be disabled during build
I: Current time: Wed Dec 18 01:56:20 +14 2024
I: pbuilder-time-stamp: 1734436580
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 [smalt_0.7.6-13.dsc]
I: copying [./smalt_0.7.6.orig.tar.gz]
I: copying [./smalt_0.7.6-13.debian.tar.xz]
I: Extracting source
gpgv: Signature made Fri Jan 12 06:08:11 2024
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tillea@rki.de"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./smalt_0.7.6-13.dsc: no acceptable signature found
dpkg-source: info: extracting smalt in smalt-0.7.6
dpkg-source: info: unpacking smalt_0.7.6.orig.tar.gz
dpkg-source: info: unpacking smalt_0.7.6-13.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 2to3.patch
dpkg-source: info: applying add-runstatedir.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/5012/tmp/hooks/D01_modify_environment starting
debug: Running on virt32a.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Dec 17 11:57 /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/5012/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/5012/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=fa718fc6645c4be68c3221436ea197e6
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=5012
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.fYXfy97G/pbuilderrc_yUZ6 --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.fYXfy97G/b2 --logfile b2/build.log smalt_0.7.6-13.dsc'
SUDO_GID=113
SUDO_UID=107
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://10.0.0.15:3142/
I: uname -a
Linux i-capture-the-hostname 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/5012/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), zlib1g-dev, python3, samtools, libbambamc-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19680 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on python3; however:
Package python3 is not installed.
pbuilder-satisfydepends-dummy depends on samtools; however:
Package samtools is not installed.
pbuilder-satisfydepends-dummy depends on libbambamc-dev; however:
Package libbambamc-dev is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbambamc-dev{a} libbambamc0{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnsl2{a} libpipeline1{a} libpkgconf3{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tzdata{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget
0 packages upgraded, 75 newly installed, 0 to remove and 0 not upgraded.
Need to get 29.2 MB of archives. After unpacking 103 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main armhf libpython3.12-minimal armhf 3.12.8-3 [802 kB]
Get: 2 http://deb.debian.org/debian unstable/main armhf libexpat1 armhf 2.6.4-1 [83.5 kB]
Get: 3 http://deb.debian.org/debian unstable/main armhf python3.12-minimal armhf 3.12.8-3 [1794 kB]
Get: 4 http://deb.debian.org/debian unstable/main armhf python3-minimal armhf 3.12.7-1 [26.8 kB]
Get: 5 http://deb.debian.org/debian unstable/main armhf media-types all 10.1.0 [26.9 kB]
Get: 6 http://deb.debian.org/debian unstable/main armhf netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian unstable/main armhf tzdata all 2024b-4 [256 kB]
Get: 8 http://deb.debian.org/debian unstable/main armhf libkrb5support0 armhf 1.21.3-3 [30.0 kB]
Get: 9 http://deb.debian.org/debian unstable/main armhf libcom-err2 armhf 1.47.2~rc1-2 [22.9 kB]
Get: 10 http://deb.debian.org/debian unstable/main armhf libk5crypto3 armhf 1.21.3-3 [75.8 kB]
Get: 11 http://deb.debian.org/debian unstable/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B]
Get: 12 http://deb.debian.org/debian unstable/main armhf libkrb5-3 armhf 1.21.3-3 [283 kB]
Get: 13 http://deb.debian.org/debian unstable/main armhf libgssapi-krb5-2 armhf 1.21.3-3 [114 kB]
Get: 14 http://deb.debian.org/debian unstable/main armhf libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get: 15 http://deb.debian.org/debian unstable/main armhf libtirpc3t64 armhf 1.3.4+ds-1.3+b1 [71.3 kB]
Get: 16 http://deb.debian.org/debian unstable/main armhf libnsl2 armhf 1.3.0-3+b3 [35.0 kB]
Get: 17 http://deb.debian.org/debian unstable/main armhf readline-common all 8.2-6 [69.4 kB]
Get: 18 http://deb.debian.org/debian unstable/main armhf libreadline8t64 armhf 8.2-6 [146 kB]
Get: 19 http://deb.debian.org/debian unstable/main armhf libpython3.12-stdlib armhf 3.12.8-3 [1824 kB]
Get: 20 http://deb.debian.org/debian unstable/main armhf python3.12 armhf 3.12.8-3 [677 kB]
Get: 21 http://deb.debian.org/debian unstable/main armhf libpython3-stdlib armhf 3.12.7-1 [9712 B]
Get: 22 http://deb.debian.org/debian unstable/main armhf python3 armhf 3.12.7-1 [27.8 kB]
Get: 23 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB]
Get: 24 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB]
Get: 25 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB]
Get: 26 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3+b1 [42.3 kB]
Get: 27 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.22.5-3 [195 kB]
Get: 28 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB]
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Get: 30 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.2-12 [83.9 kB]
Get: 31 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB]
Get: 32 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB]
Get: 33 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB]
Get: 34 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB]
Get: 35 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get: 36 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get: 37 http://deb.debian.org/debian unstable/main armhf autopoint all 0.22.5-3 [723 kB]
Get: 38 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.21 [88.9 kB]
Get: 39 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-8 [517 kB]
Get: 40 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 41 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 42 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 43 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 44 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.192-4 [184 kB]
Get: 45 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB]
Get: 46 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-5+b1 [9088 kB]
Get: 47 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB]
Get: 48 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.22.5-3 [1488 kB]
Get: 49 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 50 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 51 http://deb.debian.org/debian unstable/main armhf debhelper all 13.21 [919 kB]
Get: 52 http://deb.debian.org/debian unstable/main armhf libbambamc0 armhf 0.0.50-6+b2 [32.4 kB]
Get: 53 http://deb.debian.org/debian unstable/main armhf libpkgconf3 armhf 1.8.1-4 [31.8 kB]
Get: 54 http://deb.debian.org/debian unstable/main armhf pkgconf-bin armhf 1.8.1-4 [29.2 kB]
Get: 55 http://deb.debian.org/debian unstable/main armhf pkgconf armhf 1.8.1-4 [26.1 kB]
Get: 56 http://deb.debian.org/debian unstable/main armhf pkg-config armhf 1.8.1-4 [14.0 kB]
Get: 57 http://deb.debian.org/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB]
Get: 58 http://deb.debian.org/debian unstable/main armhf libbambamc-dev armhf 0.0.50-6+b2 [45.0 kB]
Get: 59 http://deb.debian.org/debian unstable/main armhf libbrotli1 armhf 1.1.0-2+b6 [282 kB]
Get: 60 http://deb.debian.org/debian unstable/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-8 [18.2 kB]
Get: 61 http://deb.debian.org/debian unstable/main armhf libsasl2-2 armhf 2.1.28+dfsg1-8 [50.2 kB]
Get: 62 http://deb.debian.org/debian unstable/main armhf libldap-2.5-0 armhf 2.5.18+dfsg-3+b1 [163 kB]
Get: 63 http://deb.debian.org/debian unstable/main armhf libnghttp2-14 armhf 1.64.0-1 [62.9 kB]
Get: 64 http://deb.debian.org/debian unstable/main armhf libnghttp3-9 armhf 1.6.0-2 [56.8 kB]
Get: 65 http://deb.debian.org/debian unstable/main armhf libngtcp2-16 armhf 1.9.1-1 [115 kB]
Get: 66 http://deb.debian.org/debian unstable/main armhf libngtcp2-crypto-gnutls8 armhf 1.9.1-1 [15.8 kB]
Get: 67 http://deb.debian.org/debian unstable/main armhf libpsl5t64 armhf 0.21.2-1.1+b1 [55.8 kB]
Get: 68 http://deb.debian.org/debian unstable/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b5 [53.2 kB]
Get: 69 http://deb.debian.org/debian unstable/main armhf libssh2-1t64 armhf 1.11.1-1 [227 kB]
Get: 70 http://deb.debian.org/debian unstable/main armhf libcurl3t64-gnutls armhf 8.11.1-1 [311 kB]
Get: 71 http://deb.debian.org/debian unstable/main armhf libdeflate0 armhf 1.22-1 [36.3 kB]
Get: 72 http://deb.debian.org/debian unstable/main armhf libhtscodecs2 armhf 1.6.1-1 [63.1 kB]
Get: 73 http://deb.debian.org/debian unstable/main armhf libhts3t64 armhf 1.20+ds-2 [401 kB]
Get: 74 http://deb.debian.org/debian unstable/main armhf libncurses6 armhf 6.5-2+b1 [82.3 kB]
Get: 75 http://deb.debian.org/debian unstable/main armhf samtools armhf 1.20-3 [620 kB]
Fetched 29.2 MB in 1s (43.7 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libpython3.12-minimal:armhf.
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Preparing to unpack .../libpython3.12-minimal_3.12.8-3_armhf.deb ...
Unpacking libpython3.12-minimal:armhf (3.12.8-3) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../libexpat1_2.6.4-1_armhf.deb ...
Unpacking libexpat1:armhf (2.6.4-1) ...
Selecting previously unselected package python3.12-minimal.
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Unpacking python3.12-minimal (3.12.8-3) ...
Setting up libpython3.12-minimal:armhf (3.12.8-3) ...
Setting up libexpat1:armhf (2.6.4-1) ...
Setting up python3.12-minimal (3.12.8-3) ...
Selecting previously unselected package python3-minimal.
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Unpacking python3-minimal (3.12.7-1) ...
Selecting previously unselected package media-types.
Preparing to unpack .../01-media-types_10.1.0_all.deb ...
Unpacking media-types (10.1.0) ...
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Preparing to unpack .../02-netbase_6.4_all.deb ...
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Preparing to unpack .../03-tzdata_2024b-4_all.deb ...
Unpacking tzdata (2024b-4) ...
Selecting previously unselected package libkrb5support0:armhf.
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Unpacking libkrb5support0:armhf (1.21.3-3) ...
Selecting previously unselected package libcom-err2:armhf.
Preparing to unpack .../05-libcom-err2_1.47.2~rc1-2_armhf.deb ...
Unpacking libcom-err2:armhf (1.47.2~rc1-2) ...
Selecting previously unselected package libk5crypto3:armhf.
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Unpacking libk5crypto3:armhf (1.21.3-3) ...
Selecting previously unselected package libkeyutils1:armhf.
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Unpacking libkeyutils1:armhf (1.6.3-4) ...
Selecting previously unselected package libkrb5-3:armhf.
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Unpacking libkrb5-3:armhf (1.21.3-3) ...
Selecting previously unselected package libgssapi-krb5-2:armhf.
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Unpacking libgssapi-krb5-2:armhf (1.21.3-3) ...
Selecting previously unselected package libtirpc-common.
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Unpacking libtirpc-common (1.3.4+ds-1.3) ...
Selecting previously unselected package libtirpc3t64:armhf.
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Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3 to /lib/arm-linux-gnueabihf/libtirpc.so.3.usr-is-merged by libtirpc3t64'
Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0 to /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
Unpacking libtirpc3t64:armhf (1.3.4+ds-1.3+b1) ...
Selecting previously unselected package libnsl2:armhf.
Preparing to unpack .../12-libnsl2_1.3.0-3+b3_armhf.deb ...
Unpacking libnsl2:armhf (1.3.0-3+b3) ...
Selecting previously unselected package readline-common.
Preparing to unpack .../13-readline-common_8.2-6_all.deb ...
Unpacking readline-common (8.2-6) ...
Selecting previously unselected package libreadline8t64:armhf.
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Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64'
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Current default time zone: 'Etc/UTC'
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Run 'dpkg-reconfigure tzdata' if you wish to change it.
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Not building database; man-db/auto-update is not 'true'.
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Processing triggers for libc-bin (2.40-4) ...
Reading package lists...
Building dependency tree...
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-> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/5012/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/5012/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/smalt-0.7.6/ && 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 > ../smalt_0.7.6-13_source.changes
dpkg-buildpackage: info: source package smalt
dpkg-buildpackage: info: source version 0.7.6-13
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_auto_clean
make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6'
dh_auto_clean
rm -rf test/*.pyc misc/*.pyc test/tmp
find . -type d -name __pycache__ | xargs rm -rf
make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
debian/rules override_dh_autoreconf
make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6'
echo "Do nothing - fails because auf broken upstream autoconf stuff"
Do nothing - fails because auf broken upstream autoconf stuff
make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6'
dh_auto_configure -- CONFIG_SHELL=/bin/bash
./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 CONFIG_SHELL=/bin/bash
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking for icc... no
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 we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... none
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for ranlib... ranlib
checking for a Python interpreter with version >= 2.6... python3
checking for python3... /usr/bin/python3
checking for python3 version... 3.1
checking for python3 platform... linux
checking for python3 script directory... ${prefix}/lib/python3.1/site-packages
checking for python3 extension module directory... ${exec_prefix}/lib/python3.1/site-packages
checking for samtools... yes
checking for sam_open in -lbam... no
checking for BAMBAMC... yes
checking for gzread in -lz... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking pthread.h usability... yes
checking pthread.h presence... yes
checking for pthread.h... yes
checking semaphore.h usability... yes
checking semaphore.h presence... yes
checking for semaphore.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdint.h... (cached) yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking emmintrin.h usability... no
checking emmintrin.h presence... no
checking for emmintrin.h... no
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating test/Makefile
config.status: creating test/data/Makefile
config.status: creating misc/Makefile
config.status: creating config.h
config.status: executing depfiles commands
make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
debian/rules override_dh_auto_build-arch
make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6'
dh_auto_build -a
make -j4
make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6'
make all-recursive
make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6'
Making all in src
make[4]: Entering directory '/build/reproducible-path/smalt-0.7.6/src'
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c elib.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c filio.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sequence.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libsgm_a-score.o `test -f 'score.c' || echo './'`score.c
sequence.c: In function 'make3BitMangledCodec':
sequence.c:298:14: warning: comparison of integer expressions of different signedness: 'int' and 'enum SEQ_CONSTANTS' [-Wsign-compare]
298 | for (i=1; i<SIZE_CODTAB; i++) {
| ^
sequence.c: In function 'seqCodecCreateFromAlphabet':
sequence.c:372:14: warning: comparison of integer expressions of different signedness: 'int' and 'enum SEQ_CONSTANTS' [-Wsign-compare]
372 | for (i=0; i<SIZE_DECODTAB; i++)
| ^
sequence.c:378:14: warning: comparison of integer expressions of different signedness: 'int' and 'enum SEQ_CONSTANTS' [-Wsign-compare]
378 | for (i=0; i<SIZE_CODTAB; i++) {
| ^
score.c:49:21: warning: 'LN0P25' defined but not used [-Wunused-const-variable=]
49 | static const double LN0P25 = -1.386294; /* natural logarithm of 1/4 */
| ^~~~~~
sequence.c: In function 'fprintSeqFastqSequence':
sequence.c:1700:16: warning: comparison of integer expressions of different signedness: 'short int' and 'enum SEQ_CONSTANTS' [-Wsign-compare]
1700 | if (linewidth>OUTBUFSIZE) linewidth = OUTBUFSIZE;
| ^
sequence.c: In function 'seqFastqGetConstSequence':
sequence.c:2079:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
2079 | if (length)
| ^~
sequence.c:2081:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
2081 | return NULL;
| ^~~~~~
sequence.c: In function 'seqFastqGetSequence':
sequence.c:2094:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
2094 | if (length)
| ^~
sequence.c:2096:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
2096 | return NULL;
| ^~~~~~
sequence.c: In function 'seqIOopen':
sequence.c:489:5: warning: this statement may fall through [-Wimplicit-fallthrough=]
489 | strcpy(p->fmode, "r");
| ^~~~~~~~~~~~~~~~~~~~~
sequence.c:491:3: note: here
491 | case SEQIO_WRITE_GZIP_FASTA:
| ^~~~
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libsgm_a-diffstr.o `test -f 'diffstr.c' || echo './'`diffstr.c
diffstr.c: In function 'diffStrGetDiffStats':
diffstr.c:978:22: warning: the comparison will always evaluate as 'true' for the pointer operand in 'diffstrp + 1' must not be NULL [-Waddress]
978 | if (diffstrp+1 != NULL) {
| ^~
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libsgm_a-alibuffer.o `test -f 'alibuffer.c' || echo './'`alibuffer.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libsgm_a-alignment.o `test -f 'alignment.c' || echo './'`alignment.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libsgm_a-sort.o `test -f 'sort.c' || echo './'`sort.c
alignment.c:478:13: warning: 'blankALITRACK' defined but not used [-Wunused-function]
478 | static void blankALITRACK(ALITRACK *trackp, const ALIBAND *bandp)
| ^~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libsgm_a-array.o `test -f 'array.c' || echo './'`array.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libsgm_a-interval.o `test -f 'interval.c' || echo './'`interval.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libsgm_a-hashidx.o `test -f 'hashidx.c' || echo './'`hashidx.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libsgm_a-hashhit.o `test -f 'hashhit.c' || echo './'`hashhit.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libsgm_a-segment.o `test -f 'segment.c' || echo './'`segment.c
hashidx.c: In function 'countPerfectKey':
hashidx.c:191:77: warning: unused parameter 'tuplectr' [-Wunused-parameter]
191 | static int countPerfectKey(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr)
| ~~~~~~~~~~^~~~~~~~
hashidx.c: In function 'countCollisionKey':
hashidx.c:206:79: warning: unused parameter 'tuplectr' [-Wunused-parameter]
206 | static int countCollisionKey(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr)
| ~~~~~~~~~~^~~~~~~~
hashidx.c: In function 'collectWords':
hashidx.c:223:74: warning: unused parameter 'tuplectr' [-Wunused-parameter]
223 | static int collectWords(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr)
| ~~~~~~~~~~^~~~~~~~
hashidx.c: In function 'countWords':
hashidx.c:265:72: warning: unused parameter 'tuplectr' [-Wunused-parameter]
265 | static int countWords(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr)
| ~~~~~~~~~~^~~~~~~~
hashidx.c: At top level:
hashidx.c:446:18: warning: 'getWordHisto' defined but not used [-Wunused-function]
446 | static WORDNUM_t getWordHisto(WORDNUM_t *counts, HASHNUM_t n, const HashTable *htp)
| ^~~~~~~~~~~~
hashidx.c:63:19: warning: 'HASHTABFIL_READERRMSG' defined but not used [-Wunused-const-variable=]
63 | static const char HASHTABFIL_READERRMSG[] = "when reading hash table file";
| ^~~~~~~~~~~~~~~~~~~~~
hashhit.c: In function 'hashCreateHitList':
hashhit.c:1559:18: warning: comparison of integer expressions of different signedness: 'int' and 'enum <anonymous>' [-Wsign-compare]
1559 | if (maxnhits < HITLST_MINSIZ) maxnhits = HITLST_MINSIZ;
| ^
segment.c:1375:12: warning: 'checkCANDARRsequential' defined but not used [-Wunused-function]
1375 | static int checkCANDARRsequential(const CANDARR candr, SEGNUM_t *rvc_offs)
| ^~~~~~~~~~~~~~~~~~~~~~
segment.c:1330:13: warning: 'labelSEGCANDWithinInsertRange' defined but not used [-Wunused-function]
1330 | static void labelSEGCANDWithinInsertRange (SEGCAND *candAp, SEGNUM_t nsegA,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o smalt-smalt.o `test -f 'smalt.c' || echo './'`smalt.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o smalt-menu.o `test -f 'menu.c' || echo './'`menu.c
smalt.c: In function 'cleanupSmaltOutput':
smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter]
659 | static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op)
| ~~~~~~~~^~~~~~~
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o smalt-threads.o `test -f 'threads.c' || echo './'`threads.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o smalt-infmt.o `test -f 'infmt.c' || echo './'`infmt.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o smalt-results.o `test -f 'results.c' || echo './'`results.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o smalt-resultpairs.o `test -f 'resultpairs.c' || echo './'`resultpairs.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o smalt-report.o `test -f 'report.c' || echo './'`report.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o smalt-rmap.o `test -f 'rmap.c' || echo './'`rmap.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o smalt-insert.o `test -f 'insert.c' || echo './'`insert.c
rm -f libseq.a
ar cru libseq.a elib.o filio.o sequence.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libseq.a
rm -f libsgm.a
ar cru libsgm.a libsgm_a-score.o libsgm_a-diffstr.o libsgm_a-alibuffer.o libsgm_a-alignment.o libsgm_a-sort.o libsgm_a-array.o libsgm_a-interval.o libsgm_a-hashidx.o libsgm_a-hashhit.o libsgm_a-segment.o libseq.a
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libsgm.a
gcc -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o smalt smalt-smalt.o smalt-menu.o smalt-threads.o smalt-infmt.o smalt-results.o smalt-resultpairs.o smalt-report.o smalt-rmap.o smalt-insert.o libsgm.a libseq.a -lbambamc -lz -lm -lpthread -lz
make[4]: Leaving directory '/build/reproducible-path/smalt-0.7.6/src'
Making all in test
make[4]: Entering directory '/build/reproducible-path/smalt-0.7.6/test'
make[5]: Entering directory '/build/reproducible-path/smalt-0.7.6/test'
make[5]: Nothing to be done for 'all-am'.
make[5]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test'
make[4]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test'
Making all in misc
make[4]: Entering directory '/build/reproducible-path/smalt-0.7.6/misc'
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c simread.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c rsample.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c fetchseq.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c splitreads.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c mixreads.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c splitmates.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c readstats.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c trunkreads.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c basqcol.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c basqual.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c simqual.c
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o diffstr.o `test -f '../src/diffstr.c' || echo './'`../src/diffstr.c
../src/diffstr.c: In function 'diffStrGetDiffStats':
../src/diffstr.c:978:22: warning: the comparison will always evaluate as 'true' for the pointer operand in 'diffstrp + 1' must not be NULL [-Waddress]
978 | if (diffstrp+1 != NULL) {
| ^~
gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o fetchseq fetchseq.o ../src/libseq.a -lz
gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o splitreads splitreads.o ../src/libseq.a -lz
gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o mixreads mixreads.o ../src/libseq.a -lz
gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o splitmates splitmates.o ../src/libseq.a -lz
gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o readstats readstats.o ../src/libseq.a -lz
gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o trunkreads trunkreads.o ../src/libseq.a -lz
gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o basqcol basqcol.o basqual.o ../src/libseq.a -lz
gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o simread simread.o rsample.o ../src/libsgm.a ../src/libseq.a -lm -lz
gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o simqual simqual.o basqual.o diffstr.o ../src/libseq.a -lm -lz
make[4]: Leaving directory '/build/reproducible-path/smalt-0.7.6/misc'
make[4]: Entering directory '/build/reproducible-path/smalt-0.7.6'
make[4]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
make[3]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
make -C test sequenceReverseComplement_test
make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6/test'
gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c sequenceReverseComplement_test.c
gcc -I../src/ -I../test -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o sequenceReverseComplement_test sequenceReverseComplement_test.o ../src/libseq.a -lz
make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test'
make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
dh_auto_build -Nsmalt
make -j4
make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6'
make all-recursive
make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6'
Making all in src
make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6/src'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/build/reproducible-path/smalt-0.7.6/src'
Making all in test
make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6/test'
make[4]: Entering directory '/build/reproducible-path/smalt-0.7.6/test'
make[4]: Nothing to be done for 'all-am'.
make[4]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test'
make[3]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test'
Making all in misc
make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6/misc'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/build/reproducible-path/smalt-0.7.6/misc'
make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6'
make[3]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
dh_auto_test
make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1
make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6'
Making check in src
make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6/src'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6/src'
Making check in test
make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6/test'
make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6/test'
make sequenceReverseComplement_test smalt_Xali_test
make[4]: Entering directory '/build/reproducible-path/smalt-0.7.6/test'
make[4]: 'sequenceReverseComplement_test' is up to date.
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o smalt_Xali_test-smalt.o `test -f '../src/smalt.c' || echo './'`../src/smalt.c
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o smalt_Xali_test-menu.o `test -f '../src/menu.c' || echo './'`../src/menu.c
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o smalt_Xali_test-threads.o `test -f '../src/threads.c' || echo './'`../src/threads.c
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o smalt_Xali_test-infmt.o `test -f '../src/infmt.c' || echo './'`../src/infmt.c
../src/smalt.c: In function 'cleanupSmaltOutput':
../src/smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter]
659 | static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op)
| ~~~~~~~~^~~~~~~
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o smalt_Xali_test-results.o `test -f '../src/results.c' || echo './'`../src/results.c
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o smalt_Xali_test-resultpairs.o `test -f '../src/resultpairs.c' || echo './'`../src/resultpairs.c
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o smalt_Xali_test-insert.o `test -f '../src/insert.c' || echo './'`../src/insert.c
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o smalt_Xali_test-report.o `test -f '../src/report.c' || echo './'`../src/report.c
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o smalt_Xali_test-rmap.o `test -f '../src/rmap.c' || echo './'`../src/rmap.c
gcc -I../src/ -I../test -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o smalt_Xali_test smalt_Xali_test-smalt.o smalt_Xali_test-menu.o smalt_Xali_test-threads.o smalt_Xali_test-infmt.o smalt_Xali_test-results.o smalt_Xali_test-resultpairs.o smalt_Xali_test-insert.o smalt_Xali_test-report.o smalt_Xali_test-rmap.o ../src/libsgm.a ../src/libseq.a -lbambamc -lz -lm -lpthread -lz
make[4]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test'
make check-TESTS
make[4]: Entering directory '/build/reproducible-path/smalt-0.7.6/test'
/build/reproducible-path/smalt-0.7.6/test/formats.py:32: SyntaxWarning: invalid escape sequence '\d'
CIGARSTR = compile("^cigar:([ABCDNRSP]):(\d{2})\s+(\S+)\s+(\d+)\s+(\d+)\s+([*+-])\s+" \
/build/reproducible-path/smalt-0.7.6/test/formats.py:33: SyntaxWarning: invalid escape sequence '\S'
"(\S+)\s+(\d+)\s+(\d+)\s+\+\s+(\d+)\s+(.+)$")
PASS: splitReads_test.py
/build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:13: SyntaxWarning: invalid escape sequence '\d'
"Bbf^BcfBbdcfBdcfcddYbaB\dfYcc\ec_efeed\_cTebcacced"\
/build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:14: SyntaxWarning: invalid escape sequence '\e'
"bebf`^fa^cV`fde^\ecc`d`cbccfeTbdbeZcefccf^fccbfBc!\n",
/build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:20: SyntaxWarning: invalid escape sequence '\`'
"edff^Yc^`dY`\\fefa^ddcYb^ef`adfdB\`f\`c`defce`adde!\n",
/build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:25: SyntaxWarning: invalid escape sequence '\B'
"Yfffcc\BYBf`dedBeeaZf^c^adff`BbfeTB_bdf\`YfdeBfBdd"\
/build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:26: SyntaxWarning: invalid escape sequence '\e'
"eB_ae\eVff]dTedc_dcff^cVa_^d\\affdfdfddcadbbBT^fBd!\n",
/build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:32: SyntaxWarning: invalid escape sequence '\c'
"B``bdZffbeMUcUaTfeceb`V^fecaddde\cfW^de[Bececec`B!\n",
/build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:37: SyntaxWarning: invalid escape sequence '\e'
"daBZddeYdBfe`fBf`ecfdfcf`c\eacXdbLe^b``ccadK]e]^_T"\
/build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:38: SyntaxWarning: invalid escape sequence '\T'
"fccbcd\Tffb^Yfdfdf^efa\[fbfdad`X\\Ue_^eBfcfcfNfdf^!\n"
PASS: results_split_test.py
PASS: ouform_cigar_test.py
PASS: sample_test.py
PASS: cigar_test.py
PASS: mthread_test.py
PASS: ioform_test.py
/build/reproducible-path/smalt-0.7.6/test/./xali_test.py:76: SyntaxWarning: invalid escape sequence '\S'
REFNAMNO = compile("^\S+_(\d+)")
/build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:5: SyntaxWarning: invalid escape sequence '\S'
SAMSTR = re.compile("^(\S+)\t(\d+)\t(\S+)\t(\d+)\t(\d+)\t(\S+)\t(\S+)\t"\
/build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:6: SyntaxWarning: invalid escape sequence '\d'
"(\d+)\t([\+\-]*\d+)\t(\S+)\t(\S+)"\
/build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:8: SyntaxWarning: invalid escape sequence '\S'
TAGSTR = re.compile("^(\S{2}):([iZ]):(\S+)")
/build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:13: SyntaxWarning: invalid escape sequence '\S'
QNAMSTR = re.compile("^(\S+)\/([12])$")
/build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:14: SyntaxWarning: invalid escape sequence '\d'
ALISCOR = re.compile("\tAS:i:(\d+)")
/build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:15: SyntaxWarning: invalid escape sequence '\d'
CLIPSTART = re.compile("^(\d+)([HS])")
/build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:16: SyntaxWarning: invalid escape sequence '\d'
CLIPEND = re.compile("(\d+)([HS])$")
PASS: xali_test.py
PASS: bam_cigar_test.py
==================
All 9 tests passed
==================
make[4]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test'
make[3]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test'
make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test'
Making check in misc
make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6/misc'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6/misc'
make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6'
make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
create-stamp debian/debhelper-build-stamp
dh_prep
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6'
# upstream install does install more files than needed
make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
debian/rules override_dh_install-indep
make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6'
dh_install
# fix path to smalt executable in examples
for py in `ls test/*.py` ; do \
sed 's#PROGNAM = "../src/smalt"#PROGNAM = "/usr/bin/smalt"#' ${py} > debian/smalt-examples/usr/share/doc/smalt/${py} ; \
done
make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
dh_install -Nsmalt-examples
dh_installdocs
dh_installchangelogs
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
dh_md5sums
dh_builddeb
dpkg-deb: building package 'smalt' in '../smalt_0.7.6-13_armhf.deb'.
dpkg-deb: building package 'smalt-dbgsym' in '../smalt-dbgsym_0.7.6-13_armhf.deb'.
dpkg-deb: building package 'smalt-examples' in '../smalt-examples_0.7.6-13_all.deb'.
dpkg-genbuildinfo --build=binary -O../smalt_0.7.6-13_armhf.buildinfo
dpkg-genchanges --build=binary -O../smalt_0.7.6-13_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/5012/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/5012/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/5012 and its subdirectories
I: Current time: Wed Dec 18 02:09:26 +14 2024
I: pbuilder-time-stamp: 1734437366