I: pbuilder: network access will be disabled during build
I: Current time: Sat Jan 24 12:17:12 +14 2026
I: pbuilder-time-stamp: 1769206632
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
gpgv: Signature made Sun Dec  1 12:08:12 2024 
gpgv:                using RSA key 52D5BD0E7D4DB084E34B5865D4A41CFADDB20DB5
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./primer3_2.6.1-5.dsc: no acceptable signature found
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/2383716/tmp/hooks/D01_modify_environment starting
debug: Running on codethink03-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 Jan 23 22:17 /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/2383716/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/2383716/tmp/hooks/D02_print_environment starting
I: set
  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 '
  DIRSTACK=()
  DISTRIBUTION=unstable
  EUID=0
  FUNCNAME=([0]="Echo" [1]="main")
  GROUPS=()
  HOME=/root
  HOSTNAME=i-capture-the-hostname
  HOSTTYPE=aarch64
  HOST_ARCH=arm64
  IFS=' 	
  '
  INVOCATION_ID=5d6d1141fa9645218414882d831e704e
  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=2383716
  PS4='+ '
  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.U5pAHwT7/pbuilderrc_M6rR --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.U5pAHwT7/b2 --logfile b2/build.log primer3_2.6.1-5.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 i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Nov 22  2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/2383716/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: arm64
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 ... 20084 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
 pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
  Package debhelper-compat is not installed.

Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
  autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} 
The following packages are RECOMMENDED but will NOT be installed:
  curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 
0 packages upgraded, 29 newly installed, 0 to remove and 0 not upgraded.
Need to get 19.4 MB of archives. After unpacking 77.7 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB]
Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB]
Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-3 [198 kB]
Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB]
Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-6 [1130 kB]
Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-12 [91.4 kB]
Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB]
Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB]
Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB]
Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-3 [723 kB]
Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.22 [90.5 kB]
Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB]
Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 21 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 22 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get: 23 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get: 24 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB]
Get: 25 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB]
Get: 26 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-3 [1532 kB]
Get: 27 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 28 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 29 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.22 [919 kB]
Fetched 19.4 MB in 0s (124 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sensible-utils.
(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 ... 20084 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_arm64.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:arm64.
Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ...
Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ...
Unpacking file (1:5.45-3+b1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.22.5-3_arm64.deb ...
Unpacking gettext-base (0.22.5-3) ...
Selecting previously unselected package libuchardet0:arm64.
Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ...
Unpacking libuchardet0:arm64 (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.23.0-6_arm64.deb ...
Unpacking groff-base (1.23.0-6) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.40.2-12_arm64.deb ...
Unpacking bsdextrautils (2.40.2-12) ...
Selecting previously unselected package libpipeline1:arm64.
Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ...
Unpacking libpipeline1:arm64 (1.5.8-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ...
Unpacking man-db (2.13.0-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-4_arm64.deb ...
Unpacking m4 (1.4.19-4) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../11-autoconf_2.72-3_all.deb ...
Unpacking autoconf (2.72-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../14-autopoint_0.22.5-3_all.deb ...
Unpacking autopoint (0.22.5-3) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../15-libdebhelper-perl_13.22_all.deb ...
Unpacking libdebhelper-perl (13.22) ...
Selecting previously unselected package libtool.
Preparing to unpack .../16-libtool_2.4.7-8_all.deb ...
Unpacking libtool (2.4.7-8) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../17-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.14.0-1) ...
Selecting previously unselected package libelf1t64:arm64.
Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ...
Unpacking libelf1t64:arm64 (0.192-4) ...
Selecting previously unselected package dwz.
Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ...
Unpacking dwz (0.15-1+b1) ...
Selecting previously unselected package libicu72:arm64.
Preparing to unpack .../23-libicu72_72.1-5+b1_arm64.deb ...
Unpacking libicu72:arm64 (72.1-5+b1) ...
Selecting previously unselected package libxml2:arm64.
Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ...
Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../25-gettext_0.22.5-3_arm64.deb ...
Unpacking gettext (0.22.5-3) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../28-debhelper_13.22_all.deb ...
Unpacking debhelper (13.22) ...
Setting up libpipeline1:arm64 (1.5.8-1) ...
Setting up libicu72:arm64 (72.1-5+b1) ...
Setting up bsdextrautils (2.40.2-12) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.22) ...
Setting up libmagic1t64:arm64 (1:5.45-3+b1) ...
Setting up gettext-base (0.22.5-3) ...
Setting up m4 (1.4.19-4) ...
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:arm64 (0.192-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up autopoint (0.22.5-3) ...
Setting up autoconf (2.72-3) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:arm64 (0.0.8-1+b2) ...
Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.0-1) ...
Setting up gettext (0.22.5-3) ...
Setting up libtool (2.4.7-8) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.14.0-1) ...
Setting up groff-base (1.23.0-6) ...
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 (13.22) ...
Processing triggers for libc-bin (2.40-4) ...
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: user script /srv/workspace/pbuilder/2383716/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/2383716/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/primer3-2.6.1/ && 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  > ../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 arm64
 debian/rules clean
dh clean --sourcedirectory=src
   dh_auto_clean -O--sourcedirectory=src
	cd src && make -j12 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 -j12 "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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -g -Wall -O2 -ffloat-store  -Wl,-z,relro -Wl,-z,now -g -o thal_primer.o thal.c
cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++
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;
      |               ^~~
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 -mbranch-protection=standard -g -Wall -O2 -ffloat-store  -Wl,-z,relro -Wl,-z,now -g -o thal_parameters.o thal_parameters.c
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;
      |                          ^~~
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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o thal_main.o thal_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 -mbranch-protection=standard -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
ar rv liboligotm.a oligotm.o
ar: 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 -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o  -lm
creating liboligotm.a
a - oligotm.o
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 -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o oligotm oligotm_main.c liboligotm.a  -lm
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;}
      |           ~~~~^~~~~
ar rv libmasker.a masker.o
ar: creating libmasker.a
a - masker.o
ranlib libmasker.a
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 -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o amplicon3_core amplicontm_main.c libamplicontm.a  -lm
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/aarch64-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/aarch64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk'
ar rv libdpal.a dpal_primer.o
ar: creating libdpal.a
a - dpal_primer.o
ranlib libdpal.a
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/aarch64-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/aarch64-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/aarch64-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/aarch64-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 -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o ntdpal ntdpal_main.o dpal.o
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/aarch64-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/aarch64-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:
/usr/include/aarch64-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/aarch64-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/aarch64-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/aarch64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk'
ar rv libthal.a thal_primer.o
ar: creating libthal.a
a - thal_primer.o
ranlib libthal.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 -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o ntthal thal_main.o thal.o thal_parameters.o -lm
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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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, Fri Jan 23 22:19:14 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...1s [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...0s [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...1s [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...1s [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 3 s (0.05 min)

DONE Fri Jan 23 22:19:17 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, Fri Jan 23 22:19:17 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...0s [OK]
primer_task_th...1s [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...2s [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...9s [OK]
primer_tm_lc_masking...0s [OK]
primer_tm_lc_masking_formatted...0s [OK]
primer_start_codon...1s [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...1s [OK]
primer_windows_newlines...0s [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...1s [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...2s [OK]
primer_list_files...[OK]
primer1...0s [OK]
primer1_list_files...[OK]
primer_mispriming...0s [OK]
primer_mispriming_formatted...0s [OK]
primer_mispriming_boundary1...1s [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...2s [OK]
long_seq...1s [OK]
primer_position_penalty...1s [OK]
primer_position_penalty_formatted...1s [OK]
p3-tmpl-mispriming...0s [OK]
primer_poly_x...0s [OK]
primer_three_prime_distance...0s [OK]
primer_obj_fn...5s [OK]
p3_3_prime_n...0s [OK]
primer_masker...4s [OK]
primer_masker_formatted...6s [OK]
primer_overhang...0s [OK]
primer_overhang_th...24s [OK]
primer_mispriming_th...16s [OK]
th-w-other-tasks...18s [OK]
th-w-other-tasks_list_files...[OK]
primer_new_tasks_th...24s [OK]
primer_sec_struct_thal...16s [OK]
primer_thermod_align...57s [OK]
primer_thermod_align_formatted...62s [OK]
primer1_th...208s [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 Fri Jan 23 22:27:06 2026...288s [OK]

Tests in p3test.pl ran for 757 s (12.6166666666667 min)

DONE Fri Jan 23 22:31:54 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 -j12 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 -j12 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
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 from: /lib/ld-linux-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged
   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' in '../primer3_2.6.1-5_arm64.deb'.
dpkg-deb: building package 'primer3-examples' in '../primer3-examples_2.6.1-5_all.deb'.
dpkg-deb: building package 'primer3-dbgsym' in '../primer3-dbgsym_2.6.1-5_arm64.deb'.
 dpkg-genbuildinfo --build=binary -O../primer3_2.6.1-5_arm64.buildinfo
 dpkg-genchanges --build=binary -O../primer3_2.6.1-5_arm64.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: user script /srv/workspace/pbuilder/2383716/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/2383716/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/2383716 and its subdirectories
I: Current time: Sat Jan 24 12:36:45 +14 2026
I: pbuilder-time-stamp: 1769207805