Diff of the two buildlogs:
--
--- b1/build.log 2025-02-20 22:44:12.585942936 +0000
+++ b2/build.log 2025-02-20 22:46:36.491448292 +0000
@@ -1,6 +1,6 @@
I: pbuilder: network access will be disabled during build
-I: Current time: Wed Mar 25 17:04:28 -12 2026
-I: pbuilder-time-stamp: 1774501468
+I: Current time: Fri Feb 21 12:44:15 +14 2025
+I: pbuilder-time-stamp: 1740091455
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
@@ -28,52 +28,84 @@
dpkg-source: info: applying 0006-Make-vcflib-smithwaterman-and-fastahack-external-inc.patch
I: Not using root during the build.
I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/1279144/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/68020/tmp/hooks/D01_modify_environment starting
+debug: Running on codethink04-arm64.
+I: Changing host+domainname to test build reproducibility
+I: Adding a custom variable just for the fun of it...
+I: Changing /bin/sh to bash
+'/bin/sh' -> '/bin/bash'
+lrwxrwxrwx 1 root root 9 Feb 20 22:44 /bin/sh -> /bin/bash
+I: Setting pbuilder2's login shell to /bin/bash
+I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
+I: user script /srv/workspace/pbuilder/68020/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/68020/tmp/hooks/D02_print_environment starting
I: set
- BUILDDIR='/build/reproducible-path'
- BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
- BUILDUSERNAME='pbuilder1'
- BUILD_ARCH='arm64'
- DEBIAN_FRONTEND='noninteractive'
+ BASH=/bin/sh
+ BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
+ BASH_ALIASES=()
+ BASH_ARGC=()
+ BASH_ARGV=()
+ BASH_CMDS=()
+ BASH_LINENO=([0]="12" [1]="0")
+ BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
+ BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+ BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu")
+ BASH_VERSION='5.2.37(1)-release'
+ BUILDDIR=/build/reproducible-path
+ BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+ BUILDUSERNAME=pbuilder2
+ BUILD_ARCH=arm64
+ DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
- DISTRIBUTION='trixie'
- HOME='/root'
- HOST_ARCH='arm64'
+ DIRSTACK=()
+ DISTRIBUTION=trixie
+ EUID=0
+ FUNCNAME=([0]="Echo" [1]="main")
+ GROUPS=()
+ HOME=/root
+ HOSTNAME=i-capture-the-hostname
+ HOSTTYPE=aarch64
+ HOST_ARCH=arm64
IFS='
'
- INVOCATION_ID='b4cfe536fd584d77b064cb22a1a02432'
- 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='1279144'
- PS1='# '
- PS2='> '
+ INVOCATION_ID=702c416a2aec4a8f87620f5e0c670e7e
+ LANG=C
+ LANGUAGE=nl_BE:nl
+ LC_ALL=C
+ MACHTYPE=aarch64-unknown-linux-gnu
+ MAIL=/var/mail/root
+ OPTERR=1
+ OPTIND=1
+ OSTYPE=linux-gnu
+ PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
+ PBCURRENTCOMMANDLINEOPERATION=build
+ PBUILDER_OPERATION=build
+ PBUILDER_PKGDATADIR=/usr/share/pbuilder
+ PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
+ PBUILDER_SYSCONFDIR=/etc
+ PIPESTATUS=([0]="0")
+ POSIXLY_CORRECT=y
+ PPID=68020
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.fM5JKmnC/pbuilderrc_005W --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.fM5JKmnC/b1 --logfile b1/build.log freebayes_1.3.9-1.dsc'
- SUDO_GID='109'
- SUDO_UID='104'
- SUDO_USER='jenkins'
- TERM='unknown'
- TZ='/usr/share/zoneinfo/Etc/GMT+12'
- USER='root'
- _='/usr/bin/systemd-run'
- http_proxy='http://192.168.101.4:3128'
+ PWD=/
+ SHELL=/bin/bash
+ SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
+ SHLVL=3
+ SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.fM5JKmnC/pbuilderrc_aH7r --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.fM5JKmnC/b2 --logfile b2/build.log freebayes_1.3.9-1.dsc'
+ SUDO_GID=109
+ SUDO_UID=104
+ SUDO_USER=jenkins
+ TERM=unknown
+ TZ=/usr/share/zoneinfo/Etc/GMT-14
+ UID=0
+ USER=root
+ _='I: set'
+ http_proxy=http://192.168.101.4:3128
I: uname -a
- Linux codethink03-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux
+ Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux
I: ls -l /bin
- lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/1279144/tmp/hooks/D02_print_environment finished
+ lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/68020/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
@@ -381,7 +413,7 @@
Get: 244 http://deb.debian.org/debian trixie/main arm64 sysstat arm64 12.7.5-2+b1 [596 kB]
Get: 245 http://deb.debian.org/debian trixie/main arm64 parallel all 20240222+ds-2 [2163 kB]
Get: 246 http://deb.debian.org/debian trixie/main arm64 samtools arm64 1.21-1 [637 kB]
-Fetched 132 MB in 1s (98.7 MB/s)
+Fetched 132 MB in 1s (147 MB/s)
Preconfiguring packages ...
Selecting previously unselected package libpython3.13-minimal:arm64.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19923 files and directories currently installed.)
@@ -1189,8 +1221,8 @@
Setting up tzdata (2025a-2) ...
Current default time zone: 'Etc/UTC'
-Local time is now: Thu Mar 26 05:05:42 UTC 2026.
-Universal Time is now: Thu Mar 26 05:05:42 UTC 2026.
+Local time is now: Thu Feb 20 22:45:04 UTC 2025.
+Universal Time is now: Thu Feb 20 22:45:04 UTC 2025.
Run 'dpkg-reconfigure tzdata' if you wish to change it.
Setting up zip (3.0-14+b1) ...
@@ -1414,7 +1446,11 @@
Building tag database...
-> Finished parsing the build-deps
I: Building the package
-I: Running cd /build/reproducible-path/freebayes-1.3.9/ && 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 > ../freebayes_1.3.9-1_source.changes
+I: user script /srv/workspace/pbuilder/68020/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for trixie
+I: user script /srv/workspace/pbuilder/68020/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/freebayes-1.3.9/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../freebayes_1.3.9-1_source.changes
dpkg-buildpackage: info: source package freebayes
dpkg-buildpackage: info: source version 1.3.9-1
dpkg-buildpackage: info: source distribution unstable
@@ -1490,13 +1526,11 @@
cd build && LC_ALL=C.UTF-8 ninja -j12 -v
[1/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Bias.cpp.o -MF libfreebayes_common.a.p/src_Bias.cpp.o.d -o libfreebayes_common.a.p/src_Bias.cpp.o -c ../src/Bias.cpp
[2/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_IndelAllele.cpp.o -MF libfreebayes_common.a.p/src_IndelAllele.cpp.o.d -o libfreebayes_common.a.p/src_IndelAllele.cpp.o -c ../src/IndelAllele.cpp
-[3/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Dirichlet.cpp.o -MF libfreebayes_common.a.p/src_Dirichlet.cpp.o.d -o libfreebayes_common.a.p/src_Dirichlet.cpp.o -c ../src/Dirichlet.cpp
+[3/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Ewens.cpp.o -MF libfreebayes_common.a.p/src_Ewens.cpp.o.d -o libfreebayes_common.a.p/src_Ewens.cpp.o -c ../src/Ewens.cpp
[4/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Contamination.cpp.o -MF libfreebayes_common.a.p/src_Contamination.cpp.o.d -o libfreebayes_common.a.p/src_Contamination.cpp.o -c ../src/Contamination.cpp
[5/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_CNV.cpp.o -MF libfreebayes_common.a.p/src_CNV.cpp.o.d -o libfreebayes_common.a.p/src_CNV.cpp.o -c ../src/CNV.cpp
-[6/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Ewens.cpp.o -MF libfreebayes_common.a.p/src_Ewens.cpp.o.d -o libfreebayes_common.a.p/src_Ewens.cpp.o -c ../src/Ewens.cpp
-[7/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Multinomial.cpp.o -MF libfreebayes_common.a.p/src_Multinomial.cpp.o.d -o libfreebayes_common.a.p/src_Multinomial.cpp.o -c ../src/Multinomial.cpp
-[8/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_LeftAlign.cpp.o -MF libfreebayes_common.a.p/src_LeftAlign.cpp.o.d -o libfreebayes_common.a.p/src_LeftAlign.cpp.o -c ../src/LeftAlign.cpp
-[9/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_BedReader.cpp.o -MF libfreebayes_common.a.p/src_BedReader.cpp.o.d -o libfreebayes_common.a.p/src_BedReader.cpp.o -c ../src/BedReader.cpp
+[6/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Dirichlet.cpp.o -MF libfreebayes_common.a.p/src_Dirichlet.cpp.o.d -o libfreebayes_common.a.p/src_Dirichlet.cpp.o -c ../src/Dirichlet.cpp
+[7/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_BedReader.cpp.o -MF libfreebayes_common.a.p/src_BedReader.cpp.o.d -o libfreebayes_common.a.p/src_BedReader.cpp.o -c ../src/BedReader.cpp
In file included from ../src/BedReader.cpp:14:
/usr/include/SeqLib/IntervalTree.h:85:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor]
85 | ~TIntervalTree<T,K>() {
@@ -1514,6 +1548,8 @@
124 | intervalVector& ivals,
| ^~~~~~~~~~~~~~
/usr/include/SeqLib/IntervalTree.h:124:13: note: remove the ‘< >’
+[8/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Multinomial.cpp.o -MF libfreebayes_common.a.p/src_Multinomial.cpp.o.d -o libfreebayes_common.a.p/src_Multinomial.cpp.o -c ../src/Multinomial.cpp
+[9/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_NonCall.cpp.o -MF libfreebayes_common.a.p/src_NonCall.cpp.o.d -o libfreebayes_common.a.p/src_NonCall.cpp.o -c ../src/NonCall.cpp
[10/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -MF libfreebayes_common.a.p/src_SegfaultHandler.cpp.o.d -o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -c ../src/SegfaultHandler.cpp
[11/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Result.cpp.o -MF libfreebayes_common.a.p/src_Result.cpp.o.d -o libfreebayes_common.a.p/src_Result.cpp.o -c ../src/Result.cpp
[12/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_FBFasta.cpp.o -MF libfreebayes_common.a.p/src_FBFasta.cpp.o.d -o libfreebayes_common.a.p/src_FBFasta.cpp.o -c ../src/FBFasta.cpp
@@ -1531,12 +1567,12 @@
../src/FBFasta.cpp:315:9: note: call to ‘void free(void*)’ here
315 | free(seq);
| ~~~~^~~~~
-[13/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_NonCall.cpp.o -MF libfreebayes_common.a.p/src_NonCall.cpp.o.d -o libfreebayes_common.a.p/src_NonCall.cpp.o -c ../src/NonCall.cpp
-[14/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Marginals.cpp.o -MF libfreebayes_common.a.p/src_Marginals.cpp.o.d -o libfreebayes_common.a.p/src_Marginals.cpp.o -c ../src/Marginals.cpp
+[13/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Marginals.cpp.o -MF libfreebayes_common.a.p/src_Marginals.cpp.o.d -o libfreebayes_common.a.p/src_Marginals.cpp.o -c ../src/Marginals.cpp
+[14/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_LeftAlign.cpp.o -MF libfreebayes_common.a.p/src_LeftAlign.cpp.o.d -o libfreebayes_common.a.p/src_LeftAlign.cpp.o -c ../src/LeftAlign.cpp
[15/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Parameters.cpp.o -MF libfreebayes_common.a.p/src_Parameters.cpp.o.d -o libfreebayes_common.a.p/src_Parameters.cpp.o -c ../src/Parameters.cpp
-[16/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Sample.cpp.o -MF libfreebayes_common.a.p/src_Sample.cpp.o.d -o libfreebayes_common.a.p/src_Sample.cpp.o -c ../src/Sample.cpp
-[17/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_DataLikelihood.cpp.o -MF libfreebayes_common.a.p/src_DataLikelihood.cpp.o.d -o libfreebayes_common.a.p/src_DataLikelihood.cpp.o -c ../src/DataLikelihood.cpp
-[18/27] c++ -Ibamleftalign.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ bamleftalign.p/src_bamleftalign.cpp.o -MF bamleftalign.p/src_bamleftalign.cpp.o.d -o bamleftalign.p/src_bamleftalign.cpp.o -c ../src/bamleftalign.cpp
+[16/27] c++ -Ibamleftalign.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ bamleftalign.p/src_bamleftalign.cpp.o -MF bamleftalign.p/src_bamleftalign.cpp.o.d -o bamleftalign.p/src_bamleftalign.cpp.o -c ../src/bamleftalign.cpp
+[17/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Sample.cpp.o -MF libfreebayes_common.a.p/src_Sample.cpp.o.d -o libfreebayes_common.a.p/src_Sample.cpp.o -c ../src/Sample.cpp
+[18/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_DataLikelihood.cpp.o -MF libfreebayes_common.a.p/src_DataLikelihood.cpp.o.d -o libfreebayes_common.a.p/src_DataLikelihood.cpp.o -c ../src/DataLikelihood.cpp
[19/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Allele.cpp.o -MF libfreebayes_common.a.p/src_Allele.cpp.o.d -o libfreebayes_common.a.p/src_Allele.cpp.o -c ../src/Allele.cpp
[20/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Utility.cpp.o -MF libfreebayes_common.a.p/src_Utility.cpp.o.d -o libfreebayes_common.a.p/src_Utility.cpp.o -c ../src/Utility.cpp
In file included from ../contrib/ttmath/ttmathint.h:48,
@@ -1654,8 +1690,8 @@
64 | ~ListElement<T>() {
| ^
../contrib/multichoose/multipermute.h:64:5: note: remove the ‘< >’
-[22/27] c++ -Ifreebayes.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ freebayes.p/src_freebayes.cpp.o -MF freebayes.p/src_freebayes.cpp.o.d -o freebayes.p/src_freebayes.cpp.o -c ../src/freebayes.cpp
-[23/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_ResultData.cpp.o -MF libfreebayes_common.a.p/src_ResultData.cpp.o.d -o libfreebayes_common.a.p/src_ResultData.cpp.o -c ../src/ResultData.cpp
+[22/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_ResultData.cpp.o -MF libfreebayes_common.a.p/src_ResultData.cpp.o.d -o libfreebayes_common.a.p/src_ResultData.cpp.o -c ../src/ResultData.cpp
+[23/27] c++ -Ifreebayes.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ freebayes.p/src_freebayes.cpp.o -MF freebayes.p/src_freebayes.cpp.o.d -o freebayes.p/src_freebayes.cpp.o -c ../src/freebayes.cpp
[24/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I../contrib/multichoose -I/usr/include/vcflib -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_AlleleParser.cpp.o -MF libfreebayes_common.a.p/src_AlleleParser.cpp.o.d -o libfreebayes_common.a.p/src_AlleleParser.cpp.o -c ../src/AlleleParser.cpp
[25/27] rm -f libfreebayes_common.a && gcc-ar csrDT libfreebayes_common.a libfreebayes_common.a.p/src_Allele.cpp.o libfreebayes_common.a.p/src_AlleleParser.cpp.o libfreebayes_common.a.p/src_BedReader.cpp.o libfreebayes_common.a.p/src_Bias.cpp.o libfreebayes_common.a.p/src_CNV.cpp.o libfreebayes_common.a.p/src_Contamination.cpp.o libfreebayes_common.a.p/src_DataLikelihood.cpp.o libfreebayes_common.a.p/src_Dirichlet.cpp.o libfreebayes_common.a.p/src_Ewens.cpp.o libfreebayes_common.a.p/src_FBFasta.cpp.o libfreebayes_common.a.p/src_Genotype.cpp.o libfreebayes_common.a.p/src_IndelAllele.cpp.o libfreebayes_common.a.p/src_LeftAlign.cpp.o libfreebayes_common.a.p/src_Marginals.cpp.o libfreebayes_common.a.p/src_Multinomial.cpp.o libfreebayes_common.a.p/src_NonCall.cpp.o libfreebayes_common.a.p/src_Parameters.cpp.o libfreebayes_common.a.p/src_Result.cpp.o libfreebayes_common.a.p/src_ResultData.cpp.o libfreebayes_common.a.p/src_Sample.cpp.o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o libfreebayes_common.a.p/src_Utility.cpp.o
[26/27] c++ -o bamleftalign bamleftalign.p/src_bamleftalign.cpp.o -I/usr/include/fastahack -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/freebayes-1.3.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group libfreebayes_common.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so -pthread /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libvcflib.so /usr/lib/aarch64-linux-gnu/libseqlib.so /usr/lib/libbwa.a /usr/lib/aarch64-linux-gnu/libfastahack.so /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libwfa2.so /usr/lib/aarch64-linux-gnu/libtabixpp.so -Wl,--end-group
@@ -1671,21 +1707,21 @@
ninja: Entering directory `/build/reproducible-path/freebayes-1.3.9/build'
ninja: no work to do.
1/5 T00 RUNNING
->>> UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MESON_TEST_ITERATION=1 MALLOC_PERTURB_=107 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /usr/bin/prove -e bash -v t/00_region_and_target_handling.t
+>>> ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=36 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /usr/bin/prove -e bash -v t/00_region_and_target_handling.t
2/5 T01 RUNNING
->>> UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=248 MESON_TEST_ITERATION=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /usr/bin/prove -e bash -v t/01_call_variants.t
+>>> MALLOC_PERTURB_=116 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /usr/bin/prove -e bash -v t/01_call_variants.t
3/5 T01b RUNNING
->>> MALLOC_PERTURB_=58 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MESON_TEST_ITERATION=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /usr/bin/prove -e bash -v t/01b_call_variants.t
+>>> MALLOC_PERTURB_=76 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /usr/bin/prove -e bash -v t/01b_call_variants.t
4/5 T02 RUNNING
->>> UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=147 MESON_TEST_ITERATION=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /usr/bin/prove -e bash -v t/02_multi_bam.t
+>>> ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MALLOC_PERTURB_=228 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /usr/bin/prove -e bash -v t/02_multi_bam.t
5/5 T03 RUNNING
->>> UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 MESON_TEST_ITERATION=1 MALLOC_PERTURB_=239 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /usr/bin/prove -e bash -v t/03_reference_bases.t
+>>> ASAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1 UBSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 MESON_TEST_ITERATION=1 MALLOC_PERTURB_=241 MSAN_OPTIONS=halt_on_error=1:abort_on_error=1:print_summary=1:print_stacktrace=1 /usr/bin/prove -e bash -v t/03_reference_bases.t
-5/5 T03 OK 0.49s
+5/5 T03 OK 0.52s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
t/03_reference_bases.t ..
1..3
@@ -1694,11 +1730,11 @@
ok 3 - freebayes does not put lowercase IUPAC bases in VCFs
ok
All tests successful.
-Files=1, Tests=3, 0 wallclock secs ( 0.02 usr 0.01 sys + 0.05 cusr 0.00 csys = 0.08 CPU)
+Files=1, Tests=3, 0 wallclock secs ( 0.02 usr 0.00 sys + 0.04 cusr 0.01 csys = 0.07 CPU)
Result: PASS
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
-4/5 T02 OK 0.94s
+4/5 T02 OK 1.01s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
t/02_multi_bam.t ..
1..7
@@ -1711,11 +1747,11 @@
ok 7 - freebayes rejects two BAMs with the same name
ok
All tests successful.
-Files=1, Tests=7, 1 wallclock secs ( 0.02 usr 0.00 sys + 0.15 cusr 0.03 csys = 0.20 CPU)
+Files=1, Tests=7, 1 wallclock secs ( 0.02 usr 0.00 sys + 0.13 cusr 0.05 csys = 0.20 CPU)
Result: PASS
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
-1/5 T00 OK 1.10s
+1/5 T00 OK 1.12s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
t/00_region_and_target_handling.t ..
1..12
@@ -1733,11 +1769,11 @@
ok 12 - region outside of bounds error
ok
All tests successful.
-Files=1, Tests=12, 1 wallclock secs ( 0.03 usr 0.00 sys + 0.13 cusr 0.04 csys = 0.20 CPU)
+Files=1, Tests=12, 1 wallclock secs ( 0.02 usr 0.00 sys + 0.13 cusr 0.04 csys = 0.19 CPU)
Result: PASS
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
-3/5 T01b OK 4.73s
+3/5 T01b OK 5.77s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
t/01b_call_variants.t ..
1..10
@@ -1753,11 +1789,11 @@
ok 10 - freebayes correctly uses CNV map with multiple entries
ok
All tests successful.
-Files=1, Tests=10, 5 wallclock secs ( 0.01 usr 0.01 sys + 3.43 cusr 0.19 csys = 3.64 CPU)
+Files=1, Tests=10, 6 wallclock secs ( 0.02 usr 0.00 sys + 3.52 cusr 0.21 csys = 3.75 CPU)
Result: PASS
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
-2/5 T01 OK 7.59s
+2/5 T01 OK 8.06s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
stdout:
t/01_call_variants.t ..
@@ -1780,13 +1816,13 @@
ok 16 - !
ok
All tests successful.
-Files=1, Tests=16, 8 wallclock secs ( 0.02 usr 0.00 sys + 4.95 cusr 1.09 csys = 6.06 CPU)
+Files=1, Tests=16, 8 wallclock secs ( 0.02 usr 0.00 sys + 4.90 cusr 1.13 csys = 6.05 CPU)
Result: PASS
stderr:
[E::idx_find_and_load] Could not retrieve index file for '-'
Random access with SetRegion not available for STDIN reading (no index file)
ERROR(freebayes): Could not SetRegion to q:1..10000
-t/01_call_variants.t: line 108: 1318916 Aborted freebayes -f tiny/q.fa.gz -@ tiny/q_spiked.vcf.gz -r q:1-10000 -l - < tiny/NA12878.chr22.tiny.bam > /dev/null 2> /dev/null
+t/01_call_variants.t: line 108: 109139 Aborted freebayes -f tiny/q.fa.gz -@ tiny/q_spiked.vcf.gz -r q:1-10000 -l - < tiny/NA12878.chr22.tiny.bam > /dev/null 2> /dev/null
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
@@ -1844,12 +1880,14 @@
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: including full source code in upload
I: copying local configuration
+I: user script /srv/workspace/pbuilder/68020/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/68020/tmp/hooks/B01_cleanup finished
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/1279144 and its subdirectories
-I: Current time: Wed Mar 25 17:07:11 -12 2026
-I: pbuilder-time-stamp: 1774501631
+I: removing directory /srv/workspace/pbuilder/68020 and its subdirectories
+I: Current time: Fri Feb 21 12:46:35 +14 2025
+I: pbuilder-time-stamp: 1740091595