Running as unit: rb-build-amd64_10-53809.service; invocation ID: 7835306e4c9046f1a2c993420f37157c ==================================================================================== Thu Sep 18 07:45:16 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_10) on jenkins, called using "ionos5-amd64 ionos1-amd64" as arguments. Thu Sep 18 07:45:16 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-vlsJ43We" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Sep 18 07:45:16 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Thu Sep 18 07:45:16 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-HpW6i6' Thu Sep 18 07:45:16 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Thu Sep 18 07:45:16 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-XET1BF' ok, let's check if phast is building anywhere yet… ok, phast is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of phast in unstable on amd64 on jenkins now. 1st build will be done on ionos5-amd64.debian.net. 2nd build will be done on ionos1-amd64.debian.net. ============================================================================= Thu Sep 18 07:45:25 UTC 2025 I: starting to build phast/unstable/amd64 on jenkins on '2025-09-18 07:45' Thu Sep 18 07:45:25 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_10/53809/console.log 1758181525 amd64 unstable phast Thu Sep 18 07:45:25 UTC 2025 I: Downloading source for unstable/phast=1.7+dfsg-2 --2025-09-18 07:45:25-- http://deb.debian.org/debian/pool/main/p/phast/phast_1.7%2bdfsg-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2218 (2.2K) [text/prs.lines.tag] Saving to: ‘phast_1.7+dfsg-2.dsc’ 0K .. 100% 263M=0s 2025-09-18 07:45:25 (263 MB/s) - ‘phast_1.7+dfsg-2.dsc’ saved [2218/2218] --2025-09-18 07:45:25-- http://deb.debian.org/debian/pool/main/p/phast/phast_1.7%2bdfsg-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2218 (2.2K) [text/prs.lines.tag] Saving to: ‘phast_1.7+dfsg-2.dsc’ 0K .. 100% 263M=0s 2025-09-18 07:45:25 (263 MB/s) - ‘phast_1.7+dfsg-2.dsc’ saved [2218/2218] Thu Sep 18 07:45:25 UTC 2025 I: phast_1.7+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: phast Binary: phast Architecture: any Version: 1.7+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: http://compgen.cshl.edu/phast/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/phast Vcs-Git: https://salsa.debian.org/med-team/phast.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), liblapack-dev | liblapack.so, libblas-dev | libblas.so, liblapacke-dev, libtmglib-dev, libpcre2-dev, help2man Package-List: phast deb science optional arch=any Checksums-Sha1: 718957dc45971f6f249cecd243ada1efe4034eb5 1809648 phast_1.7+dfsg.orig.tar.xz 65b16e2c78c347704a757e47213c1004da402c7c 58712 phast_1.7+dfsg-2.debian.tar.xz Checksums-Sha256: 56131c493daa49de2cb2031d620e056e7f10a361284798716274c0d006ff2c0e 1809648 phast_1.7+dfsg.orig.tar.xz b8326097fe92e0a8d43e5a5283e78209b0e8e9742e5ad2c5f53c7d3433daa7d6 58712 phast_1.7+dfsg-2.debian.tar.xz Files: fb92e0faf0f68e257f20633a5832f530 1809648 phast_1.7+dfsg.orig.tar.xz 82891b7557ea3ee0165a041306e1be1f 58712 phast_1.7+dfsg-2.debian.tar.xz Dgit: a1cd2a946900d5c55078600c12724d6602712021 debian archive/debian/1.7+dfsg-2 https://git.dgit.debian.org/phast -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmd66U4UHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdoSHw//Ulr4fOJXcZZkBbLcvauHVAGkvaZP x0a7Uk/4xNrJfZyOfUgDVnNBHD5Vj/xskyHoi5SdwyFsNUxcv4KJV6AWKYENnGrA AAYudS9yq8Usch4REfkkECooSC27gbVJDsJr1d0vXOFbLrIRzQ6I4JAD6TT7dthf zpcbDyLJA3Uepz0qXEGKQmi5WUx2q07NYJtBFCpvf74xYGCjQX8WZpG8m/0/MKC0 hOfdhlAPMiQjPKMyCorEK+NwlkTsnuQ4ni0imYO/pzMoTdIMJ+KwaDa7zKqDAjh6 Tv0nDTb32WhJVLQiu49GmC2lIfey0nVeWBUloT2+LNMRNlRxNgKcc9OszviSNZwK h/6375+AnPfoGjJNkAzMKtXm5zkbIkXkawFcb8Nuzdod4UExV7yll0sF0AWmRjBh qKAenxkmAkBoN4pLk0m+4gHriTYH45edO9OLzclLIXMwQKr/puyxWCHT0JPv5yCU ASrNPypn9YvV1DLmG3bysQxEeo/JRZb5Xb16Umyewnye/ZwI8uRo9y+RiKlRbMi+ q1R3M/+OIVOxGJAE3PuPvqO+cFHFXXmWdUlIsiMMyJ+J9WxkJWi69knGO90UI0ut 5oD1e0PGFfgtUnJK+9I8MIKKtQ9cF2c5GCPZOcTdGSrQtO8ngMnNVNqwAjD405ug ERnrfs59Ra3to9U= =UAH5 -----END PGP SIGNATURE----- Thu Sep 18 07:45:25 UTC 2025 I: Checking whether the package is not for us Thu Sep 18 07:45:25 UTC 2025 I: Starting 1st build on remote node ionos5-amd64.debian.net. Thu Sep 18 07:45:25 UTC 2025 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Thu Sep 18 07:45:25 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Thu Sep 18 07:45:25 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-mt8Gzu' ==================================================================================== Wed Oct 21 14:08:26 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos5-amd64, called using "1 phast unstable /srv/reproducible-results/rbuild-debian/r-b-build.4IydX6S2 1.7+dfsg-2" as arguments. Wed Oct 21 14:08:26 UTC 2026 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-8p9OSb5f" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Oct 21 14:08:26 UTC 2026 I: Downloading source for unstable/phast=1.7+dfsg-2 Reading package lists... NOTICE: 'phast' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/phast.git Please use: git clone https://salsa.debian.org/med-team/phast.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1871 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main phast 1.7+dfsg-2 (dsc) [2218 B] Get:2 http://deb.debian.org/debian unstable/main phast 1.7+dfsg-2 (tar) [1810 kB] Get:3 http://deb.debian.org/debian unstable/main phast 1.7+dfsg-2 (diff) [58.7 kB] Fetched 1871 kB in 0s (60.6 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'phast' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/phast.git Please use: git clone https://salsa.debian.org/med-team/phast.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1871 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main phast 1.7+dfsg-2 (dsc) [2218 B] Get:2 http://deb.debian.org/debian unstable/main phast 1.7+dfsg-2 (tar) [1810 kB] Get:3 http://deb.debian.org/debian unstable/main phast 1.7+dfsg-2 (diff) [58.7 kB] Fetched 1871 kB in 0s (60.6 MB/s) Download complete and in download only mode ============================================================================= Building phast in unstable on amd64 on ionos5-amd64 now. Date: Wed Oct 21 14:08:26 UTC 2026 Date UTC: Wed Oct 21 14:08:26 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Wed Oct 21 02:08:26 -12 2026 I: pbuilder-time-stamp: 1792591706 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 [phast_1.7+dfsg-2.dsc] I: copying [./phast_1.7+dfsg.orig.tar.xz] I: copying [./phast_1.7+dfsg-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./phast_1.7+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting phast in phast-1.7+dfsg dpkg-source: info: unpacking phast_1.7+dfsg.orig.tar.xz dpkg-source: info: unpacking phast_1.7+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying clapack.patch dpkg-source: info: applying do_not_install_to_opt.patch dpkg-source: info: applying use_debian_packaged_libpcre.patch dpkg-source: info: applying use_debian_packaged_help2man.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying pcre2.patch dpkg-source: info: applying gcc-14.patch dpkg-source: info: applying make.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1882834/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='16350d8d50794435bab6edfa7630b1b6' 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='1882834' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.4IydX6S2/pbuilderrc_GqBW --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.4IydX6S2/b1 --logfile b1/build.log phast_1.7+dfsg-2.dsc' SUDO_GID='110' SUDO_HOME='/var/lib/jenkins' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1882834/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team 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), liblapack-dev | liblapack.so, libblas-dev | libblas.so, liblapacke-dev, libtmglib-dev, libpcre2-dev, help2man dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 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. pbuilder-satisfydepends-dummy depends on liblapack-dev | liblapack.so; however: Package liblapack-dev is not installed. Package liblapack.so is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev | libblas.so; however: Package libblas-dev is not installed. Package libblas.so is not installed. pbuilder-satisfydepends-dummy depends on liblapacke-dev; however: Package liblapacke-dev is not installed. pbuilder-satisfydepends-dummy depends on libtmglib-dev; however: Package libtmglib-dev is not installed. pbuilder-satisfydepends-dummy depends on libpcre2-dev; however: Package libpcre2-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man 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} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} liblapack-dev{a} liblapack3{a} liblapacke{a} liblapacke-dev{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpipeline1{a} libtmglib-dev{a} libtmglib3{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{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, 44 newly installed, 0 to remove and 0 not upgraded. Need to get 24.1 MB of archives. After unpacking 107 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 23 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.1-7 [229 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.1-7 [5894 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libtmglib3 amd64 3.12.1-7 [143 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 liblapacke amd64 3.12.1-7 [441 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libtmglib-dev amd64 3.12.1-7 [148 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 liblapacke-dev amd64 3.12.1-7 [440 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libpcre2-16-0 amd64 10.46-1 [281 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libpcre2-32-0 amd64 10.46-1 [268 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libpcre2-posix3 amd64 10.46-1 [63.9 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libpcre2-dev amd64 10.46-1 [853 kB] Fetched 24.1 MB in 1s (31.8 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 ... 19917 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../09-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... 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Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up file (1:5.46-5) ... Setting up libpcre2-16-0:amd64 (10.46-1) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up autotools-dev (20240727.1) ... Setting up libpcre2-32-0:amd64 (10.46-1) ... Setting up libblas3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up libgfortran5:amd64 (15.2.0-4) ... Setting up autoconf (2.72-3.1) ... Setting up libpcre2-posix3:amd64 (10.46-1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up libblas-dev:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up liblapack3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-2+b1) ... Setting up libpcre2-dev:amd64 (10.46-1) ... Setting up libtool (2.5.4-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (21) ... Setting up libtmglib3:amd64 (3.12.1-7) ... Setting up liblapack-dev:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up liblapacke:amd64 (3.12.1-7) ... Setting up libtmglib-dev:amd64 (3.12.1-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up liblapacke-dev:amd64 (3.12.1-7) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.26) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/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 dpkg-buildpackage: info: source package phast dpkg-buildpackage: info: source version 1.7+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/phast-1.7+dfsg' dh_auto_clean cd src && /usr/bin/make clean make[2]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib' cat: /build/reproducible-path/phast-1.7+dfsg/src/lib/../version: No such file or directory for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/reproducible-path/phast-1.7+dfsg/src/lib/$dir && /usr/bin/make clean ; done make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/base' cat: /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/base' make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/msa' cat: /build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/msa' make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/feature' cat: /build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/feature' make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/hmm' cat: /build/reproducible-path/phast-1.7+dfsg/src/lib/hmm/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/hmm' make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo' cat: /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo' make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm' cat: /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/motif' cat: /build/reproducible-path/phast-1.7+dfsg/src/lib/motif/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/motif' rm -f /build/reproducible-path/phast-1.7+dfsg/src/lib/../../lib/* make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/dless' cat: /build/reproducible-path/phast-1.7+dfsg/src/dless/../version: No such file or directory rm -f *.o dless.help dlessP.help /build/reproducible-path/phast-1.7+dfsg/src/dless/../../bin/dless /build/reproducible-path/phast-1.7+dfsg/src/dless/../../bin/dlessP make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/dless' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/exoniphy' cat: /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../version: No such file or directory rm -f *.o *.help /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../bin/exoniphy make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/exoniphy' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phastCons' cat: /build/reproducible-path/phast-1.7+dfsg/src/phastCons/../version: No such file or directory rm -f *.o /build/reproducible-path/phast-1.7+dfsg/src/phastCons/../../bin/phastCons phastCons.help make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phastCons' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phastOdds' cat: /build/reproducible-path/phast-1.7+dfsg/src/phastOdds/../version: No such file or directory rm -f *.o *.help /build/reproducible-path/phast-1.7+dfsg/src/phastOdds/../../bin/phastOdds make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phastOdds' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phastMotif' cat: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../version: No such file or directory rm -f *.o /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../bin/phastMotif make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phastMotif' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloFit' cat: /build/reproducible-path/phast-1.7+dfsg/src/phyloFit/../version: No such file or directory rm -f *.o /build/reproducible-path/phast-1.7+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.help make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloFit' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloBoot' cat: /build/reproducible-path/phast-1.7+dfsg/src/phyloBoot/../version: No such file or directory rm -f *.o *.help /build/reproducible-path/phast-1.7+dfsg/src/phyloBoot/../../bin/phyloBoot make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloBoot' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloP' cat: /build/reproducible-path/phast-1.7+dfsg/src/phyloP/../version: No such file or directory rm -f *.o /build/reproducible-path/phast-1.7+dfsg/src/phyloP/../../bin/phyloP phyloP.help make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloP' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/prequel' cat: /build/reproducible-path/phast-1.7+dfsg/src/prequel/../version: No such file or directory rm -f *.o /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsDecode /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsEncode /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsScoreMatrix /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsTrain /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/prequel pbsDecode.help pbsEncode.help pbsScoreMatrix.help pbsTrain.help prequel.help make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/prequel' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/util' cat: /build/reproducible-path/phast-1.7+dfsg/src/util/../version: No such file or directory rm -f *.o *.help /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/all_dists /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/base_evolve /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/chooseLines /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/clean_genes /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/consEntropy /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/convert_coords /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/display_rate_matrix /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/draw_tree /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/eval_predictions /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/hmm_train /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/hmm_tweak /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/hmm_view /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/indelFit /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/indelHistory /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/maf_parse /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/makeHKY /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/modFreqs /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/msa_diff /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/msa_split /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/msa_view /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/phast /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/phastBias /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/refeature /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/stringiphy /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/treeGen /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/tree_doctor make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/util' rm -rf ../bin ../lib ../doc make[2]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build 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 ) make[2]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src' mkdir -p ../bin ../lib for dir in lib dless exoniphy phastCons phastOdds phastMotif phyloFit phyloBoot phyloP prequel util ; do cd /build/reproducible-path/phast-1.7+dfsg/src/$dir && make ; done make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/reproducible-path/phast-1.7+dfsg/src/lib/$dir && make ; done make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/base' 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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_complex_matrix.c -o phast_complex_matrix.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_complex_vector.c -o phast_complex_vector.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_eigen.c -o phast_eigen.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_hashtable.c -o phast_hashtable.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_list_of_lists.c -o phast_list_of_lists.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_lists.c -o phast_lists.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_markov_matrix.c -o phast_markov_matrix.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_matrix.c -o phast_matrix.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_memory_handler.c -o phast_memory_handler.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_misc.c -o phast_misc.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 phast_misc.c: In function 'make_name_hash': phast_misc.c:673:46: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 673 | pcre2_compile_context *map_re = str_re_new("^[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*(->|=)[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from phast_misc.c:16: /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_misc.c: In function 'phast_fclose': phast_misc.c:301:5: warning: pointer 'f' used after 'fclose' [-Wuse-after-free] 301 | unregister_open_file(f); | ^~~~~~~~~~~~~~~~~~~~~~~ phast_misc.c:300:5: note: call to 'fclose' here 300 | fclose(f); | ^~~~~~~~~ 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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_numerical_opt.c -o phast_numerical_opt.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_prob_matrix.c -o phast_prob_matrix.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_prob_vector.c -o phast_prob_vector.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_stringsplus.c -o phast_stringsplus.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 phast_stringsplus.c: In function 'str_re_match_sub': phast_stringsplus.c:501:25: warning: pointer targets in passing argument 2 of 'pcre2_match_8' differ in signedness [-Wpointer-sign] 501 | rc = pcre2_match(re, s->chars, s->length, offset, 0, match_data, NULL); | ~^~~~~~~ | | | char * In file included from phast_stringsplus.c:16: /usr/include/pcre2.h:1011:1: note: expected 'PCRE2_SPTR8' {aka 'const unsigned char *'} but argument is of type 'char *' 1011 | PCRE2_TYPES_STRUCTURES_AND_FUNCTIONS | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ phast_stringsplus.c:504:52: warning: 'ovector' may be used uninitialized [-Wmaybe-uninitialized] 504 | if (first_match != NULL) (*first_match) = ovector[0]; | ~~~~~~~^~~ phast_stringsplus.c:491:15: note: 'ovector' was declared here 491 | PCRE2_SIZE *ovector; | ^~~~~~~ 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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_vector.c -o phast_vector.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 ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar: creating /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/base' make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/msa' 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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_local_alignment.c -o phast_local_alignment.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 phast_local_alignment.c: In function 'la_read_lav': phast_local_alignment.c:50:55: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 50 | pcre2_compile_context *stanza_start_re = str_re_new("^([dshaxm])[[:space:]]*{"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/local_alignment.h:36, from phast_local_alignment.c:32: /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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_maf.c -o phast_maf.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 phast_maf.c: In function 'maf_read_cats_subset': phast_maf.c:29:41: warning: variable 'block_no' set but not used [-Wunused-but-set-variable] 29 | int i, start_idx, length, max_tuples, block_no, | ^~~~~~~~ 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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_maf_block.c -o phast_maf_block.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_msa.c -o phast_msa.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 phast_msa.c: In function 'msa_read_fasta': phast_msa.c:264:29: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 264 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*([^[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | 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 phast_msa.c:39: /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:257:40: warning: variable 'line_no' set but not used [-Wunused-but-set-variable] 257 | int maxlen, i, nseqs, j, do_toupper, line_no; | ^~~~~~~ phast_msa.c: In function 'msa_read_seq_fasta': phast_msa.c:1929:29: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 1929 | descrip_re = str_re_new("^[[:space:]]*>"); | ^~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c: In function 'msa_format_for_content': phast_msa.c:2590:22: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 2590 | ss_re = str_re_new("^NSEQS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2591:26: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 2591 | phylip_re = str_re_new("^([[:space:]]*([0-9]+))[[:space:]]*[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2592:25: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 2592 | fasta_re = str_re_new("^>.*"); | ^~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2593:23: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 2593 | lav_re = str_re_new("^#:lav.*"); | ^~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2594:23: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 2594 | maf_re = str_re_new("^##maf"); | ^~~~~~~~ | | | char * /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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_multi_msa.c -o phast_multi_msa.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 phast_multi_msa.c: In function 'multimsa_new_from_files': phast_multi_msa.c:54:49: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 54 | pcre2_compile_context *blocks_re = str_re_new("#[[:space:]]*BLOCKS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | 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 phast_multi_msa.c:37: /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_multi_msa.c:55:47: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 55 | pcre2_compile_context *alph_re = str_re_new("#[[:space:]]*ALPHABET[[:space:]]*=[[:space:]]*([A-Z]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_multi_msa.c:56:49: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 56 | pcre2_compile_context *format_re = str_re_new("#[[:space:]]*FORMAT[[:space:]]*=[[:space:]]*([A-Z]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_sufficient_stats.c -o phast_sufficient_stats.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 phast_sufficient_stats.c: In function 'ss_from_msas': phast_sufficient_stats.c:140:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] 140 | else | ^~~~ phast_sufficient_stats.c:142:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' 142 | max_tuples = pow_bounded(strlen(msa->alphabet) + (int)strlen(msa->missing) + 1, | ^~~~~~~~~~ phast_sufficient_stats.c: In function 'ss_read': phast_sufficient_stats.c:661:25: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 661 | nseqs_re = str_re_new("NSEQS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | 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 /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/sufficient_stats.h:20, from phast_sufficient_stats.c:11: /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:662:26: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 662 | length_re = str_re_new("LENGTH[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:663:30: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 663 | tuple_size_re = str_re_new("TUPLE_SIZE[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:664:27: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 664 | ntuples_re = str_re_new("NTUPLES[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:665:25: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 665 | names_re = str_re_new("NAMES[[:space:]]*=[[:space:]]*(.*)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:666:24: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 666 | alph_re = str_re_new("ALPHABET[[:space:]]*=[[:space:]]*([-.^A-Za-z ]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:667:25: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 667 | ncats_re = str_re_new("NCATS[[:space:]]*=[[:space:]]*([-0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:668:26: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 668 | offset_re = str_re_new("IDX_OFFSET[[:space:]]*=[[:space:]]*([-0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:669:25: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 669 | tuple_re = str_re_new("^([0-9]+)[[:space:]]+([-.^A-Za-z ]+)[[:space:]]+([0-9.[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:670:25: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 670 | order_re = str_re_new("TUPLE_IDX_ORDER:"); | ^~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/msa' make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/feature' 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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_bed.c -o phast_bed.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 phast_bed.c: In function 'gff_print_bed': phast_bed.c:143:52: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 143 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/gff.h:21, from phast_bed.c:15: /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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_category_map.c -o phast_category_map.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 phast_category_map.c: In function 'cm_read': phast_category_map.c:39:31: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 39 | cat_range_re = str_re_new("^[[:space:]]*([^[:space:]]+)[[:space:]]+([[:digit:]]+)(-([[:digit:]]+))?([[:space:]]+([[: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/category_map.h:92, from phast_category_map.c:10: /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:40:27: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 40 | ncats_re = str_re_new("^[[:space:]]*NCATS[[:space:]]*=[[:space:]]*([[:digit:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:41:26: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 41 | fill_re = str_re_new("^[[:space:]]*FILL_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:42:27: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 42 | label_re = str_re_new("^[[:space:]]*LABELLING_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:43:28: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 43 | extend_re = str_re_new("^[[:space:]]*FEATURE_EXTEND[[:space:]]*:[[:space:]]*(.+)[[:space:]]*\\((.+)\\)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_genepred.c -o phast_genepred.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_gff.c -o phast_gff.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 phast_gff.c: In function 'gff_read_set': phast_gff.c:56:38: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 56 | spec_comment_re = str_re_new("^[[:space:]]*##[[:space:]]*([^[:space:]]+)[[:space:]]+([^[:space:]]+)([[:space:]]+([^[:space:]]+))?"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/gff.h:21, from phast_gff.c:13: /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_gff.c: In function 'gff_new_feature_genomic_pos': phast_gff.c:272:24: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 272 | posre = str_re_new("(chr[_a-zA-Z0-9]+):([0-9]+)-([0-9]+)([-+])?"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_gff.c: In function 'gff_group': phast_gff.c:688:23: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 688 | tag_re = str_re_new(tmpstr); | ^~~~~~ | | | char * /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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_wig.c -o phast_wig.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 ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/feature' make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/hmm' 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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/hmm/../../..\" -fno-strict-aliasing -c phast_em.c -o phast_em.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/hmm/../../..\" -fno-strict-aliasing -c phast_hmm.c -o phast_hmm.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 ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/hmm' make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo' 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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_bgc_hmm.c -o phast_bgc_hmm.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_cons.c -o phast_cons.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_dgamma.c -o phast_dgamma.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_column.c -o phast_fit_column.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_em.c -o phast_fit_em.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_feature.c -o phast_fit_feature.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_indel_history.c -o phast_indel_history.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_indel_mod.c -o phast_indel_mod.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_fit.c -o phast_phylo_fit.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 phast_phylo_fit.c:41:25: error: conflicting types for 'phyloFit_struct_new'; have 'struct phyloFit_struct *(int)' 41 | struct phyloFit_struct* phyloFit_struct_new(int rphast) { | ^~~~~~~~~~~~~~~~~~~ In file included from phast_phylo_fit.c:33: /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/phylo_fit.h:69:25: note: previous declaration of 'phyloFit_struct_new' with type 'struct phyloFit_struct *(void)' 69 | struct phyloFit_struct* phyloFit_struct_new(); | ^~~~~~~~~~~~~~~~~~~ make[4]: *** [Makefile:13: phast_phylo_fit.o] Error 1 make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo' make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm' 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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c phast_gap_patterns.c -o phast_gap_patterns.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c phast_phylo_hmm.c -o phast_phylo_hmm.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 ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/motif' 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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/motif/../../..\" -fno-strict-aliasing -c phast_motif.c -o phast_motif.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 phast_motif.c: In function 'mtf_print': phast_motif.c:1411:21: warning: '%s' directive argument is null [-Wformat-overflow=] 1411 | fprintf(F, "\t%s\n", (char*)lst_get_ptr(notfound, i)); | ^~ phast_motif.c: In function 'mtf_print_html': phast_motif.c:1604:23: warning: '%s' directive argument is null [-Wformat-overflow=] 1604 | fprintf(F, "
  • %s\n", (char*)lst_get_ptr(notfound, i)); | ^~ 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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/motif/../../..\" -fno-strict-aliasing -c phast_tfbs.c -o phast_tfbs.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 phast_tfbs.c: In function 'pwm_read': phast_tfbs.c:147:24: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 147 | pssm_re = str_re_new("^letter-probability matrix: alength= ([0-9]+) w= ([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | 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 phast_tfbs.c:16: /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_tfbs.c:148:30: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 148 | motif_name_re = str_re_new("^MOTIF[[:space:]]+(.+?)[[:space:]].*"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_tfbs.c: In function 'ms_read': phast_tfbs.c:229:29: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 229 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*(.+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_tfbs.c:219:32: warning: variable 'line_no' set but not used [-Wunused-but-set-variable] 219 | int i, nseqs, j, do_toupper, line_no; | ^~~~~~~ ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/motif' make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/dless' ../munge-help.sh dless.help_src > dless.help ../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 : warning: 'PHAST_HOME' redefined : note: this is the location of the previous definition : note: this is the location of the previous definition : warning: 'PHAST_HOME' redefined : note: this is the location of the previous definition dlessP.c: In function 'do_p_values': dlessP.c:199:45: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 199 | pcre2_compile_context *id_re = str_re_new(".*id \"([^\"]*)\""); | ^~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/trees.h:25, from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/tree_model.h:26, from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/bd_phylo_hmm.h:22, from dlessP.c:17: /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 -L/build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/dless/../../bin/dless dless.o phast_bd_phylo_hmm.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/dless/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/dless/../../bin/dlessP dlessP.o phast_bd_phylo_hmm.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now /usr/bin/ld: dlessP.o: in function `do_p_values': ./src/dless/./src/dless/dlessP.c:232:(.text+0x43b): undefined reference to `tr_create_copy' /usr/bin/ld: ./src/dless/./src/dless/dlessP.c:252:(.text+0x4c4): undefined reference to `tr_reroot' /usr/bin/ld: ./src/dless/./src/dless/dlessP.c:264:(.text+0x4ee): undefined reference to `tr_total_len' /usr/bin/ld: ./src/dless/./src/dless/dlessP.c:264:(.text+0x507): undefined reference to `sub_define_jump_process' /usr/bin/ld: ./src/dless/./src/dless/dlessP.c:265:(.text+0x52f): undefined reference to `sub_p_value_joint_many' /usr/bin/ld: ./src/dless/./src/dless/dlessP.c:268:(.text+0x541): undefined reference to `tr_free' /usr/bin/ld: ./src/dless/./src/dless/dlessP.c:269:(.text+0x549): undefined reference to `sub_free_jump_process' /usr/bin/ld: ./src/dless/./src/dless/dlessP.c:222:(.text+0xcfc): undefined reference to `tr_total_len' /usr/bin/ld: ./src/dless/./src/dless/dlessP.c:222:(.text+0xd12): undefined reference to `sub_define_jump_process' /usr/bin/ld: ./src/dless/./src/dless/dlessP.c:223:(.text+0xd2d): undefined reference to `sub_p_value_many' /usr/bin/ld: ./src/dless/./src/dless/dlessP.c:225:(.text+0xd3a): undefined reference to `sub_free_jump_process' /usr/bin/ld: dlessP.o: in function `main': ./src/dless/./src/dless/dlessP.c:103:(.text.startup+0x31d): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/dless/./src/dless/dlessP.c:132:(.text.startup+0x3f4): undefined reference to `tm_prune' /usr/bin/ld: ./src/dless/./src/dless/dlessP.c:144:(.text.startup+0x424): undefined reference to `tr_name_ancestors' /usr/bin/ld: phast_bd_phylo_hmm.o: in function `bd_new': ./src/dless/./src/dless/phast_bd_phylo_hmm.c:92:(.text+0x634): undefined reference to `tm_create_copy' /usr/bin/ld: ./src/dless/./src/dless/phast_bd_phylo_hmm.c:94:(.text+0x67f): undefined reference to `tr_partition_nodes' /usr/bin/ld: ./src/dless/./src/dless/phast_bd_phylo_hmm.c:103:(.text+0x715): undefined reference to `tm_reinit' /usr/bin/ld: ./src/dless/./src/dless/phast_bd_phylo_hmm.c:144:(.text+0xb77): undefined reference to `tr_partition_nodes' /usr/bin/ld: ./src/dless/./src/dless/phast_bd_phylo_hmm.c:164:(.text+0xca7): undefined reference to `im_new' /usr/bin/ld: phast_bd_phylo_hmm.o: in function `bd_handle_missing_data': ./src/dless/./src/dless/phast_bd_phylo_hmm.c:234:(.text+0x10e4): undefined reference to `tr_postorder' /usr/bin/ld: ./src/dless/./src/dless/phast_bd_phylo_hmm.c:260:(.text+0x1236): undefined reference to `tr_preorder' /usr/bin/ld: phast_bd_phylo_hmm.o: in function `bd_add_indel_emissions': ./src/dless/./src/dless/phast_bd_phylo_hmm.c:316:(.text+0x1767): undefined reference to `im_column_logl' /usr/bin/ld: dless.o: in function `main': ./src/dless/./src/dless/dless.c:146:(.text.startup+0x4da): undefined reference to `ih_new_from_file' /usr/bin/ld: ./src/dless/./src/dless/dless.c:171:(.text.startup+0x68e): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/dless/./src/dless/dless.c:179:(.text.startup+0x6c1): undefined reference to `tm_is_reversible' /usr/bin/ld: ./src/dless/./src/dless/dless.c:209:(.text.startup+0x784): undefined reference to `tm_prune' /usr/bin/ld: ./src/dless/./src/dless/dless.c:221:(.text.startup+0x7b5): undefined reference to `tr_name_ancestors' /usr/bin/ld: ./src/dless/./src/dless/dless.c:237:(.text.startup+0x11d9): undefined reference to `ih_reconstruct' /usr/bin/ld: phast_bd_phylo_hmm.o: in function `bd_new': ./src/dless/./src/dless/phast_bd_phylo_hmm.c:92:(.text+0x634): undefined reference to `tm_create_copy' /usr/bin/ld: ./src/dless/./src/dless/phast_bd_phylo_hmm.c:94:(.text+0x67f): undefined reference to `tr_partition_nodes' /usr/bin/ld: ./src/dless/./src/dless/phast_bd_phylo_hmm.c:103:(.text+0x715): undefined reference to `tm_reinit' /usr/bin/ld: ./src/dless/./src/dless/phast_bd_phylo_hmm.c:144:(.text+0xb77): undefined reference to `tr_partition_nodes' /usr/bin/ld: ./src/dless/./src/dless/phast_bd_phylo_hmm.c:164:(.text+0xca7): undefined reference to `im_new' /usr/bin/ld: phast_bd_phylo_hmm.o: in function `bd_handle_missing_data': ./src/dless/./src/dless/phast_bd_phylo_hmm.c:234:(.text+0x10e4): undefined reference to `tr_postorder' /usr/bin/ld: ./src/dless/./src/dless/phast_bd_phylo_hmm.c:260:(.text+0x1236): undefined reference to `tr_preorder' /usr/bin/ld: phast_bd_phylo_hmm.o: in function `bd_add_indel_emissions': ./src/dless/./src/dless/phast_bd_phylo_hmm.c:316:(.text+0x1767): undefined reference to `im_column_logl' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_rates_cross': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:361:(.text+0xf6c): undefined reference to `DiscreteGamma' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:364:(.text+0xf8a): undefined reference to `tm_reinit' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:371:(.text+0xfc9): undefined reference to `tm_create_copy' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:376:(.text+0xfe0): undefined reference to `tm_scale_branchlens' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:453:(.text+0x13b2): undefined reference to `tm_free' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_free': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:469:(.text+0x154d): undefined reference to `tm_free' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_compute_emissions': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:597:(.text+0x18c6): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:597:(.text+0x1d80): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:597:(.text+0x1fbb): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_set_branch_len_factors': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:1182:(.text+0x3d1f): undefined reference to `tr_total_len' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_estim_mods_em': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:1099:(.text+0x3f94): undefined reference to `tm_params_new_init_from_model' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:1109:(.text+0x4049): undefined reference to `tm_fit' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:1087:(.text+0x40a0): undefined reference to `subst_mod_is_codon_model' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_gap_patterns.o): in function `gp_create_gapcats': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_gap_patterns.c:163:(.text+0x71c): undefined reference to `tr_inorder' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_gap_patterns.o): in function `gp_set_phylo_patterns': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_gap_patterns.c:244:(.text+0xf45): undefined reference to `tr_postorder' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_gap_patterns.o): in function `gp_set_patterns': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_gap_patterns.c:419:(.text+0x1721): undefined reference to `tr_partition_leaves' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_rates_cross': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:361:(.text+0xf6c): undefined reference to `DiscreteGamma' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:364:(.text+0xf8a): undefined reference to `tm_reinit' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:371:(.text+0xfc9): undefined reference to `tm_create_copy' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:376:(.text+0xfe0): undefined reference to `tm_scale_branchlens' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:453:(.text+0x13b2): undefined reference to `tm_free' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_free': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:469:(.text+0x154d): undefined reference to `tm_free' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_compute_emissions': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:597:(.text+0x18c6): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:597:(.text+0x1d80): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:597:(.text+0x1fbb): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_set_branch_len_factors': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:1182:(.text+0x3d1f): undefined reference to `tr_total_len' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_estim_mods_em': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:1099:(.text+0x3f94): undefined reference to `tm_params_new_init_from_model' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:1109:(.text+0x4049): undefined reference to `tm_fit' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:1087:(.text+0x40a0): undefined reference to `subst_mod_is_codon_model' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_gap_patterns.o): in function `gp_create_gapcats': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_gap_patterns.c:163:(.text+0x71c): undefined reference to `tr_inorder' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_gap_patterns.o): in function `gp_set_phylo_patterns': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_gap_patterns.c:244:(.text+0xf45): undefined reference to `tr_postorder' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_gap_patterns.o): in function `gp_set_patterns': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_gap_patterns.c:419:(.text+0x1721): undefined reference to `tr_partition_leaves' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' collect2: error: ld returned 1 exit status make[3]: *** [Makefile:25: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../bin/dlessP] Error 1 make[3]: *** Waiting for unfinished jobs.... collect2: error: ld returned 1 exit status make[3]: *** [Makefile:25: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../bin/dless] Error 1 make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/dless' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/exoniphy' ../munge-help.sh exoniphy.help_src > exoniphy.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/exoniphy/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../..\" -fno-strict-aliasing -c exoniphy.c -o exoniphy.o : warning: 'PHAST_HOME' redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../bin/exoniphy exoniphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now /usr/bin/ld: exoniphy.o: in function `main': ./src/exoniphy/./src/exoniphy/exoniphy.c:225:(.text.startup+0x243): undefined reference to `tr_new_from_file' /usr/bin/ld: ./src/exoniphy/./src/exoniphy/exoniphy.c:367:(.text.startup+0x472): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/exoniphy/./src/exoniphy/exoniphy.c:374:(.text.startup+0x4be): undefined reference to `tm_extrapolate_and_prune' /usr/bin/ld: ./src/exoniphy/./src/exoniphy/exoniphy.c:381:(.text.startup+0x82f): undefined reference to `tm_prune' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_rates_cross': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:361:(.text+0xf6c): undefined reference to `DiscreteGamma' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:364:(.text+0xf8a): undefined reference to `tm_reinit' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:371:(.text+0xfc9): undefined reference to `tm_create_copy' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:376:(.text+0xfe0): undefined reference to `tm_scale_branchlens' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:453:(.text+0x13b2): undefined reference to `tm_free' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_free': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:469:(.text+0x154d): undefined reference to `tm_free' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_compute_emissions': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:597:(.text+0x18c6): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:597:(.text+0x1d80): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:597:(.text+0x1fbb): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_set_branch_len_factors': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:1182:(.text+0x3d1f): undefined reference to `tr_total_len' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_estim_mods_em': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:1099:(.text+0x3f94): undefined reference to `tm_params_new_init_from_model' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:1109:(.text+0x4049): undefined reference to `tm_fit' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:1087:(.text+0x40a0): undefined reference to `subst_mod_is_codon_model' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../lib/libphast.a(phast_gap_patterns.o): in function `gp_create_gapcats': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_gap_patterns.c:163:(.text+0x71c): undefined reference to `tr_inorder' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../lib/libphast.a(phast_gap_patterns.o): in function `gp_set_phylo_patterns': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_gap_patterns.c:244:(.text+0xf45): undefined reference to `tr_postorder' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../lib/libphast.a(phast_gap_patterns.o): in function `gp_set_patterns': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_gap_patterns.c:419:(.text+0x1721): undefined reference to `tr_partition_leaves' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' collect2: error: ld returned 1 exit status make[3]: *** [Makefile:22: /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../bin/exoniphy] Error 1 make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/exoniphy' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phastCons' ../munge-help.sh phastCons.help_src > phastCons.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/phastCons/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/phastCons/../..\" -fno-strict-aliasing -c phastCons.c -o phastCons.o : warning: 'PHAST_HOME' redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.7+dfsg/src/phastCons/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/phastCons/../../bin/phastCons phastCons.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now /usr/bin/ld: phastCons.o: in function `main': ./src/phastCons/./src/phastCons/phastCons.c:26:(.text.startup+0x47): undefined reference to `phastCons_struct_new' /usr/bin/ld: ./src/phastCons/./src/phastCons/phastCons.c:275:(.text.startup+0x14a): undefined reference to `tr_new_from_file' /usr/bin/ld: ./src/phastCons/./src/phastCons/phastCons.c:328:(.text.startup+0x25d): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/phastCons/./src/phastCons/phastCons.c:362:(.text.startup+0xa06): undefined reference to `phastCons' /usr/bin/ld: ./src/phastCons/./src/phastCons/phastCons.c:341:(.text.startup+0xa43): undefined reference to `tr_leaf_names' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastCons/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' collect2: error: ld returned 1 exit status make[3]: *** [Makefile:22: /build/reproducible-path/phast-1.7+dfsg/src/phastCons/../../bin/phastCons] Error 1 make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phastCons' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phastOdds' ../munge-help.sh phastOdds.help_src > phastOdds.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/phastOdds/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/phastOdds/../..\" -fno-strict-aliasing -c phastOdds.c -o phastOdds.o : warning: 'PHAST_HOME' redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.7+dfsg/src/phastOdds/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/phastOdds/../../bin/phastOdds phastOdds.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now /usr/bin/ld: phastOdds.o: in function `main': ./src/phastOdds/./src/phastOdds/phastOdds.c:85:(.text.startup+0x269): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/phastOdds/./src/phastOdds/phastOdds.c:74:(.text.startup+0x359): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/phastOdds/./src/phastOdds/phastOdds.c:180:(.text.startup+0x615): undefined reference to `tm_prune' /usr/bin/ld: ./src/phastOdds/./src/phastOdds/phastOdds.c:193:(.text.startup+0x6b5): undefined reference to `tm_prune' /usr/bin/ld: ./src/phastOdds/./src/phastOdds/phastOdds.c:330:(.text.startup+0xe9e): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: ./src/phastOdds/./src/phastOdds/phastOdds.c:336:(.text.startup+0xf0e): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: ./src/phastOdds/./src/phastOdds/phastOdds.c:330:(.text.startup+0x1699): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: ./src/phastOdds/./src/phastOdds/phastOdds.c:336:(.text.startup+0x1719): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastOdds/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' collect2: error: ld returned 1 exit status make[3]: *** [Makefile:22: /build/reproducible-path/phast-1.7+dfsg/src/phastOdds/../../bin/phastOdds] Error 1 make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phastOdds' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phastMotif' 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/phastMotif/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../..\" -fno-strict-aliasing -c phastMotif.c -o phastMotif.o : warning: 'PHAST_HOME' redefined : note: this is the location of the previous definition phastMotif.c: In function 'main': phastMotif.c:131:13: warning: variable 'separate_backgd' set but not used [-Wunused-but-set-variable] 131 | int i, j, separate_backgd = 0, | ^~~~~~~~~~~~~~~ gcc -L/build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../bin/phastMotif phastMotif.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now /usr/bin/ld: phastMotif.o: in function `main': ./src/phastMotif/./src/phastMotif/phastMotif.c:153:(.text.startup+0x14f): undefined reference to `tr_new_from_file' /usr/bin/ld: ./src/phastMotif/./src/phastMotif/phastMotif.c:161:(.text.startup+0x23c): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/phastMotif/./src/phastMotif/phastMotif.c:342:(.text.startup+0x1124): undefined reference to `tr_create_copy' /usr/bin/ld: ./src/phastMotif/./src/phastMotif/phastMotif.c:342:(.text.startup+0x1146): undefined reference to `tm_new' /usr/bin/ld: ./src/phastMotif/./src/phastMotif/phastMotif.c:344:(.text.startup+0x1165): undefined reference to `tm_params_init' /usr/bin/ld: ./src/phastMotif/./src/phastMotif/phastMotif.c:344:(.text.startup+0x1186): undefined reference to `tm_fit' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `mtf_new': ./src/lib/motif/./src/lib/motif/phast_motif.c:1218:(.text+0x1d3): undefined reference to `tm_create_copy' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:1220:(.text+0x1fc): undefined reference to `tm_create_copy' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:1221:(.text+0x20d): undefined reference to `tm_free_rmp' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:1225:(.text+0x250): undefined reference to `tm_init_rmp' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:1232:(.text+0x291): undefined reference to `tm_scale_branchlens' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `phy_compute_emissions': ./src/lib/motif/./src/lib/motif/phast_motif.c:316:(.text+0x39d): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `mtf_compute_conditional': ./src/lib/motif/./src/lib/motif/phast_motif.c:397:(.text+0x784): undefined reference to `tm_unpack_params' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:398:(.text+0x791): undefined reference to `tm_get_nparams' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `phy_compute_emissions': ./src/lib/motif/./src/lib/motif/phast_motif.c:316:(.text+0x103d): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `phy_estim_mods': ./src/lib/motif/./src/lib/motif/phast_motif.c:333:(.text+0x10f2): undefined reference to `tm_params_new_init_from_model' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:336:(.text+0x1189): undefined reference to `tm_fit' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `mtf_compute_inner_derivs_phy': ./src/lib/motif/./src/lib/motif/phast_motif.c:631:(.text+0x133f): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:632:(.text+0x1357): undefined reference to `tm_unpack_params' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:633:(.text+0x1375): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:639:(.text+0x13f7): undefined reference to `tm_unpack_params' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:640:(.text+0x141b): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `mtf_compute_conditional_grad': ./src/lib/motif/./src/lib/motif/phast_motif.c:506:(.text+0x22af): undefined reference to `tm_get_nparams' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `mtf_new': ./src/lib/motif/./src/lib/motif/phast_motif.c:1218:(.text+0x4a01): undefined reference to `tm_create_copy' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:1220:(.text+0x4a2c): undefined reference to `tm_create_copy' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:1221:(.text+0x4a3d): undefined reference to `tm_free_rmp' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:1225:(.text+0x4a80): undefined reference to `tm_init_rmp' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:1232:(.text+0x4ac1): undefined reference to `tm_scale_branchlens' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `mtf_free': ./src/lib/motif/./src/lib/motif/phast_motif.c:1262:(.text+0x4b19): undefined reference to `tm_free' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `phy_estim_mods': ./src/lib/motif/./src/lib/motif/phast_motif.c:333:(.text+0x70f3): undefined reference to `tm_params_new_init_from_model' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:336:(.text+0x7184): undefined reference to `tm_fit' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `mtf_find': ./src/lib/motif/./src/lib/motif/phast_motif.c:183:(.text+0x8836): undefined reference to `tm_params_new_init_from_model' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:160:(.text+0x8a86): undefined reference to `tm_get_nparams' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `mtf_print': ./src/lib/motif/./src/lib/motif/phast_motif.c:1355:(.text+0x9104): undefined reference to `tr_total_len' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:1356:(.text+0x9128): undefined reference to `tr_total_len' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `mtf_print_html': ./src/lib/motif/./src/lib/motif/phast_motif.c:1496:(.text+0x9cb8): undefined reference to `tr_total_len' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:1497:(.text+0x9cdd): undefined reference to `tr_total_len' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `phy_compute_emissions': ./src/lib/motif/./src/lib/motif/phast_motif.c:316:(.text.unlikely+0xe): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:316:(.text.unlikely+0x29): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' collect2: error: ld returned 1 exit status make[3]: *** [Makefile:16: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../bin/phastMotif] Error 1 make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phastMotif' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloFit' ../munge-help.sh phyloFit.help_src > phyloFit.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/phyloFit/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/phyloFit/../..\" -fno-strict-aliasing -c phyloFit.c -o phyloFit.o : warning: 'PHAST_HOME' redefined : note: this is the location of the previous definition phyloFit.c: In function 'main': phyloFit.c:100:8: error: too many arguments to function 'phyloFit_struct_new'; expected 0, have 1 100 | pf = phyloFit_struct_new(0); | ^~~~~~~~~~~~~~~~~~~ ~ In file included from phyloFit.c:29: /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/phylo_fit.h:69:25: note: declared here 69 | struct phyloFit_struct* phyloFit_struct_new(); | ^~~~~~~~~~~~~~~~~~~ make[3]: *** [Makefile:20: phyloFit.o] Error 1 make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloFit' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloBoot' ../munge-help.sh phyloBoot.help_src > phyloBoot.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/phyloBoot/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/phyloBoot/../..\" -fno-strict-aliasing -c phyloBoot.c -o phyloBoot.o : warning: 'PHAST_HOME' redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.7+dfsg/src/phyloBoot/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/phyloBoot/../../bin/phyloBoot phyloBoot.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now /usr/bin/ld: phyloBoot.o: in function `set_param_descriptions': ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:28:(.text+0x139): undefined reference to `tm_get_nratevarparams' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:29:(.text+0x144): undefined reference to `tm_get_nratematparams' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:48:(.text+0x1b2): undefined reference to `tr_preorder' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:56:(.text+0x2a4): undefined reference to `tm_is_reversible' /usr/bin/ld: phyloBoot.o: in function `main': ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:484:(.text.startup+0x206): undefined reference to `tm_params_new_init_from_model' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:484:(.text.startup+0x2c1): undefined reference to `tm_params_new_init_from_model' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:247:(.text.startup+0x387): undefined reference to `tr_new_from_file' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:250:(.text.startup+0x47e): undefined reference to `tm_get_subst_mod_type' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:209:(.text.startup+0x619): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:267:(.text.startup+0x691): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:392:(.text.startup+0x79c): undefined reference to `tm_generate_msa_scaleLst' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:447:(.text.startup+0x879): undefined reference to `tm_create_copy' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:448:(.text.startup+0x896): undefined reference to `tm_reinit' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:454:(.text.startup+0x8ac): undefined reference to `tm_params_new_init_from_model' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:467:(.text.startup+0x902): undefined reference to `tm_fit_em' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:475:(.text.startup+0x961): undefined reference to `tm_print' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:513:(.text.startup+0xb73): undefined reference to `tm_free' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:469:(.text.startup+0xbd1): undefined reference to `tm_fit' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:444:(.text.startup+0xdbe): undefined reference to `tr_create_copy' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:444:(.text.startup+0xde8): undefined reference to `tm_new' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:456:(.text.startup+0xe19): undefined reference to `tm_params_init' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:452:(.text.startup+0xe29): undefined reference to `tm_params_init_random' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:295:(.text.startup+0xe7f): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:300:(.text.startup+0xecf): undefined reference to `tm_create_copy' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:301:(.text.startup+0xeea): undefined reference to `tm_scale_branchlens' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:397:(.text.startup+0xfbb): undefined reference to `tm_generate_msa' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:452:(.text.startup+0x1040): undefined reference to `tm_params_init_random' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:546:(.text.startup+0x1528): undefined reference to `tm_unpack_params' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:548:(.text.startup+0x1554): undefined reference to `tm_print' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:395:(.text.startup+0x161b): undefined reference to `tm_generate_msa_random_subtree' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:245:(.text.startup+0x163a): undefined reference to `tr_new_from_string' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:298:(.text.startup+0x18d6): undefined reference to `tm_scale_branchlens' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:421:(.text.startup+0x192e): undefined reference to `subst_mod_is_codon_model' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:421:(.text.startup+0x1938): undefined reference to `tm_order' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:316:(.text.startup+0x19fa): undefined reference to `subst_mod_is_codon_model' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:316:(.text.startup+0x1a04): undefined reference to `tm_order' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:351:(.text.startup+0x1a5e): undefined reference to `subst_mod_is_codon_model' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:351:(.text.startup+0x1a68): undefined reference to `tm_order' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:333:(.text.startup+0x1add): undefined reference to `subst_mod_is_reversible' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:336:(.text.startup+0x1b24): undefined reference to `tr_new_from_string' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:331:(.text.startup+0x1b6f): undefined reference to `tr_new_from_string' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phyloBoot/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' collect2: error: ld returned 1 exit status make[3]: *** [Makefile:22: /build/reproducible-path/phast-1.7+dfsg/src/phyloBoot/../../bin/phyloBoot] Error 1 make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloBoot' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloP' ../munge-help.sh phyloP.help_src > phyloP.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/phyloP/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/phyloP/../..\" -fno-strict-aliasing -c phyloP.c -o phyloP.o : warning: 'PHAST_HOME' redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.7+dfsg/src/phyloP/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/phyloP/../../bin/phyloP phyloP.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now /usr/bin/ld: phyloP.o: in function `main': ./src/phyloP/./src/phyloP/phyloP.c:16:(.text.startup+0x40): undefined reference to `phyloP_struct_new' /usr/bin/ld: ./src/phyloP/./src/phyloP/phyloP.c:166:(.text.startup+0x421): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/phyloP/./src/phyloP/phyloP.c:199:(.text.startup+0x467): undefined reference to `phyloP' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phyloP/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' collect2: error: ld returned 1 exit status make[3]: *** [Makefile:23: /build/reproducible-path/phast-1.7+dfsg/src/phyloP/../../bin/phyloP] Error 1 make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloP' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/prequel' ../munge-help.sh pbsDecode.help_src > pbsDecode.help ../munge-help.sh pbsEncode.help_src > pbsEncode.help ../munge-help.sh pbsScoreMatrix.help_src > pbsScoreMatrix.help ../munge-help.sh pbsTrain.help_src > pbsTrain.help ../munge-help.sh prequel.help_src > prequel.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/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsDecode.c -o pbsDecode.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 phast_simplex_grid.c -o phast_simplex_grid.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 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 : 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 pbsTrain.c -o pbsTrain.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/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 : 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 phast_pbs_code.c: In function 'pbs_new_from_file': phast_pbs_code.c:88:48: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 88 | pcre2_compile_context *nrows_re = str_re_new("##NROWS[[:space:]]*=[[:space:]]*([0-9]+)"), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/pbs_code.h:8, from phast_pbs_code.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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_pbs_code.c:89:32: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 89 | *dimension_re = str_re_new("##DIMENSION[[:space:]]*=[[:space:]]*([0-9]+)"), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_pbs_code.c:90:29: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 90 | *nbytes_re = str_re_new("##NBYTES[[:space:]]*=[[:space:]]*([0-9]+)"), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_pbs_code.c:91:31: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 91 | *codesize_re = str_re_new("##CODESIZE[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ prequel.c: In function 'main': prequel.c:285:32: warning: '.bin' directive writing 4 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 285 | sprintf(out_fname, "%s.%s.bin", out_root, n->name); | ^~~~ In file included from /usr/include/stdio.h:970, from prequel.c:11: In function 'sprintf', inlined from 'main' at prequel.c:285:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 6 or more bytes (assuming 261) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ prequel.c: In function 'main': prequel.c:253:32: warning: '.fa' directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 253 | sprintf(out_fname, "%s.%s.fa", out_root, n->name); | ^~~ In function 'sprintf', inlined from 'main' at prequel.c:253:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 5 or more bytes (assuming 260) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ prequel.c: In function 'main': prequel.c:203:32: warning: '.probs' directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 203 | sprintf(out_fname, "%s.%s.probs", out_root, n->name); | ^~~~~~ In function 'sprintf', inlined from 'main' at prequel.c:203:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 8 or more bytes (assuming 263) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -L/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsDecode pbsDecode.o phast_simplex_grid.o phast_pbs_code.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/prequel/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsEncode pbsEncode.o phast_simplex_grid.o phast_pbs_code.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/prequel/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsScoreMatrix pbsScoreMatrix.o phast_simplex_grid.o phast_pbs_code.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/prequel/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsTrain pbsTrain.o phast_simplex_grid.o phast_pbs_code.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/prequel/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/prequel prequel.o phast_simplex_grid.o phast_pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now /usr/bin/ld: prequel.o: in function `do_indels': ./src/prequel/./src/prequel/prequel.c:320:(.text+0xb0): undefined reference to `tr_get_node' /usr/bin/ld: ./src/prequel/./src/prequel/prequel.c:329:(.text+0xe8): undefined reference to `tr_postorder' /usr/bin/ld: ./src/prequel/./src/prequel/prequel.c:388:(.text+0x296): undefined reference to `tr_partition_nodes' /usr/bin/ld: ./src/prequel/./src/prequel/prequel.c:327:(.text+0xc7e): undefined reference to `tm_build_seq_idx' /usr/bin/ld: prequel.o: in function `main': ./src/prequel/./src/prequel/prequel.c:122:(.text.startup+0x2b5): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/prequel/./src/prequel/prequel.c:127:(.text.startup+0x2db): undefined reference to `tm_prune' /usr/bin/ld: ./src/prequel/./src/prequel/prequel.c:139:(.text.startup+0x312): undefined reference to `tr_name_ancestors' /usr/bin/ld: ./src/prequel/./src/prequel/prequel.c:148:(.text.startup+0x34f): undefined reference to `tl_new_tree_posteriors' /usr/bin/ld: ./src/prequel/./src/prequel/prequel.c:158:(.text.startup+0xbea): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' /usr/bin/ld: pbsScoreMatrix.o: in function `main': ./src/prequel/./src/prequel/pbsScoreMatrix.c:64:(.text.startup+0x226): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/prequel/./src/prequel/pbsScoreMatrix.c:106:(.text.startup+0x382): undefined reference to `tm_set_subst_matrix' /usr/bin/ld: ./src/prequel/./src/prequel/pbsScoreMatrix.c:64:(.text.startup+0x884): undefined reference to `tm_new_from_file' collect2: error: ld returned 1 exit status /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' make[3]: *** [Makefile:25: /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsEncode] Error 1 make[3]: *** Waiting for unfinished jobs.... collect2: error: ld returned 1 exit status collect2: error: ld returned 1 exit status make[3]: *** [Makefile:25: /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsScoreMatrix] Error 1 /usr/bin/ld: make[3]: *** [Makefile:25: /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/prequel] Error 1 /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' collect2: error: ld returned 1 exit status make[3]: *** [Makefile:25: /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsDecode] Error 1 collect2: error: ld returned 1 exit status make[3]: *** [Makefile:25: /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsTrain] Error 1 make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/prequel' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/util' ../munge-help.sh base_evolve.help_src > base_evolve.help ../munge-help.sh clean_genes.help_src > clean_genes.help ../munge-help.sh consEntropy.help_src > consEntropy.help ../munge-help.sh indelFit.help_src > indelFit.help ../munge-help.sh indelHistory.help_src > indelHistory.help ../munge-help.sh makeHKY.help_src > makeHKY.help ../munge-help.sh modFreqs.help_src > modFreqs.help ../munge-help.sh msa_diff.help_src > msa_diff.help ../munge-help.sh phast.help_src > phast.help ../munge-help.sh phastBias.help_src > phastBias.help ../munge-help.sh treeGen.help_src > treeGen.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/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 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 convert_coords.c -o convert_coords.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 : 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 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 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 : 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 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 : 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 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 : 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 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 : 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 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 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 : 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 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 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 : 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 : warning: 'PHAST_HOME' redefined : note: this is the location of the previous definition : 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/convert_coords convert_coords.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 : 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/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/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 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 -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 /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/util/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' 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' && | ^~ In file included from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/tree_model.h:26, from tree_doctor.c:14: /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 */ | ^~~~ collect2: error: ld returned 1 exit status make[3]: *** [Makefile:20: /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/chooseLines] Error 1 make[3]: *** Waiting for unfinished jobs.... /usr/bin/ld: draw_tree.o: in function `main': ./src/util/./src/util/draw_tree.c:84:(.text.startup+0x104): undefined reference to `tr_new_from_file' /usr/bin/ld: ./src/util/./src/util/draw_tree.c:86:(.text.startup+0x120): undefined reference to `tr_print_ps' /usr/bin/ld: ./src/util/./src/util/draw_tree.c:80:(.text.startup+0x143): undefined reference to `tm_new_from_file' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/util/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' collect2: error: ld returned 1 exit status make[3]: *** [Makefile:20: /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/draw_tree] Error 1 /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/util/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' collect2: error: ld returned 1 exit status make[3]: *** [Makefile:20: /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/convert_coords] Error 1 /usr/bin/ld: makeHKY.o: in function `main': ./src/util/./src/util/makeHKY.c:60:(.text.startup+0x307): undefined reference to `tr_new_from_file' /usr/bin/ld: ./src/util/./src/util/makeHKY.c:90:(.text.startup+0x3c9): undefined reference to `tm_new' /usr/bin/ld: ./src/util/./src/util/makeHKY.c:91:(.text.startup+0x3de): undefined reference to `tm_set_HKY_matrix' /usr/bin/ld: ./src/util/./src/util/makeHKY.c:92:(.text.startup+0x3e6): undefined reference to `tm_scale_rate_matrix' /usr/bin/ld: ./src/util/./src/util/makeHKY.c:94:(.text.startup+0x3f5): undefined reference to `tm_print' /usr/bin/ld: ./src/util/./src/util/makeHKY.c:87:(.text.startup+0x4b7): undefined reference to `tr_new_from_string' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/util/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' collect2: error: ld returned 1 exit status make[3]: *** [Makefile:20: /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/makeHKY] Error 1 make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/util' make[2]: *** [Makefile:9: all] Error 2 make[2]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src' make[1]: *** [Makefile:6: all] Error 2 make[1]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg' dh_auto_build: error: make -j42 "INSTALL=install --strip-program=true" returned exit code 2 make: *** [debian/rules:6: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/1882834 and its subdirectories Starting cleanup. All cleanup done. Wed Oct 21 14:11:07 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-8p9OSb5f, removing. /srv/reproducible-results/rbuild-debian/r-b-build.4IydX6S2: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 07:48 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 07:45 b2 -rw-rw-r-- 1 jenkins jenkins 2218 Jan 5 2025 phast_1.7+dfsg-2.dsc -rw------- 1 jenkins jenkins 3321 Sep 18 07:45 rbuildlog.Lql7EiD /srv/reproducible-results/rbuild-debian/r-b-build.4IydX6S2/b1: total 208 -rw-r--r-- 1 jenkins jenkins 211450 Sep 18 07:48 build.log /srv/reproducible-results/rbuild-debian/r-b-build.4IydX6S2/b2: total 0 Thu Sep 18 07:48:08 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Oct 21 02:08:26 -12 2026 I: pbuilder-time-stamp: 1792591706 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 [phast_1.7+dfsg-2.dsc] I: copying [./phast_1.7+dfsg.orig.tar.xz] I: copying [./phast_1.7+dfsg-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./phast_1.7+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting phast in phast-1.7+dfsg dpkg-source: info: unpacking phast_1.7+dfsg.orig.tar.xz dpkg-source: info: unpacking phast_1.7+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying clapack.patch dpkg-source: info: applying do_not_install_to_opt.patch dpkg-source: info: applying use_debian_packaged_libpcre.patch dpkg-source: info: applying use_debian_packaged_help2man.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying pcre2.patch dpkg-source: info: applying gcc-14.patch dpkg-source: info: applying make.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1882834/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='16350d8d50794435bab6edfa7630b1b6' 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='1882834' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.4IydX6S2/pbuilderrc_GqBW --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.4IydX6S2/b1 --logfile b1/build.log phast_1.7+dfsg-2.dsc' SUDO_GID='110' SUDO_HOME='/var/lib/jenkins' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1882834/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team 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), liblapack-dev | liblapack.so, libblas-dev | libblas.so, liblapacke-dev, libtmglib-dev, libpcre2-dev, help2man dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 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. pbuilder-satisfydepends-dummy depends on liblapack-dev | liblapack.so; however: Package liblapack-dev is not installed. Package liblapack.so is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev | libblas.so; however: Package libblas-dev is not installed. Package libblas.so is not installed. pbuilder-satisfydepends-dummy depends on liblapacke-dev; however: Package liblapacke-dev is not installed. pbuilder-satisfydepends-dummy depends on libtmglib-dev; however: Package libtmglib-dev is not installed. pbuilder-satisfydepends-dummy depends on libpcre2-dev; however: Package libpcre2-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man 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} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} liblapack-dev{a} liblapack3{a} liblapacke{a} liblapacke-dev{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpipeline1{a} libtmglib-dev{a} libtmglib3{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{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, 44 newly installed, 0 to remove and 0 not upgraded. Need to get 24.1 MB of archives. After unpacking 107 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 23 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.1-7 [229 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.1-7 [5894 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libtmglib3 amd64 3.12.1-7 [143 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 liblapacke amd64 3.12.1-7 [441 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libtmglib-dev amd64 3.12.1-7 [148 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 liblapacke-dev amd64 3.12.1-7 [440 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libpcre2-16-0 amd64 10.46-1 [281 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libpcre2-32-0 amd64 10.46-1 [268 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libpcre2-posix3 amd64 10.46-1 [63.9 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libpcre2-dev amd64 10.46-1 [853 kB] Fetched 24.1 MB in 1s (31.8 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 ... 19917 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../09-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-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 .../20-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... 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Preparing to unpack .../33-libgfortran5_15.2.0-4_amd64.deb ... Unpacking libgfortran5:amd64 (15.2.0-4) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../34-liblapack3_3.12.1-7_amd64.deb ... Unpacking liblapack3:amd64 (3.12.1-7) ... Selecting previously unselected package liblapack-dev:amd64. Preparing to unpack .../35-liblapack-dev_3.12.1-7_amd64.deb ... Unpacking liblapack-dev:amd64 (3.12.1-7) ... Selecting previously unselected package libtmglib3:amd64. Preparing to unpack .../36-libtmglib3_3.12.1-7_amd64.deb ... Unpacking libtmglib3:amd64 (3.12.1-7) ... Selecting previously unselected package liblapacke:amd64. Preparing to unpack .../37-liblapacke_3.12.1-7_amd64.deb ... Unpacking liblapacke:amd64 (3.12.1-7) ... Selecting previously unselected package libtmglib-dev:amd64. Preparing to unpack .../38-libtmglib-dev_3.12.1-7_amd64.deb ... Unpacking libtmglib-dev:amd64 (3.12.1-7) ... Selecting previously unselected package liblapacke-dev:amd64. Preparing to unpack .../39-liblapacke-dev_3.12.1-7_amd64.deb ... Unpacking liblapacke-dev:amd64 (3.12.1-7) ... Selecting previously unselected package libpcre2-16-0:amd64. Preparing to unpack .../40-libpcre2-16-0_10.46-1_amd64.deb ... Unpacking libpcre2-16-0:amd64 (10.46-1) ... Selecting previously unselected package libpcre2-32-0:amd64. Preparing to unpack .../41-libpcre2-32-0_10.46-1_amd64.deb ... Unpacking libpcre2-32-0:amd64 (10.46-1) ... Selecting previously unselected package libpcre2-posix3:amd64. Preparing to unpack .../42-libpcre2-posix3_10.46-1_amd64.deb ... Unpacking libpcre2-posix3:amd64 (10.46-1) ... Selecting previously unselected package libpcre2-dev:amd64. Preparing to unpack .../43-libpcre2-dev_10.46-1_amd64.deb ... Unpacking libpcre2-dev:amd64 (10.46-1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up bsdextrautils (2.41.1-3) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up file (1:5.46-5) ... Setting up libpcre2-16-0:amd64 (10.46-1) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up autotools-dev (20240727.1) ... Setting up libpcre2-32-0:amd64 (10.46-1) ... Setting up libblas3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up libgfortran5:amd64 (15.2.0-4) ... Setting up autoconf (2.72-3.1) ... Setting up libpcre2-posix3:amd64 (10.46-1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up libblas-dev:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up liblapack3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-2+b1) ... Setting up libpcre2-dev:amd64 (10.46-1) ... Setting up libtool (2.5.4-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (21) ... Setting up libtmglib3:amd64 (3.12.1-7) ... Setting up liblapack-dev:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up liblapacke:amd64 (3.12.1-7) ... Setting up libtmglib-dev:amd64 (3.12.1-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up liblapacke-dev:amd64 (3.12.1-7) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.26) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/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 dpkg-buildpackage: info: source package phast dpkg-buildpackage: info: source version 1.7+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/phast-1.7+dfsg' dh_auto_clean cd src && /usr/bin/make clean make[2]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib' cat: /build/reproducible-path/phast-1.7+dfsg/src/lib/../version: No such file or directory for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/reproducible-path/phast-1.7+dfsg/src/lib/$dir && /usr/bin/make clean ; done make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/base' cat: /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/base' make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/msa' cat: /build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/msa' make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/feature' cat: /build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/feature' make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/hmm' cat: /build/reproducible-path/phast-1.7+dfsg/src/lib/hmm/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/hmm' make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo' cat: /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo' make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm' cat: /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/motif' cat: /build/reproducible-path/phast-1.7+dfsg/src/lib/motif/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/motif' rm -f /build/reproducible-path/phast-1.7+dfsg/src/lib/../../lib/* make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/dless' cat: /build/reproducible-path/phast-1.7+dfsg/src/dless/../version: No such file or directory rm -f *.o dless.help dlessP.help /build/reproducible-path/phast-1.7+dfsg/src/dless/../../bin/dless /build/reproducible-path/phast-1.7+dfsg/src/dless/../../bin/dlessP make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/dless' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/exoniphy' cat: /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../version: No such file or directory rm -f *.o *.help /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../bin/exoniphy make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/exoniphy' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phastCons' cat: /build/reproducible-path/phast-1.7+dfsg/src/phastCons/../version: No such file or directory rm -f *.o /build/reproducible-path/phast-1.7+dfsg/src/phastCons/../../bin/phastCons phastCons.help make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phastCons' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phastOdds' cat: /build/reproducible-path/phast-1.7+dfsg/src/phastOdds/../version: No such file or directory rm -f *.o *.help /build/reproducible-path/phast-1.7+dfsg/src/phastOdds/../../bin/phastOdds make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phastOdds' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phastMotif' cat: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../version: No such file or directory rm -f *.o /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../bin/phastMotif make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phastMotif' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloFit' cat: /build/reproducible-path/phast-1.7+dfsg/src/phyloFit/../version: No such file or directory rm -f *.o /build/reproducible-path/phast-1.7+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.help make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloFit' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloBoot' cat: /build/reproducible-path/phast-1.7+dfsg/src/phyloBoot/../version: No such file or directory rm -f *.o *.help /build/reproducible-path/phast-1.7+dfsg/src/phyloBoot/../../bin/phyloBoot make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloBoot' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloP' cat: /build/reproducible-path/phast-1.7+dfsg/src/phyloP/../version: No such file or directory rm -f *.o /build/reproducible-path/phast-1.7+dfsg/src/phyloP/../../bin/phyloP phyloP.help make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloP' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/prequel' cat: /build/reproducible-path/phast-1.7+dfsg/src/prequel/../version: No such file or directory rm -f *.o /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsDecode /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsEncode /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsScoreMatrix /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsTrain /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/prequel pbsDecode.help pbsEncode.help pbsScoreMatrix.help pbsTrain.help prequel.help make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/prequel' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/util' cat: /build/reproducible-path/phast-1.7+dfsg/src/util/../version: No such file or directory rm -f *.o *.help /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/all_dists /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/base_evolve /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/chooseLines /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/clean_genes /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/consEntropy /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/convert_coords /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/display_rate_matrix /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/draw_tree /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/eval_predictions /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/hmm_train /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/hmm_tweak /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/hmm_view /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/indelFit /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/indelHistory /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/maf_parse /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/makeHKY /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/modFreqs /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/msa_diff /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/msa_split /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/msa_view /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/phast /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/phastBias /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/refeature /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/stringiphy /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/treeGen /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/tree_doctor make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/util' rm -rf ../bin ../lib ../doc make[2]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build 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 ) make[2]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src' mkdir -p ../bin ../lib for dir in lib dless exoniphy phastCons phastOdds phastMotif phyloFit phyloBoot phyloP prequel util ; do cd /build/reproducible-path/phast-1.7+dfsg/src/$dir && make ; done make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/reproducible-path/phast-1.7+dfsg/src/lib/$dir && make ; done make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/base' 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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_complex_matrix.c -o phast_complex_matrix.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_complex_vector.c -o phast_complex_vector.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_eigen.c -o phast_eigen.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_hashtable.c -o phast_hashtable.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_list_of_lists.c -o phast_list_of_lists.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_lists.c -o phast_lists.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_markov_matrix.c -o phast_markov_matrix.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_matrix.c -o phast_matrix.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_memory_handler.c -o phast_memory_handler.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_misc.c -o phast_misc.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 phast_misc.c: In function 'make_name_hash': phast_misc.c:673:46: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 673 | pcre2_compile_context *map_re = str_re_new("^[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*(->|=)[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from phast_misc.c:16: /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_misc.c: In function 'phast_fclose': phast_misc.c:301:5: warning: pointer 'f' used after 'fclose' [-Wuse-after-free] 301 | unregister_open_file(f); | ^~~~~~~~~~~~~~~~~~~~~~~ phast_misc.c:300:5: note: call to 'fclose' here 300 | fclose(f); | ^~~~~~~~~ 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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_numerical_opt.c -o phast_numerical_opt.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_prob_matrix.c -o phast_prob_matrix.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_prob_vector.c -o phast_prob_vector.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_stringsplus.c -o phast_stringsplus.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 phast_stringsplus.c: In function 'str_re_match_sub': phast_stringsplus.c:501:25: warning: pointer targets in passing argument 2 of 'pcre2_match_8' differ in signedness [-Wpointer-sign] 501 | rc = pcre2_match(re, s->chars, s->length, offset, 0, match_data, NULL); | ~^~~~~~~ | | | char * In file included from phast_stringsplus.c:16: /usr/include/pcre2.h:1011:1: note: expected 'PCRE2_SPTR8' {aka 'const unsigned char *'} but argument is of type 'char *' 1011 | PCRE2_TYPES_STRUCTURES_AND_FUNCTIONS | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ phast_stringsplus.c:504:52: warning: 'ovector' may be used uninitialized [-Wmaybe-uninitialized] 504 | if (first_match != NULL) (*first_match) = ovector[0]; | ~~~~~~~^~~ phast_stringsplus.c:491:15: note: 'ovector' was declared here 491 | PCRE2_SIZE *ovector; | ^~~~~~~ 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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_vector.c -o phast_vector.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 ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar: creating /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/base' make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/msa' 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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_local_alignment.c -o phast_local_alignment.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 phast_local_alignment.c: In function 'la_read_lav': phast_local_alignment.c:50:55: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 50 | pcre2_compile_context *stanza_start_re = str_re_new("^([dshaxm])[[:space:]]*{"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/local_alignment.h:36, from phast_local_alignment.c:32: /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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_maf.c -o phast_maf.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 phast_maf.c: In function 'maf_read_cats_subset': phast_maf.c:29:41: warning: variable 'block_no' set but not used [-Wunused-but-set-variable] 29 | int i, start_idx, length, max_tuples, block_no, | ^~~~~~~~ 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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_maf_block.c -o phast_maf_block.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_msa.c -o phast_msa.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 phast_msa.c: In function 'msa_read_fasta': phast_msa.c:264:29: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 264 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*([^[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | 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 phast_msa.c:39: /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:257:40: warning: variable 'line_no' set but not used [-Wunused-but-set-variable] 257 | int maxlen, i, nseqs, j, do_toupper, line_no; | ^~~~~~~ phast_msa.c: In function 'msa_read_seq_fasta': phast_msa.c:1929:29: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 1929 | descrip_re = str_re_new("^[[:space:]]*>"); | ^~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c: In function 'msa_format_for_content': phast_msa.c:2590:22: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 2590 | ss_re = str_re_new("^NSEQS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2591:26: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 2591 | phylip_re = str_re_new("^([[:space:]]*([0-9]+))[[:space:]]*[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2592:25: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 2592 | fasta_re = str_re_new("^>.*"); | ^~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2593:23: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 2593 | lav_re = str_re_new("^#:lav.*"); | ^~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2594:23: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 2594 | maf_re = str_re_new("^##maf"); | ^~~~~~~~ | | | char * /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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_multi_msa.c -o phast_multi_msa.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 phast_multi_msa.c: In function 'multimsa_new_from_files': phast_multi_msa.c:54:49: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 54 | pcre2_compile_context *blocks_re = str_re_new("#[[:space:]]*BLOCKS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | 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 phast_multi_msa.c:37: /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_multi_msa.c:55:47: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 55 | pcre2_compile_context *alph_re = str_re_new("#[[:space:]]*ALPHABET[[:space:]]*=[[:space:]]*([A-Z]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_multi_msa.c:56:49: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 56 | pcre2_compile_context *format_re = str_re_new("#[[:space:]]*FORMAT[[:space:]]*=[[:space:]]*([A-Z]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_sufficient_stats.c -o phast_sufficient_stats.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 phast_sufficient_stats.c: In function 'ss_from_msas': phast_sufficient_stats.c:140:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] 140 | else | ^~~~ phast_sufficient_stats.c:142:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' 142 | max_tuples = pow_bounded(strlen(msa->alphabet) + (int)strlen(msa->missing) + 1, | ^~~~~~~~~~ phast_sufficient_stats.c: In function 'ss_read': phast_sufficient_stats.c:661:25: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 661 | nseqs_re = str_re_new("NSEQS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | 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 /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/sufficient_stats.h:20, from phast_sufficient_stats.c:11: /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:662:26: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 662 | length_re = str_re_new("LENGTH[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:663:30: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 663 | tuple_size_re = str_re_new("TUPLE_SIZE[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:664:27: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 664 | ntuples_re = str_re_new("NTUPLES[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:665:25: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 665 | names_re = str_re_new("NAMES[[:space:]]*=[[:space:]]*(.*)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:666:24: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 666 | alph_re = str_re_new("ALPHABET[[:space:]]*=[[:space:]]*([-.^A-Za-z ]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:667:25: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 667 | ncats_re = str_re_new("NCATS[[:space:]]*=[[:space:]]*([-0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:668:26: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 668 | offset_re = str_re_new("IDX_OFFSET[[:space:]]*=[[:space:]]*([-0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:669:25: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 669 | tuple_re = str_re_new("^([0-9]+)[[:space:]]+([-.^A-Za-z ]+)[[:space:]]+([0-9.[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:670:25: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 670 | order_re = str_re_new("TUPLE_IDX_ORDER:"); | ^~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/msa' make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/feature' 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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_bed.c -o phast_bed.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 phast_bed.c: In function 'gff_print_bed': phast_bed.c:143:52: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 143 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/gff.h:21, from phast_bed.c:15: /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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_category_map.c -o phast_category_map.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 phast_category_map.c: In function 'cm_read': phast_category_map.c:39:31: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 39 | cat_range_re = str_re_new("^[[:space:]]*([^[:space:]]+)[[:space:]]+([[:digit:]]+)(-([[:digit:]]+))?([[:space:]]+([[: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/category_map.h:92, from phast_category_map.c:10: /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:40:27: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 40 | ncats_re = str_re_new("^[[:space:]]*NCATS[[:space:]]*=[[:space:]]*([[:digit:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:41:26: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 41 | fill_re = str_re_new("^[[:space:]]*FILL_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:42:27: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 42 | label_re = str_re_new("^[[:space:]]*LABELLING_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:43:28: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 43 | extend_re = str_re_new("^[[:space:]]*FEATURE_EXTEND[[:space:]]*:[[:space:]]*(.+)[[:space:]]*\\((.+)\\)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_genepred.c -o phast_genepred.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_gff.c -o phast_gff.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 phast_gff.c: In function 'gff_read_set': phast_gff.c:56:38: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 56 | spec_comment_re = str_re_new("^[[:space:]]*##[[:space:]]*([^[:space:]]+)[[:space:]]+([^[:space:]]+)([[:space:]]+([^[:space:]]+))?"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/gff.h:21, from phast_gff.c:13: /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_gff.c: In function 'gff_new_feature_genomic_pos': phast_gff.c:272:24: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 272 | posre = str_re_new("(chr[_a-zA-Z0-9]+):([0-9]+)-([0-9]+)([-+])?"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_gff.c: In function 'gff_group': phast_gff.c:688:23: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 688 | tag_re = str_re_new(tmpstr); | ^~~~~~ | | | char * /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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_wig.c -o phast_wig.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 ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/feature' make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/hmm' 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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/hmm/../../..\" -fno-strict-aliasing -c phast_em.c -o phast_em.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/hmm/../../..\" -fno-strict-aliasing -c phast_hmm.c -o phast_hmm.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 ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/hmm' make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo' 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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_bgc_hmm.c -o phast_bgc_hmm.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_cons.c -o phast_cons.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_dgamma.c -o phast_dgamma.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_column.c -o phast_fit_column.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_em.c -o phast_fit_em.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_feature.c -o phast_fit_feature.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_indel_history.c -o phast_indel_history.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_indel_mod.c -o phast_indel_mod.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_fit.c -o phast_phylo_fit.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 phast_phylo_fit.c:41:25: error: conflicting types for 'phyloFit_struct_new'; have 'struct phyloFit_struct *(int)' 41 | struct phyloFit_struct* phyloFit_struct_new(int rphast) { | ^~~~~~~~~~~~~~~~~~~ In file included from phast_phylo_fit.c:33: /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/phylo_fit.h:69:25: note: previous declaration of 'phyloFit_struct_new' with type 'struct phyloFit_struct *(void)' 69 | struct phyloFit_struct* phyloFit_struct_new(); | ^~~~~~~~~~~~~~~~~~~ make[4]: *** [Makefile:13: phast_phylo_fit.o] Error 1 make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo' make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm' 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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c phast_gap_patterns.c -o phast_gap_patterns.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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c phast_phylo_hmm.c -o phast_phylo_hmm.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 ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/motif' 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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/motif/../../..\" -fno-strict-aliasing -c phast_motif.c -o phast_motif.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 phast_motif.c: In function 'mtf_print': phast_motif.c:1411:21: warning: '%s' directive argument is null [-Wformat-overflow=] 1411 | fprintf(F, "\t%s\n", (char*)lst_get_ptr(notfound, i)); | ^~ phast_motif.c: In function 'mtf_print_html': phast_motif.c:1604:23: warning: '%s' directive argument is null [-Wformat-overflow=] 1604 | fprintf(F, "
  • %s\n", (char*)lst_get_ptr(notfound, i)); | ^~ 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/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/motif/../../..\" -fno-strict-aliasing -c phast_tfbs.c -o phast_tfbs.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 phast_tfbs.c: In function 'pwm_read': phast_tfbs.c:147:24: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 147 | pssm_re = str_re_new("^letter-probability matrix: alength= ([0-9]+) w= ([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | 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 phast_tfbs.c:16: /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_tfbs.c:148:30: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 148 | motif_name_re = str_re_new("^MOTIF[[:space:]]+(.+?)[[:space:]].*"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_tfbs.c: In function 'ms_read': phast_tfbs.c:229:29: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 229 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*(.+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_tfbs.c:219:32: warning: variable 'line_no' set but not used [-Wunused-but-set-variable] 219 | int i, nseqs, j, do_toupper, line_no; | ^~~~~~~ ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/motif' make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/dless' ../munge-help.sh dless.help_src > dless.help ../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 : warning: 'PHAST_HOME' redefined : note: this is the location of the previous definition : note: this is the location of the previous definition : warning: 'PHAST_HOME' redefined : note: this is the location of the previous definition dlessP.c: In function 'do_p_values': dlessP.c:199:45: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 199 | pcre2_compile_context *id_re = str_re_new(".*id \"([^\"]*)\""); | ^~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/trees.h:25, from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/tree_model.h:26, from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/bd_phylo_hmm.h:22, from dlessP.c:17: /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 -L/build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/dless/../../bin/dless dless.o phast_bd_phylo_hmm.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/dless/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/dless/../../bin/dlessP dlessP.o phast_bd_phylo_hmm.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now /usr/bin/ld: dlessP.o: in function `do_p_values': ./src/dless/./src/dless/dlessP.c:232:(.text+0x43b): undefined reference to `tr_create_copy' /usr/bin/ld: ./src/dless/./src/dless/dlessP.c:252:(.text+0x4c4): undefined reference to `tr_reroot' /usr/bin/ld: ./src/dless/./src/dless/dlessP.c:264:(.text+0x4ee): undefined reference to `tr_total_len' /usr/bin/ld: ./src/dless/./src/dless/dlessP.c:264:(.text+0x507): undefined reference to `sub_define_jump_process' /usr/bin/ld: ./src/dless/./src/dless/dlessP.c:265:(.text+0x52f): undefined reference to `sub_p_value_joint_many' /usr/bin/ld: ./src/dless/./src/dless/dlessP.c:268:(.text+0x541): undefined reference to `tr_free' /usr/bin/ld: ./src/dless/./src/dless/dlessP.c:269:(.text+0x549): undefined reference to `sub_free_jump_process' /usr/bin/ld: ./src/dless/./src/dless/dlessP.c:222:(.text+0xcfc): undefined reference to `tr_total_len' /usr/bin/ld: ./src/dless/./src/dless/dlessP.c:222:(.text+0xd12): undefined reference to `sub_define_jump_process' /usr/bin/ld: ./src/dless/./src/dless/dlessP.c:223:(.text+0xd2d): undefined reference to `sub_p_value_many' /usr/bin/ld: ./src/dless/./src/dless/dlessP.c:225:(.text+0xd3a): undefined reference to `sub_free_jump_process' /usr/bin/ld: dlessP.o: in function `main': ./src/dless/./src/dless/dlessP.c:103:(.text.startup+0x31d): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/dless/./src/dless/dlessP.c:132:(.text.startup+0x3f4): undefined reference to `tm_prune' /usr/bin/ld: ./src/dless/./src/dless/dlessP.c:144:(.text.startup+0x424): undefined reference to `tr_name_ancestors' /usr/bin/ld: phast_bd_phylo_hmm.o: in function `bd_new': ./src/dless/./src/dless/phast_bd_phylo_hmm.c:92:(.text+0x634): undefined reference to `tm_create_copy' /usr/bin/ld: ./src/dless/./src/dless/phast_bd_phylo_hmm.c:94:(.text+0x67f): undefined reference to `tr_partition_nodes' /usr/bin/ld: ./src/dless/./src/dless/phast_bd_phylo_hmm.c:103:(.text+0x715): undefined reference to `tm_reinit' /usr/bin/ld: ./src/dless/./src/dless/phast_bd_phylo_hmm.c:144:(.text+0xb77): undefined reference to `tr_partition_nodes' /usr/bin/ld: ./src/dless/./src/dless/phast_bd_phylo_hmm.c:164:(.text+0xca7): undefined reference to `im_new' /usr/bin/ld: phast_bd_phylo_hmm.o: in function `bd_handle_missing_data': ./src/dless/./src/dless/phast_bd_phylo_hmm.c:234:(.text+0x10e4): undefined reference to `tr_postorder' /usr/bin/ld: ./src/dless/./src/dless/phast_bd_phylo_hmm.c:260:(.text+0x1236): undefined reference to `tr_preorder' /usr/bin/ld: phast_bd_phylo_hmm.o: in function `bd_add_indel_emissions': ./src/dless/./src/dless/phast_bd_phylo_hmm.c:316:(.text+0x1767): undefined reference to `im_column_logl' /usr/bin/ld: dless.o: in function `main': ./src/dless/./src/dless/dless.c:146:(.text.startup+0x4da): undefined reference to `ih_new_from_file' /usr/bin/ld: ./src/dless/./src/dless/dless.c:171:(.text.startup+0x68e): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/dless/./src/dless/dless.c:179:(.text.startup+0x6c1): undefined reference to `tm_is_reversible' /usr/bin/ld: ./src/dless/./src/dless/dless.c:209:(.text.startup+0x784): undefined reference to `tm_prune' /usr/bin/ld: ./src/dless/./src/dless/dless.c:221:(.text.startup+0x7b5): undefined reference to `tr_name_ancestors' /usr/bin/ld: ./src/dless/./src/dless/dless.c:237:(.text.startup+0x11d9): undefined reference to `ih_reconstruct' /usr/bin/ld: phast_bd_phylo_hmm.o: in function `bd_new': ./src/dless/./src/dless/phast_bd_phylo_hmm.c:92:(.text+0x634): undefined reference to `tm_create_copy' /usr/bin/ld: ./src/dless/./src/dless/phast_bd_phylo_hmm.c:94:(.text+0x67f): undefined reference to `tr_partition_nodes' /usr/bin/ld: ./src/dless/./src/dless/phast_bd_phylo_hmm.c:103:(.text+0x715): undefined reference to `tm_reinit' /usr/bin/ld: ./src/dless/./src/dless/phast_bd_phylo_hmm.c:144:(.text+0xb77): undefined reference to `tr_partition_nodes' /usr/bin/ld: ./src/dless/./src/dless/phast_bd_phylo_hmm.c:164:(.text+0xca7): undefined reference to `im_new' /usr/bin/ld: phast_bd_phylo_hmm.o: in function `bd_handle_missing_data': ./src/dless/./src/dless/phast_bd_phylo_hmm.c:234:(.text+0x10e4): undefined reference to `tr_postorder' /usr/bin/ld: ./src/dless/./src/dless/phast_bd_phylo_hmm.c:260:(.text+0x1236): undefined reference to `tr_preorder' /usr/bin/ld: phast_bd_phylo_hmm.o: in function `bd_add_indel_emissions': ./src/dless/./src/dless/phast_bd_phylo_hmm.c:316:(.text+0x1767): undefined reference to `im_column_logl' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_rates_cross': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:361:(.text+0xf6c): undefined reference to `DiscreteGamma' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:364:(.text+0xf8a): undefined reference to `tm_reinit' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:371:(.text+0xfc9): undefined reference to `tm_create_copy' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:376:(.text+0xfe0): undefined reference to `tm_scale_branchlens' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:453:(.text+0x13b2): undefined reference to `tm_free' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_free': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:469:(.text+0x154d): undefined reference to `tm_free' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_compute_emissions': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:597:(.text+0x18c6): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:597:(.text+0x1d80): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:597:(.text+0x1fbb): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_set_branch_len_factors': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:1182:(.text+0x3d1f): undefined reference to `tr_total_len' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_estim_mods_em': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:1099:(.text+0x3f94): undefined reference to `tm_params_new_init_from_model' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:1109:(.text+0x4049): undefined reference to `tm_fit' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:1087:(.text+0x40a0): undefined reference to `subst_mod_is_codon_model' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_gap_patterns.o): in function `gp_create_gapcats': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_gap_patterns.c:163:(.text+0x71c): undefined reference to `tr_inorder' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_gap_patterns.o): in function `gp_set_phylo_patterns': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_gap_patterns.c:244:(.text+0xf45): undefined reference to `tr_postorder' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_gap_patterns.o): in function `gp_set_patterns': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_gap_patterns.c:419:(.text+0x1721): undefined reference to `tr_partition_leaves' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_rates_cross': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:361:(.text+0xf6c): undefined reference to `DiscreteGamma' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:364:(.text+0xf8a): undefined reference to `tm_reinit' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:371:(.text+0xfc9): undefined reference to `tm_create_copy' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:376:(.text+0xfe0): undefined reference to `tm_scale_branchlens' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:453:(.text+0x13b2): undefined reference to `tm_free' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_free': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:469:(.text+0x154d): undefined reference to `tm_free' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_compute_emissions': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:597:(.text+0x18c6): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:597:(.text+0x1d80): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:597:(.text+0x1fbb): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_set_branch_len_factors': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:1182:(.text+0x3d1f): undefined reference to `tr_total_len' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_estim_mods_em': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:1099:(.text+0x3f94): undefined reference to `tm_params_new_init_from_model' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:1109:(.text+0x4049): undefined reference to `tm_fit' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:1087:(.text+0x40a0): undefined reference to `subst_mod_is_codon_model' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_gap_patterns.o): in function `gp_create_gapcats': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_gap_patterns.c:163:(.text+0x71c): undefined reference to `tr_inorder' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_gap_patterns.o): in function `gp_set_phylo_patterns': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_gap_patterns.c:244:(.text+0xf45): undefined reference to `tr_postorder' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_gap_patterns.o): in function `gp_set_patterns': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_gap_patterns.c:419:(.text+0x1721): undefined reference to `tr_partition_leaves' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' collect2: error: ld returned 1 exit status make[3]: *** [Makefile:25: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../bin/dlessP] Error 1 make[3]: *** Waiting for unfinished jobs.... collect2: error: ld returned 1 exit status make[3]: *** [Makefile:25: /build/reproducible-path/phast-1.7+dfsg/src/dless/../../bin/dless] Error 1 make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/dless' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/exoniphy' ../munge-help.sh exoniphy.help_src > exoniphy.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/exoniphy/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../..\" -fno-strict-aliasing -c exoniphy.c -o exoniphy.o : warning: 'PHAST_HOME' redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../bin/exoniphy exoniphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now /usr/bin/ld: exoniphy.o: in function `main': ./src/exoniphy/./src/exoniphy/exoniphy.c:225:(.text.startup+0x243): undefined reference to `tr_new_from_file' /usr/bin/ld: ./src/exoniphy/./src/exoniphy/exoniphy.c:367:(.text.startup+0x472): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/exoniphy/./src/exoniphy/exoniphy.c:374:(.text.startup+0x4be): undefined reference to `tm_extrapolate_and_prune' /usr/bin/ld: ./src/exoniphy/./src/exoniphy/exoniphy.c:381:(.text.startup+0x82f): undefined reference to `tm_prune' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_rates_cross': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:361:(.text+0xf6c): undefined reference to `DiscreteGamma' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:364:(.text+0xf8a): undefined reference to `tm_reinit' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:371:(.text+0xfc9): undefined reference to `tm_create_copy' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:376:(.text+0xfe0): undefined reference to `tm_scale_branchlens' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:453:(.text+0x13b2): undefined reference to `tm_free' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_free': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:469:(.text+0x154d): undefined reference to `tm_free' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_compute_emissions': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:597:(.text+0x18c6): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:597:(.text+0x1d80): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:597:(.text+0x1fbb): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_set_branch_len_factors': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:1182:(.text+0x3d1f): undefined reference to `tr_total_len' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../lib/libphast.a(phast_phylo_hmm.o): in function `phmm_estim_mods_em': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:1099:(.text+0x3f94): undefined reference to `tm_params_new_init_from_model' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:1109:(.text+0x4049): undefined reference to `tm_fit' /usr/bin/ld: ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_phylo_hmm.c:1087:(.text+0x40a0): undefined reference to `subst_mod_is_codon_model' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../lib/libphast.a(phast_gap_patterns.o): in function `gp_create_gapcats': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_gap_patterns.c:163:(.text+0x71c): undefined reference to `tr_inorder' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../lib/libphast.a(phast_gap_patterns.o): in function `gp_set_phylo_patterns': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_gap_patterns.c:244:(.text+0xf45): undefined reference to `tr_postorder' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../lib/libphast.a(phast_gap_patterns.o): in function `gp_set_patterns': ./src/lib/phylo_hmm/./src/lib/phylo_hmm/phast_gap_patterns.c:419:(.text+0x1721): undefined reference to `tr_partition_leaves' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' collect2: error: ld returned 1 exit status make[3]: *** [Makefile:22: /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../bin/exoniphy] Error 1 make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/exoniphy' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phastCons' ../munge-help.sh phastCons.help_src > phastCons.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/phastCons/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/phastCons/../..\" -fno-strict-aliasing -c phastCons.c -o phastCons.o : warning: 'PHAST_HOME' redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.7+dfsg/src/phastCons/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/phastCons/../../bin/phastCons phastCons.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now /usr/bin/ld: phastCons.o: in function `main': ./src/phastCons/./src/phastCons/phastCons.c:26:(.text.startup+0x47): undefined reference to `phastCons_struct_new' /usr/bin/ld: ./src/phastCons/./src/phastCons/phastCons.c:275:(.text.startup+0x14a): undefined reference to `tr_new_from_file' /usr/bin/ld: ./src/phastCons/./src/phastCons/phastCons.c:328:(.text.startup+0x25d): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/phastCons/./src/phastCons/phastCons.c:362:(.text.startup+0xa06): undefined reference to `phastCons' /usr/bin/ld: ./src/phastCons/./src/phastCons/phastCons.c:341:(.text.startup+0xa43): undefined reference to `tr_leaf_names' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastCons/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' collect2: error: ld returned 1 exit status make[3]: *** [Makefile:22: /build/reproducible-path/phast-1.7+dfsg/src/phastCons/../../bin/phastCons] Error 1 make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phastCons' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phastOdds' ../munge-help.sh phastOdds.help_src > phastOdds.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/phastOdds/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/phastOdds/../..\" -fno-strict-aliasing -c phastOdds.c -o phastOdds.o : warning: 'PHAST_HOME' redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.7+dfsg/src/phastOdds/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/phastOdds/../../bin/phastOdds phastOdds.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now /usr/bin/ld: phastOdds.o: in function `main': ./src/phastOdds/./src/phastOdds/phastOdds.c:85:(.text.startup+0x269): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/phastOdds/./src/phastOdds/phastOdds.c:74:(.text.startup+0x359): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/phastOdds/./src/phastOdds/phastOdds.c:180:(.text.startup+0x615): undefined reference to `tm_prune' /usr/bin/ld: ./src/phastOdds/./src/phastOdds/phastOdds.c:193:(.text.startup+0x6b5): undefined reference to `tm_prune' /usr/bin/ld: ./src/phastOdds/./src/phastOdds/phastOdds.c:330:(.text.startup+0xe9e): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: ./src/phastOdds/./src/phastOdds/phastOdds.c:336:(.text.startup+0xf0e): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: ./src/phastOdds/./src/phastOdds/phastOdds.c:330:(.text.startup+0x1699): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: ./src/phastOdds/./src/phastOdds/phastOdds.c:336:(.text.startup+0x1719): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastOdds/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' collect2: error: ld returned 1 exit status make[3]: *** [Makefile:22: /build/reproducible-path/phast-1.7+dfsg/src/phastOdds/../../bin/phastOdds] Error 1 make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phastOdds' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phastMotif' 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/phastMotif/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../..\" -fno-strict-aliasing -c phastMotif.c -o phastMotif.o : warning: 'PHAST_HOME' redefined : note: this is the location of the previous definition phastMotif.c: In function 'main': phastMotif.c:131:13: warning: variable 'separate_backgd' set but not used [-Wunused-but-set-variable] 131 | int i, j, separate_backgd = 0, | ^~~~~~~~~~~~~~~ gcc -L/build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../bin/phastMotif phastMotif.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now /usr/bin/ld: phastMotif.o: in function `main': ./src/phastMotif/./src/phastMotif/phastMotif.c:153:(.text.startup+0x14f): undefined reference to `tr_new_from_file' /usr/bin/ld: ./src/phastMotif/./src/phastMotif/phastMotif.c:161:(.text.startup+0x23c): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/phastMotif/./src/phastMotif/phastMotif.c:342:(.text.startup+0x1124): undefined reference to `tr_create_copy' /usr/bin/ld: ./src/phastMotif/./src/phastMotif/phastMotif.c:342:(.text.startup+0x1146): undefined reference to `tm_new' /usr/bin/ld: ./src/phastMotif/./src/phastMotif/phastMotif.c:344:(.text.startup+0x1165): undefined reference to `tm_params_init' /usr/bin/ld: ./src/phastMotif/./src/phastMotif/phastMotif.c:344:(.text.startup+0x1186): undefined reference to `tm_fit' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `mtf_new': ./src/lib/motif/./src/lib/motif/phast_motif.c:1218:(.text+0x1d3): undefined reference to `tm_create_copy' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:1220:(.text+0x1fc): undefined reference to `tm_create_copy' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:1221:(.text+0x20d): undefined reference to `tm_free_rmp' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:1225:(.text+0x250): undefined reference to `tm_init_rmp' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:1232:(.text+0x291): undefined reference to `tm_scale_branchlens' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `phy_compute_emissions': ./src/lib/motif/./src/lib/motif/phast_motif.c:316:(.text+0x39d): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `mtf_compute_conditional': ./src/lib/motif/./src/lib/motif/phast_motif.c:397:(.text+0x784): undefined reference to `tm_unpack_params' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:398:(.text+0x791): undefined reference to `tm_get_nparams' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `phy_compute_emissions': ./src/lib/motif/./src/lib/motif/phast_motif.c:316:(.text+0x103d): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `phy_estim_mods': ./src/lib/motif/./src/lib/motif/phast_motif.c:333:(.text+0x10f2): undefined reference to `tm_params_new_init_from_model' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:336:(.text+0x1189): undefined reference to `tm_fit' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `mtf_compute_inner_derivs_phy': ./src/lib/motif/./src/lib/motif/phast_motif.c:631:(.text+0x133f): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:632:(.text+0x1357): undefined reference to `tm_unpack_params' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:633:(.text+0x1375): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:639:(.text+0x13f7): undefined reference to `tm_unpack_params' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:640:(.text+0x141b): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `mtf_compute_conditional_grad': ./src/lib/motif/./src/lib/motif/phast_motif.c:506:(.text+0x22af): undefined reference to `tm_get_nparams' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `mtf_new': ./src/lib/motif/./src/lib/motif/phast_motif.c:1218:(.text+0x4a01): undefined reference to `tm_create_copy' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:1220:(.text+0x4a2c): undefined reference to `tm_create_copy' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:1221:(.text+0x4a3d): undefined reference to `tm_free_rmp' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:1225:(.text+0x4a80): undefined reference to `tm_init_rmp' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:1232:(.text+0x4ac1): undefined reference to `tm_scale_branchlens' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `mtf_free': ./src/lib/motif/./src/lib/motif/phast_motif.c:1262:(.text+0x4b19): undefined reference to `tm_free' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `phy_estim_mods': ./src/lib/motif/./src/lib/motif/phast_motif.c:333:(.text+0x70f3): undefined reference to `tm_params_new_init_from_model' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:336:(.text+0x7184): undefined reference to `tm_fit' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `mtf_find': ./src/lib/motif/./src/lib/motif/phast_motif.c:183:(.text+0x8836): undefined reference to `tm_params_new_init_from_model' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:160:(.text+0x8a86): undefined reference to `tm_get_nparams' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `mtf_print': ./src/lib/motif/./src/lib/motif/phast_motif.c:1355:(.text+0x9104): undefined reference to `tr_total_len' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:1356:(.text+0x9128): undefined reference to `tr_total_len' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `mtf_print_html': ./src/lib/motif/./src/lib/motif/phast_motif.c:1496:(.text+0x9cb8): undefined reference to `tr_total_len' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:1497:(.text+0x9cdd): undefined reference to `tr_total_len' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_motif.o): in function `phy_compute_emissions': ./src/lib/motif/./src/lib/motif/phast_motif.c:316:(.text.unlikely+0xe): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: ./src/lib/motif/./src/lib/motif/phast_motif.c:316:(.text.unlikely+0x29): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' collect2: error: ld returned 1 exit status make[3]: *** [Makefile:16: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../bin/phastMotif] Error 1 make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phastMotif' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloFit' ../munge-help.sh phyloFit.help_src > phyloFit.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/phyloFit/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/phyloFit/../..\" -fno-strict-aliasing -c phyloFit.c -o phyloFit.o : warning: 'PHAST_HOME' redefined : note: this is the location of the previous definition phyloFit.c: In function 'main': phyloFit.c:100:8: error: too many arguments to function 'phyloFit_struct_new'; expected 0, have 1 100 | pf = phyloFit_struct_new(0); | ^~~~~~~~~~~~~~~~~~~ ~ In file included from phyloFit.c:29: /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/phylo_fit.h:69:25: note: declared here 69 | struct phyloFit_struct* phyloFit_struct_new(); | ^~~~~~~~~~~~~~~~~~~ make[3]: *** [Makefile:20: phyloFit.o] Error 1 make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloFit' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloBoot' ../munge-help.sh phyloBoot.help_src > phyloBoot.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/phyloBoot/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/phyloBoot/../..\" -fno-strict-aliasing -c phyloBoot.c -o phyloBoot.o : warning: 'PHAST_HOME' redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.7+dfsg/src/phyloBoot/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/phyloBoot/../../bin/phyloBoot phyloBoot.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now /usr/bin/ld: phyloBoot.o: in function `set_param_descriptions': ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:28:(.text+0x139): undefined reference to `tm_get_nratevarparams' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:29:(.text+0x144): undefined reference to `tm_get_nratematparams' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:48:(.text+0x1b2): undefined reference to `tr_preorder' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:56:(.text+0x2a4): undefined reference to `tm_is_reversible' /usr/bin/ld: phyloBoot.o: in function `main': ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:484:(.text.startup+0x206): undefined reference to `tm_params_new_init_from_model' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:484:(.text.startup+0x2c1): undefined reference to `tm_params_new_init_from_model' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:247:(.text.startup+0x387): undefined reference to `tr_new_from_file' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:250:(.text.startup+0x47e): undefined reference to `tm_get_subst_mod_type' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:209:(.text.startup+0x619): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:267:(.text.startup+0x691): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:392:(.text.startup+0x79c): undefined reference to `tm_generate_msa_scaleLst' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:447:(.text.startup+0x879): undefined reference to `tm_create_copy' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:448:(.text.startup+0x896): undefined reference to `tm_reinit' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:454:(.text.startup+0x8ac): undefined reference to `tm_params_new_init_from_model' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:467:(.text.startup+0x902): undefined reference to `tm_fit_em' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:475:(.text.startup+0x961): undefined reference to `tm_print' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:513:(.text.startup+0xb73): undefined reference to `tm_free' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:469:(.text.startup+0xbd1): undefined reference to `tm_fit' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:444:(.text.startup+0xdbe): undefined reference to `tr_create_copy' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:444:(.text.startup+0xde8): undefined reference to `tm_new' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:456:(.text.startup+0xe19): undefined reference to `tm_params_init' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:452:(.text.startup+0xe29): undefined reference to `tm_params_init_random' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:295:(.text.startup+0xe7f): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:300:(.text.startup+0xecf): undefined reference to `tm_create_copy' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:301:(.text.startup+0xeea): undefined reference to `tm_scale_branchlens' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:397:(.text.startup+0xfbb): undefined reference to `tm_generate_msa' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:452:(.text.startup+0x1040): undefined reference to `tm_params_init_random' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:546:(.text.startup+0x1528): undefined reference to `tm_unpack_params' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:548:(.text.startup+0x1554): undefined reference to `tm_print' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:395:(.text.startup+0x161b): undefined reference to `tm_generate_msa_random_subtree' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:245:(.text.startup+0x163a): undefined reference to `tr_new_from_string' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:298:(.text.startup+0x18d6): undefined reference to `tm_scale_branchlens' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:421:(.text.startup+0x192e): undefined reference to `subst_mod_is_codon_model' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:421:(.text.startup+0x1938): undefined reference to `tm_order' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:316:(.text.startup+0x19fa): undefined reference to `subst_mod_is_codon_model' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:316:(.text.startup+0x1a04): undefined reference to `tm_order' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:351:(.text.startup+0x1a5e): undefined reference to `subst_mod_is_codon_model' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:351:(.text.startup+0x1a68): undefined reference to `tm_order' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:333:(.text.startup+0x1add): undefined reference to `subst_mod_is_reversible' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:336:(.text.startup+0x1b24): undefined reference to `tr_new_from_string' /usr/bin/ld: ./src/phyloBoot/./src/phyloBoot/phyloBoot.c:331:(.text.startup+0x1b6f): undefined reference to `tr_new_from_string' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phyloBoot/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' collect2: error: ld returned 1 exit status make[3]: *** [Makefile:22: /build/reproducible-path/phast-1.7+dfsg/src/phyloBoot/../../bin/phyloBoot] Error 1 make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloBoot' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloP' ../munge-help.sh phyloP.help_src > phyloP.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/phyloP/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/phyloP/../..\" -fno-strict-aliasing -c phyloP.c -o phyloP.o : warning: 'PHAST_HOME' redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.7+dfsg/src/phyloP/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/phyloP/../../bin/phyloP phyloP.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now /usr/bin/ld: phyloP.o: in function `main': ./src/phyloP/./src/phyloP/phyloP.c:16:(.text.startup+0x40): undefined reference to `phyloP_struct_new' /usr/bin/ld: ./src/phyloP/./src/phyloP/phyloP.c:166:(.text.startup+0x421): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/phyloP/./src/phyloP/phyloP.c:199:(.text.startup+0x467): undefined reference to `phyloP' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/phyloP/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' collect2: error: ld returned 1 exit status make[3]: *** [Makefile:23: /build/reproducible-path/phast-1.7+dfsg/src/phyloP/../../bin/phyloP] Error 1 make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloP' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/prequel' ../munge-help.sh pbsDecode.help_src > pbsDecode.help ../munge-help.sh pbsEncode.help_src > pbsEncode.help ../munge-help.sh pbsScoreMatrix.help_src > pbsScoreMatrix.help ../munge-help.sh pbsTrain.help_src > pbsTrain.help ../munge-help.sh prequel.help_src > prequel.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/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsDecode.c -o pbsDecode.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 phast_simplex_grid.c -o phast_simplex_grid.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 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 : 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 pbsTrain.c -o pbsTrain.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/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 : 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 phast_pbs_code.c: In function 'pbs_new_from_file': phast_pbs_code.c:88:48: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 88 | pcre2_compile_context *nrows_re = str_re_new("##NROWS[[:space:]]*=[[:space:]]*([0-9]+)"), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/pbs_code.h:8, from phast_pbs_code.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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_pbs_code.c:89:32: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 89 | *dimension_re = str_re_new("##DIMENSION[[:space:]]*=[[:space:]]*([0-9]+)"), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_pbs_code.c:90:29: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 90 | *nbytes_re = str_re_new("##NBYTES[[:space:]]*=[[:space:]]*([0-9]+)"), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_pbs_code.c:91:31: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 91 | *codesize_re = str_re_new("##CODESIZE[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ prequel.c: In function 'main': prequel.c:285:32: warning: '.bin' directive writing 4 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 285 | sprintf(out_fname, "%s.%s.bin", out_root, n->name); | ^~~~ In file included from /usr/include/stdio.h:970, from prequel.c:11: In function 'sprintf', inlined from 'main' at prequel.c:285:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 6 or more bytes (assuming 261) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ prequel.c: In function 'main': prequel.c:253:32: warning: '.fa' directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 253 | sprintf(out_fname, "%s.%s.fa", out_root, n->name); | ^~~ In function 'sprintf', inlined from 'main' at prequel.c:253:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 5 or more bytes (assuming 260) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ prequel.c: In function 'main': prequel.c:203:32: warning: '.probs' directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 203 | sprintf(out_fname, "%s.%s.probs", out_root, n->name); | ^~~~~~ In function 'sprintf', inlined from 'main' at prequel.c:203:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 8 or more bytes (assuming 263) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -L/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsDecode pbsDecode.o phast_simplex_grid.o phast_pbs_code.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/prequel/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsEncode pbsEncode.o phast_simplex_grid.o phast_pbs_code.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/prequel/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsScoreMatrix pbsScoreMatrix.o phast_simplex_grid.o phast_pbs_code.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/prequel/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsTrain pbsTrain.o phast_simplex_grid.o phast_pbs_code.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/prequel/../../lib -o /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/prequel prequel.o phast_simplex_grid.o phast_pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now /usr/bin/ld: prequel.o: in function `do_indels': ./src/prequel/./src/prequel/prequel.c:320:(.text+0xb0): undefined reference to `tr_get_node' /usr/bin/ld: ./src/prequel/./src/prequel/prequel.c:329:(.text+0xe8): undefined reference to `tr_postorder' /usr/bin/ld: ./src/prequel/./src/prequel/prequel.c:388:(.text+0x296): undefined reference to `tr_partition_nodes' /usr/bin/ld: ./src/prequel/./src/prequel/prequel.c:327:(.text+0xc7e): undefined reference to `tm_build_seq_idx' /usr/bin/ld: prequel.o: in function `main': ./src/prequel/./src/prequel/prequel.c:122:(.text.startup+0x2b5): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/prequel/./src/prequel/prequel.c:127:(.text.startup+0x2db): undefined reference to `tm_prune' /usr/bin/ld: ./src/prequel/./src/prequel/prequel.c:139:(.text.startup+0x312): undefined reference to `tr_name_ancestors' /usr/bin/ld: ./src/prequel/./src/prequel/prequel.c:148:(.text.startup+0x34f): undefined reference to `tl_new_tree_posteriors' /usr/bin/ld: ./src/prequel/./src/prequel/prequel.c:158:(.text.startup+0xbea): undefined reference to `tl_compute_log_likelihood' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' /usr/bin/ld: pbsScoreMatrix.o: in function `main': ./src/prequel/./src/prequel/pbsScoreMatrix.c:64:(.text.startup+0x226): undefined reference to `tm_new_from_file' /usr/bin/ld: ./src/prequel/./src/prequel/pbsScoreMatrix.c:106:(.text.startup+0x382): undefined reference to `tm_set_subst_matrix' /usr/bin/ld: ./src/prequel/./src/prequel/pbsScoreMatrix.c:64:(.text.startup+0x884): undefined reference to `tm_new_from_file' collect2: error: ld returned 1 exit status /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' make[3]: *** [Makefile:25: /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsEncode] Error 1 make[3]: *** Waiting for unfinished jobs.... collect2: error: ld returned 1 exit status collect2: error: ld returned 1 exit status make[3]: *** [Makefile:25: /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsScoreMatrix] Error 1 /usr/bin/ld: make[3]: *** [Makefile:25: /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/prequel] Error 1 /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' collect2: error: ld returned 1 exit status make[3]: *** [Makefile:25: /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsDecode] Error 1 collect2: error: ld returned 1 exit status make[3]: *** [Makefile:25: /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsTrain] Error 1 make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/prequel' make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/util' ../munge-help.sh base_evolve.help_src > base_evolve.help ../munge-help.sh clean_genes.help_src > clean_genes.help ../munge-help.sh consEntropy.help_src > consEntropy.help ../munge-help.sh indelFit.help_src > indelFit.help ../munge-help.sh indelHistory.help_src > indelHistory.help ../munge-help.sh makeHKY.help_src > makeHKY.help ../munge-help.sh modFreqs.help_src > modFreqs.help ../munge-help.sh msa_diff.help_src > msa_diff.help ../munge-help.sh phast.help_src > phast.help ../munge-help.sh phastBias.help_src > phastBias.help ../munge-help.sh treeGen.help_src > treeGen.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/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 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 convert_coords.c -o convert_coords.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 : 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 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 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 : 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 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 : 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 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 : 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 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 : 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 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 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 : 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 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 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 : 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 : warning: 'PHAST_HOME' redefined : note: this is the location of the previous definition : 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/convert_coords convert_coords.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 : 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/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/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 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 -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 /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/util/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' 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' && | ^~ In file included from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/tree_model.h:26, from tree_doctor.c:14: /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 */ | ^~~~ collect2: error: ld returned 1 exit status make[3]: *** [Makefile:20: /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/chooseLines] Error 1 make[3]: *** Waiting for unfinished jobs.... /usr/bin/ld: draw_tree.o: in function `main': ./src/util/./src/util/draw_tree.c:84:(.text.startup+0x104): undefined reference to `tr_new_from_file' /usr/bin/ld: ./src/util/./src/util/draw_tree.c:86:(.text.startup+0x120): undefined reference to `tr_print_ps' /usr/bin/ld: ./src/util/./src/util/draw_tree.c:80:(.text.startup+0x143): undefined reference to `tm_new_from_file' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/util/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' collect2: error: ld returned 1 exit status make[3]: *** [Makefile:20: /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/draw_tree] Error 1 /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/util/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' collect2: error: ld returned 1 exit status make[3]: *** [Makefile:20: /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/convert_coords] Error 1 /usr/bin/ld: makeHKY.o: in function `main': ./src/util/./src/util/makeHKY.c:60:(.text.startup+0x307): undefined reference to `tr_new_from_file' /usr/bin/ld: ./src/util/./src/util/makeHKY.c:90:(.text.startup+0x3c9): undefined reference to `tm_new' /usr/bin/ld: ./src/util/./src/util/makeHKY.c:91:(.text.startup+0x3de): undefined reference to `tm_set_HKY_matrix' /usr/bin/ld: ./src/util/./src/util/makeHKY.c:92:(.text.startup+0x3e6): undefined reference to `tm_scale_rate_matrix' /usr/bin/ld: ./src/util/./src/util/makeHKY.c:94:(.text.startup+0x3f5): undefined reference to `tm_print' /usr/bin/ld: ./src/util/./src/util/makeHKY.c:87:(.text.startup+0x4b7): undefined reference to `tr_new_from_string' /usr/bin/ld: /build/reproducible-path/phast-1.7+dfsg/src/util/../../lib/libphast.a(phast_memory_handler.o): in function `tm_rmp_protect': ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x360): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x185): undefined reference to `tm_get_nparams' /usr/bin/ld: ./src/lib/base/./src/lib/base/phast_memory_handler.c:506:(.text+0x1ac): undefined reference to `tm_get_nparams' collect2: error: ld returned 1 exit status make[3]: *** [Makefile:20: /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/makeHKY] Error 1 make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/util' make[2]: *** [Makefile:9: all] Error 2 make[2]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src' make[1]: *** [Makefile:6: all] Error 2 make[1]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg' dh_auto_build: error: make -j42 "INSTALL=install --strip-program=true" returned exit code 2 make: *** [debian/rules:6: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/1882834 and its subdirectories phast failed to build from source. removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/phast_1.7+dfsg-2.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/phast_1.7+dfsg-2.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/phast_1.7+dfsg-2.build1.log.gz' Thu Sep 18 07:48:08 UTC 2025 W: No second build log, what happened? Compressing the 1st log... b1/build.log: 92.1% -- replaced with stdout INSERT 0 1 INSERT 0 1 DELETE 1 [2025-09-18 07:48:09] INFO: Starting at 2025-09-18 07:48:09.161934 [2025-09-18 07:48:09] INFO: Generating the pages of 1 package(s) [2025-09-18 07:48:09] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/phast didn't produce a buildlog, even though it has been built. [2025-09-18 07:48:09] INFO: Finished at 2025-09-18 07:48:09.413730, took: 0:00:00.251799 Thu Sep 18 07:48:09 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/phast.html Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/phast_1.7+dfsg-2.rbuild.log: 91.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/phast_1.7+dfsg-2.rbuild.log.gz [2025-09-18 07:48:09] INFO: Starting at 2025-09-18 07:48:09.725645 [2025-09-18 07:48:09] INFO: Generating the pages of 1 package(s) [2025-09-18 07:48:09] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/phast_1.7+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/phast_1.7+dfsg-2.diff.gz is missing [2025-09-18 07:48:09] INFO: Finished at 2025-09-18 07:48:09.991903, took: 0:00:00.266262 All cleanup done. Thu Sep 18 07:48:10 UTC 2025 - total duration: 0h 2m 52s. Thu Sep 18 07:48:10 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-vlsJ43We, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 2min 53.994s CPU time consumed: 2.506s Memory peak: 39.7M (swap: 0B)