Sun Mar 2 06:50:38 UTC 2025 I: starting to build soapaligner/trixie/amd64 on jenkins on '2025-03-02 06:50'
Sun Mar 2 06:50:38 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_6/34019/console.log
Sun Mar 2 06:50:38 UTC 2025 I: Downloading source for trixie/soapaligner=2.20-5
--2025-03-02 06:50:38-- http://deb.debian.org/debian/pool/main/s/soapaligner/soapaligner_2.20-5.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2039 (2.0K) [text/prs.lines.tag]
Saving to: ‘soapaligner_2.20-5.dsc’
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2025-03-02 06:50:38 (287 MB/s) - ‘soapaligner_2.20-5.dsc’ saved [2039/2039]
Sun Mar 2 06:50:38 UTC 2025 I: soapaligner_2.20-5.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: soapaligner
Binary: soapaligner
Architecture: any-amd64
Version: 2.20-5
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>
Homepage: https://web.archive.org/web/20190127081222/http://soap.genomics.org.cn/soapaligner.html
Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/soapaligner
Vcs-Git: https://salsa.debian.org/med-team/soapaligner.git
Build-Depends: debhelper-compat (= 13)
Package-List:
soapaligner deb science optional arch=any-amd64,x32
Checksums-Sha1:
b99762edeee90352f191511f0d26db32ab9e43d1 110922 soapaligner_2.20.orig.tar.gz
3a8105fb94fe86e89a53059b09ad5f9ecc119022 6408 soapaligner_2.20-5.debian.tar.xz
Checksums-Sha256:
c5253dddc35e289723f3daada4a3a083111ff6fb9898bc8241dab6f6f972d456 110922 soapaligner_2.20.orig.tar.gz
16c6459f2b63507fd99dfc1e278f0b5bea7092a9934880b88498b8b015fd0ae3 6408 soapaligner_2.20-5.debian.tar.xz
Files:
ca75753697b12749c42356f366738fef 110922 soapaligner_2.20.orig.tar.gz
94c9ac888c01e1e6c2d7fd85b3850b02 6408 soapaligner_2.20-5.debian.tar.xz
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Sun Mar 2 06:50:38 UTC 2025 I: Checking whether the package is not for us
Sun Mar 2 06:50:38 UTC 2025 I: Starting 1st build on remote node ionos5-amd64.debian.net.
Sun Mar 2 06:50:38 UTC 2025 I: Preparing to do remote build '1' on ionos5-amd64.debian.net.
Sun Mar 2 06:51:14 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sat Apr 4 01:13:39 -12 2026
I: pbuilder-time-stamp: 1775308419
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: Copying source file
I: copying [soapaligner_2.20-5.dsc]
I: copying [./soapaligner_2.20.orig.tar.gz]
I: copying [./soapaligner_2.20-5.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./soapaligner_2.20-5.dsc: unsupported subcommand
dpkg-source: info: extracting soapaligner in soapaligner-2.20
dpkg-source: info: unpacking soapaligner_2.20.orig.tar.gz
dpkg-source: info: unpacking soapaligner_2.20-5.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying compiler_options.patch
dpkg-source: info: applying linkerror.patch
dpkg-source: info: applying UsageDoublette.patch
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying gcc-10.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/3974150/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='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='9a0919b88a714cc09ee1617b2c0ab62a'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='3974150'
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.4wr504AH/pbuilderrc_Hw2k --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.4wr504AH/b1 --logfile b1/build.log soapaligner_2.20-5.dsc'
SUDO_GID='110'
SUDO_UID='105'
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 ionos5-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) 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/3974150/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13)
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19802 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.
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} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a}
The following packages are RECOMMENDED but will NOT be installed:
curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded.
Need to get 20.6 MB of archives. After unpacking 77.9 MB will be used.
Writing extended state information...
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Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
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Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB]
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Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB]
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Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB]
Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB]
Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 21 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 22 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 23 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 24 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB]
Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB]
Fetched 20.6 MB in 5s (3901 kB/s)
Preconfiguring packages ...
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(Reading database ... 19802 files and directories currently installed.)
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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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Not building database; man-db/auto-update is not 'true'.
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Processing triggers for libc-bin (2.40-7) ...
Reading package lists...
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/soapaligner-2.20/ && 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 > ../soapaligner_2.20-5_source.changes
dpkg-buildpackage: info: source package soapaligner
dpkg-buildpackage: info: source version 2.20-5
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Nilesh Patra <npatra974@gmail.com>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean
dh_auto_clean
make -j42 clean
make[1]: Entering directory '/build/reproducible-path/soapaligner-2.20'
rm -f *.o soap
make[1]: Leaving directory '/build/reproducible-path/soapaligner-2.20'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/soapaligner.substvars debian/files
rm -fr -- debian/soapaligner/ debian/tmp/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \)
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
dh_auto_build
make -j42 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/soapaligner-2.20'
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" SeqIO.c -o SeqIO.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" MiscUtilities.c -o MiscUtilities.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" MemManager.c -o MemManager.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" TextConverter.c -o TextConverter.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" r250.c -o r250.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" DNACount.c -o DNACount.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" HSP.c -o HSP.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" Timing.c -o Timing.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" BWT.c -o BWT.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" extratools.c -o extratools.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" soapio.c -o soapio.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" BWTAln.c -o BWTAln.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" Match.c -o Match.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" PairMatch.c -o PairMatch.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" stdaln.c -o stdaln.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" kstring.c -o kstring.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" soap.c -o soap.o
r250.c: In function 'randlcg':
r250.c:33:41: warning: overflow in conversion from 'long int' to 'int' changes value from '548781581296767' to '724984959' [-Woverflow]
33 | static int quotient1 = LONG_MAX / 16807L;
| ^~~~~~~~
In file included from extratools.c:1:
extratools.h:83:12: warning: inline function 'altCalMM' declared but never defined
83 | inline int altCalMM(unsigned int x);
| ^~~~~~~~
In file included from soapio.h:21,
from soapio.c:17:
extratools.h:84:12: warning: inline function 'CalMismatch' declared but never defined
84 | inline int CalMismatch(const char *,const unsigned int *,const unsigned int , const unsigned int, const unsigned int);
| ^~~~~~~~~~~
extratools.h:83:12: warning: inline function 'altCalMM' declared but never defined
83 | inline int altCalMM(unsigned int x);
| ^~~~~~~~
In file included from BWTAln.h:23,
from BWTAln.c:1:
extratools.h:84:12: warning: inline function 'CalMismatch' declared but never defined
84 | inline int CalMismatch(const char *,const unsigned int *,const unsigned int , const unsigned int, const unsigned int);
| ^~~~~~~~~~~
extratools.h:83:12: warning: inline function 'altCalMM' declared but never defined
83 | inline int altCalMM(unsigned int x);
| ^~~~~~~~
In file included from soap.c:24:
Match.h:132:13: warning: inline function 'PickupHit' declared but never defined
132 | inline void PickupHit(ALNSEQ *, const int ,int *, HITTABLE *,const unsigned int *, const unsigned int, unsigned short * );
| ^~~~~~~~~
In file included from Match.c:17:
Match.h:130:12: warning: inline function 'CheckIns' declared but never defined
130 | inline int CheckIns(HITITEM *, HITITEM *, PEAUX *);
| ^~~~~~~~
Match.h:130:12: warning: inline function 'CheckIns' declared but never defined
130 | inline int CheckIns(HITITEM *, HITITEM *, PEAUX *);
| ^~~~~~~~
In file included from BWTAln.h:23,
from Match.h:23:
extratools.h:84:12: warning: inline function 'CalMismatch' declared but never defined
84 | inline int CalMismatch(const char *,const unsigned int *,const unsigned int , const unsigned int, const unsigned int);
| ^~~~~~~~~~~
extratools.h:83:12: warning: inline function 'altCalMM' declared but never defined
83 | inline int altCalMM(unsigned int x);
| ^~~~~~~~
In file included from BWTAln.h:23,
from Match.h:23:
extratools.h:84:12: warning: inline function 'CalMismatch' declared but never defined
84 | inline int CalMismatch(const char *,const unsigned int *,const unsigned int , const unsigned int, const unsigned int);
| ^~~~~~~~~~~
extratools.h:83:12: warning: inline function 'altCalMM' declared but never defined
83 | inline int altCalMM(unsigned int x);
| ^~~~~~~~
In file included from PairMatch.c:19:
Match.h:132:13: warning: inline function 'PickupHit' declared but never defined
132 | inline void PickupHit(ALNSEQ *, const int ,int *, HITTABLE *,const unsigned int *, const unsigned int, unsigned short * );
| ^~~~~~~~~
In file included from BWTAln.h:23,
from Match.h:23:
extratools.h:84:12: warning: inline function 'CalMismatch' declared but never defined
84 | inline int CalMismatch(const char *,const unsigned int *,const unsigned int , const unsigned int, const unsigned int);
| ^~~~~~~~~~~
extratools.h:83:12: warning: inline function 'altCalMM' declared but never defined
83 | inline int altCalMM(unsigned int x);
| ^~~~~~~~
cc -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" SeqIO.o MiscUtilities.o MemManager.o TextConverter.o r250.o DNACount.o HSP.o Timing.o BWT.o extratools.o soapio.o BWTAln.o Match.o PairMatch.o stdaln.o kstring.o soap.o -o soap -Wl,-flto -Wl,-z,relro -Wl,-z,now -lm -lpthread
In function 'aln_local_core',
inlined from 'SWRescue' at PairMatch.c:167:3:
stdaln.c:740:17: warning: 'free' called on pointer 'MEM[(int * *)_1041]' with nonzero offset 4 [-Wfree-nonheap-object]
740 | MYFREE(s_array[i]);
| ^
make[1]: Leaving directory '/build/reproducible-path/soapaligner-2.20'
dh_auto_test
rm -fr -- /tmp/dh-xdg-rundir-1Ow5m0zS
create-stamp debian/debhelper-build-stamp
dh_prep
rm -f -- debian/soapaligner.substvars
rm -fr -- debian/.debhelper/generated/soapaligner/ debian/soapaligner/ debian/tmp/
dh_auto_install --destdir=debian/soapaligner/
install -m0755 -d /build/reproducible-path/soapaligner-2.20/debian/soapaligner
dh_install
install -m0755 -d debian/soapaligner/usr/bin
cp --reflink=auto -a ./soap debian/soapaligner/usr/bin/
dh_installdocs
install -m0755 -d debian/soapaligner/usr/share/doc/soapaligner
install -m0755 -d debian/soapaligner/usr/share/doc/soapaligner
cp --reflink=auto -a ./NEWS debian/soapaligner/usr/share/doc/soapaligner
chmod -R u\+rw,go=rX debian/soapaligner/usr/share/doc
install -p -m0644 debian/README.Debian debian/soapaligner/usr/share/doc/soapaligner/README.Debian
install -p -m0644 debian/copyright debian/soapaligner/usr/share/doc/soapaligner/copyright
dh_installchangelogs
install -m0755 -d debian/soapaligner/usr/share/doc/soapaligner
install -p -m0644 debian/.debhelper/generated/soapaligner/dh_installchangelogs.dch.trimmed debian/soapaligner/usr/share/doc/soapaligner/changelog.Debian
dh_installman
install -m0755 -d debian/soapaligner/usr/share/man/man1/
install -p -m0644 ./soap.1 debian/soapaligner/usr/share/man/man1/soap.1
man-recode --to-code UTF-8 --suffix .dh-new debian/soapaligner/usr/share/man/man1/soap.1
mv debian/soapaligner/usr/share/man/man1/soap.1.dh-new debian/soapaligner/usr/share/man/man1/soap.1
chmod 0644 -- debian/soapaligner/usr/share/man/man1/soap.1
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
cd debian/soapaligner
chmod a-x usr/share/doc/soapaligner/NEWS usr/share/doc/soapaligner/changelog.Debian usr/share/man/man1/soap.1
gzip -9nf usr/share/doc/soapaligner/NEWS usr/share/doc/soapaligner/changelog.Debian usr/share/man/man1/soap.1
cd '/build/reproducible-path/soapaligner-2.20'
dh_fixperms
find debian/soapaligner ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/soapaligner/usr/share/doc -type f -a -true -a ! -regex 'debian/soapaligner/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/soapaligner/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/soapaligner/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/soapaligner -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/soapaligner/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
dh_missing
dh_dwz -a
dwz -- debian/soapaligner/usr/bin/soap
dh_strip -a
install -m0755 -d debian/.debhelper/soapaligner/dbgsym-root/usr/lib/debug/.build-id/0b
objcopy --only-keep-debug --compress-debug-sections debian/soapaligner/usr/bin/soap debian/.debhelper/soapaligner/dbgsym-root/usr/lib/debug/.build-id/0b/6bce66ab3c86455c544e38088a9dd74f0ee525.debug
chmod 0644 -- debian/.debhelper/soapaligner/dbgsym-root/usr/lib/debug/.build-id/0b/6bce66ab3c86455c544e38088a9dd74f0ee525.debug
strip --remove-section=.comment --remove-section=.note debian/soapaligner/usr/bin/soap
objcopy --add-gnu-debuglink debian/.debhelper/soapaligner/dbgsym-root/usr/lib/debug/.build-id/0b/6bce66ab3c86455c544e38088a9dd74f0ee525.debug debian/soapaligner/usr/bin/soap
install -m0755 -d debian/.debhelper/soapaligner/dbgsym-root/usr/share/doc
ln -s soapaligner debian/.debhelper/soapaligner/dbgsym-root/usr/share/doc/soapaligner-dbgsym
install -m0755 -d debian/.debhelper/soapaligner
dh_makeshlibs -a
rm -f debian/soapaligner/DEBIAN/shlibs
dh_shlibdeps -a
install -m0755 -d debian/soapaligner/DEBIAN
dpkg-shlibdeps -Tdebian/soapaligner.substvars debian/soapaligner/usr/bin/soap
dh_installdeb
install -m0755 -d debian/soapaligner/DEBIAN
dh_gencontrol
install -m0755 -d debian/soapaligner/DEBIAN
echo misc:Depends= >> debian/soapaligner.substvars
echo misc:Pre-Depends= >> debian/soapaligner.substvars
install -m0755 -d debian/.debhelper/soapaligner/dbgsym-root/DEBIAN
dpkg-gencontrol -psoapaligner -ldebian/changelog -Tdebian/soapaligner.substvars -cdebian/control -Pdebian/.debhelper/soapaligner/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=soapaligner-dbgsym "-DDepends=soapaligner (= \${binary:Version})" "-DDescription=debug symbols for soapaligner" -DBuild-Ids=0b6bce66ab3c86455c544e38088a9dd74f0ee525 -DSection=debug -UMulti-Arch -UReplaces -UBreaks
chmod 0644 -- debian/.debhelper/soapaligner/dbgsym-root/DEBIAN/control
dpkg-gencontrol -psoapaligner -ldebian/changelog -Tdebian/soapaligner.substvars -cdebian/control -Pdebian/soapaligner
chmod 0644 -- debian/soapaligner/DEBIAN/control
dh_md5sums
install -m0755 -d debian/soapaligner/DEBIAN
cd debian/soapaligner >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/soapaligner/DEBIAN/md5sums
install -m0755 -d debian/.debhelper/soapaligner/dbgsym-root/DEBIAN
cd debian/.debhelper/soapaligner/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/soapaligner/dbgsym-root/DEBIAN/md5sums
dh_builddeb
dpkg-deb --root-owner-group --build debian/soapaligner ..
dpkg-deb --root-owner-group --build debian/.debhelper/soapaligner/dbgsym-root ..
dpkg-deb: building package 'soapaligner' in '../soapaligner_2.20-5_amd64.deb'.
dpkg-deb: building package 'soapaligner-dbgsym' in '../soapaligner-dbgsym_2.20-5_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../soapaligner_2.20-5_amd64.buildinfo
dpkg-genchanges --build=binary -O../soapaligner_2.20-5_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/3974150 and its subdirectories
I: Current time: Sat Apr 4 01:14:13 -12 2026
I: pbuilder-time-stamp: 1775308453
Sun Mar 2 06:51:14 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net.
Sun Mar 2 06:51:14 UTC 2025 I: Preparing to do remote build '2' on ionos11-amd64.debian.net.
Sun Mar 2 06:53:13 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net.
Sun Mar 2 06:53:14 UTC 2025 I: soapaligner_2.20-5_amd64.changes:
Format: 1.8
Date: Thu, 14 Jan 2021 17:05:45 +0530
Source: soapaligner
Binary: soapaligner soapaligner-dbgsym
Architecture: amd64
Version: 2.20-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Nilesh Patra <npatra974@gmail.com>
Description:
soapaligner - aligner of short reads of next generation sequencers
Closes: 979681
Changes:
soapaligner (2.20-5) unstable; urgency=medium
.
* Team Upload.
* d/p/gcc-10.patch: Fix compilation with GCC 10.
- Thank you, Logan Rosen (Closes: #979681)
* Declare compliance with policy 4.5.1
* Bump debhelper-compat version to 13
Checksums-Sha1:
b063eccf7726d2395e1df16bf6eb9651e0487710 111164 soapaligner-dbgsym_2.20-5_amd64.deb
3fcd3f9e30285b949067dacc8d07d325f0c2e772 4905 soapaligner_2.20-5_amd64.buildinfo
de2ea90a6aea414b17f009ed9c47d10071ad0e64 52664 soapaligner_2.20-5_amd64.deb
Checksums-Sha256:
6e154e24a93f3350c0e3f4374f6243fe7cac0e6c2cd8de632d2355f0de8ae5f1 111164 soapaligner-dbgsym_2.20-5_amd64.deb
42586b4c1d256efc1ddc3cb8acce63a523cbdd9001733a4e874397fc1d277d0b 4905 soapaligner_2.20-5_amd64.buildinfo
62746b4fb1501146ecb322ae2eeb0be167f6b27226333366c78eace8c866c808 52664 soapaligner_2.20-5_amd64.deb
Files:
e4830dce2dc2135a169371263fa44ceb 111164 debug optional soapaligner-dbgsym_2.20-5_amd64.deb
23f5afbf28a0c85ceed49f1a979b341c 4905 science optional soapaligner_2.20-5_amd64.buildinfo
4502cfcc006af6e6e18afc7afba7e0ce 52664 science optional soapaligner_2.20-5_amd64.deb
Sun Mar 2 06:53:15 UTC 2025 I: diffoscope 289 will be used to compare the two builds:
Running as unit: rb-diffoscope-amd64_6-34019.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.4wr504AH/soapaligner_2.20-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.4wr504AH/soapaligner_2.20-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.4wr504AH/soapaligner_2.20-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.4wr504AH/b1/soapaligner_2.20-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.4wr504AH/b2/soapaligner_2.20-5_amd64.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call diffoscope.comparators.binary.FilesystemFile
## main (total time: 0.003s)
0.003s 2 calls outputs
0.000s 1 call cleanup
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 225ms
CPU time consumed: 225ms
Sun Mar 2 06:53:19 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists.
Sun Mar 2 06:53:19 UTC 2025 I: soapaligner from trixie built successfully and reproducibly on amd64.
Sun Mar 2 06:53:20 UTC 2025 I: Submitting .buildinfo files to external archives:
Sun Mar 2 06:53:20 UTC 2025 I: Submitting 8.0K b1/soapaligner_2.20-5_amd64.buildinfo.asc
Sun Mar 2 06:53:21 UTC 2025 I: Submitting 8.0K b2/soapaligner_2.20-5_amd64.buildinfo.asc
Sun Mar 2 06:53:21 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sun Mar 2 06:53:21 UTC 2025 I: Done submitting .buildinfo files.
Sun Mar 2 06:53:21 UTC 2025 I: Removing signed soapaligner_2.20-5_amd64.buildinfo.asc files:
removed './b1/soapaligner_2.20-5_amd64.buildinfo.asc'
removed './b2/soapaligner_2.20-5_amd64.buildinfo.asc'