I: pbuilder: network access will be disabled during build
I: Current time: Mon Mar 23 03:00:20 -12 2026
I: pbuilder-time-stamp: 1774278020
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [primer3_2.6.1-5.dsc]
I: copying [./primer3_2.6.1.orig.tar.gz]
I: copying [./primer3_2.6.1-5.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./primer3_2.6.1-5.dsc: unsupported subcommand
dpkg-source: info: extracting primer3 in primer3-2.6.1
dpkg-source: info: unpacking primer3_2.6.1.orig.tar.gz
dpkg-source: info: unpacking primer3_2.6.1-5.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying primer_thermodynamic_parameters_path_2_etc.patch
dpkg-source: info: applying set_prefix.patch
dpkg-source: info: applying buildflags.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/1763574/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
DISTRIBUTION='unstable'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='c7970407c1d34910aba835c1f84df2b9'
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='1763574'
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.z0wV0gsV/pbuilderrc_wM2u --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.z0wV0gsV/b1 --logfile b1/build.log primer3_2.6.1-5.dsc'
SUDO_GID='110'
SUDO_UID='105'
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 ionos5-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/1763574/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13)
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19798 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} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a}
The following packages are RECOMMENDED but will NOT be installed:
curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded.
Need to get 20.6 MB of archives. After unpacking 77.9 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-4 [92.4 kB]
Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB]
Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB]
Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-3 [539 kB]
Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 24 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 25 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 26 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB]
Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB]
Fetched 20.6 MB in 3s (7828 kB/s)
Preconfiguring packages ...
Selecting previously unselected package sensible-utils.
(Reading database ...
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(Reading database ... 19798 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_amd64.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
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Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ...
Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ...
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Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ...
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Preparing to unpack .../04-gettext-base_0.23.1-1_amd64.deb ...
Unpacking gettext-base (0.23.1-1) ...
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Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ...
Unpacking libuchardet0:amd64 (0.0.8-1+b2) ...
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Preparing to unpack .../06-groff-base_1.23.0-7_amd64.deb ...
Unpacking groff-base (1.23.0-7) ...
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Unpacking bsdextrautils (2.40.4-4) ...
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Unpacking libpipeline1:amd64 (1.5.8-1) ...
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Preparing to unpack .../10-m4_1.4.19-5_amd64.deb ...
Unpacking m4 (1.4.19-5) ...
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Setting up libpipeline1:amd64 (1.5.8-1) ...
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Setting up bsdextrautils (2.40.4-4) ...
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Setting up libarchive-zip-perl (1.68-1) ...
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Setting up libmagic1t64:amd64 (1:5.45-3+b1) ...
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Setting up m4 (1.4.19-5) ...
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:amd64 (0.192-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up libunistring5:amd64 (1.3-1) ...
Setting up autopoint (0.23.1-1) ...
Setting up autoconf (2.72-3) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:amd64 (0.0.8-1+b2) ...
Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up automake (1:1.17-3) ...
update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.1-2) ...
Setting up gettext (0.23.1-1) ...
Setting up libtool (2.5.4-3) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up groff-base (1.23.0-7) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.24.1) ...
Processing triggers for libc-bin (2.40-7) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/primer3-2.6.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../primer3_2.6.1-5_source.changes
dpkg-buildpackage: info: source package primer3
dpkg-buildpackage: info: source version 2.6.1-5
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Ananthu C V <weepingclown@disroot.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean --sourcedirectory=src
dh_auto_clean -O--sourcedirectory=src
cd src && make -j42 clean
make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1/src'
no windows
rm -f *.o primer3_core ntdpal ntthal amplicon3_core oligotm long_seq_tm_test primer3_masker *~ libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libamplicontm.a libmasker.a libprimer3.so.1.0.0 libdpal.a.so.1.0.0 libthal.a.so.1.0.0 libthalpara.a.so.1.0.0 libamplicontm.so.1.0.0 liboligotm.so.1.2.0 libmasker.a.so.1.0.0 example.for example.rev example.int core ../*~
cd ../test/; make clean
make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/test'
echo; echo; echo 'CLEAN UP TEST DIRECTORIES'; echo; echo;
CLEAN UP TEST DIRECTORIES
rm -rf primer_list_tmp/*
rm -rf primer1_list_tmp/*
rm -rf primer1_th_list_tmp/*
rm -rf th-w-other-tasks_list_tmp/*
rm -f primer_global_err/*.tmp primer_global_err/*.tmp2 primer_global_err/*.bak
rm -f amplicon3/*.tmp amplicon3/*.jpg amplicon3/decipher*
rm -f *.tmp *.bak *.tmp.err *~
rm -f hyb_probe_only.for hyb_probe_only.int
rm -f right_only.for right_only.rev left_only.for
rm -f pcr_primers_and_io.int pcr_primers_and_io.rev pcr_primers_and_io.for
rm -f pcr_primers.rev pcr_primers.for
rm -f pick_primer_list_and_file_flag_th_[1-4].for pick_primer_list_and_file_flag_th_[1-4].rev
rm -f pick_primer_list_and_file_flag_th_[1-4].int
rm -f syntax[0-1][0-9].for syntax[0-1][0-9].int syntax[0-1][0-9].rev
rm -f oligotm.*.valg # valgrind output from oligotm_test.pl --valgrind
rm -f ntdpal.*.valg # valgrind output from dpal_test.pl --valgrind
rm -f ntthal.*.valg # valgrind output from thal_test.pl --valgrind
rm -f masker.*.valg # valgrind output from thal_test.pl --valgrind
rm -f oligotm.*.valg.* # valgrind output from oligotm_test.pl --valgrind
rm -f ntdpal.*.valg.* # valgrind output from dpal_test.pl --valgrind
rm -f ntthal.*.valg.* # valgrind output from thal_test.pl --valgrind
rm -f masker.*.valg.* # valgrind output from masker_test.pl --valgrind
rm -f *.vg */*.vg # valgrind output from p3test{,z}.pl --valgrind
rm -f *.vg.core.* # core files from crashed valgrind test
rm -f ./core # in case we crashed and left a core file
make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1/test'
make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1/src'
debian/rules execute_after_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1'
rm -rf /build/reproducible-path/primer3-2.6.1/src/debian
make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1'
dh_autoreconf_clean -O--sourcedirectory=src
dh_clean -O--sourcedirectory=src
debian/rules binary
dh binary --sourcedirectory=src
dh_update_autotools_config -O--sourcedirectory=src
dh_autoreconf -O--sourcedirectory=src
dh_auto_configure -O--sourcedirectory=src
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1'
dh_auto_build -- 'CPP=$(CXX)'
cd src && make -j42 "INSTALL=install --strip-program=true" CPP=\$\(CXX\)
make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/src'
no windows
cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g primer3_boulder_main.c
cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o format_output.o format_output.c
cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o read_boulder.o read_boulder.c
cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o print_boulder.o print_boulder.c
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -std=c++11 -Wl,-z,relro -Wl,-z,now -g -o libprimer3.o libprimer3.cc
cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o p3_seq_lib.o p3_seq_lib.c
cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o dpal_primer.o dpal.c
cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal_primer.o thal.c
cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal_parameters.o thal_parameters.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o oligotm.o oligotm.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicontm.o amplicontm.c
cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g masker.c
cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -g -Wall -Wl,-z,relro -Wl,-z,now -g -o ntdpal_main.o ntdpal_main.c
cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o dpal.o dpal.c
cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o thal_main.o thal_main.c
cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++
cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal.o thal.c
ar rv libthalpara.a thal_parameters.o
ar: creating libthalpara.a
a - thal_parameters.o
ranlib libthalpara.a
format_output.c: In function 'print_seq':
format_output.c:418:61: warning: the comparison will always evaluate as 'true' for the address of 'rev' will never be NULL [-Waddress]
418 | if (pa->pick_right_primer && (&retval->rev) != NULL
| ^~
In file included from format_output.h:41,
from format_output.c:40:
libprimer3.h:927:26: note: 'rev' declared here
927 | oligo_array fwd, intl, rev;
| ^~~
format_output.c:429:60: warning: the comparison will always evaluate as 'true' for the address of 'fwd' will never be NULL [-Waddress]
429 | if (pa->pick_left_primer && (&retval->fwd) != NULL
| ^~
libprimer3.h:927:15: note: 'fwd' declared here
927 | oligo_array fwd, intl, rev;
| ^~~
format_output.c: In function 'format_oligos':
format_output.c:851:51: warning: the comparison will always evaluate as 'true' for the address of 'fwd' will never be NULL [-Waddress]
851 | if ((pa->pick_left_primer) && ((&retval->fwd) != NULL )
| ^~
libprimer3.h:927:15: note: 'fwd' declared here
927 | oligo_array fwd, intl, rev;
| ^~~
format_output.c:858:55: warning: the comparison will always evaluate as 'true' for the address of 'intl' will never be NULL [-Waddress]
858 | if ((pa->pick_internal_oligo) && ((&retval->intl) != NULL )
| ^~
libprimer3.h:927:20: note: 'intl' declared here
927 | oligo_array fwd, intl, rev;
| ^~~~
format_output.c:865:52: warning: the comparison will always evaluate as 'true' for the address of 'rev' will never be NULL [-Waddress]
865 | if ((pa->pick_right_primer) && ((&retval->rev) != NULL )
| ^~
libprimer3.h:927:26: note: 'rev' declared here
927 | oligo_array fwd, intl, rev;
| ^~~
format_output.c:888:49: warning: the comparison will always evaluate as 'true' for the address of 'fwd' will never be NULL [-Waddress]
888 | if ((pa->pick_left_primer) && ((&retval->fwd) != NULL )
| ^~
libprimer3.h:927:15: note: 'fwd' declared here
927 | oligo_array fwd, intl, rev;
| ^~~
format_output.c:907:53: warning: the comparison will always evaluate as 'true' for the address of 'intl' will never be NULL [-Waddress]
907 | if ((pa->pick_internal_oligo) && ((&retval->intl) != NULL )
| ^~
libprimer3.h:927:20: note: 'intl' declared here
927 | oligo_array fwd, intl, rev;
| ^~~~
format_output.c:926:50: warning: the comparison will always evaluate as 'true' for the address of 'rev' will never be NULL [-Waddress]
926 | if ((pa->pick_right_primer) && ((&retval->rev) != NULL )
| ^~
libprimer3.h:927:26: note: 'rev' declared here
927 | oligo_array fwd, intl, rev;
| ^~~
ar rv liboligotm.a oligotm.o
cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm
ar: creating liboligotm.a
a - oligotm.o
libprimer3.cc: In function 'char* strstr_nocase(char*, char*)':
libprimer3.cc:6168:29: warning: pointer 'p' used after 'void free(void*)' [-Wuse-after-free]
6168 | else {free(tmp); return p;}
| ^
libprimer3.cc:6168:15: note: call to 'void free(void*)' here
6168 | else {free(tmp); return p;}
| ~~~~^~~~~
ranlib liboligotm.a
cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o oligotm oligotm_main.c liboligotm.a -lm
ar rv libamplicontm.a amplicontm.o
ar: creating libamplicontm.a
a - amplicontm.o
ranlib libamplicontm.a
cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o amplicon3_core amplicontm_main.c libamplicontm.a -lm
ar rv libmasker.a masker.o
ar: creating libmasker.a
a - masker.o
ranlib libmasker.a
ar rv libdpal.a dpal_primer.o
cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o ntdpal ntdpal_main.o dpal.o
ar: creating libdpal.a
a - dpal_primer.o
ranlib libdpal.a
In file included from /usr/include/string.h:548,
from thal.c:43:
In function 'strcpy',
inlined from 'safe_malloc' at thal.c:804:7,
inlined from 'calc_hairpin' at thal.c:1922:19:
In file included from /usr/include/string.h:548,
from thal.c:43:
In function 'strcpy',
inlined from 'safe_malloc' at thal.c:804:7,
inlined from 'calc_hairpin' at thal.c:1922:19:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull]
81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull]
81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk'
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk'
In function 'strcpy',
inlined from 'safe_malloc' at thal.c:804:7,
inlined from 'calc_bulge_internal.isra' at thal.c:2000:19:
In function 'strcpy',
inlined from 'safe_malloc' at thal.c:804:7,
inlined from 'calc_bulge_internal.isra' at thal.c:2000:19:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull]
81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull]
81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk'
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk'
In function 'strcpy',
inlined from 'safe_malloc' at thal.c:804:7,
inlined from 'maxTM' at thal.c:1542:19,
inlined from 'fillMatrix' at thal.c:1473:16:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull]
81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk'
In function 'strcpy',
inlined from 'safe_malloc' at thal.c:804:7,
inlined from 'maxTM' at thal.c:1542:19,
inlined from 'fillMatrix' at thal.c:1473:16:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull]
81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk'
cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o ntthal thal_main.o thal.o thal_parameters.o -lm
ar rv libthal.a thal_primer.o
ar: creating libthal.a
a - thal_primer.o
ranlib libthal.a
ar rv libprimer3.a libprimer3.o p3_seq_lib.o
ar: creating libprimer3.a
a - libprimer3.o
a - p3_seq_lib.o
ranlib libprimer3.a
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -std=c++11 -lstdc++ -Wl,-z,relro -Wl,-z,now -g -o primer3_core primer3_boulder_main.o format_output.o read_boulder.o print_boulder.o libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libamplicontm.a libmasker.a -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -O2 -std=c++11 -lstdc++ -Wl,-z,relro -Wl,-z,now -g -o primer3_masker masker_main.c libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libamplicontm.a libmasker.a -lm
cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++
make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1/src'
make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1'
dh_auto_test --no-parallel --sourcedirectory=test
cd test && make -j1 test
make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/test'
cd ../src; make
make[3]: Entering directory '/build/reproducible-path/primer3-2.6.1/src'
no windows
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/build/reproducible-path/primer3-2.6.1/src'
perl cmdline_test.pl
TESTING command line arguments
Test 1... [OK]
Test 2... [OK]
Test 3... [OK]
Test 4... [OK]
Test 5... [OK]
Passed all tests - [OK]
perl oligotm_test.pl
TESTING Tm CALCULATIONS
Tm tests nr 1-50: [OK]
echo; echo; echo 'TESTING ALIGNMENT CALCS'; echo; perl dpal_test.pl ;
TESTING ALIGNMENT CALCS
Error handling of too-long sequence...[OK]
Default implementations + alignment...[OK]
Default implementations + NO alignment 1...[OK]
Default implementations + NO alignment 2...[OK]
Force _dpal_generic...[OK]
Force _dpal_long_nopath_generic 1...[OK]
Force _dpal_long_nopath_generic 2...[OK]
Force long maxgap1 functions 1...[OK]
Force long maxgap1 functions 2...[OK]
echo; echo; echo 'TESTING THERMODYNAMIC ALIGNMENT CALCS'; echo; perl thal_test.pl ;
TESTING THERMODYNAMIC ALIGNMENT CALCS
Error handling of too-long sequence...
1................................... [OK]
Default implementations + alignment...[OK]
Default implementations + NO alignment 1...[OK]
Default implementations + NO alignment 2...[OK]
Default implementations + alignment (interactive)...[OK]
Default implementations + NO alignment 1 (interactive)...[OK]
Default implementations + NO alignment 2 (interactive)...[OK]
Default implementations + alignment (interactive batch inputs)...[OK]
Default implementations + alignment + HAIRPIN (interactive batch inputs)...[OK]
echo; echo; echo 'TESTING MASKER'; echo; perl masker_test.pl ;
TESTING MASKER
Default implementations...[OK]
echo; echo; echo 'TESTING amplicon3_core'; echo; perl a3test.pl
TESTING amplicon3_core
a3test.pl for amplicon3_core version 2.5.0
a3test.pl: testing ../src/amplicon3_core
START, Mon Mar 23 15:01:29 2026
plain_WNT9B...0s [OK]
plain_TBX18...0s [OK]
plain_RYK...0s [OK]
plain_WNT2...0s [OK]
plain_ROCK2...0s [OK]
plain_SFRP3...0s [OK]
plain_IFT20...0s [OK]
plain_DVL1...0s [OK]
plain_IFT88...0s [OK]
plain_FZD2...0s [OK]
plain_GAPDH...0s [OK]
plain_WNT1...0s [OK]
plain_MYH6...0s [OK]
plain_on_command_line_WNT9B...0s [OK]
plain_on_command_line_TBX18...0s [OK]
plain_on_command_line_RYK...0s [OK]
plain_on_command_line_WNT2...0s [OK]
plain_on_command_line_ROCK2...0s [OK]
plain_on_command_line_SFRP3...0s [OK]
plain_on_command_line_IFT20...0s [OK]
plain_on_command_line_DVL1...0s [OK]
plain_on_command_line_IFT88...0s [OK]
plain_on_command_line_FZD2...0s [OK]
plain_on_command_line_GAPDH...0s [OK]
plain_on_command_line_WNT1...0s [OK]
plain_on_command_line_MYH6...0s [OK]
classic_WNT9B...0s [OK]
classic_TBX18...0s [OK]
classic_RYK...0s [OK]
classic_WNT2...0s [OK]
classic_ROCK2...0s [OK]
classic_SFRP3...0s [OK]
classic_IFT20...0s [OK]
classic_DVL1...0s [OK]
classic_IFT88...0s [OK]
classic_FZD2...0s [OK]
classic_GAPDH...0s [OK]
classic_WNT1...1s [OK]
classic_MYH6...0s [OK]
heli_WNT9B...0s [OK]
heli_TBX18...0s [OK]
heli_RYK...0s [OK]
heli_WNT2...0s [OK]
heli_ROCK2...0s [OK]
heli_SFRP3...0s [OK]
heli_IFT20...0s [OK]
heli_DVL1...0s [OK]
heli_IFT88...0s [OK]
heli_FZD2...0s [OK]
heli_GAPDH...0s [OK]
heli_WNT1...0s [OK]
heli_MYH6...0s [OK]
long_WNT9B...0s [OK]
long_TBX18...0s [OK]
long_RYK...0s [OK]
long_WNT2...0s [OK]
long_ROCK2...0s [OK]
long_SFRP3...0s [OK]
long_IFT20...0s [OK]
long_DVL1...0s [OK]
long_IFT88...0s [OK]
long_FZD2...0s [OK]
long_GAPDH...0s [OK]
long_WNT1...0s [OK]
long_MYH6...0s [OK]
optimal_WNT9B...0s [OK]
optimal_TBX18...0s [OK]
optimal_RYK...0s [OK]
optimal_WNT2...0s [OK]
optimal_ROCK2...0s [OK]
optimal_SFRP3...0s [OK]
optimal_IFT20...0s [OK]
optimal_DVL1...0s [OK]
optimal_IFT88...0s [OK]
optimal_FZD2...0s [OK]
optimal_GAPDH...0s [OK]
optimal_WNT1...0s [OK]
optimal_MYH6...0s [OK]
only_mv_WNT9B...0s [OK]
only_mv_TBX18...0s [OK]
only_mv_RYK...0s [OK]
only_mv_WNT2...0s [OK]
only_mv_ROCK2...0s [OK]
only_mv_SFRP3...0s [OK]
only_mv_IFT20...0s [OK]
only_mv_DVL1...0s [OK]
only_mv_IFT88...0s [OK]
only_mv_FZD2...0s [OK]
only_mv_GAPDH...0s [OK]
only_mv_WNT1...0s [OK]
only_mv_MYH6...0s [OK]
no_dmso_WNT9B...0s [OK]
no_dmso_TBX18...0s [OK]
no_dmso_RYK...0s [OK]
no_dmso_WNT2...0s [OK]
no_dmso_ROCK2...0s [OK]
no_dmso_SFRP3...0s [OK]
no_dmso_IFT20...0s [OK]
no_dmso_DVL1...0s [OK]
no_dmso_IFT88...0s [OK]
no_dmso_FZD2...0s [OK]
no_dmso_GAPDH...0s [OK]
no_dmso_WNT1...0s [OK]
no_dmso_MYH6...0s [OK]
Tests in a3test.pl ran for 1 s (0.0166666666666667 min)
DONE Mon Mar 23 15:01:30 2026 Passed all tests - [OK]
echo; echo; echo 'TESTING primer3_core'; echo; perl p3test.pl
TESTING primer3_core
mkdir: ../test/primer_list_tmp
mkdir: ../test/primer1_list_tmp
mkdir: ../test/primer1_th_list_tmp
mkdir: ../test/th-w-other-tasks_list_tmp
p3test.pl for primer3_core version 2.6.1
p3test.pl: testing ../src/primer3_core
START, Mon Mar 23 15:01:30 2026
testing fatal errors...
./primer_global_err/annealing_temp_salt
Testing --output and --error flags on
../src/primer3_core --strict_tags ./primer_global_err/annealing_temp_salt.in --output ./primer_global_err/annealing_temp_salt.tmp --error ./primer_global_err/annealing_temp_salt.tmp2
./primer_global_err/bad_divalent_dntp_conc_1
./primer_global_err/bad_divalent_dntp_conc_2
./primer_global_err/bad_divalent_dntp_conc_3
./primer_global_err/bad_divalent_dntp_conc_4
./primer_global_err/bad_dna_conc
./primer_global_err/bad_first_base_index
./primer_global_err/bad_float_1
./primer_global_err/bad_float_2
./primer_global_err/bad_float_3
./primer_global_err/bad_float_4
./primer_global_err/bad_gc_1
./primer_global_err/bad_gc_2
./primer_global_err/bad_gc_3
./primer_global_err/bad_gc_int_1
./primer_global_err/bad_gc_int_2
./primer_global_err/bad_gc_int_3
./primer_global_err/bad_min_three_prime_distance
./primer_global_err/bad_num_ns
./primer_global_err/bad_num_ns_int
./primer_global_err/bad_product_sizes_1
./primer_global_err/bad_product_sizes_2
./primer_global_err/bad_product_sizes_3
./primer_global_err/bad_product_sizes_4
./primer_global_err/bad_salt_conc
./primer_global_err/bad_self_any
./primer_global_err/bad_self_any_int
./primer_global_err/bad_self_end
./primer_global_err/bad_self_end_int
./primer_global_err/bad_settings0
./primer_global_err/bad_settings1
./primer_global_err/bad_settings2
./primer_global_err/bad_settings3
./primer_global_err/bad_settings4
./primer_global_err/bad_settings5
./primer_global_err/bad_settings6
./primer_global_err/empty_1
./primer_global_err/empty_product_size
./primer_global_err/gc_clamp_min_size
./primer_global_err/incorrect_task
./primer_global_err/io_gc_content_obj_fn
./primer_global_err/io_obj_fn
./primer_global_err/junction_overlap_max_size
./primer_global_err/junction_overlap_min_size
./primer_global_err/max_annealing_temp
./primer_global_err/max_min_bound
./primer_global_err/max_min_bound_int
./primer_global_err/max_min_tm
./primer_global_err/max_min_tm_int
./primer_global_err/max_opt_bound
./primer_global_err/max_opt_bound_int
./primer_global_err/max_opt_tm
./primer_global_err/max_opt_tm_int
./primer_global_err/MAX_PRIMER_LENGTH
./primer_global_err/max_size_limit_int
./primer_global_err/max_size_limit_with_overhang
./primer_global_err/max_size_min_product
./primer_global_err/max_size_min_product_int
./primer_global_err/min_opt_tm
./primer_global_err/min_opt_tm_int
./primer_global_err/mishyb_obj_fn
./primer_global_err/mispr_obj_fn
./primer_global_err/must_match_length_0
./primer_global_err/must_match_length_1
./primer_global_err/must_match_length_10
./primer_global_err/must_match_length_2
./primer_global_err/must_match_length_3
./primer_global_err/must_match_length_4
./primer_global_err/must_match_length_5
./primer_global_err/must_match_length_6
./primer_global_err/must_match_length_7
./primer_global_err/must_match_length_8
./primer_global_err/must_match_length_9
./primer_global_err/no_equal
./primer_global_err/no_terminal_equal
./primer_global_err/opt_max_size
./primer_global_err/opt_max_size_int
./primer_global_err/opt_min_size
./primer_global_err/opt_min_size_int
./primer_global_err/pair_mispr
./primer_global_err/pr_gc_content_obj_fn
./primer_global_err/product_size_obj_fn
./primer_global_err/product_tm_obj_fn
./primer_global_err/repeat_lib_err
./primer_global_err/repeat_lib_err1
./primer_global_err/repeat_lib_err2
./primer_global_err/repeat_lib_err3
./primer_global_err/repeat_lib_err4
./primer_global_err/repeat_lib_err5
./primer_global_err/repeat_lib_err6
./primer_global_err/repeat_lib_int_err
./primer_global_err/repeat_lib_int_err1
./primer_global_err/repeat_lib_int_err2
./primer_global_err/repeat_lib_int_err3
./primer_global_err/repeat_lib_int_err4
./primer_global_err/repeat_lib_int_err5
./primer_global_err/repeat_lib_int_err6
./primer_global_err/seq_quality1
./primer_global_err/seq_quality2
./primer_global_err/seq_quality3
./primer_global_err/seq_quality4
./primer_global_err/too_many_product_sizes
./primer_global_err/zero_min_size
./primer_global_err/zero_num_return
[OK]
primer_must_use_th...0s [OK]
primer_sec_struct_dpal...1s [OK]
primer_task_th...0s [OK]
primer_thal_args...0s [OK]
primer_thal_max_seq_error...1s [OK]
primer_first_base_index...0s [OK]
primer_must_match...0s [OK]
test_compl_error...0s [OK]
test_left_to_right_of_right...0s [OK]
dv_conc_vs_dntp_conc...0s [OK]
primer_boundary...0s [OK]
primer_boundary1...0s [OK]
primer_boundary_formatted...0s [OK]
primer_boundary1_formatted...0s [OK]
primer3_v1_1_4_default_settings...0s [OK]
primer3web_v0_4_0_default_settings...0s [OK]
primer3web_v3_0_0_default_settings...1s [OK]
primer3web_v4_0_0_default_settings...0s [OK]
primer_internal...0s [OK]
primer_internal1...0s [OK]
primer_internal_formatted...0s [OK]
primer_internal1_formatted...0s [OK]
primer_ok_regions...0s [OK]
primer_ok_regions_formatted...0s [OK]
primer_ok_regions2...8s [OK]
primer_tm_lc_masking...0s [OK]
primer_tm_lc_masking_formatted...0s [OK]
primer_start_codon...0s [OK]
primer_task...0s [OK]
primer_task_formatted...0s [OK]
primer_renewed_tasks...0s [OK]
primer_dmso_formamide...0s [OK]
primer_new_tasks...1s [OK]
primer_new_tasks_formatted...0s [OK]
primer_internal_position...0s [OK]
primer_annealing_temp...0s [OK]
primer_windows_newlines...1s [OK]
primer_must_overlap_point...1s [OK]
primer_overlap_junction...0s [OK]
primer_all_settingsfiles...0s [OK]
primer_high_tm_load_set...0s [OK]
primer_high_gc_load_set...0s [OK]
primer_gc_end...0s [OK]
primer_check...0s [OK]
primer_must_use...0s [OK]
primer_must_use_formatted...0s [OK]
primer_syntax...0s [OK]
primer_end_pathology...0s [OK]
primer_num_best...0s [OK]
primer_quality_boundary...0s [OK]
primer...1s [OK]
primer_list_files...[OK]
primer1...0s [OK]
primer1_list_files...[OK]
primer_mispriming...0s [OK]
primer_mispriming_formatted...1s [OK]
primer_mispriming_boundary1...0s [OK]
primer_mispriming_boundary1_formatted...0s [OK]
primer_mispriming_boundary2...0s [OK]
primer_mispriming_boundary2_formatted...0s [OK]
primer_mispriming_long_lib...0s [OK]
primer_rat...0s [OK]
primer_human...1s [OK]
long_seq...0s [OK]
primer_position_penalty...1s [OK]
primer_position_penalty_formatted...0s [OK]
p3-tmpl-mispriming...0s [OK]
primer_poly_x...0s [OK]
primer_three_prime_distance...0s [OK]
primer_obj_fn...2s [OK]
p3_3_prime_n...0s [OK]
primer_masker...3s [OK]
primer_masker_formatted...2s [OK]
primer_overhang...0s [OK]
primer_overhang_th...10s [OK]
primer_mispriming_th...7s [OK]
th-w-other-tasks...13s [OK]
th-w-other-tasks_list_files...[OK]
primer_new_tasks_th...14s [OK]
primer_sec_struct_thal...12s [OK]
primer_thermod_align...33s [OK]
primer_thermod_align_formatted...32s [OK]
primer1_th...80s [OK]
primer1_th_list_files...[OK]
primer_lib_amb_codes...
NOTE: this test takes _much_ longer than the others (5 to 20 minutes or more).
starting primer_lib_amb_codes at Mon Mar 23 15:05:16 2026...160s [OK]
Tests in p3test.pl ran for 386 s (6.43333333333333 min)
DONE Mon Mar 23 15:07:56 2026 Passed all tests - [OK]
echo; echo; echo "Testing completed. You must check the test output for the string FAILED"; echo; echo;
Testing completed. You must check the test output for the string FAILED
make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1/test'
dh clean --sourcedirectory=test
dh_auto_clean -O--sourcedirectory=test
cd test && make -j42 clean
make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/test'
echo; echo; echo 'CLEAN UP TEST DIRECTORIES'; echo; echo;
CLEAN UP TEST DIRECTORIES
rm -rf primer_list_tmp/*
rm -rf primer1_list_tmp/*
rm -rf primer1_th_list_tmp/*
rm -rf th-w-other-tasks_list_tmp/*
rm -f primer_global_err/*.tmp primer_global_err/*.tmp2 primer_global_err/*.bak
rm -f amplicon3/*.tmp amplicon3/*.jpg amplicon3/decipher*
rm -f *.tmp *.bak *.tmp.err *~
rm -f hyb_probe_only.for hyb_probe_only.int
rm -f right_only.for right_only.rev left_only.for
rm -f pcr_primers_and_io.int pcr_primers_and_io.rev pcr_primers_and_io.for
rm -f pcr_primers.rev pcr_primers.for
rm -f pick_primer_list_and_file_flag_th_[1-4].for pick_primer_list_and_file_flag_th_[1-4].rev
rm -f pick_primer_list_and_file_flag_th_[1-4].int
rm -f syntax[0-1][0-9].for syntax[0-1][0-9].int syntax[0-1][0-9].rev
rm -f oligotm.*.valg # valgrind output from oligotm_test.pl --valgrind
rm -f ntdpal.*.valg # valgrind output from dpal_test.pl --valgrind
rm -f ntthal.*.valg # valgrind output from thal_test.pl --valgrind
rm -f masker.*.valg # valgrind output from thal_test.pl --valgrind
rm -f oligotm.*.valg.* # valgrind output from oligotm_test.pl --valgrind
rm -f ntdpal.*.valg.* # valgrind output from dpal_test.pl --valgrind
rm -f ntthal.*.valg.* # valgrind output from thal_test.pl --valgrind
rm -f masker.*.valg.* # valgrind output from masker_test.pl --valgrind
rm -f *.vg */*.vg # valgrind output from p3test{,z}.pl --valgrind
rm -f *.vg.core.* # core files from crashed valgrind test
rm -f ./core # in case we crashed and left a core file
make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1/test'
debian/rules execute_after_dh_auto_clean
make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1'
rm -rf /build/reproducible-path/primer3-2.6.1/src/debian
make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1'
dh_autoreconf_clean -O--sourcedirectory=test
dh_clean -O--sourcedirectory=test
make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1'
create-stamp debian/debhelper-build-stamp
dh_testroot -O--sourcedirectory=src
dh_prep -O--sourcedirectory=src
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1'
dh_auto_install -- PREFIX=debian/primer3/usr
cd src && make -j42 install DESTDIR=/build/reproducible-path/primer3-2.6.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" PREFIX=debian/primer3/usr
make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/src'
no windows
install -d "debian/primer3/usr/bin"
install -m 755 primer3_core ntdpal ntthal amplicon3_core oligotm long_seq_tm_test primer3_masker "debian/primer3/usr/bin"
make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1/src'
make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1'
dh_install -O--sourcedirectory=src
dh_installdocs -O--sourcedirectory=src
dh_installchangelogs -O--sourcedirectory=src
dh_installexamples -O--sourcedirectory=src
debian/rules execute_after_dh_installexamples
make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1'
mkdir -p /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test;
mkdir -p /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/src;
mkdir -p /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/settings_files;
mkdir -p /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/kmer_lists;
cp -aR ./test/* /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test;
cp -aR ./src/humrep_and_simple.txt /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/src;
cp -a settings_files/primer*.txt /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/settings_files;
cp -aR ./kmer_lists/*.list /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/kmer_lists;
chmod -x /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test/thal*
chmod -x /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test/amplicon3/amplicons.csv
chmod -x /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test/primer_windows_newlines_input
sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test/long_seq_tm_test.pl ;
sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test/vgrep.pl ;
make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1'
dh_installman -O--sourcedirectory=src
dh_installsystemduser -O--sourcedirectory=src
dh_lintian -O--sourcedirectory=src
dh_perl -O--sourcedirectory=src
dh_link -O--sourcedirectory=src
dh_strip_nondeterminism -O--sourcedirectory=src
dh_compress -O--sourcedirectory=src
dh_fixperms -O--sourcedirectory=src
dh_missing -O--sourcedirectory=src
dh_dwz -a -O--sourcedirectory=src
dh_strip -a -O--sourcedirectory=src
dh_makeshlibs -a -O--sourcedirectory=src
dh_shlibdeps -a -O--sourcedirectory=src
dh_installdeb -O--sourcedirectory=src
dh_gencontrol -O--sourcedirectory=src
dh_md5sums -O--sourcedirectory=src
dh_builddeb -O--sourcedirectory=src
dpkg-deb: building package 'primer3-dbgsym' in '../primer3-dbgsym_2.6.1-5_amd64.deb'.
dpkg-deb: building package 'primer3-examples' in '../primer3-examples_2.6.1-5_all.deb'.
dpkg-deb: building package 'primer3' in '../primer3_2.6.1-5_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../primer3_2.6.1-5_amd64.buildinfo
dpkg-genchanges --build=binary -O../primer3_2.6.1-5_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/1763574 and its subdirectories
I: Current time: Mon Mar 23 03:10:32 -12 2026
I: pbuilder-time-stamp: 1774278632