Diff of the two buildlogs: -- --- b1/build.log 2025-01-07 00:51:18.647883282 +0000 +++ b2/build.log 2025-01-07 00:56:37.965355901 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jan 6 12:46:18 -12 2025 -I: pbuilder-time-stamp: 1736210778 +I: Current time: Mon Feb 9 21:14:21 +14 2026 +I: pbuilder-time-stamp: 1770621261 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying make.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4071440/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4147813/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Feb 9 07:14 /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/4147813/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4147813/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=20 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + 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]="x86_64-pc-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='449680d27efe4517b8d32a8f3c63eaae' - 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='4071440' - PS1='# ' - PS2='> ' + INVOCATION_ID=a430ef907b0d4945b49922547a4d1785 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-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=4147813 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.0cfAPv0G/pbuilderrc_xyqu --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.0cfAPv0G/b1 --logfile b1/build.log phast_1.7+dfsg-2.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.0cfAPv0G/pbuilderrc_c1hu --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.0cfAPv0G/b2 --logfile b2/build.log phast_1.7+dfsg-2.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.11.10+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1~bpo12+1 (2024-12-19) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4071440/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/4147813/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -171,7 +203,7 @@ Get: 43 http://deb.debian.org/debian unstable/main amd64 libpcre2-32-0 amd64 10.44-5 [248 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libpcre2-posix3 amd64 10.44-5 [60.4 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libpcre2-dev amd64 10.44-5 [790 kB] -Fetched 31.5 MB in 5s (6130 kB/s) +Fetched 31.5 MB in 0s (86.8 MB/s) Preconfiguring packages ... Selecting previously unselected package liblocale-gettext-perl. (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 ... 19848 files and directories currently installed.) @@ -370,7 +402,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/phast-1.7+dfsg/ && 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 > ../phast_1.7+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/4147813/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/4147813/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/phast-1.7+dfsg/ && 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 > ../phast_1.7+dfsg-2_source.changes dpkg-buildpackage: info: source package phast dpkg-buildpackage: info: source version 1.7+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -467,7 +503,7 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j20 "INSTALL=install --strip-program=true" + make -j42 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/phast-1.7+dfsg' Type "make package" to create a tarball reflecting the current state of the CVS tree. (cd src; make DESTDIR= CLAPACKPATH=/usr/lib ) @@ -1154,9 +1190,9 @@ ../munge-help.sh dlessP.help_src > dlessP.help gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/dless/../..\" -fno-strict-aliasing -c dless.c -o dless.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/dless/../..\" -fno-strict-aliasing -c phast_bd_phylo_hmm.c -o phast_bd_phylo_hmm.o -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/dless/../..\" -fno-strict-aliasing -c dlessP.c -o dlessP.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/dless/../..\" -fno-strict-aliasing -c dlessP.c -o dlessP.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined @@ -1240,18 +1276,18 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/prequel/../..\" -fno-strict-aliasing -c phast_pbs_code.c -o phast_pbs_code.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsEncode.c -o pbsEncode.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsScoreMatrix.c -o pbsScoreMatrix.o +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsTrain.c -o pbsTrain.o +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/prequel/../..\" -fno-strict-aliasing -c prequel.c -o prequel.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined -: warning: "PHAST_HOME" redefined : note: this is the location of the previous definition +: warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsTrain.c -o pbsTrain.o : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/prequel/../..\" -fno-strict-aliasing -c prequel.c -o prequel.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined @@ -1353,102 +1389,97 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c all_dists.c -o all_dists.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c base_evolve.c -o base_evolve.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c chooseLines.c -o chooseLines.o +: warning: "PHAST_HOME" redefined +: note: this is the location of the previous definition gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c clean_genes.c -o clean_genes.o -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c consEntropy.c -o consEntropy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c consEntropy.c -o consEntropy.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c convert_coords.c -o convert_coords.o -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c display_rate_matrix.c -o display_rate_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c display_rate_matrix.c -o display_rate_matrix.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c draw_tree.c -o draw_tree.o -: warning: "PHAST_HOME" redefined -: note: this is the location of the previous definition -: warning: "PHAST_HOME" redefined -: note: this is the location of the previous definition gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c eval_predictions.c -o eval_predictions.o -: warning: "PHAST_HOME" redefined -: note: this is the location of the previous definition gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_train.c -o hmm_train.o +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_tweak.c -o hmm_tweak.o +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_view.c -o hmm_view.o +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c indelFit.c -o indelFit.o +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c indelHistory.c -o indelHistory.o +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c maf_parse.c -o maf_parse.o +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c makeHKY.c -o makeHKY.o +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c modFreqs.c -o modFreqs.o +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_diff.c -o msa_diff.o +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_split.c -o msa_split.o +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_view.c -o msa_view.o +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c phast.c -o phast.o +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c phastBias.c -o phastBias.o +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c refeature.c -o refeature.o +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c stringiphy.c -o stringiphy.o +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c treeGen.c -o treeGen.o +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c tree_doctor.c -o tree_doctor.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_tweak.c -o hmm_tweak.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_view.c -o hmm_view.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c indelFit.c -o indelFit.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition +msa_view.c: In function 'fill_with_Ns': +msa_view.c:361:49: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] + 361 | pcre2_compile_context* fill_N_re = str_re_new("([[:digit:]]+):([[:digit:]]+)-([[:digit:]]+)"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | + | char * +In file included from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/gff.h:21, + from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/msa.h:19, + from msa_view.c:14: +/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *' + 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined +: warning: "PHAST_HOME" redefined +: note: this is the location of the previous definition : note: this is the location of the previous definition -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c indelHistory.c -o indelHistory.o -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c maf_parse.c -o maf_parse.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c makeHKY.c -o makeHKY.o -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c modFreqs.c -o modFreqs.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_diff.c -o msa_diff.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_split.c -o msa_split.o display_rate_matrix.c: In function 'do_context_dependent_ti_tv': display_rate_matrix.c:204:8: warning: variable 'tuple_i' set but not used [-Wunused-but-set-variable] 204 | char tuple_i[mod->order+2], tuple_j[mod->order+2]; | ^~~~~~~ : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_view.c -o msa_view.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c phast.c -o phast.o -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c phastBias.c -o phastBias.o -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c refeature.c -o refeature.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c stringiphy.c -o stringiphy.o -msa_view.c: In function 'fill_with_Ns': -msa_view.c:361:49: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] - 361 | pcre2_compile_context* fill_N_re = str_re_new("([[:digit:]]+):([[:digit:]]+)-([[:digit:]]+)"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | char * -In file included from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/gff.h:21, - from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/msa.h:19, - from msa_view.c:14: -/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *' - 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c treeGen.c -o treeGen.o -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c tree_doctor.c -o tree_doctor.o -gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/base_evolve base_evolve.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition -gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/convert_coords convert_coords.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/draw_tree draw_tree.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/hmm_view hmm_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now +: warning: "PHAST_HOME" redefined +: note: this is the location of the previous definition tree_doctor.c: In function 'main': tree_doctor.c:348:19: warning: the comparison will always evaluate as 'true' for the address of 'name' will never be NULL [-Waddress] 348 | if (n->name != NULL && n->name[0] != '\0' && @@ -1458,23 +1489,28 @@ /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/trees.h:47:8: note: 'name' declared here 47 | char name [STR_MED_LEN]; /**< Name of this node i.e. 'Drosophila 23' usually one of the sequence names */ | ^~~~ -gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/indelFit indelFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/indelHistory indelHistory.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now +gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now +gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/convert_coords convert_coords.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now +gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now +gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/base_evolve base_evolve.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now +gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/draw_tree draw_tree.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/makeHKY makeHKY.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/msa_diff msa_diff.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/phastBias phastBias.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/refeature refeature.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/all_dists all_dists.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/consEntropy consEntropy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now +gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/indelHistory indelHistory.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now +gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/hmm_view hmm_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now +gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/all_dists all_dists.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now +gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/stringiphy stringiphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now +gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/msa_diff msa_diff.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now +gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/indelFit indelFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/hmm_train hmm_train.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/hmm_tweak hmm_tweak.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/stringiphy stringiphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/tree_doctor tree_doctor.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/eval_predictions eval_predictions.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/maf_parse maf_parse.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/treeGen treeGen.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now +gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/maf_parse maf_parse.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now +gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/eval_predictions eval_predictions.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/msa_view msa_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/msa_split msa_split.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/display_rate_matrix display_rate_matrix.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now @@ -1534,7 +1570,7 @@ make[1]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/phast-1.7+dfsg' -cd test && PATH=/build/reproducible-path/phast-1.7+dfsg/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games /usr/bin/make msa_view +cd test && PATH=/build/reproducible-path/phast-1.7+dfsg/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path /usr/bin/make msa_view make[2]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/test' *** Testing msa_view *** msa_view hmrc.ss -i SS --end 10000 > hmrc.fa @@ -1562,14 +1598,14 @@ if ! diff --brief hmrc_sub_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --summary -i SS > hmrc_summary if ! diff --brief -b hmrc_summary hmrc_summary_correct ; then echo "ERROR" ; exit 1 ; fi --e Passed all tests. +Passed all tests. make[2]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/test' make[1]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/phast/ - make -j20 install DESTDIR=/build/reproducible-path/phast-1.7\+dfsg/debian/phast AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + make -j42 install DESTDIR=/build/reproducible-path/phast-1.7\+dfsg/debian/phast AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/phast-1.7+dfsg' (cd src; make install DESTDIR=/build/reproducible-path/phast-1.7+dfsg/debian/phast ) make[2]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src' @@ -1612,12 +1648,14 @@ 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/4147813/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4147813/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/4071440 and its subdirectories -I: Current time: Mon Jan 6 12:51:17 -12 2025 -I: pbuilder-time-stamp: 1736211077 +I: removing directory /srv/workspace/pbuilder/4147813 and its subdirectories +I: Current time: Mon Feb 9 21:19:37 +14 2026 +I: pbuilder-time-stamp: 1770621577