Mon Mar 17 11:14:11 UTC 2025 I: starting to build trf/unstable/amd64 on jenkins on '2025-03-17 11:13'
Mon Mar 17 11:14:11 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_16/49925/console.log
Mon Mar 17 11:14:11 UTC 2025 I: Downloading source for unstable/trf=4.09.1-6
--2025-03-17 11:14:11-- http://deb.debian.org/debian/pool/main/t/trf/trf_4.09.1-6.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2054 (2.0K) [text/prs.lines.tag]
Saving to: ‘trf_4.09.1-6.dsc’
0K .. 100% 302M=0s
2025-03-17 11:14:11 (302 MB/s) - ‘trf_4.09.1-6.dsc’ saved [2054/2054]
Mon Mar 17 11:14:11 UTC 2025 I: trf_4.09.1-6.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: trf
Binary: trf, trf-examples
Architecture: any all
Version: 4.09.1-6
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://tandem.bu.edu/trf/trf.html
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/trf
Vcs-Git: https://salsa.debian.org/med-team/trf.git
Testsuite: autopkgtest
Testsuite-Triggers: bc, html2text
Build-Depends: debhelper-compat (= 13)
Package-List:
trf deb science optional arch=any
trf-examples deb science optional arch=all
Checksums-Sha1:
d9edd62b0b916cc539534fbe22eabffdea8139ac 274103 trf_4.09.1.orig.tar.gz
e498088e451e922e383c5504da1bd637c0170fa4 16056 trf_4.09.1-6.debian.tar.xz
Checksums-Sha256:
516015b625473350c3d1c9b83cac86baea620c8418498ab64c0a67029c3fb28a 274103 trf_4.09.1.orig.tar.gz
38e74c5ffad47861b2d3d70a4aec273f6904980b3ff856d75e84177a6252aa84 16056 trf_4.09.1-6.debian.tar.xz
Files:
8569300f69776b65e22ad12caa682ab8 274103 trf_4.09.1.orig.tar.gz
1646377eb9c320a6187df65064a0168a 16056 trf_4.09.1-6.debian.tar.xz
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Mon Mar 17 11:14:11 UTC 2025 I: Checking whether the package is not for us
Mon Mar 17 11:14:11 UTC 2025 I: Starting 1st build on remote node ionos15-amd64.debian.net.
Mon Mar 17 11:14:11 UTC 2025 I: Preparing to do remote build '1' on ionos15-amd64.debian.net.
Mon Mar 17 11:15:00 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sun Apr 19 05:37:13 -12 2026
I: pbuilder-time-stamp: 1776620233
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 [trf_4.09.1-6.dsc]
I: copying [./trf_4.09.1.orig.tar.gz]
I: copying [./trf_4.09.1-6.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./trf_4.09.1-6.dsc: unsupported subcommand
dpkg-source: info: extracting trf in trf-4.09.1
dpkg-source: info: unpacking trf_4.09.1.orig.tar.gz
dpkg-source: info: unpacking trf_4.09.1-6.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying fix-exit-code.patch
dpkg-source: info: applying typo.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/4188863/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='unstable'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='d89eebb3857943fbbf64be9d73b89739'
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='4188863'
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.8BXgdDiJ/pbuilderrc_eJNa --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.8BXgdDiJ/b1 --logfile b1/build.log trf_4.09.1-6.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 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/4188863/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 ... 19784 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} libicu76{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 20.9 MB of archives. After unpacking 80.8 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-2 [337 kB]
Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-2 [109 kB]
Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-2 [43.5 kB]
Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB]
Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-7 [294 kB]
Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB]
Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB]
Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 24 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 25 http://deb.debian.org/debian unstable/main amd64 libicu76 amd64 76.1-3 [9721 kB]
Get: 26 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.3+b1 [699 kB]
Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB]
Fetched 20.9 MB in 3s (8090 kB/s)
Preconfiguring packages ...
Selecting previously unselected package sensible-utils.
(Reading database ...
(Reading database ... 5%
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(Reading database ... 19784 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%3a5.46-2_amd64.deb ...
Unpacking libmagic-mgc (1:5.46-2) ...
Selecting previously unselected package libmagic1t64:amd64.
Preparing to unpack .../02-libmagic1t64_1%3a5.46-2_amd64.deb ...
Unpacking libmagic1t64:amd64 (1:5.46-2) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.46-2_amd64.deb ...
Unpacking file (1:5.46-2) ...
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Preparing to unpack .../04-gettext-base_0.23.1-1_amd64.deb ...
Unpacking gettext-base (0.23.1-1) ...
Selecting previously unselected package libuchardet0:amd64.
Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ...
Unpacking libuchardet0:amd64 (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.23.0-7_amd64.deb ...
Unpacking groff-base (1.23.0-7) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.40.4-5_amd64.deb ...
Unpacking bsdextrautils (2.40.4-5) ...
Selecting previously unselected package libpipeline1:amd64.
Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ...
Unpacking libpipeline1:amd64 (1.5.8-1) ...
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Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ...
Unpacking man-db (2.13.0-1) ...
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Preparing to unpack .../10-m4_1.4.19-7_amd64.deb ...
Unpacking m4 (1.4.19-7) ...
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Unpacking autoconf (2.72-3) ...
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Unpacking autotools-dev (20220109.1) ...
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Preparing to unpack .../13-automake_1%3a1.17-3_all.deb ...
Unpacking automake (1:1.17-3) ...
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Unpacking libdebhelper-perl (13.24.1) ...
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Unpacking libunistring5:amd64 (1.3-1) ...
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Unpacking libicu76:amd64 (76.1-3) ...
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Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.3+b1_amd64.deb ...
Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.3+b1) ...
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Setting up libpipeline1:amd64 (1.5.8-1) ...
Setting up bsdextrautils (2.40.4-5) ...
Setting up libmagic-mgc (1:5.46-2) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.24.1) ...
Setting up libmagic1t64:amd64 (1:5.46-2) ...
Setting up gettext-base (0.23.1-1) ...
Setting up m4 (1.4.19-7) ...
Setting up file (1:5.46-2) ...
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 libicu76:amd64 (76.1-3) ...
Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.3+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 (2.5.4-4) ...
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 (2.41-6) ...
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/trf-4.09.1/ && 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 > ../trf_4.09.1-6_source.changes
dpkg-buildpackage: info: source package trf
dpkg-buildpackage: info: source version 4.09.1-6
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 amd64
debian/rules clean
dh clean
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether sleep supports fractional seconds... yes
checking filesystem timestamp resolution... 0.01
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking xargs -n works... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... none
checking for ranlib... ranlib
checking whether ln -s works... yes
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for limits.h... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for size_t... yes
checking for GNU libc compatible malloc... yes
checking for GNU libc compatible realloc... yes
checking for library containing floor... -lm
checking for sqrt... yes
checking for memset... yes
checking for strchr... yes
checking for strerror... yes
checking for strstr... yes
checking for strtol... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands
dh_auto_build
make -j42
make[1]: Entering directory '/build/reproducible-path/trf-4.09.1'
make all-recursive
make[2]: Entering directory '/build/reproducible-path/trf-4.09.1'
Making all in src
make[3]: Entering directory '/build/reproducible-path/trf-4.09.1/src'
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fno-align-functions -fno-align-loops -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/trf-4.09.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o trf-trf.o `test -f 'trf.c' || echo './'`trf.c
In file included from trfrun.h:89,
from trf.c:30:
tr30dat.h:49:9: note: '#pragma message: You forgot to define a platform when compiling. Setting UNIXCONSOLE.'
49 | #pragma message( \
| ^~~~~~~
In file included from trfrun.h:91:
trfclean.h: In function 'GetList':
trfclean.h:166:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
166 | fgets( hsequence, 255, fp );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
trfclean.h:170:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
170 | fgets( hparameters, 255, fp );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
trfclean.h: In function 'CleanAlignments':
trfclean.h:484:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
484 | fgets( string2, 260, al_fp );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
trfclean.h:485:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
485 | fgets( string3, 260, al_fp );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
trfclean.h:502:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
502 | fgets( string2, 260, al_fp );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
trfclean.h: In function 'BreakAlignments':
trfclean.h:568:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
568 | fgets( headlns[i], 200, al_fp );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
trfclean.h:593:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
593 | fgets( buffer, 200, al_fp );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
trfrun.h: In function 'TRF':
trfrun.h:696:30: warning: '%s' directive writing up to 259 bytes into a region of size between 0 and 259 [-Wformat-overflow=]
696 | sprintf( htmlstring, "%s.%s.html", paramset.outputprefix, paramstring );
| ^~ ~~~~~~~~~~~
In file included from /usr/include/stdio.h:970,
from trf.c:26:
In function 'sprintf',
inlined from 'TRF' at trfrun.h:696:5:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 7 and 525 bytes into a destination of size 260
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
trfrun.h: In function 'TRF':
trfrun.h:697:29: warning: '%s' directive writing up to 259 bytes into a region of size between 0 and 259 [-Wformat-overflow=]
697 | sprintf( txtstring, "%s.%s.txt.html", paramset.outputprefix, paramstring );
| ^~ ~~~~~~~~~~~
In function 'sprintf',
inlined from 'TRF' at trfrun.h:697:5:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 11 and 529 bytes into a destination of size 260
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
trfrun.h: In function 'TRF':
trfrun.h:698:29: warning: '%s' directive writing up to 259 bytes into a region of size between 0 and 259 [-Wformat-overflow=]
698 | sprintf( datstring, "%s.%s.dat", paramset.outputprefix, paramstring );
| ^~ ~~~~~~~~~~~
In function 'sprintf',
inlined from 'TRF' at trfrun.h:698:5:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 6 and 524 bytes into a destination of size 260
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
trfrun.h: In function 'TRF':
trfrun.h:699:30: warning: '%s' directive writing up to 259 bytes into a region of size between 0 and 259 [-Wformat-overflow=]
699 | sprintf( maskstring, "%s.%s.mask", paramset.outputprefix, paramstring );
| ^~ ~~~~~~~~~~~
In function 'sprintf',
inlined from 'TRF' at trfrun.h:699:5:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 7 and 525 bytes into a destination of size 260
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
trfrun.h: In function 'TRFControlRoutine':
trfrun.h:323:27: warning: '.summary.html' directive writing 13 bytes into a region of size between 0 and 259 [-Wformat-overflow=]
323 | sprintf( desth, "%s.%s.summary.html", prefix, paramstring );
| ^~~~~~~~~~~~~
In function 'sprintf',
inlined from 'TRFControlRoutine' at trfrun.h:323:5:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 15 or more bytes (assuming 274) into a destination of size 260
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
trfrun.h: In function 'TRFControlRoutine':
trfrun.h:335:31: warning: '.mask' directive writing 5 bytes into a region of size between 0 and 259 [-Wformat-overflow=]
335 | sprintf( destm, "%s.%s.mask", prefix, paramstring );
| ^~~~~
In function 'sprintf',
inlined from 'TRFControlRoutine' at trfrun.h:335:9:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 7 or more bytes (assuming 266) into a destination of size 260
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
trfrun.h: In function 'TRFControlRoutine':
trfrun.h:348:35: warning: '.dat' directive writing 4 bytes into a region of size between 0 and 259 [-Wformat-overflow=]
348 | sprintf( destd, "%s.%s.dat", prefix, paramstring );
| ^~~~
In function 'sprintf',
inlined from 'TRFControlRoutine' at trfrun.h:348:13:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 6 or more bytes (assuming 265) into a destination of size 260
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
trfrun.h: In function 'TRFControlRoutine':
trfrun.h:499:32: warning: '%s' directive writing up to 259 bytes into a region of size between 0 and 259 [-Wformat-overflow=]
499 | sprintf( outh, "%s.%s.1.html", input, paramstring );
| ^~ ~~~~~~~~~~~
In function 'sprintf',
inlined from 'TRFControlRoutine' at trfrun.h:499:13:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 9 and 527 bytes into a destination of size 260
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
trfrun.h: In function 'TRFControlRoutine':
trfrun.h:520:42: warning: '%s' directive writing up to 259 bytes into a region of size between 247 and 256 [-Wformat-overflow=]
520 | sprintf( maskstring, "%s.s%d.%s.mask", prefix, i, paramstring );
| ^~ ~~~~~~~~~~~
In function 'sprintf',
inlined from 'TRFControlRoutine' at trfrun.h:520:13:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 278) into a destination of size 260
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
trfrun.h: In function 'TRFControlRoutine':
trfrun.h:528:36: warning: '%s' directive writing up to 259 bytes into a region of size between 247 and 256 [-Wformat-overflow=]
528 | sprintf( outm, "%s.s%d.%s.mask", prefix, i, paramstring );
| ^~ ~~~~~~~~~~~
In function 'sprintf',
inlined from 'TRFControlRoutine' at trfrun.h:528:13:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 278) into a destination of size 260
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
trfrun.h: In function 'TRFControlRoutine':
trfrun.h:196:39: warning: '.dat' directive writing 4 bytes into a region of size between 0 and 259 [-Wformat-overflow=]
196 | sprintf( destd, "%s.%s.dat", prefix, paramstring );
| ^~~~
In function 'sprintf',
inlined from 'TRFControlRoutine' at trfrun.h:196:17:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 6 or more bytes (assuming 265) into a destination of size 260
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
trfrun.h: In function 'TRFControlRoutine':
trfrun.h:288:33: warning: '.mask' directive writing 5 bytes into a region of size between 0 and 259 [-Wformat-overflow=]
288 | maskstring, "%s.%s.mask", paramset.outputprefix, paramstring );
| ^~~~~
In function 'sprintf',
inlined from 'TRFControlRoutine' at trfrun.h:287:13:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 7 or more bytes (assuming 266) into a destination of size 260
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
gcc -fno-align-functions -fno-align-loops -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/trf-4.09.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o trf trf-trf.o -lm
make[3]: Leaving directory '/build/reproducible-path/trf-4.09.1/src'
make[3]: Entering directory '/build/reproducible-path/trf-4.09.1'
make[3]: Leaving directory '/build/reproducible-path/trf-4.09.1'
make[2]: Leaving directory '/build/reproducible-path/trf-4.09.1'
make[1]: Leaving directory '/build/reproducible-path/trf-4.09.1'
dh_auto_test
make -j42 check "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1
make[1]: Entering directory '/build/reproducible-path/trf-4.09.1'
Making check in src
make[2]: Entering directory '/build/reproducible-path/trf-4.09.1/src'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/reproducible-path/trf-4.09.1/src'
make[2]: Entering directory '/build/reproducible-path/trf-4.09.1'
make[2]: Leaving directory '/build/reproducible-path/trf-4.09.1'
make[1]: Leaving directory '/build/reproducible-path/trf-4.09.1'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install
make -j42 install DESTDIR=/build/reproducible-path/trf-4.09.1/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/build/reproducible-path/trf-4.09.1'
Making install in src
make[2]: Entering directory '/build/reproducible-path/trf-4.09.1/src'
make[3]: Entering directory '/build/reproducible-path/trf-4.09.1/src'
make[3]: Nothing to be done for 'install-data-am'.
/usr/bin/mkdir -p '/build/reproducible-path/trf-4.09.1/debian/tmp/usr/bin'
/usr/bin/install -c trf '/build/reproducible-path/trf-4.09.1/debian/tmp/usr/bin'
make install-exec-hook
make[4]: Entering directory '/build/reproducible-path/trf-4.09.1/src'
ln -s /build/reproducible-path/trf-4.09.1/debian/tmp/usr/bin/trf \
/build/reproducible-path/trf-4.09.1/debian/tmp/usr/bin/trf4.10.0-rc.2.linux64.exe
make[4]: Leaving directory '/build/reproducible-path/trf-4.09.1/src'
make[3]: Leaving directory '/build/reproducible-path/trf-4.09.1/src'
make[2]: Leaving directory '/build/reproducible-path/trf-4.09.1/src'
make[2]: Entering directory '/build/reproducible-path/trf-4.09.1'
make[3]: Entering directory '/build/reproducible-path/trf-4.09.1'
make[3]: Nothing to be done for 'install-exec-am'.
/usr/bin/mkdir -p '/build/reproducible-path/trf-4.09.1/debian/tmp/usr/share/doc/trf'
/usr/bin/install -c -m 644 README.md '/build/reproducible-path/trf-4.09.1/debian/tmp/usr/share/doc/trf'
make[3]: Leaving directory '/build/reproducible-path/trf-4.09.1'
make[2]: Leaving directory '/build/reproducible-path/trf-4.09.1'
make[1]: Leaving directory '/build/reproducible-path/trf-4.09.1'
debian/rules override_dh_install
make[1]: Entering directory '/build/reproducible-path/trf-4.09.1'
dh_install
find debian -name "*.exe" -delete
make[1]: Leaving directory '/build/reproducible-path/trf-4.09.1'
dh_installdocs
dh_installchangelogs
dh_installman
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'trf' in '../trf_4.09.1-6_amd64.deb'.
dpkg-deb: building package 'trf-dbgsym' in '../trf-dbgsym_4.09.1-6_amd64.deb'.
dpkg-deb: building package 'trf-examples' in '../trf-examples_4.09.1-6_all.deb'.
dpkg-genbuildinfo --build=binary -O../trf_4.09.1-6_amd64.buildinfo
dpkg-genchanges --build=binary -O../trf_4.09.1-6_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/4188863 and its subdirectories
I: Current time: Sun Apr 19 05:38:00 -12 2026
I: pbuilder-time-stamp: 1776620280
Mon Mar 17 11:15:01 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net.
Mon Mar 17 11:15:01 UTC 2025 I: Preparing to do remote build '2' on ionos11-amd64.debian.net.
Mon Mar 17 11:17:15 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net.
Mon Mar 17 11:17:15 UTC 2025 I: trf_4.09.1-6_amd64.changes:
Format: 1.8
Date: Sun, 02 Oct 2022 14:59:22 +0200
Source: trf
Binary: trf trf-dbgsym trf-examples
Architecture: amd64 all
Version: 4.09.1-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
trf - locate and display tandem repeats in DNA sequences
trf-examples - locate and display tandem repeats in DNA sequences (examples)
Changes:
trf (4.09.1-6) unstable; urgency=medium
.
* d/control: add myself to uploaders.
* d/watch: fix watch file; use git mode.
* d/control: declare compliance to standards version 4.6.1.
* typo.patch: added; fix typo caught by lintian.
* d/copyright: bump copyright year for debian/*.
Checksums-Sha1:
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2fe014e4b32f2064185327b2cb0d1fe3bec18aeb 19256 trf-examples_4.09.1-6_all.deb
e9254c08647af6abbcf898b09b76b8771880e88d 5094 trf_4.09.1-6_amd64.buildinfo
ed778250b89104f1a02387fda8bcb9ce85cfdb79 58416 trf_4.09.1-6_amd64.deb
Checksums-Sha256:
ec5cb3f9a3451fcae87ebc84640a37691a5b819c88fb4a2db7845a8280b3dd32 79160 trf-dbgsym_4.09.1-6_amd64.deb
8622e59612a6c4056642ef21d8db3ab490a23d6ebfd8be50cf4c8f079b9990dc 19256 trf-examples_4.09.1-6_all.deb
41d320b556d27b52203e4f1e6d8dba72462cc54c2130b6d5bcf7e87ca5670657 5094 trf_4.09.1-6_amd64.buildinfo
80b40b9ab0dc2b4ec8a3dde54568dcccea226ad0645cc436ac8501b4256334a5 58416 trf_4.09.1-6_amd64.deb
Files:
cbcc719bf59f78aa862c24d4f889fc1a 79160 debug optional trf-dbgsym_4.09.1-6_amd64.deb
f2a90c9a136d205c7ec7878d07f89dac 19256 science optional trf-examples_4.09.1-6_all.deb
663d6f22bcdba6d91f58a0f8b7f3ccbe 5094 science optional trf_4.09.1-6_amd64.buildinfo
074b99f40c95b42407c79b0eeff909cc 58416 science optional trf_4.09.1-6_amd64.deb
Mon Mar 17 11:17:16 UTC 2025 I: diffoscope 289 will be used to compare the two builds:
Running as unit: rb-diffoscope-amd64_16-49925.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.8BXgdDiJ/trf_4.09.1-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.8BXgdDiJ/trf_4.09.1-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.8BXgdDiJ/trf_4.09.1-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.8BXgdDiJ/b1/trf_4.09.1-6_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.8BXgdDiJ/b2/trf_4.09.1-6_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: 217ms
CPU time consumed: 218ms
Mon Mar 17 11:17:17 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists.
Mon Mar 17 11:17:17 UTC 2025 I: trf from unstable built successfully and reproducibly on amd64.
Mon Mar 17 11:17:18 UTC 2025 I: Submitting .buildinfo files to external archives:
Mon Mar 17 11:17:18 UTC 2025 I: Submitting 8.0K b1/trf_4.09.1-6_amd64.buildinfo.asc
Mon Mar 17 11:17:18 UTC 2025 I: Submitting 8.0K b2/trf_4.09.1-6_amd64.buildinfo.asc
Mon Mar 17 11:17:19 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Mon Mar 17 11:17:19 UTC 2025 I: Done submitting .buildinfo files.
Mon Mar 17 11:17:19 UTC 2025 I: Removing signed trf_4.09.1-6_amd64.buildinfo.asc files:
removed './b1/trf_4.09.1-6_amd64.buildinfo.asc'
removed './b2/trf_4.09.1-6_amd64.buildinfo.asc'