I: pbuilder: network access will be disabled during build
I: Current time: Sun Mar 29 19:34:48 -12 2026
I: pbuilder-time-stamp: 1774856088
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: using eatmydata during job
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
dpkg-source: warning: cannot verify inline signature for ./smalt_0.7.6-13.dsc: unsupported subcommand
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/41280/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='i386'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='4557e5b3c5cb44f9946621d394163a5e'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
LD_LIBRARY_PATH='/usr/lib/libeatmydata'
LD_PRELOAD='libeatmydata.so'
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='41280'
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.4tU1zcxd/pbuilderrc_K7CE --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.4tU1zcxd/b1 --logfile b1/build.log smalt_0.7.6-13.dsc'
SUDO_GID='112'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://213.165.73.152:3128'
I: uname -a
Linux ionos6-i386 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/41280/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: i386
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 ... 19788 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} libffi8{a} libfile-stripnondeterminism-perl{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-0{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{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} python3.13{a} python3.13-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, 78 newly installed, 0 to remove and 0 not upgraded.
Need to get 34.4 MB of archives. After unpacking 122 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main i386 libpython3.13-minimal i386 3.13.2-1 [859 kB]
Get: 2 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.4-1 [107 kB]
Get: 3 http://deb.debian.org/debian trixie/main i386 python3.13-minimal i386 3.13.2-1 [2266 kB]
Get: 4 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.13.1-2 [27.0 kB]
Get: 5 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB]
Get: 6 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian trixie/main i386 tzdata all 2025a-2 [259 kB]
Get: 8 http://deb.debian.org/debian trixie/main i386 libffi8 i386 3.4.7-1 [21.4 kB]
Get: 9 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-6 [69.4 kB]
Get: 10 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-6 [173 kB]
Get: 11 http://deb.debian.org/debian trixie/main i386 libpython3.13-stdlib i386 3.13.2-1 [1985 kB]
Get: 12 http://deb.debian.org/debian trixie/main i386 python3.13 i386 3.13.2-1 [745 kB]
Get: 13 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.13.1-2 [9952 B]
Get: 14 http://deb.debian.org/debian trixie/main i386 python3 i386 3.13.1-2 [28.0 kB]
Get: 15 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 16 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 17 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 18 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 19 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.23.1-1 [245 kB]
Get: 20 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 21 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-7 [1199 kB]
Get: 22 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.4-4 [96.4 kB]
Get: 23 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 24 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 25 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-5 [301 kB]
Get: 26 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB]
Get: 27 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 28 http://deb.debian.org/debian trixie/main i386 automake all 1:1.17-3 [862 kB]
Get: 29 http://deb.debian.org/debian trixie/main i386 autopoint all 0.23.1-1 [770 kB]
Get: 30 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 31 http://deb.debian.org/debian trixie/main i386 libtool all 2.5.4-3 [539 kB]
Get: 32 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 33 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 34 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 35 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 36 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 37 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 38 http://deb.debian.org/debian trixie/main i386 libunistring5 i386 1.3-1 [458 kB]
Get: 39 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-6 [9582 kB]
Get: 40 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB]
Get: 41 http://deb.debian.org/debian trixie/main i386 gettext i386 0.23.1-1 [1714 kB]
Get: 42 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 43 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 44 http://deb.debian.org/debian trixie/main i386 debhelper all 13.24.1 [920 kB]
Get: 45 http://deb.debian.org/debian trixie/main i386 libbambamc0 i386 0.0.50-6+b2 [43.7 kB]
Get: 46 http://deb.debian.org/debian trixie/main i386 libpkgconf3 i386 1.8.1-4 [38.4 kB]
Get: 47 http://deb.debian.org/debian trixie/main i386 pkgconf-bin i386 1.8.1-4 [30.6 kB]
Get: 48 http://deb.debian.org/debian trixie/main i386 pkgconf i386 1.8.1-4 [26.2 kB]
Get: 49 http://deb.debian.org/debian trixie/main i386 pkg-config i386 1.8.1-4 [14.0 kB]
Get: 50 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB]
Get: 51 http://deb.debian.org/debian trixie/main i386 libbambamc-dev i386 0.0.50-6+b2 [58.4 kB]
Get: 52 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB]
Get: 53 http://deb.debian.org/debian trixie/main i386 libcom-err2 i386 1.47.2-1 [24.3 kB]
Get: 54 http://deb.debian.org/debian trixie/main i386 libidn2-0 i386 2.3.7-2+b1 [130 kB]
Get: 55 http://deb.debian.org/debian trixie/main i386 libp11-kit0 i386 0.25.5-3 [423 kB]
Get: 56 http://deb.debian.org/debian trixie/main i386 libtasn1-6 i386 4.20.0-2 [51.6 kB]
Get: 57 http://deb.debian.org/debian trixie/main i386 libgnutls30t64 i386 3.8.9-2 [1462 kB]
Get: 58 http://deb.debian.org/debian trixie/main i386 libkrb5support0 i386 1.21.3-4 [35.0 kB]
Get: 59 http://deb.debian.org/debian trixie/main i386 libk5crypto3 i386 1.21.3-4 [83.7 kB]
Get: 60 http://deb.debian.org/debian trixie/main i386 libkeyutils1 i386 1.6.3-4 [9600 B]
Get: 61 http://deb.debian.org/debian trixie/main i386 libkrb5-3 i386 1.21.3-4 [354 kB]
Get: 62 http://deb.debian.org/debian trixie/main i386 libgssapi-krb5-2 i386 1.21.3-4 [149 kB]
Get: 63 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8+b1 [20.9 kB]
Get: 64 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-8+b1 [61.3 kB]
Get: 65 http://deb.debian.org/debian trixie/main i386 libldap2 i386 2.6.9+dfsg-1 [205 kB]
Get: 66 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB]
Get: 67 http://deb.debian.org/debian trixie/main i386 libnghttp3-9 i386 1.6.0-2 [75.9 kB]
Get: 68 http://deb.debian.org/debian trixie/main i386 libngtcp2-16 i386 1.9.1-1 [151 kB]
Get: 69 http://deb.debian.org/debian trixie/main i386 libngtcp2-crypto-gnutls8 i386 1.9.1-1 [19.1 kB]
Get: 70 http://deb.debian.org/debian trixie/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB]
Get: 71 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB]
Get: 72 http://deb.debian.org/debian trixie/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB]
Get: 73 http://deb.debian.org/debian trixie/main i386 libcurl3t64-gnutls i386 8.12.1-2 [411 kB]
Get: 74 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.23-1+b1 [48.4 kB]
Get: 75 http://deb.debian.org/debian trixie/main i386 libhtscodecs2 i386 1.6.1-2 [70.9 kB]
Get: 76 http://deb.debian.org/debian trixie/main i386 libhts3t64 i386 1.21+ds-1 [506 kB]
Get: 77 http://deb.debian.org/debian trixie/main i386 libncurses6 i386 6.5+20250216-1 [112 kB]
Get: 78 http://deb.debian.org/debian trixie/main i386 samtools i386 1.21-1 [700 kB]
Fetched 34.4 MB in 0s (89.0 MB/s)
Preconfiguring packages ...
Selecting previously unselected package libpython3.13-minimal:i386.
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Setting up libpython3.13-minimal:i386 (3.13.2-1) ...
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Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
Unpacking libreadline8t64:i386 (8.2-6) ...
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Current default time zone: 'Etc/UTC'
Local time is now: Mon Mar 30 07:35:10 UTC 2026.
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Run 'dpkg-reconfigure tzdata' if you wish to change it.
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update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
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Processing triggers for libc-bin (2.40-7) ...
Reading package lists...
Building dependency tree...
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/smalt-0.7.6/ && 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 > ../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 i386
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=i686-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/i386-linux-gnu --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... yes
checking emmintrin.h presence... yes
checking for emmintrin.h... yes
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
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 -j22
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.. -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 -Wformat -Werror=format-security -c elib.c
gcc -DHAVE_CONFIG_H -I. -I.. -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 -Wformat -Werror=format-security -c filio.c
gcc -DHAVE_CONFIG_H -I. -I.. -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 -Wformat -Werror=format-security -c sequence.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-score.o `test -f 'score.c' || echo './'`score.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-diffstr.o `test -f 'diffstr.c' || echo './'`diffstr.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-alibuffer.o `test -f 'alibuffer.c' || echo './'`alibuffer.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-alignment.o `test -f 'alignment.c' || echo './'`alignment.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-swsimd.o `test -f 'swsimd.c' || echo './'`swsimd.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-sort.o `test -f 'sort.c' || echo './'`sort.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-array.o `test -f 'array.c' || echo './'`array.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-interval.o `test -f 'interval.c' || echo './'`interval.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-hashidx.o `test -f 'hashidx.c' || echo './'`hashidx.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-hashhit.o `test -f 'hashhit.c' || echo './'`hashhit.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-segment.o `test -f 'segment.c' || echo './'`segment.c
gcc -DHAVE_CONFIG_H -I. -I.. -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 -Wformat -Werror=format-security -c -o smalt-smalt.o `test -f 'smalt.c' || echo './'`smalt.c
gcc -DHAVE_CONFIG_H -I. -I.. -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 -Wformat -Werror=format-security -c -o smalt-menu.o `test -f 'menu.c' || echo './'`menu.c
gcc -DHAVE_CONFIG_H -I. -I.. -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 -Wformat -Werror=format-security -c -o smalt-threads.o `test -f 'threads.c' || echo './'`threads.c
gcc -DHAVE_CONFIG_H -I. -I.. -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 -Wformat -Werror=format-security -c -o smalt-infmt.o `test -f 'infmt.c' || echo './'`infmt.c
gcc -DHAVE_CONFIG_H -I. -I.. -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 -Wformat -Werror=format-security -c -o smalt-results.o `test -f 'results.c' || echo './'`results.c
gcc -DHAVE_CONFIG_H -I. -I.. -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 -Wformat -Werror=format-security -c -o smalt-resultpairs.o `test -f 'resultpairs.c' || echo './'`resultpairs.c
gcc -DHAVE_CONFIG_H -I. -I.. -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 -Wformat -Werror=format-security -c -o smalt-report.o `test -f 'report.c' || echo './'`report.c
gcc -DHAVE_CONFIG_H -I. -I.. -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 -Wformat -Werror=format-security -c -o smalt-rmap.o `test -f 'rmap.c' || echo './'`rmap.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)
| ~~~~~~~~~~^~~~~~~~
diffstr.c: In function 'diffStrGetDiffStats':
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)
| ~~~~~~~~~~^~~~~~~~
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) {
| ^~
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)
| ~~~~~~~~~~^~~~~~~~
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++) {
| ^
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;
| ^
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;
| ^
gcc -DHAVE_CONFIG_H -I. -I.. -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 -Wformat -Werror=format-security -c -o smalt-insert.o `test -f 'insert.c' || echo './'`insert.c
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 */
| ^~~~~~
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,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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':
alignment.c:478:13: warning: 'blankALITRACK' defined but not used [-Wunused-function]
478 | static void blankALITRACK(ALITRACK *trackp, const ALIBAND *bandp)
| ^~~~~~~~~~~~~
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:
| ^~~~
smalt.c: In function 'cleanupSmaltOutput':
smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter]
659 | static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op)
| ~~~~~~~~^~~~~~~
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-swsimd.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 -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.. -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 -Wformat -Werror=format-security -c simread.c
gcc -DHAVE_CONFIG_H -I. -I.. -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 -Wformat -Werror=format-security -c rsample.c
gcc -DHAVE_CONFIG_H -I. -I.. -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 -Wformat -Werror=format-security -c fetchseq.c
gcc -DHAVE_CONFIG_H -I. -I.. -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 -Wformat -Werror=format-security -c splitreads.c
gcc -DHAVE_CONFIG_H -I. -I.. -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 -Wformat -Werror=format-security -c mixreads.c
gcc -DHAVE_CONFIG_H -I. -I.. -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 -Wformat -Werror=format-security -c splitmates.c
gcc -DHAVE_CONFIG_H -I. -I.. -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 -Wformat -Werror=format-security -c readstats.c
gcc -DHAVE_CONFIG_H -I. -I.. -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 -Wformat -Werror=format-security -c trunkreads.c
gcc -DHAVE_CONFIG_H -I. -I.. -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 -Wformat -Werror=format-security -c basqcol.c
gcc -DHAVE_CONFIG_H -I. -I.. -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 -Wformat -Werror=format-security -c basqual.c
gcc -DHAVE_CONFIG_H -I. -I.. -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 -Wformat -Werror=format-security -c simqual.c
gcc -DHAVE_CONFIG_H -I. -I.. -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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.. -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 -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 -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 -j22
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 -j22 check "TESTSUITEFLAGS=-j22 --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 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -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 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -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 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -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 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-infmt.o `test -f '../src/infmt.c' || echo './'`../src/infmt.c
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -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 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -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 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -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 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -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 -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-rmap.o `test -f '../src/rmap.c' || echo './'`../src/rmap.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 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -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
dwz: debian/smalt/usr/bin/smalt: DWARF compression not beneficial - old size 241265 new size 245119
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'smalt-dbgsym' in '../smalt-dbgsym_0.7.6-13_i386.deb'.
dpkg-deb: building package 'smalt' in '../smalt_0.7.6-13_i386.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_i386.buildinfo
dpkg-genchanges --build=binary -O../smalt_0.7.6-13_i386.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/41280 and its subdirectories
I: Current time: Sun Mar 29 19:37:43 -12 2026
I: pbuilder-time-stamp: 1774856263