Mon Feb 24 21:52:24 UTC 2025 I: starting to build quicktree/trixie/amd64 on jenkins on '2025-02-24 21:52'
Mon Feb 24 21:52:24 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_8/48623/console.log
Mon Feb 24 21:52:24 UTC 2025 I: Downloading source for trixie/quicktree=2.5-6
--2025-02-24 21:52:25-- http://deb.debian.org/debian/pool/main/q/quicktree/quicktree_2.5-6.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2019 (2.0K) [text/prs.lines.tag]
Saving to: ‘quicktree_2.5-6.dsc’
0K . 100% 298M=0s
2025-02-24 21:52:25 (298 MB/s) - ‘quicktree_2.5-6.dsc’ saved [2019/2019]
Mon Feb 24 21:52:25 UTC 2025 I: quicktree_2.5-6.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: quicktree
Binary: quicktree, libquicktree-dev
Architecture: any
Version: 2.5-6
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>
Homepage: https://github.com/khowe/quicktree/
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/quicktree
Vcs-Git: https://salsa.debian.org/med-team/quicktree.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), help2man, dh-exec
Package-List:
libquicktree-dev deb libdevel optional arch=any
quicktree deb science optional arch=any
Checksums-Sha1:
7694e325400b1775b3682b14ada2a8ba301fbd94 39784 quicktree_2.5.orig.tar.gz
3a22d2a452231f1d91434dcf029b5df9fab4afc5 5872 quicktree_2.5-6.debian.tar.xz
Checksums-Sha256:
731aa845ce3f1f0645bd0df2b54df75f78fce065d6a3ddc47fedf4bdcb11c248 39784 quicktree_2.5.orig.tar.gz
ac8993853ea900963d4c854969e7d250b7f637029eada0b93a9c6aff197e01a4 5872 quicktree_2.5-6.debian.tar.xz
Files:
e7fcd348f16de227383461373565b8de 39784 quicktree_2.5.orig.tar.gz
b4b7cee711ae26366501b2fd12cccd56 5872 quicktree_2.5-6.debian.tar.xz
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Mon Feb 24 21:52:25 UTC 2025 I: Checking whether the package is not for us
Mon Feb 24 21:52:25 UTC 2025 I: Starting 1st build on remote node ionos15-amd64.debian.net.
Mon Feb 24 21:52:25 UTC 2025 I: Preparing to do remote build '1' on ionos15-amd64.debian.net.
Mon Feb 24 21:52:53 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sun Mar 29 16:15:26 -12 2026
I: pbuilder-time-stamp: 1774844126
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 [quicktree_2.5-6.dsc]
I: copying [./quicktree_2.5.orig.tar.gz]
I: copying [./quicktree_2.5-6.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./quicktree_2.5-6.dsc: unsupported subcommand
dpkg-source: info: extracting quicktree in quicktree-2.5
dpkg-source: info: unpacking quicktree_2.5.orig.tar.gz
dpkg-source: info: unpacking quicktree_2.5-6.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying fixMake.patch
dpkg-source: info: applying create_lib.patch
dpkg-source: info: applying fix_build_warnings.patch
dpkg-source: info: applying add_CPPFLAGS.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/685038/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='929806f991674c5b92b08a63f75adcf8'
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='685038'
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.2MMPFWJ9/pbuilderrc_c1Xb --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.2MMPFWJ9/b1 --logfile b1/build.log quicktree_2.5-6.dsc'
SUDO_GID='111'
SUDO_UID='106'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://213.165.73.152:3128'
I: uname -a
Linux ionos15-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/685038/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), help2man, dh-exec
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.
pbuilder-satisfydepends-dummy depends on help2man; however:
Package help2man is not installed.
pbuilder-satisfydepends-dummy depends on dh-exec; however:
Package dh-exec is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} liblocale-gettext-perl{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, 33 newly installed, 0 to remove and 0 not upgraded.
Need to get 20.8 MB of archives. After unpacking 78.7 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB]
Get: 2 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 4 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 5 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 6 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 7 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 8 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 9 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-4 [92.4 kB]
Get: 10 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 11 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 12 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB]
Get: 13 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB]
Get: 14 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 15 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB]
Get: 16 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 17 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 18 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB]
Get: 19 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 20 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 21 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 22 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 23 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 24 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 25 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 26 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 27 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB]
Get: 28 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 29 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 30 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 31 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB]
Get: 32 http://deb.debian.org/debian trixie/main amd64 dh-exec amd64 0.30 [25.6 kB]
Get: 33 http://deb.debian.org/debian trixie/main amd64 help2man amd64 1.49.3 [198 kB]
Fetched 20.8 MB in 0s (130 MB/s)
Preconfiguring packages ...
Selecting previously unselected package liblocale-gettext-perl.
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(Reading database ... 19802 files and directories currently installed.)
Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_amd64.deb ...
Unpacking liblocale-gettext-perl (1.07-7+b1) ...
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Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
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Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:amd64.
Preparing to unpack .../03-libmagic1t64_1%3a5.45-3+b1_amd64.deb ...
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Preparing to unpack .../04-file_1%3a5.45-3+b1_amd64.deb ...
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Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_amd64.deb ...
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Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
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Setting up libpipeline1:amd64 (1.5.8-1) ...
Setting up libicu72:amd64 (72.1-6) ...
Setting up bsdextrautils (2.40.4-4) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.24.1) ...
Setting up libmagic1t64:amd64 (1:5.45-3+b1) ...
Setting up gettext-base (0.23.1-1) ...
Setting up m4 (1.4.19-5) ...
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:amd64 (0.192-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up libunistring5:amd64 (1.3-1) ...
Setting up autopoint (0.23.1-1) ...
Setting up autoconf (2.72-3) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:amd64 (0.0.8-1+b2) ...
Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up liblocale-gettext-perl (1.07-7+b1) ...
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 (2.5.4-3) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up help2man (1.49.3) ...
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) ...
Setting up dh-exec (0.30) ...
Processing triggers for libc-bin (2.40-7) ...
Reading package lists...
Building dependency tree...
Reading state information...
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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/quicktree-2.5/ && 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 > ../quicktree_2.5-6_source.changes
dpkg-buildpackage: info: source package quicktree
dpkg-buildpackage: info: source version 2.5-6
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Lance Lin <lq27267@gmail.com>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
dpkg-source: info: using options from quicktree-2.5/debian/source/options: --extend-diff-ignore=(^|/)(src\/quicktree\.c|src\/tree\.c)$
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/quicktree-2.5'
dh_auto_clean
make -j42 clean
make[2]: Entering directory '/build/reproducible-path/quicktree-2.5'
rm -f ./*.o quicktree
make[2]: Leaving directory '/build/reproducible-path/quicktree-2.5'
rm -f quicktree.1
rm -f libquicktree.a
make[1]: Leaving directory '/build/reproducible-path/quicktree-2.5'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/quicktree.substvars debian/libquicktree-dev.substvars debian/files
rm -fr -- debian/quicktree/ debian/tmp/ debian/libquicktree-dev/
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
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/quicktree-2.5'
sed -i 's/expexted/expected/' src/tree.c
sed -i 's/optio\\n/option/' src/quicktree.c
dh_auto_build
make -j42 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/build/reproducible-path/quicktree-2.5'
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/quicktree-2.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -Wunused-result -c -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -o ./align.o ./src/align.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/quicktree-2.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -Wunused-result -c -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -o ./cluster.o ./src/cluster.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/quicktree-2.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -Wunused-result -c -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -o ./distancemat.o ./src/distancemat.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/quicktree-2.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -Wunused-result -c -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -o ./options.o ./src/options.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/quicktree-2.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -Wunused-result -c -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -o ./util.o ./src/util.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/quicktree-2.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -Wunused-result -c -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -o ./sequence.o ./src/sequence.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/quicktree-2.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -Wunused-result -c -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -o ./quicktree.o ./src/quicktree.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/quicktree-2.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -Wunused-result -c -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -o ./buildtree.o ./src/buildtree.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/quicktree-2.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -Wunused-result -c -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -o ./tree.o ./src/tree.c
cc -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -o quicktree ./align.o ./cluster.o ./distancemat.o ./options.o ./util.o ./sequence.o ./quicktree.o ./buildtree.o ./tree.o -lm
ar rc libquicktree.a ./buildtree.o ./cluster.o ./distancemat.o ./options.o ./util.o ./sequence.o ./tree.o
make[2]: Leaving directory '/build/reproducible-path/quicktree-2.5'
help2man -i debian/quicktree.htm --no-discard-stderr ./quicktree > quicktree.1
make[1]: Leaving directory '/build/reproducible-path/quicktree-2.5'
dh_auto_test
rm -fr -- /tmp/dh-xdg-rundir-7sPzOpX6
create-stamp debian/debhelper-build-stamp
dh_prep
rm -f -- debian/quicktree.substvars debian/libquicktree-dev.substvars
rm -fr -- debian/.debhelper/generated/quicktree/ debian/quicktree/ debian/tmp/ debian/.debhelper/generated/libquicktree-dev/ debian/libquicktree-dev/
dh_auto_install
install -m0755 -d /build/reproducible-path/quicktree-2.5/debian/tmp
dh_install
install -m0755 -d debian/quicktree/usr/bin
cp --reflink=auto -a ./quicktree debian/quicktree/usr/bin/
install -m0755 -d debian/libquicktree-dev/usr/include/quicktree
cp --reflink=auto -a ./include/align.h ./include/aln2dist.h ./include/aln2tree.h ./include/buildtree.h ./include/cluster.h ./include/dist2tree.h ./include/distancemat.h ./include/options.h ./include/sequence.h ./include/tree.h ./include/util.h ./include/version.h debian/libquicktree-dev/usr/include/quicktree/
install -m0755 -d debian/libquicktree-dev/usr/lib/x86_64-linux-gnu
cp --reflink=auto -a ./libquicktree.a debian/libquicktree-dev/usr/lib/x86_64-linux-gnu/
dh_installdocs
install -m0755 -d debian/quicktree/usr/share/doc/quicktree
install -p -m0644 debian/copyright debian/quicktree/usr/share/doc/quicktree/copyright
install -m0755 -d debian/libquicktree-dev/usr/share/doc/libquicktree-dev
install -p -m0644 debian/copyright debian/libquicktree-dev/usr/share/doc/libquicktree-dev/copyright
dh_installchangelogs
install -m0755 -d debian/quicktree/usr/share/doc/quicktree
install -p -m0644 debian/.debhelper/generated/quicktree/dh_installchangelogs.dch.trimmed debian/quicktree/usr/share/doc/quicktree/changelog.Debian
install -m0755 -d debian/libquicktree-dev/usr/share/doc/libquicktree-dev
install -p -m0644 debian/.debhelper/generated/libquicktree-dev/dh_installchangelogs.dch.trimmed debian/libquicktree-dev/usr/share/doc/libquicktree-dev/changelog.Debian
dh_installexamples
install -m0755 -d debian/quicktree/usr/share/doc/quicktree/examples
cp --reflink=auto -a ./debian/tests/data/cysprot.stockholm debian/quicktree/usr/share/doc/quicktree/examples
dh_installman
install -m0755 -d debian/quicktree/usr/share/man/man1/
install -p -m0644 ./quicktree.1 debian/quicktree/usr/share/man/man1/quicktree.1
man-recode --to-code UTF-8 --suffix .dh-new debian/quicktree/usr/share/man/man1/quicktree.1
mv debian/quicktree/usr/share/man/man1/quicktree.1.dh-new debian/quicktree/usr/share/man/man1/quicktree.1
chmod 0644 -- debian/quicktree/usr/share/man/man1/quicktree.1
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
cd debian/quicktree
cd debian/libquicktree-dev
chmod a-x usr/share/doc/quicktree/changelog.Debian usr/share/man/man1/quicktree.1
chmod a-x usr/share/doc/libquicktree-dev/changelog.Debian
gzip -9nf usr/share/doc/quicktree/changelog.Debian usr/share/man/man1/quicktree.1
gzip -9nf usr/share/doc/libquicktree-dev/changelog.Debian
cd '/build/reproducible-path/quicktree-2.5'
cd '/build/reproducible-path/quicktree-2.5'
dh_fixperms
find debian/quicktree ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/libquicktree-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/quicktree/usr/share/doc -type f -a -true -a ! -regex 'debian/quicktree/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libquicktree-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libquicktree-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/quicktree/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/libquicktree-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/quicktree/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libquicktree-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/quicktree -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/libquicktree-dev -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/quicktree/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
find debian/libquicktree-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
dh_missing
dh_dwz -a
dwz -- debian/quicktree/usr/bin/quicktree
dh_strip -a
strip --strip-debug --remove-section=.comment --remove-section=.note --enable-deterministic-archives -R .gnu.lto_\* -R .gnu.debuglto_\* -N __gnu_lto_slim -N __gnu_lto_v1 debian/libquicktree-dev/usr/lib/x86_64-linux-gnu/libquicktree.a
install -m0755 -d debian/.debhelper/quicktree/dbgsym-root/usr/lib/debug/.build-id/7a
objcopy --only-keep-debug --compress-debug-sections debian/quicktree/usr/bin/quicktree debian/.debhelper/quicktree/dbgsym-root/usr/lib/debug/.build-id/7a/94a567a31a877c4efccb1e83b84bece9955019.debug
chmod 0644 -- debian/.debhelper/quicktree/dbgsym-root/usr/lib/debug/.build-id/7a/94a567a31a877c4efccb1e83b84bece9955019.debug
strip --remove-section=.comment --remove-section=.note debian/quicktree/usr/bin/quicktree
objcopy --add-gnu-debuglink debian/.debhelper/quicktree/dbgsym-root/usr/lib/debug/.build-id/7a/94a567a31a877c4efccb1e83b84bece9955019.debug debian/quicktree/usr/bin/quicktree
install -m0755 -d debian/.debhelper/quicktree/dbgsym-root/usr/share/doc
ln -s quicktree debian/.debhelper/quicktree/dbgsym-root/usr/share/doc/quicktree-dbgsym
install -m0755 -d debian/.debhelper/quicktree
dh_makeshlibs -a
rm -f debian/quicktree/DEBIAN/shlibs
rm -f debian/libquicktree-dev/DEBIAN/shlibs
dh_shlibdeps -a
install -m0755 -d debian/quicktree/DEBIAN
dpkg-shlibdeps -Tdebian/quicktree.substvars debian/quicktree/usr/bin/quicktree
dh_installdeb
install -m0755 -d debian/quicktree/DEBIAN
install -m0755 -d debian/libquicktree-dev/DEBIAN
dh_gencontrol
install -m0755 -d debian/libquicktree-dev/DEBIAN
echo misc:Depends= >> debian/libquicktree-dev.substvars
echo misc:Pre-Depends= >> debian/libquicktree-dev.substvars
dpkg-gencontrol -plibquicktree-dev -ldebian/changelog -Tdebian/libquicktree-dev.substvars -cdebian/control -Pdebian/libquicktree-dev
install -m0755 -d debian/quicktree/DEBIAN
echo misc:Depends= >> debian/quicktree.substvars
echo misc:Pre-Depends= >> debian/quicktree.substvars
install -m0755 -d debian/.debhelper/quicktree/dbgsym-root/DEBIAN
dpkg-gencontrol -pquicktree -ldebian/changelog -Tdebian/quicktree.substvars -cdebian/control -Pdebian/.debhelper/quicktree/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=quicktree-dbgsym "-DDepends=quicktree (= \${binary:Version})" "-DDescription=debug symbols for quicktree" -DBuild-Ids=7a94a567a31a877c4efccb1e83b84bece9955019 -DSection=debug -UMulti-Arch -UReplaces -UBreaks
dpkg-gencontrol: warning: Depends field of package libquicktree-dev: substitution variable ${shlibs:Depends} used, but is not defined
chmod 0644 -- debian/libquicktree-dev/DEBIAN/control
chmod 0644 -- debian/.debhelper/quicktree/dbgsym-root/DEBIAN/control
dpkg-gencontrol -pquicktree -ldebian/changelog -Tdebian/quicktree.substvars -cdebian/control -Pdebian/quicktree
chmod 0644 -- debian/quicktree/DEBIAN/control
dh_md5sums
install -m0755 -d debian/quicktree/DEBIAN
install -m0755 -d debian/libquicktree-dev/DEBIAN
cd debian/quicktree >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
cd debian/libquicktree-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/quicktree/DEBIAN/md5sums
install -m0755 -d debian/.debhelper/quicktree/dbgsym-root/DEBIAN
chmod 0644 -- debian/libquicktree-dev/DEBIAN/md5sums
cd debian/.debhelper/quicktree/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/quicktree/dbgsym-root/DEBIAN/md5sums
dh_builddeb
dpkg-deb --root-owner-group --build debian/quicktree ..
dpkg-deb --root-owner-group --build debian/.debhelper/quicktree/dbgsym-root ..
dpkg-deb --root-owner-group --build debian/libquicktree-dev ..
dpkg-deb: building package 'quicktree' in '../quicktree_2.5-6_amd64.deb'.
dpkg-deb: building package 'quicktree-dbgsym' in '../quicktree-dbgsym_2.5-6_amd64.deb'.
dpkg-deb: building package 'libquicktree-dev' in '../libquicktree-dev_2.5-6_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../quicktree_2.5-6_amd64.buildinfo
dpkg-genchanges --build=binary -O../quicktree_2.5-6_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-source: info: using options from quicktree-2.5/debian/source/options: --extend-diff-ignore=(^|/)(src\/quicktree\.c|src\/tree\.c)$
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/685038 and its subdirectories
I: Current time: Sun Mar 29 16:15:52 -12 2026
I: pbuilder-time-stamp: 1774844152
Mon Feb 24 21:52:53 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net.
Mon Feb 24 21:52:53 UTC 2025 I: Preparing to do remote build '2' on ionos11-amd64.debian.net.
Mon Feb 24 21:54:00 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net.
Mon Feb 24 21:54:01 UTC 2025 I: quicktree_2.5-6_amd64.changes:
Format: 1.8
Date: Tue, 03 Oct 2023 19:27:53 +0700
Source: quicktree
Binary: libquicktree-dev quicktree quicktree-dbgsym
Architecture: amd64
Version: 2.5-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Lance Lin <lq27267@gmail.com>
Description:
libquicktree-dev - Neighbor-Joining algorithm for phylogenies (development)
quicktree - Neighbor-Joining algorithm for phylogenies
Closes: 1048270
Changes:
quicktree (2.5-6) unstable; urgency=medium
.
* Team upload.
* d/control: Update Standards-Version to 4.6.2
* d/rules: Clean libquicktree.a (Closes: #1048270)
* d/source/options: Ignore changes to source files
* d/copyright: Update year for debian/* files to 2023
* d/patches/fix_build_warnings.patch: Fix minor build warnings for
incorrect format type and suggested parentheses
* d/patches/add_CPPFLAGS.patch: Passes CPPFLAGS for hardening with
D_FORTIFY_SOURCE
Checksums-Sha1:
49b37f06bf174317fb1bba79823655b20a2b220a 26120 libquicktree-dev_2.5-6_amd64.deb
cd9bacdcdd8350f722ac28034c3828bfaba5ef80 43828 quicktree-dbgsym_2.5-6_amd64.deb
5c544c9dcd1a815b036a83d106fed965ad409cc1 5222 quicktree_2.5-6_amd64.buildinfo
34ba23cb6f1f8592169c91f1ee5b999760145cbd 21628 quicktree_2.5-6_amd64.deb
Checksums-Sha256:
0f9bcaa4de156b151cadeeb3aa223b3dd0cb9d96330e0242d452c9253e8a6caf 26120 libquicktree-dev_2.5-6_amd64.deb
609a33710cf1d27eb128298f3a8b16e550006231997b3a4d44f4655be1a46d2b 43828 quicktree-dbgsym_2.5-6_amd64.deb
fe4d18cf5c65ee07c2b7b497d0b351b020594e592daa0543226b2dbd7c374528 5222 quicktree_2.5-6_amd64.buildinfo
2f826c23ed7304abe99040c5a0da913c3b5c051f45e0224b71221b7e7a3ca2a2 21628 quicktree_2.5-6_amd64.deb
Files:
9c6b513e6397d03f0c5d2ff6c153057d 26120 libdevel optional libquicktree-dev_2.5-6_amd64.deb
593f5df1c942c20748bbebebfde205c5 43828 debug optional quicktree-dbgsym_2.5-6_amd64.deb
19bf463187547b5bceba4081f2a6ef62 5222 science optional quicktree_2.5-6_amd64.buildinfo
4f9a3a0d991e31cb663aba9364695674 21628 science optional quicktree_2.5-6_amd64.deb
Mon Feb 24 21:54:02 UTC 2025 I: diffoscope 289 will be used to compare the two builds:
Running as unit: rb-diffoscope-amd64_8-48623.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.2MMPFWJ9/quicktree_2.5-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.2MMPFWJ9/quicktree_2.5-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.2MMPFWJ9/quicktree_2.5-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.2MMPFWJ9/b1/quicktree_2.5-6_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.2MMPFWJ9/b2/quicktree_2.5-6_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: 235ms
CPU time consumed: 236ms
Mon Feb 24 21:54:02 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists.
Mon Feb 24 21:54:03 UTC 2025 I: quicktree from trixie built successfully and reproducibly on amd64.
Mon Feb 24 21:54:04 UTC 2025 I: Submitting .buildinfo files to external archives:
Mon Feb 24 21:54:04 UTC 2025 I: Submitting 8.0K b1/quicktree_2.5-6_amd64.buildinfo.asc
Mon Feb 24 21:54:06 UTC 2025 I: Submitting 8.0K b2/quicktree_2.5-6_amd64.buildinfo.asc
Mon Feb 24 21:54:08 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Mon Feb 24 21:54:08 UTC 2025 I: Done submitting .buildinfo files.
Mon Feb 24 21:54:08 UTC 2025 I: Removing signed quicktree_2.5-6_amd64.buildinfo.asc files:
removed './b1/quicktree_2.5-6_amd64.buildinfo.asc'
removed './b2/quicktree_2.5-6_amd64.buildinfo.asc'