Mon Jan 6 20:46:52 UTC 2025 I: starting to build rate4site/trixie/i386 on jenkins on '2025-01-06 20:46'
Mon Jan 6 20:46:52 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_11/41597/console.log
Mon Jan 6 20:46:52 UTC 2025 I: Downloading source for trixie/rate4site=3.0.0-8
--2025-01-06 20:46:52-- http://deb.debian.org/debian/pool/main/r/rate4site/rate4site_3.0.0-8.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: ‘rate4site_3.0.0-8.dsc’
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2025-01-06 20:46:52 (305 MB/s) - ‘rate4site_3.0.0-8.dsc’ saved [2054/2054]
Mon Jan 6 20:46:52 UTC 2025 I: rate4site_3.0.0-8.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: rate4site
Binary: rate4site
Architecture: any
Version: 3.0.0-8
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Guy Yachdav <gyachdav@rostlab.org>, Laszlo Kajan <lkajan@debian.org>, Andreas Tille <tille@debian.org>
Homepage: https://www.tau.ac.il/~itaymay/cp/rate4site.html
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/rate4site
Vcs-Git: https://salsa.debian.org/med-team/rate4site.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13)
Package-List:
rate4site deb science optional arch=any
Checksums-Sha1:
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bb0429162f4a7752031730289dfa5cd8fe7901d0 4684 rate4site_3.0.0-8.debian.tar.xz
Checksums-Sha256:
5f748131bc2d10383c35c3141a835efa4ec1e7088cd9d8970e8024021aa509ac 303488 rate4site_3.0.0.orig.tar.gz
66fe3297b77dabf92715dd161c1267cfaa141027385c491279a12532cd3a4165 4684 rate4site_3.0.0-8.debian.tar.xz
Files:
c06ec2429d1535bf91e8dbcaed537d30 303488 rate4site_3.0.0.orig.tar.gz
c1c1e4f19082338f936827542fbfb816 4684 rate4site_3.0.0-8.debian.tar.xz
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Mon Jan 6 20:46:52 UTC 2025 I: Checking whether the package is not for us
Mon Jan 6 20:46:52 UTC 2025 I: Starting 1st build on remote node ionos6-i386.debian.net.
Mon Jan 6 20:46:52 UTC 2025 I: Preparing to do remote build '1' on ionos6-i386.debian.net.
Mon Jan 6 20:48:14 UTC 2025 I: Deleting $TMPDIR on ionos6-i386.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sun Feb 8 15:09:58 -12 2026
I: pbuilder-time-stamp: 1770606598
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: using eatmydata during job
I: Copying source file
I: copying [rate4site_3.0.0-8.dsc]
I: copying [./rate4site_3.0.0.orig.tar.gz]
I: copying [./rate4site_3.0.0-8.debian.tar.xz]
I: Extracting source
gpgv: Signature made Thu Jan 20 10:57:32 2022
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./rate4site_3.0.0-8.dsc: no acceptable signature found
dpkg-source: info: extracting rate4site in rate4site-3.0.0
dpkg-source: info: unpacking rate4site_3.0.0.orig.tar.gz
dpkg-source: info: unpacking rate4site_3.0.0-8.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying spelling.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/128180/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='i386'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='6b95c82de6a74a319bc052d3ee7a5007'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
LD_LIBRARY_PATH='/usr/lib/libeatmydata'
LD_PRELOAD='libeatmydata.so'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='128180'
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.9ptsD2q1/pbuilderrc_8nCb --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.9ptsD2q1/b1 --logfile b1/build.log rate4site_3.0.0-8.dsc'
SUDO_GID='112'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://213.165.73.152:3128'
I: uname -a
Linux ionos6-i386 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) 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/128180/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13)
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19951 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} 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, 29 newly installed, 0 to remove and 0 not upgraded.
Need to get 20.1 MB of archives. After unpacking 75.8 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 4 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 5 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-3 [201 kB]
Get: 6 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 7 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-7 [1199 kB]
Get: 8 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.2-13 [95.9 kB]
Get: 9 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 10 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 11 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB]
Get: 12 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-3 [723 kB]
Get: 16 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.23 [90.6 kB]
Get: 17 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-8 [517 kB]
Get: 18 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 21 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 22 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 23 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 24 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-5+b1 [9583 kB]
Get: 25 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB]
Get: 26 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-3 [1631 kB]
Get: 27 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 28 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 29 http://deb.debian.org/debian trixie/main i386 debhelper all 13.23 [919 kB]
Fetched 20.1 MB in 0s (90.1 MB/s)
Preconfiguring packages ...
Selecting previously unselected package sensible-utils.
(Reading database ...
(Reading database ... 5%
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(Reading database ... 19951 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_i386.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
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Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_i386.deb ...
Unpacking libmagic1t64:i386 (1:5.45-3+b1) ...
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Preparing to unpack .../03-file_1%3a5.45-3+b1_i386.deb ...
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Preparing to unpack .../04-gettext-base_0.22.5-3_i386.deb ...
Unpacking gettext-base (0.22.5-3) ...
Selecting previously unselected package libuchardet0:i386.
Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_i386.deb ...
Unpacking libuchardet0:i386 (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.23.0-7_i386.deb ...
Unpacking groff-base (1.23.0-7) ...
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Preparing to unpack .../07-bsdextrautils_2.40.2-13_i386.deb ...
Unpacking bsdextrautils (2.40.2-13) ...
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Preparing to unpack .../08-libpipeline1_1.5.8-1_i386.deb ...
Unpacking libpipeline1:i386 (1.5.8-1) ...
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Unpacking m4 (1.4.19-4) ...
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Setting up libpipeline1:i386 (1.5.8-1) ...
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Setting up bsdextrautils (2.40.2-13) ...
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Setting up libarchive-zip-perl (1.68-1) ...
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Setting up libmagic1t64:i386 (1:5.45-3+b1) ...
Setting up gettext-base (0.22.5-3) ...
Setting up m4 (1.4.19-4) ...
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:i386 (0.192-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up autopoint (0.22.5-3) ...
Setting up autoconf (2.72-3) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:i386 (0.0.8-1+b2) ...
Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.0-1) ...
Setting up gettext (0.22.5-3) ...
Setting up libtool (2.4.7-8) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.14.0-1) ...
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 (13.23) ...
Processing triggers for libc-bin (2.40-4) ...
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/rate4site-3.0.0/ && 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 > ../rate4site_3.0.0-8_source.changes
dpkg-buildpackage: info: source package rate4site
dpkg-buildpackage: info: source version 3.0.0-8
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
debian/rules clean
dh clean
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
configure.ac:5: warning: 'AM_CONFIG_HEADER': this macro is obsolete.
configure.ac:5: You should use the 'AC_CONFIG_HEADERS' macro instead.
./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from...
aclocal.m4:745: AM_CONFIG_HEADER is expanded from...
configure.ac:5: the top level
configure.ac:17: warning: The macro 'AC_HEADER_STDC' is obsolete.
configure.ac:17: You should run autoupdate.
./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from...
configure.ac:17: the top level
configure.ac:8: installing './compile'
dh_auto_configure
./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking for a BSD-compatible install... /usr/bin/install -c
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 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
./configure: line 4580: test: syntax error: `-O2' unexpected
checking for g++... g++
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... unsupported
checking for g++ option to enable C++98 features... none needed
checking dependency style of g++... none
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 grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for string... yes
checking for iostream... yes
checking for size_t... yes
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking for g++ option to enable C++11 features... (cached) unsupported
checking for g++ option to enable C++98 features... (cached) none needed
checking dependency style of g++... (cached) none
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking for g++ option to enable C++11 features... (cached) unsupported
checking for g++ option to enable C++98 features... (cached) none needed
checking dependency style of g++... (cached) none
checking for ranlib... ranlib
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/phylogeny/Makefile
config.status: creating src/rate4site/Makefile
config.status: creating config.h
config.status: executing depfiles commands
dh_auto_build
make -j22
make[1]: Entering directory '/build/reproducible-path/rate4site-3.0.0'
make all-recursive
make[2]: Entering directory '/build/reproducible-path/rate4site-3.0.0'
Making all in src/phylogeny
make[3]: Entering directory '/build/reproducible-path/rate4site-3.0.0/src/phylogeny'
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o alphabet.o alphabet.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o sequenceContainer.o sequenceContainer.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o sequence.o sequence.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o mulAlphabet.o mulAlphabet.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o someUtil.o someUtil.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o logFile.o logFile.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o gainLossAlphabet.o gainLossAlphabet.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o pijAccelerator.o pijAccelerator.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o replacementModel.o replacementModel.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o distribution.o distribution.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o readTree.o readTree.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o errorMsg.o errorMsg.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o nucleotide.o nucleotide.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o amino.o amino.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o geneticCodeHolder.o geneticCodeHolder.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o codon.o codon.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o doubleRep.o doubleRep.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o uniDistribution.o uniDistribution.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o generalGammaDistribution.o generalGammaDistribution.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o readDatMatrix.o readDatMatrix.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o datMatrixHolder.o datMatrixHolder.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o nucJC.o nucJC.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o aaJC.o aaJC.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o gtrModel.o gtrModel.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o fromQtoPt.o fromQtoPt.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o distanceTable.o distanceTable.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o nj.o nj.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o njConstrain.o njConstrain.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o numRec.o numRec.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o uniformDistribution.o uniformDistribution.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computePijComponent.o computePijComponent.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o stochasticProcess.o stochasticProcess.cpp
someUtil.cpp: In function 'void createDir(const std::string&, const std::string&)':
someUtil.cpp:507:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
507 | system(sysCall.c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o suffStatComponent.o suffStatComponent.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o unObservableData.o unObservableData.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o likeDist.o likeDist.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o countTableComponent.o countTableComponent.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o fastStartTree.o fastStartTree.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o bestAlpha.o bestAlpha.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o gammaDistribution.o gammaDistribution.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o siteSpecificRate.o siteSpecificRate.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o likelihoodComputation.o likelihoodComputation.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o recognizeFormat.o recognizeFormat.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o bblEM.o bblEM.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o hky.o hky.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o bestGtrModelParams.o bestGtrModelParams.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o tamura92.o tamura92.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o bestHKYparam.o bestHKYparam.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o bestTamura92param.o bestTamura92param.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o talRandom.o talRandom.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computeCounts.o computeCounts.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computeDownAlg.o computeDownAlg.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computeUpAlg.o computeUpAlg.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computeUpAlgFactors.o computeUpAlgFactors.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o gammaUtilities.o gammaUtilities.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o seqContainerTreeMap.o seqContainerTreeMap.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o treeUtil.o treeUtil.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o matrixUtils.o matrixUtils.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o simulateJumps.o simulateJumps.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o treeIt.o treeIt.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o tree.o tree.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o likeDistPropEB.o likeDistPropEB.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o phylipFormat.o phylipFormat.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o maseFormat.o maseFormat.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o clustalFormat.o clustalFormat.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o fastaFormat.o fastaFormat.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o molphyFormat.o molphyFormat.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o getRandomWeights.o getRandomWeights.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o nexusFormat.o nexusFormat.cpp
rm -f libphylo.a
ar cru libphylo.a alphabet.o sequenceContainer.o sequence.o mulAlphabet.o someUtil.o logFile.o gainLossAlphabet.o pijAccelerator.o replacementModel.o distribution.o readTree.o errorMsg.o nucleotide.o amino.o geneticCodeHolder.o codon.o doubleRep.o evaluateCharacterFreq.o uniDistribution.o generalGammaDistribution.o readDatMatrix.o datMatrixHolder.o chebyshevAccelerator.o nucJC.o aaJC.o gtrModel.o fromQtoPt.o distanceTable.o nj.o njConstrain.o numRec.o uniformDistribution.o computePijComponent.o stochasticProcess.o suffStatComponent.o unObservableData.o likeDist.o countTableComponent.o fastStartTree.o likelihoodComputationFactors.o bestAlpha.o gammaDistribution.o siteSpecificRate.o likelihoodComputation.o recognizeFormat.o bblEM.o hky.o bestGtrModelParams.o tamura92.o bestHKYparam.o bestTamura92param.o talRandom.o computeSubstitutionCounts.o fromCountTableComponentToDistance.o computeCounts.o computeDownAlg.o computeUpAlg.o computeUpAlgFactors.o gammaUtilities.o seqContainerTreeMap.o treeUtil.o matrixUtils.o simulateCodonsJumps.o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o multipleStochasticProcess.o simulateJumps.o simulateJumpsAbstract.o treeIt.o likelihoodComputationGL.o tree.o bblEMProportionalEB.o fromCountTableComponentToDistancePropEB.o likeDistPropEB.o bblLSProportionalEB.o phylipFormat.o maseFormat.o clustalFormat.o fastaFormat.o phylipSequentialFormat.o molphyFormat.o getRandomWeights.o nexusFormat.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libphylo.a
make[3]: Leaving directory '/build/reproducible-path/rate4site-3.0.0/src/phylogeny'
Making all in src/rate4site
make[3]: Entering directory '/build/reproducible-path/rate4site-3.0.0/src/rate4site'
g++ -DHAVE_CONFIG_H -I. -I../.. -DDOUBLEREP -Wdate-time -D_FORTIFY_SOURCE=2 -I../../src/phylogeny/ -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o rate4site-rate4siteOptions.o `test -f 'rate4siteOptions.cpp' || echo './'`rate4siteOptions.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -DDOUBLEREP -Wdate-time -D_FORTIFY_SOURCE=2 -I../../src/phylogeny/ -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o rate4site-rate4site.o `test -f 'rate4site.cpp' || echo './'`rate4site.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../../src/phylogeny/ -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o rate4siteOptions.o rate4siteOptions.cpp
g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../../src/phylogeny/ -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o rate4site.o rate4site.cpp
sed -e 's|__pkgdatadir__|/usr/share/rate4site|g;s|__examplesdir__||g;s|__sysconfdir__|/etc|g;s|__bindir__|/usr/bin|g;s|__PACKAGE_VERSION__|3.0.0|g' "rate4site.cpp" | \
pod2man --utf8 -c 'User Commands' -r "3.0.0" -name RATE4SITE > "rate4site.1"
g++ -I../../src/phylogeny/ -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -Wl,-z,relro -Wl,-z,now -o rate4site_doublerep rate4siteOptions.o rate4site.o ../../src/phylogeny/libphylo.a
g++ -I../../src/phylogeny/ -g -O2 -ffile-prefix-map=/build/reproducible-path/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -Wl,-z,relro -Wl,-z,now -o rate4site rate4site-rate4siteOptions.o rate4site-rate4site.o ../../src/phylogeny/libphylo.a
make[3]: Leaving directory '/build/reproducible-path/rate4site-3.0.0/src/rate4site'
make[3]: Entering directory '/build/reproducible-path/rate4site-3.0.0'
make[3]: Leaving directory '/build/reproducible-path/rate4site-3.0.0'
make[2]: Leaving directory '/build/reproducible-path/rate4site-3.0.0'
make[1]: Leaving directory '/build/reproducible-path/rate4site-3.0.0'
dh_auto_test
make -j22 check "TESTSUITEFLAGS=-j22 --verbose" VERBOSE=1
make[1]: Entering directory '/build/reproducible-path/rate4site-3.0.0'
Making check in src/phylogeny
make[2]: Entering directory '/build/reproducible-path/rate4site-3.0.0/src/phylogeny'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/reproducible-path/rate4site-3.0.0/src/phylogeny'
Making check in src/rate4site
make[2]: Entering directory '/build/reproducible-path/rate4site-3.0.0/src/rate4site'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/reproducible-path/rate4site-3.0.0/src/rate4site'
make[2]: Entering directory '/build/reproducible-path/rate4site-3.0.0'
make[2]: Leaving directory '/build/reproducible-path/rate4site-3.0.0'
make[1]: Leaving directory '/build/reproducible-path/rate4site-3.0.0'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install --destdir=debian/rate4site/
make -j22 install DESTDIR=/build/reproducible-path/rate4site-3.0.0/debian/rate4site AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/build/reproducible-path/rate4site-3.0.0'
Making install in src/phylogeny
make[2]: Entering directory '/build/reproducible-path/rate4site-3.0.0/src/phylogeny'
make[3]: Entering directory '/build/reproducible-path/rate4site-3.0.0/src/phylogeny'
/usr/bin/mkdir -p '/build/reproducible-path/rate4site-3.0.0/debian/rate4site/usr/lib/i386-linux-gnu'
/usr/bin/install -c -m 644 libphylo.a '/build/reproducible-path/rate4site-3.0.0/debian/rate4site/usr/lib/i386-linux-gnu'
/usr/bin/mkdir -p '/build/reproducible-path/rate4site-3.0.0/debian/rate4site/usr/include/libphylo'
/usr/bin/install -c -m 644 replacementMatrixSource/mitochondriaAscidian.code replacementMatrixSource/mitochondriaProtozoan.code replacementMatrixSource/nuclearCiliate.code replacementMatrixSource/mitochondriaEchinoderm.code replacementMatrixSource/mitochondriaVertebrate.code replacementMatrixSource/nuclearEuplotid.code replacementMatrixSource/mitochondriaFlatworm.code replacementMatrixSource/mitochondriaYeast.code replacementMatrixSource/nuclearStandard.code replacementMatrixSource/mitochondriaInvertebrate.code replacementMatrixSource/nuclearBlepharisma.code cpREV45.dat.q dayhoff.dat.q jones.dat.q mtREV24.dat.q wag.dat.q HIVb.dat.q HIVw.dat.q adrianCodon.dat.q LG.dat.q replacementMatrixSource/cpREV45.dat replacementMatrixSource/dayhoff.dat replacementMatrixSource/jones.dat replacementMatrixSource/mtREV24.dat replacementMatrixSource/wag.dat getopt.h errorMsg.h definitions.h doubleRep.h ConversionUtils.h sequenceContainer.h sequence.h alphabet.h mulAlphabet.h someUtil.h logFile.h gainLossAlphabet.h pijAccelerator.h replacementModel.h distribution.h '/build/reproducible-path/rate4site-3.0.0/debian/rate4site/usr/include/libphylo'
/usr/bin/install -c -m 644 readTree.h nucleotide.h amino.h geneticCodeHolder.h codon.h evaluateCharacterFreq.h uniDistribution.h generalGammaDistribution.h readDatMatrix.h datMatrixHolder.h chebyshevAccelerator.h nucJC.h aaJC.h gtrModel.h fromQtoPt.h trivialAccelerator.h distanceMethod.h distanceTable.h nj.h njConstrain.h distances2Tree.h numRec.h uniformDistribution.h checkcovFanctors.h likelihoodComputation.h computePijComponent.h stochasticProcess.h suffStatComponent.h unObservableData.h likeDist.h countTableComponent.h jcDistance.h fastStartTree.h checkcovFanctorsWithFactors.h likelihoodComputationFactors.h bestAlpha.h gammaDistribution.h siteSpecificRate.h recognizeFormat.h bblEM.h '/build/reproducible-path/rate4site-3.0.0/debian/rate4site/usr/include/libphylo'
/usr/bin/install -c -m 644 bestGtrModelParams.h tamura92.h bestHKYparam.h hky.h bestTamura92param.h talRandom.h computeSubstitutionCounts.h fromCountTableComponentToDistance.h computeCounts.h computeDownAlg.h computeUpAlg.h gammaUtilities.h seqContainerTreeMap.h treeUtil.h matrixUtils.h computePosteriorExpectationOfSubstitutions.h computePosteriorExpectationOfSubstitutions_nonReversibleSp.h multipleStochasticProcess.h simulateJumps.h simulateJumpsAbstract.h simulateCodonsJumps.h treeIt.h likelihoodComputationGL.h tree.h bblEMProportionalEB.h fromCountTableComponentToDistancePropEB.h likeDistPropEB.h bblLSProportionalEB.h phylipFormat.h maseFormat.h clustalFormat.h fastaFormat.h phylipSequentialFormat.h molphyFormat.h getRandomWeights.h nexusFormat.h '/build/reproducible-path/rate4site-3.0.0/debian/rate4site/usr/include/libphylo'
( cd '/build/reproducible-path/rate4site-3.0.0/debian/rate4site/usr/lib/i386-linux-gnu' && ranlib libphylo.a )
make[3]: Leaving directory '/build/reproducible-path/rate4site-3.0.0/src/phylogeny'
make[2]: Leaving directory '/build/reproducible-path/rate4site-3.0.0/src/phylogeny'
Making install in src/rate4site
make[2]: Entering directory '/build/reproducible-path/rate4site-3.0.0/src/rate4site'
make[3]: Entering directory '/build/reproducible-path/rate4site-3.0.0/src/rate4site'
/usr/bin/mkdir -p '/build/reproducible-path/rate4site-3.0.0/debian/rate4site/usr/bin'
/usr/bin/mkdir -p '/build/reproducible-path/rate4site-3.0.0/debian/rate4site/usr/share/man/man1'
/usr/bin/install -c rate4site rate4site_doublerep '/build/reproducible-path/rate4site-3.0.0/debian/rate4site/usr/bin'
/usr/bin/install -c -m 644 rate4site.1 '/build/reproducible-path/rate4site-3.0.0/debian/rate4site/usr/share/man/man1'
make[3]: Leaving directory '/build/reproducible-path/rate4site-3.0.0/src/rate4site'
make[2]: Leaving directory '/build/reproducible-path/rate4site-3.0.0/src/rate4site'
make[2]: Entering directory '/build/reproducible-path/rate4site-3.0.0'
make[3]: Entering directory '/build/reproducible-path/rate4site-3.0.0'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/build/reproducible-path/rate4site-3.0.0'
make[2]: Leaving directory '/build/reproducible-path/rate4site-3.0.0'
make[1]: Leaving directory '/build/reproducible-path/rate4site-3.0.0'
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 'rate4site' in '../rate4site_3.0.0-8_i386.deb'.
dpkg-deb: building package 'rate4site-dbgsym' in '../rate4site-dbgsym_3.0.0-8_i386.deb'.
dpkg-genbuildinfo --build=binary -O../rate4site_3.0.0-8_i386.buildinfo
dpkg-genchanges --build=binary -O../rate4site_3.0.0-8_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/128180 and its subdirectories
I: Current time: Sun Feb 8 15:11:12 -12 2026
I: pbuilder-time-stamp: 1770606672
Mon Jan 6 20:48:15 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos12-i386.debian.net.
Mon Jan 6 20:48:15 UTC 2025 I: Preparing to do remote build '2' on ionos12-i386.debian.net.
Mon Jan 6 20:50:16 UTC 2025 I: Deleting $TMPDIR on ionos12-i386.debian.net.
Mon Jan 6 20:50:16 UTC 2025 I: rate4site_3.0.0-8_i386.changes:
Format: 1.8
Date: Thu, 20 Jan 2022 11:42:04 +0100
Source: rate4site
Binary: rate4site rate4site-dbgsym
Architecture: i386
Version: 3.0.0-8
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
rate4site - detector of conserved amino-acid sites
Changes:
rate4site (3.0.0-8) unstable; urgency=medium
.
* Upstream download vanished
* Standards-Version: 4.6.0 (routine-update)
Checksums-Sha1:
63ccab8955207623ecba6c24308d57c029dee01d 9892776 rate4site-dbgsym_3.0.0-8_i386.deb
8c7fa9bbff45259c0ee5a43ace692ebabe54b003 4944 rate4site_3.0.0-8_i386.buildinfo
28cee5fe6077c7a15402b194d2d3d6c620360f4c 669168 rate4site_3.0.0-8_i386.deb
Checksums-Sha256:
820a1817d57b1d9db7cdf34afadb4a134e15f4925019f9713ef749e3f7476112 9892776 rate4site-dbgsym_3.0.0-8_i386.deb
1887d79c181f7b2eedb441129b9aae01166576146dfe27193f611ed5848cca6e 4944 rate4site_3.0.0-8_i386.buildinfo
79ed448a4423cd6598054dba71bf8597168953640c82c40d25a7c6e993c0d1d4 669168 rate4site_3.0.0-8_i386.deb
Files:
a4444d6c322e2fc6e34ded29887e9001 9892776 debug optional rate4site-dbgsym_3.0.0-8_i386.deb
f523d7273fd7344ec66eedaac208b7e4 4944 science optional rate4site_3.0.0-8_i386.buildinfo
16a860b490abdec6e061237ca1259515 669168 science optional rate4site_3.0.0-8_i386.deb
Mon Jan 6 20:50:17 UTC 2025 I: diffoscope 284 will be used to compare the two builds:
Running as unit: rb-diffoscope-i386_11-41597.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.9ptsD2q1/rate4site_3.0.0-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.9ptsD2q1/rate4site_3.0.0-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.9ptsD2q1/rate4site_3.0.0-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.9ptsD2q1/b1/rate4site_3.0.0-8_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.9ptsD2q1/b2/rate4site_3.0.0-8_i386.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call abc.DotChangesFile
## main (total time: 0.437s)
0.437s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.106s)
0.106s 12 calls diffoscope.comparators.binary.FilesystemFile
## specialize (total time: 0.000s)
0.000s 1 call specialize
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 748ms
CPU time consumed: 744ms
Mon Jan 6 20:50:23 UTC 2025 I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists.
Mon Jan 6 20:50:23 UTC 2025 I: rate4site from trixie built successfully and reproducibly on i386.
Mon Jan 6 20:50:24 UTC 2025 I: Submitting .buildinfo files to external archives:
Mon Jan 6 20:50:24 UTC 2025 I: Submitting 8.0K b1/rate4site_3.0.0-8_i386.buildinfo.asc
Mon Jan 6 20:50:25 UTC 2025 I: Submitting 8.0K b2/rate4site_3.0.0-8_i386.buildinfo.asc
Mon Jan 6 20:50:26 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Mon Jan 6 20:50:26 UTC 2025 I: Done submitting .buildinfo files.
Mon Jan 6 20:50:26 UTC 2025 I: Removing signed rate4site_3.0.0-8_i386.buildinfo.asc files:
removed './b1/rate4site_3.0.0-8_i386.buildinfo.asc'
removed './b2/rate4site_3.0.0-8_i386.buildinfo.asc'