Thu Mar 6 01:27:25 UTC 2025 I: starting to build kma/unstable/arm64 on jenkins on '2025-03-06 01:27'
Thu Mar 6 01:27:25 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_4/60359/console.log
Thu Mar 6 01:27:25 UTC 2025 I: Downloading source for unstable/kma=1.4.21-1
--2025-03-06 01:27:25-- http://deb.debian.org/debian/pool/main/k/kma/kma_1.4.21-1.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2113 (2.1K) [text/prs.lines.tag]
Saving to: ‘kma_1.4.21-1.dsc’
0K .. 100% 337M=0s
2025-03-06 01:27:25 (337 MB/s) - ‘kma_1.4.21-1.dsc’ saved [2113/2113]
Thu Mar 6 01:27:25 UTC 2025 I: kma_1.4.21-1.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: kma
Binary: kma
Architecture: any
Version: 1.4.21-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>, Étienne Mollier <emollier@debian.org>
Homepage: https://bitbucket.org/genomicepidemiology/kma
Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/kma
Vcs-Git: https://salsa.debian.org/med-team/kma.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), architecture-is-64-bit, zlib1g-dev
Package-List:
kma deb science optional arch=any
Checksums-Sha1:
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2e808ed411325e9e20272b28b305295bad4b8d35 6772 kma_1.4.21-1.debian.tar.xz
Checksums-Sha256:
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1c74f5c5de280cc5e0c5432b470d6c09ad49db6d1e3650c34c261ea05e92646e 6772 kma_1.4.21-1.debian.tar.xz
Files:
328817cee52c11d4a59b021072647541 630940 kma_1.4.21.orig.tar.xz
c75e4bb797b83bb6cc7d433fe19088e2 6772 kma_1.4.21-1.debian.tar.xz
Dgit: 44fded90fae5a14dbfd28c3f57b9430ff77c7658 debian archive/debian/1.4.21-1 https://git.dgit.debian.org/kma
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Thu Mar 6 01:27:25 UTC 2025 I: Checking whether the package is not for us
Thu Mar 6 01:27:25 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net.
Thu Mar 6 01:27:25 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net.
Thu Mar 6 01:27:59 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Tue Apr 7 19:50:27 -12 2026
I: pbuilder-time-stamp: 1775634627
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 [kma_1.4.21-1.dsc]
I: copying [./kma_1.4.21.orig.tar.xz]
I: copying [./kma_1.4.21-1.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./kma_1.4.21-1.dsc: unsupported subcommand
dpkg-source: info: extracting kma in kma-1.4.21
dpkg-source: info: unpacking kma_1.4.21.orig.tar.xz
dpkg-source: info: unpacking kma_1.4.21-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying blhc.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/1542345/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='arm64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
DISTRIBUTION='unstable'
HOME='/root'
HOST_ARCH='arm64'
IFS='
'
INVOCATION_ID='d39068b7ac9c46adb759c4fcf106c022'
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='1542345'
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.7c0JjRRl/pbuilderrc_ajMc --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.7c0JjRRl/b1 --logfile b1/build.log kma_1.4.21-1.dsc'
SUDO_GID='109'
SUDO_UID='104'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://192.168.101.4:3128'
I: uname -a
Linux codethink03-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/1542345/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: arm64
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), architecture-is-64-bit, zlib1g-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 ... 19897 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 architecture-is-64-bit; however:
Package architecture-is-64-bit is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-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:
architecture-properties{a} 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} zlib1g-dev{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, 32 newly installed, 0 to remove and 0 not upgraded.
Need to get 21.0 MB of archives. After unpacking 81.6 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB]
Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB]
Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB]
Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB]
Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB]
Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-5 [92.0 kB]
Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB]
Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB]
Get: 11 http://deb.debian.org/debian unstable/main arm64 architecture-properties arm64 0.2.6 [2336 B]
Get: 12 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-6 [285 kB]
Get: 13 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB]
Get: 14 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 15 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-3 [862 kB]
Get: 16 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB]
Get: 17 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 18 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB]
Get: 19 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 20 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 21 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 22 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 23 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get: 24 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get: 25 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB]
Get: 26 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB]
Get: 27 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b2 [630 kB]
Get: 28 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB]
Get: 29 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 30 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 31 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB]
Get: 32 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB]
Fetched 21.0 MB in 0s (96.8 MB/s)
Preconfiguring packages ...
Selecting previously unselected package sensible-utils.
(Reading database ...
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(Reading database ... 19897 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:arm64.
Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ...
Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ...
Unpacking file (1:5.45-3+b1) ...
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Preparing to unpack .../04-gettext-base_0.23.1-1_arm64.deb ...
Unpacking gettext-base (0.23.1-1) ...
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Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ...
Unpacking libuchardet0:arm64 (0.0.8-1+b2) ...
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Preparing to unpack .../06-groff-base_1.23.0-7_arm64.deb ...
Unpacking groff-base (1.23.0-7) ...
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Preparing to unpack .../07-bsdextrautils_2.40.4-5_arm64.deb ...
Unpacking bsdextrautils (2.40.4-5) ...
Selecting previously unselected package libpipeline1:arm64.
Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ...
Unpacking libpipeline1:arm64 (1.5.8-1) ...
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Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ...
Unpacking man-db (2.13.0-1) ...
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Preparing to unpack .../10-architecture-properties_0.2.6_arm64.deb ...
Unpacking architecture-properties:arm64 (0.2.6) ...
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Preparing to unpack .../11-m4_1.4.19-6_arm64.deb ...
Unpacking m4 (1.4.19-6) ...
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Unpacking libtool (2.5.4-4) ...
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Setting up libpipeline1:arm64 (1.5.8-1) ...
Setting up libicu72:arm64 (72.1-6) ...
Setting up bsdextrautils (2.40.4-5) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up architecture-properties:arm64 (0.2.6) ...
Setting up libdebhelper-perl (13.24.1) ...
Setting up libmagic1t64:arm64 (1:5.45-3+b1) ...
Setting up gettext-base (0.23.1-1) ...
Setting up m4 (1.4.19-6) ...
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:arm64 (0.192-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up libunistring5:arm64 (1.3-1) ...
Setting up autopoint (0.23.1-1) ...
Setting up autoconf (2.72-3) ...
Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:arm64 (0.0.8-1+b2) ...
Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Setting up automake (1:1.17-3) ...
update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.1-2) ...
Setting up gettext (0.23.1-1) ...
Setting up libtool (2.5.4-4) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up groff-base (1.23.0-7) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.24.1) ...
Processing triggers for libc-bin (2.41-3) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/kma-1.4.21/ && 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 > ../kma_1.4.21-1_source.changes
dpkg-buildpackage: info: source package kma
dpkg-buildpackage: info: source version 1.4.21-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean
dh_auto_clean
make -j12 clean
make[1]: Entering directory '/build/reproducible-path/kma-1.4.21'
rm -f align.o alnfrags.o ankers.o assembly.o chain.o compdna.o compkmers.o compress.o conclave.o db.o decon.o dist.o ef.o filebuff.o frags.o hashmap.o hashmapcci.o hashmapkma.o hashmapkmers.o hashtable.o index.o kma.o kmapipe.o kmeranker.o kmers.o kmmap.o loadupdate.o makeindex.o matrix.o mt1.o nw.o pherror.o printconsensus.o qc.o qseqs.o qualcheck.o runinput.o runkma.o sam.o savekmers.o seq2fasta.o seqmenttree.o seqparse.o shm.o sparse.o spltdb.o stdnuc.o stdstat.o trim.o tmp.o tsv.o update.o updateindex.o updatescores.o valueshash.o vcf.o xml.o kma kma_index kma_shm kma_update libkma.a
make[1]: Leaving directory '/build/reproducible-path/kma-1.4.21'
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
dh_auto_build
make -j12 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/kma-1.4.21'
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o align.o align.c
make[1]: Circular pherror.h <- pherror.h dependency dropped.
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alnfrags.o alnfrags.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ankers.o ankers.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o assembly.o assembly.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o chain.o chain.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o compdna.o compdna.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o compkmers.o compkmers.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o compress.o compress.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o conclave.o conclave.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o db.o db.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o decon.o decon.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dist.o dist.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ef.o ef.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filebuff.o filebuff.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o frags.o frags.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashmap.o hashmap.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashmapcci.o hashmapcci.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashmapkma.o hashmapkma.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashmapkmers.o hashmapkmers.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o index.o index.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kma.o kma.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmapipe.o kmapipe.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmeranker.o kmeranker.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmers.o kmers.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmmap.o kmmap.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loadupdate.o loadupdate.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o makeindex.o makeindex.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o matrix.o matrix.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mt1.o mt1.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o nw.o nw.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o pherror.o pherror.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o printconsensus.o printconsensus.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o qc.o qc.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o qseqs.o qseqs.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o qualcheck.o qualcheck.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o runinput.o runinput.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o runkma.o runkma.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o savekmers.o savekmers.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seq2fasta.o seq2fasta.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seqmenttree.o seqmenttree.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seqparse.o seqparse.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o shm.o shm.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sparse.o sparse.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o spltdb.o spltdb.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stdnuc.o stdnuc.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stdstat.o stdstat.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o trim.o trim.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp.o tmp.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv.o tsv.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o update.o update.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o updateindex.o updateindex.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o updatescores.o updatescores.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o valueshash.o valueshash.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o xml.o xml.c
ar -csr libkma.a align.o alnfrags.o ankers.o assembly.o chain.o compdna.o compkmers.o compress.o conclave.o db.o decon.o dist.o ef.o filebuff.o frags.o hashmap.o hashmapcci.o hashmapkma.o hashmapkmers.o hashtable.o index.o kma.o kmapipe.o kmeranker.o kmers.o kmmap.o loadupdate.o makeindex.o matrix.o mt1.o nw.o pherror.o printconsensus.o qc.o qseqs.o qualcheck.o runinput.o runkma.o sam.o savekmers.o seq2fasta.o seqmenttree.o seqparse.o shm.o sparse.o spltdb.o stdnuc.o stdstat.o trim.o tmp.o tsv.o update.o updateindex.o updatescores.o valueshash.o vcf.o xml.o
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -o kma main.c libkma.a -lm -lpthread -lz -Wl,-z,relro -Wl,-z,now
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -o kma_index kma_index.c libkma.a -lm -lz -Wl,-z,relro -Wl,-z,now
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -o kma_shm kma_shm.c libkma.a -Wl,-z,relro -Wl,-z,now
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kma-1.4.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -o kma_update kma_update.c libkma.a -Wl,-z,relro -Wl,-z,now
make[1]: Leaving directory '/build/reproducible-path/kma-1.4.21'
dh_auto_test
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install --destdir=debian/kma/
dh_install
dh_installdocs
dh_installchangelogs
dh_installman
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dwz: debian/kma/usr/bin/kma: DWARF compression not beneficial - old size 463485 new size 467221
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-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'kma' in '../kma_1.4.21-1_arm64.deb'.
dpkg-deb: building package 'kma-dbgsym' in '../kma-dbgsym_1.4.21-1_arm64.deb'.
dpkg-genbuildinfo --build=binary -O../kma_1.4.21-1_arm64.buildinfo
dpkg-genchanges --build=binary -O../kma_1.4.21-1_arm64.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: including full 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/1542345 and its subdirectories
I: Current time: Tue Apr 7 19:50:57 -12 2026
I: pbuilder-time-stamp: 1775634657
Thu Mar 6 01:27:59 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net.
Thu Mar 6 01:27:59 UTC 2025 I: Preparing to do remote build '2' on codethink04-arm64.debian.net.
Thu Mar 6 01:28:43 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net.
Thu Mar 6 01:28:44 UTC 2025 I: kma_1.4.21-1_arm64.changes:
Format: 1.8
Date: Wed, 05 Mar 2025 13:46:24 +0100
Source: kma
Binary: kma kma-dbgsym
Architecture: arm64
Version: 1.4.21-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
kma - mapping genomic sequences to raw reads directly against redundant
Changes:
kma (1.4.21-1) unstable; urgency=medium
.
* New upstream version 1.4.21
* d/control: declare compliance to standards version 4.7.2.
* typos.patch: delete: applied upstream.
Checksums-Sha1:
5b86238fc907d74eb2d29fc7e7ad965a73ff2453 696192 kma-dbgsym_1.4.21-1_arm64.deb
cb1e4eb078cdc84297ca7e2dc23caa4a57e30f6c 4887 kma_1.4.21-1_arm64.buildinfo
40fe856e7df893a59ab6a469bc360e6f2d99cb93 211472 kma_1.4.21-1_arm64.deb
Checksums-Sha256:
0d56016a185d83e5e28fc168772707eb438be456508bfd644a98c82026d47cab 696192 kma-dbgsym_1.4.21-1_arm64.deb
4ec74d6ff260ff79e5a1ae012a64d1f3ebda482ea82b64e65e52e7257445ff16 4887 kma_1.4.21-1_arm64.buildinfo
0f699eee5e96ebc0bc824b78d220f229b63da981f412be9de989ddaa7507d869 211472 kma_1.4.21-1_arm64.deb
Files:
5ad0b029424a36a6a291359acf833611 696192 debug optional kma-dbgsym_1.4.21-1_arm64.deb
fe53bd9b454d069ec23513021b7e3043 4887 science optional kma_1.4.21-1_arm64.buildinfo
6db7f259cc554a79c3e9901ef7f6ac86 211472 science optional kma_1.4.21-1_arm64.deb
Thu Mar 6 01:28:45 UTC 2025 I: diffoscope 289 will be used to compare the two builds:
Running as unit: rb-diffoscope-arm64_4-60359.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.7c0JjRRl/kma_1.4.21-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.7c0JjRRl/kma_1.4.21-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.7c0JjRRl/kma_1.4.21-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.7c0JjRRl/b1/kma_1.4.21-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.7c0JjRRl/b2/kma_1.4.21-1_arm64.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: 230ms
CPU time consumed: 231ms
Thu Mar 6 01:28:46 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists.
Thu Mar 6 01:28:46 UTC 2025 I: kma from unstable built successfully and reproducibly on arm64.
Thu Mar 6 01:28:48 UTC 2025 I: Submitting .buildinfo files to external archives:
Thu Mar 6 01:28:48 UTC 2025 I: Submitting 8.0K b1/kma_1.4.21-1_arm64.buildinfo.asc
Thu Mar 6 01:28:50 UTC 2025 I: Submitting 8.0K b2/kma_1.4.21-1_arm64.buildinfo.asc
Thu Mar 6 01:28:52 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Thu Mar 6 01:28:52 UTC 2025 I: Done submitting .buildinfo files.
Thu Mar 6 01:28:52 UTC 2025 I: Removing signed kma_1.4.21-1_arm64.buildinfo.asc files:
removed './b1/kma_1.4.21-1_arm64.buildinfo.asc'
removed './b2/kma_1.4.21-1_arm64.buildinfo.asc'