Running as unit: rb-build-arm64_15-71323.service ==================================================================================== Thu Nov 21 02:25:18 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_15) on jenkins, called using "codethink01-arm64 codethink04-arm64" as arguments. Thu Nov 21 02:25:18 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-0Y5UFKSf" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Nov 21 02:25:18 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink01-arm64.debian.net is marked as down. Thu Nov 21 02:25:18 UTC 2024 - checking via ssh if codethink01-arm64.debian.net is up. removed '/tmp/read-only-fs-test-f2NDVV' Thu Nov 21 02:25:19 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Thu Nov 21 02:25:19 UTC 2024 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-OoZRxa' ok, let's check if phast is building anywhere yet… ok, phast is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of phast in trixie on arm64 on jenkins now. 1st build will be done on codethink01-arm64.debian.net. 2nd build will be done on codethink04-arm64.debian.net. ============================================================================= Thu Nov 21 02:25:31 UTC 2024 I: starting to build phast/trixie/arm64 on jenkins on '2024-11-21 02:25' Thu Nov 21 02:25:31 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_15/71323/console.log 1732155931 arm64 trixie phast Thu Nov 21 02:25:31 UTC 2024 I: Downloading source for trixie/phast=1.6+dfsg-6 --2024-11-21 02:25:31-- http://deb.debian.org/debian/pool/main/p/phast/phast_1.6%2bdfsg-6.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_1.6+dfsg-6.dsc’ 0K .. 100% 239M=0s 2024-11-21 02:25:31 (239 MB/s) - ‘phast_1.6+dfsg-6.dsc’ saved [2218/2218] --2024-11-21 02:25:31-- http://deb.debian.org/debian/pool/main/p/phast/phast_1.6%2bdfsg-6.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_1.6+dfsg-6.dsc’ 0K .. 100% 239M=0s 2024-11-21 02:25:31 (239 MB/s) - ‘phast_1.6+dfsg-6.dsc’ saved [2218/2218] Thu Nov 21 02:25:31 UTC 2024 I: phast_1.6+dfsg-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: phast Binary: phast Architecture: any Version: 1.6+dfsg-6 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: 5bf657d4f4556f8848c6e4f362b407ec998cf10a 1808800 phast_1.6+dfsg.orig.tar.xz 3d222e3f22a904910f4f732143da1fcb759d9573 59204 phast_1.6+dfsg-6.debian.tar.xz Checksums-Sha256: 7deae15e8bd8ce8e11b251b42795e0595dd86271360b08d15e6ba107ae66863f 1808800 phast_1.6+dfsg.orig.tar.xz bb1615d418e5b718c7ea1b9ecdef1d4fea54d1f38c18a10b9d53401ef460755a 59204 phast_1.6+dfsg-6.debian.tar.xz Files: b625b9d3abbe0fdc31468820121b30e9 1808800 phast_1.6+dfsg.orig.tar.xz c7d85106e1e9f1afa300e6f0895ccc0f 59204 phast_1.6+dfsg-6.debian.tar.xz Dgit: c8e4e0f7a6923b7596177679f43f17cc3bdb9afd debian archive/debian/1.6+dfsg-6 https://git.dgit.debian.org/phast -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmaqnokUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdoDjQ//W0UPexRQcQGcxlE9XSWKEPvGt/gv jGsCCLDU+d301nIMbqr+jdn8KJpakzT5q16d6oaZ53yWzOCHSgq7fawDluw/BX3j wS/e7y7IhHX10MKLDpWiAv7nu1BBphRXEiNjWduJEe/n9Qomwzf/Hl8jouZ/SWgV VuGMJW1XeHvA0BX4LSmWfMWvOc4nR9+4uh01V/c4Mu2kN4N/llgvysWWZWLuymE1 RmnuV+k1xNbGQBjPYt6Fr+kVgGpqL8BQ/L9MW2fAWwysxwgYCbFrLjyZC/hAyJ/2 1GfPU4WNfUJErbGAAmCcrBUCG2aO+DnErre+vYYIffGiFN+fVNnaySchR5ik+Ur6 1HBLEGzfMh2Xk+i01Y7sPi9G6UXXlLc/QaZk4Q20e66DBRL37o/Ant/o5aVfecOo 6ol1vz1343aY2vuceDmxUUqo31DoPxfomkzPCTgEkfOeiwte8SuA1pTyIjzeJdj6 Tl6mYnatU3TGTzt9t5m4098ziPmLqJljKiy3LpUXNUEusvH0yQRkqL9sejqoWfCl AhX0xHVF6/45y5hNEvt/oVnRZJqGRUSwlr58C0bsqE5m6gtiRYLEMJEcnzf83yI0 yKnHsLeWpt6gLAw+BtTOAyvzy/pqIEqw0ibGgU+zPQi2QUIq7y+9127tPRt/eYAo NpDWd7nT9la+fV8= =CgqX -----END PGP SIGNATURE----- Thu Nov 21 02:25:31 UTC 2024 I: Checking whether the package is not for us Thu Nov 21 02:25:31 UTC 2024 I: Starting 1st build on remote node codethink01-arm64.debian.net. Thu Nov 21 02:25:31 UTC 2024 I: Preparing to do remote build '1' on codethink01-arm64.debian.net. Thu Nov 21 02:25:31 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink01-arm64.debian.net is marked as down. Thu Nov 21 02:25:31 UTC 2024 - checking via ssh if codethink01-arm64.debian.net is up. removed '/tmp/read-only-fs-test-nuftlR' ==================================================================================== Wed Dec 24 08:48:33 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink01-arm64, called using "1 phast trixie /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn 1.6+dfsg-6" as arguments. Wed Dec 24 08:48:33 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-jGQ24daR" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Dec 24 08:48:33 UTC 2025 I: Downloading source for trixie/phast=1.6+dfsg-6 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 1870 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main phast 1.6+dfsg-6 (dsc) [2218 B] Get:2 http://deb.debian.org/debian trixie/main phast 1.6+dfsg-6 (tar) [1809 kB] Get:3 http://deb.debian.org/debian trixie/main phast 1.6+dfsg-6 (diff) [59.2 kB] Fetched 1870 kB in 0s (13.4 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 1870 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main phast 1.6+dfsg-6 (dsc) [2218 B] Get:2 http://deb.debian.org/debian trixie/main phast 1.6+dfsg-6 (tar) [1809 kB] Get:3 http://deb.debian.org/debian trixie/main phast 1.6+dfsg-6 (diff) [59.2 kB] Fetched 1870 kB in 0s (13.4 MB/s) Download complete and in download only mode ============================================================================= Building phast in trixie on arm64 on codethink01-arm64 now. Date: Wed Dec 24 08:48:33 GMT 2025 Date UTC: Wed Dec 24 08:48:33 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Tue Dec 23 20:48:34 -12 2025 I: pbuilder-time-stamp: 1766566114 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] tar: ./dev/shm: time stamp 2027-01-26 00:52:16 is 34401821.609963636 s in the future tar: ./etc/resolv.conf: time stamp 2027-01-26 00:52:16 is 34401821.609490316 s in the future tar: ./etc/mailname: time stamp 2027-01-26 00:52:16 is 34401821.609435716 s in the future tar: ./etc/hostname: time stamp 2027-01-26 00:52:16 is 34401821.609397076 s in the future tar: ./etc/hosts: time stamp 2027-01-26 00:52:16 is 34401821.609359876 s in the future tar: ./tmp: time stamp 2027-01-26 00:52:21 is 34401826.603924956 s in the future tar: ./var/cache/apt: time stamp 2027-01-26 00:52:21 is 34401821.425953076 s in the future tar: ./var/lib/apt/lists/partial: time stamp 2027-01-26 00:52:17 is 34401817.395332076 s in the future tar: ./run/shm: time stamp 2027-01-26 00:52:16 is 34401816.015226876 s in the future tar: ./run: time stamp 2027-01-26 00:52:16 is 34401816.006278396 s in the future tar: ./etc: time stamp 2027-01-26 00:52:16 is 34401816.006202476 s in the future tar: ./dev: time stamp 2027-01-26 00:52:16 is 34401816.006191916 s in the future 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_1.6+dfsg-6.dsc] I: copying [./phast_1.6+dfsg.orig.tar.xz] I: copying [./phast_1.6+dfsg-6.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Jul 31 20:28:57 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./phast_1.6+dfsg-6.dsc: no acceptable signature found dpkg-source: info: extracting phast in phast-1.6+dfsg dpkg-source: info: unpacking phast_1.6+dfsg.orig.tar.xz dpkg-source: info: unpacking phast_1.6+dfsg-6.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 fix_test_makefile.patch dpkg-source: info: applying pcre2.patch dpkg-source: info: applying gcc-14.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4111687/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='7cefe57d4f8b4a118db06f539197c79d' 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='4111687' 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.eewESGYn/pbuilderrc_mrRd --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/b1 --logfile b1/build.log phast_1.6+dfsg-6.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink01-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4111687/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team 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 ... 20087 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} libicu72{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} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 44 newly installed, 0 to remove and 0 not upgraded. Need to get 27.7 MB of archives. After unpacking 126 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-8 [517 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 23 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-3+b1 [98.9 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libblas-dev arm64 3.12.0-3+b1 [106 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-8 [361 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-3+b1 [1812 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 liblapack-dev arm64 3.12.0-3+b1 [3709 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libtmglib3 arm64 3.12.0-3+b1 [98.8 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 liblapacke arm64 3.12.0-3+b1 [336 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libtmglib-dev arm64 3.12.0-3+b1 [103 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 liblapacke-dev arm64 3.12.0-3+b1 [322 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libpcre2-16-0 arm64 10.42-4+b2 [220 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libpcre2-32-0 arm64 10.42-4+b2 [211 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libpcre2-posix3 arm64 10.42-4+b2 [55.9 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libpcre2-dev arm64 10.42-4+b2 [683 kB] Fetched 27.7 MB in 0s (166 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 20087 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../09-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... 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_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../22-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package help2man. Preparing to unpack .../30-help2man_1.49.3+b1_arm64.deb ... Unpacking help2man (1.49.3+b1) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../31-libblas3_3.12.0-3+b1_arm64.deb ... Unpacking libblas3:arm64 (3.12.0-3+b1) ... Selecting previously unselected package libblas-dev:arm64. Preparing to unpack .../32-libblas-dev_3.12.0-3+b1_arm64.deb ... Unpacking libblas-dev:arm64 (3.12.0-3+b1) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../33-libgfortran5_14.2.0-8_arm64.deb ... Unpacking libgfortran5:arm64 (14.2.0-8) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../34-liblapack3_3.12.0-3+b1_arm64.deb ... Unpacking liblapack3:arm64 (3.12.0-3+b1) ... Selecting previously unselected package liblapack-dev:arm64. Preparing to unpack .../35-liblapack-dev_3.12.0-3+b1_arm64.deb ... Unpacking liblapack-dev:arm64 (3.12.0-3+b1) ... Selecting previously unselected package libtmglib3:arm64. Preparing to unpack .../36-libtmglib3_3.12.0-3+b1_arm64.deb ... Unpacking libtmglib3:arm64 (3.12.0-3+b1) ... Selecting previously unselected package liblapacke:arm64. Preparing to unpack .../37-liblapacke_3.12.0-3+b1_arm64.deb ... Unpacking liblapacke:arm64 (3.12.0-3+b1) ... Selecting previously unselected package libtmglib-dev:arm64. Preparing to unpack .../38-libtmglib-dev_3.12.0-3+b1_arm64.deb ... Unpacking libtmglib-dev:arm64 (3.12.0-3+b1) ... Selecting previously unselected package liblapacke-dev:arm64. Preparing to unpack .../39-liblapacke-dev_3.12.0-3+b1_arm64.deb ... Unpacking liblapacke-dev:arm64 (3.12.0-3+b1) ... Selecting previously unselected package libpcre2-16-0:arm64. Preparing to unpack .../40-libpcre2-16-0_10.42-4+b2_arm64.deb ... Unpacking libpcre2-16-0:arm64 (10.42-4+b2) ... Selecting previously unselected package libpcre2-32-0:arm64. Preparing to unpack .../41-libpcre2-32-0_10.42-4+b2_arm64.deb ... Unpacking libpcre2-32-0:arm64 (10.42-4+b2) ... Selecting previously unselected package libpcre2-posix3:arm64. Preparing to unpack .../42-libpcre2-posix3_10.42-4+b2_arm64.deb ... Unpacking libpcre2-posix3:arm64 (10.42-4+b2) ... Selecting previously unselected package libpcre2-dev:arm64. Preparing to unpack .../43-libpcre2-dev_10.42-4+b2_arm64.deb ... Unpacking libpcre2-dev:arm64 (10.42-4+b2) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libpcre2-16-0:arm64 (10.42-4+b2) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up libpcre2-32-0:arm64 (10.42-4+b2) ... Setting up libblas3:arm64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up autopoint (0.22.5-2) ... Setting up libgfortran5:arm64 (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up libpcre2-posix3:arm64 (10.42-4+b2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up libblas-dev:arm64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:arm64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libpcre2-dev:arm64 (10.42-4+b2) ... Setting up libtool (2.4.7-8) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3+b1) ... Setting up dh-autoreconf (20) ... Setting up libtmglib3:arm64 (3.12.0-3+b1) ... Setting up liblapack-dev:arm64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up liblapacke:arm64 (3.12.0-3+b1) ... Setting up libtmglib-dev:arm64 (3.12.0-3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up liblapacke-dev:arm64 (3.12.0-3+b1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... 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-1.6+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_1.6+dfsg-6_source.changes dpkg-buildpackage: info: source package phast dpkg-buildpackage: info: source version 1.6+dfsg-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/phast-1.6+dfsg' dh_auto_clean cd src && make clean make[2]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/reproducible-path/phast-1.6+dfsg/src/lib/$dir && make clean ; done make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/base' rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/base' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/msa' rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/msa' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/feature' rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/feature' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/hmm' rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/hmm' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo' rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo_hmm' rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/motif' rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/motif' rm -f /build/reproducible-path/phast-1.6+dfsg/src/lib/../../lib/* make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/dless' rm -f *.o dless.help dlessP.help /build/reproducible-path/phast-1.6+dfsg/src/dless/../../bin/dless /build/reproducible-path/phast-1.6+dfsg/src/dless/../../bin/dlessP make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/dless' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/exoniphy' rm -f *.o *.help /build/reproducible-path/phast-1.6+dfsg/src/exoniphy/../../bin/exoniphy make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/exoniphy' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/phastCons' rm -f *.o /build/reproducible-path/phast-1.6+dfsg/src/phastCons/../../bin/phastCons phastCons.help make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phastCons' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/phastOdds' rm -f *.o *.help /build/reproducible-path/phast-1.6+dfsg/src/phastOdds/../../bin/phastOdds make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phastOdds' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/phastMotif' rm -f *.o /build/reproducible-path/phast-1.6+dfsg/src/phastMotif/../../bin/phastMotif make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phastMotif' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloFit' rm -f *.o /build/reproducible-path/phast-1.6+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.help make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloFit' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloBoot' rm -f *.o *.help /build/reproducible-path/phast-1.6+dfsg/src/phyloBoot/../../bin/phyloBoot make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloBoot' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloP' rm -f *.o /build/reproducible-path/phast-1.6+dfsg/src/phyloP/../../bin/phyloP phyloP.help make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloP' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/prequel' rm -f *.o /build/reproducible-path/phast-1.6+dfsg/src/prequel/../../bin/pbsDecode /build/reproducible-path/phast-1.6+dfsg/src/prequel/../../bin/pbsEncode /build/reproducible-path/phast-1.6+dfsg/src/prequel/../../bin/pbsScoreMatrix /build/reproducible-path/phast-1.6+dfsg/src/prequel/../../bin/pbsTrain /build/reproducible-path/phast-1.6+dfsg/src/prequel/../../bin/prequel pbsDecode.help pbsEncode.help pbsScoreMatrix.help pbsTrain.help prequel.help make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/prequel' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/util' rm -f *.o *.help /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/all_dists /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/base_evolve /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/chooseLines /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/clean_genes /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/consEntropy /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/convert_coords /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/display_rate_matrix /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/draw_tree /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/eval_predictions /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/hmm_train /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/hmm_tweak /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/hmm_view /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/indelFit /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/indelHistory /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/maf_parse /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/makeHKY /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/modFreqs /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/msa_diff /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/msa_split /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/msa_view /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/phast /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/phastBias /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/refeature /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/stringiphy /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/treeGen /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/tree_doctor make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/util' rm -rf ../bin ../lib ../doc make[2]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg/src' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mkdir -p ../bin ../lib for dir in lib dless exoniphy phastCons phastOdds phastMotif phyloFit phyloBoot phyloP prequel util ; do cd /build/reproducible-path/phast-1.6+dfsg/src/$dir && make ; done make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/reproducible-path/phast-1.6+dfsg/src/lib/$dir && make ; done make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/base' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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:672:46: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 672 | 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-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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:935:1: note: expected 'PCRE2_SPTR8' {aka 'const unsigned char *'} but argument is of type 'char *' 935 | 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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+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-1.6+dfsg/src/lib/base/../../../lib/libphast.a ar rs /build/reproducible-path/phast-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+dfsg/src/lib/base' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/msa' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/../include/phast/local_alignment.h:36, from phast_local_alignment.c:32: /build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_msa.c:39: /build/reproducible-path/phast-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_multi_msa.c:37: /build/reproducible-path/phast-1.6+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-1.6+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-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/msa.h:19, from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/sufficient_stats.h:20, from phast_sufficient_stats.c:11: /build/reproducible-path/phast-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+dfsg/src/lib/msa' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/feature' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/../include/phast/gff.h:21, from phast_bed.c:15: /build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/category_map.h:92, from phast_category_map.c:10: /build/reproducible-path/phast-1.6+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-1.6+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-1.6+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:]]*(.*)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:43:28: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 43 | extend_re = str_re_new("^[[:space:]]*FEATURE_EXTEND[[:space:]]*:[[:space:]]*(.+)[[:space:]]*\\((.+)\\)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/../include/phast/gff.h:21, from phast_gff.c:13: /build/reproducible-path/phast-1.6+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-1.6+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-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+dfsg/src/lib/feature' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/hmm' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/hmm' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_p.c -o phast_phylo_p.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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_p_print.c -o phast_phylo_p_print.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_p_print.c: In function 'print_feats_generic': phast_phylo_p_print.c:752:50: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 752 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_phylo_p_print.c:17: /build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_subst_distrib.c -o phast_subst_distrib.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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_subst_mods.c -o phast_subst_mods.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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_tree_likelihoods.c -o phast_tree_likelihoods.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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_tree_model.c -o phast_tree_model.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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_trees.c -o phast_trees.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-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo_hmm' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/motif' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_tfbs.c:16: /build/reproducible-path/phast-1.6+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-1.6+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-1.6+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-1.6+dfsg/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/motif' make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/dless/../..\" -fno-strict-aliasing -c dless.c -o dless.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition make[3]: *** No rule to make target 'bd_phylo_hmm.o', needed by '/build/reproducible-path/phast-1.6+dfsg/src/dless/../../bin/dless'. Stop. make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/dless' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/exoniphy/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/exoniphy/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/exoniphy/../../bin/exoniphy exoniphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/exoniphy' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/phastCons/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/phastCons/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/phastCons/../../bin/phastCons phastCons.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phastCons' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/phastOdds/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/phastOdds/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/phastOdds/../../bin/phastOdds phastOdds.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phastOdds' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/phastMotif' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/phastMotif/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/phastMotif/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/phastMotif/../../bin/phastMotif phastMotif.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phastMotif' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/phyloFit/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 gcc -L/build/reproducible-path/phast-1.6+dfsg/src/phyloFit/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloFit' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/phyloBoot/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/phyloBoot/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/phyloBoot/../../bin/phyloBoot phyloBoot.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloBoot' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/phyloP/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/phyloP/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/phyloP/../../bin/phyloP phyloP.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloP' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsDecode.c -o pbsDecode.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition make[3]: *** No rule to make target 'simplex_grid.o', needed by '/build/reproducible-path/phast-1.6+dfsg/src/prequel/../../bin/pbsDecode'. Stop. make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/prequel' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c all_dists.c -o all_dists.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/all_dists all_dists.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c base_evolve.c -o base_evolve.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/base_evolve base_evolve.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c chooseLines.c -o chooseLines.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c clean_genes.c -o clean_genes.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/clean_genes clean_genes.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/consEntropy consEntropy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/convert_coords convert_coords.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 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]; | ^~~~~~~ gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/display_rate_matrix display_rate_matrix.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/draw_tree draw_tree.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c eval_predictions.c -o eval_predictions.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/eval_predictions eval_predictions.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/hmm_train hmm_train.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_tweak.c -o hmm_tweak.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/hmm_tweak hmm_tweak.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_view.c -o hmm_view.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/hmm_view hmm_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c indelFit.c -o indelFit.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/indelFit indelFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/indelHistory indelHistory.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/maf_parse maf_parse.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/makeHKY makeHKY.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/msa_diff msa_diff.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/msa_split msa_split.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 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-1.6+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/msa.h:19, from msa_view.c:14: /build/reproducible-path/phast-1.6+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-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/msa_view msa_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c phast.c -o phast.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c phastBias.c -o phastBias.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/phastBias phastBias.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c refeature.c -o refeature.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/refeature refeature.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c stringiphy.c -o stringiphy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/stringiphy stringiphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c treeGen.c -o treeGen.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/treeGen treeGen.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c tree_doctor.c -o tree_doctor.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition 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-1.6+dfsg/src/../include/phast/tree_model.h:26, from tree_doctor.c:14: /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/trees.h:47:8: note: 'name' declared here 47 | char name [STR_MED_LEN]; /**< Name of this node i.e. 'Drosophila 23' usually one of the sequence names */ | ^~~~ gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/tree_doctor tree_doctor.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/util' mkdir -p ../doc/man/ Generating man pages... USAGE: convert_coords -m -f [-s ] [-d ] [-p] [-n] [-i PHYLIP|FASTA|MPM] DESCRIPTION: Converts coordinates of features in a GFF file according to a multiple alignment. Will map from the coordinate system of any sequence to any other sequence; can also map to or from the coordinate system of the entire alignment. In addition, supports translation of coordinates by specified offset. OPTIONS: -m (required) Name of file in which alignment is defined. -f (required) Name of file in which features are defined (GFF). -s Index of frame of reference for feature coordinates, as defined in the GFF file. Use an integer 1-N (if N seqs) or 0 to indicate the coordinate system of the alignment as a whole. Default behavior is to match features with alignment sequences by name (feature by feature). -d Index of destination frame of reference. Default is 0 (whole MSA). -p Positive coordinate offset. This value will be added to all coordinates. Useful when the alignment (or sequence) for which the coordinates are specified is a sub-alignment of yours. -n Negative coordinate offset. This value will be subtracted from all coordinates. Useful when your alignment is a sub-alignment of the alignment (or sequence) for which the coordinates are specified. -i FASTA|PHYLIP|MPM|SS Alignment format. Default is to guess format from file contents PROGRAM: draw_tree DESCRIPTION: Produces a simple postscript rendering of a tree. USAGE: draw_tree [-dbvs] | OPTIONS: (Required) File name of tree (expected to be in Newick format, unless filename ends with '.mod', in which case expected to be a tree model file). -d Print "diagonal" branches, instead of "right-angle" or "square" ones (produces a "cladogram", as opposed to a "phenogram"). This option implies -s. -b Suppress branch lengths. -v Vertical layout. -s Don't draw branches to scale. Done. make[2]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/phast-1.6+dfsg' cd test && PATH=/build/reproducible-path/phast-1.6+dfsg/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games make msa_view make[2]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/test' *** Testing msa_view *** msa_view hmrc.ss -i SS --end 10000 > hmrc.fa if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.fa -o PHYLIP > hmrc.ph msa_view hmrc.ph -i PHYLIP > hmrc.fa if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ph --out-format MPM --in-format PHYLIP > hmrc.mpm msa_view hmrc.mpm --in-format MPM > hmrc.fa if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.fa -o SS > hmrc_short_a.ss msa_view hmrc.ss --end 10000 -i SS -o SS > hmrc_short_b.ss if ! diff --brief hmrc_short_[ab].ss ; then echo "ERROR" ; exit 1 ; fi msa_view --seqs human,cow hmrc_short_a.ss -i SS -o SS | msa_view - -i SS > hm_a.fa msa_view --seqs human,cow hmrc.fa > hm_b.fa if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --gap-strip ANY -i SS -o SS | msa_view - -i SS > hmrc_nogaps_a.fa msa_view hmrc.ss -i SS | msa_view - --gap-strip ANY > hmrc_nogaps_b.fa if ! diff --brief hmrc_nogaps_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.fa --seqs human,cow --gap-strip ALL > hm_a.fa msa_view hmrc_short_a.ss --seqs human,cow -i SS --gap-strip ALL > hm_b.fa if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --start 10000 --end 20000 -i SS > hmrc_sub_a.fa msa_view hmrc.ss -i SS | msa_view - --start 10000 --end 20000 > hmrc_sub_b.fa if ! diff --brief hmrc_sub_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --summary -i SS > hmrc_summary if ! diff --brief -b hmrc_summary hmrc_summary_correct ; then echo "ERROR" ; exit 1 ; fi -e Passed all tests. make[2]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/test' make[1]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/phast/ make -j12 install DESTDIR=/build/reproducible-path/phast-1.6\+dfsg/debian/phast AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/phast-1.6+dfsg' (cd src; make install DESTDIR=/build/reproducible-path/phast-1.6+dfsg/debian/phast ) make[2]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mkdir -p /build/reproducible-path/phast-1.6+dfsg/debian/phast/usr/bin/ mkdir -p /build/reproducible-path/phast-1.6+dfsg/debian/phast/usr/share/phast/data/ mkdir -p /build/reproducible-path/phast-1.6+dfsg/debian/phast/usr/share/man/man1/ cp ../bin/* /build/reproducible-path/phast-1.6+dfsg/debian/phast/usr/bin/ cp -R ../data/* /build/reproducible-path/phast-1.6+dfsg/debian/phast/usr/share/phast/data/ cp -R ../doc/man/* /build/reproducible-path/phast-1.6+dfsg/debian/phast/usr/share/man/man1/ make[2]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/phast-1.6+dfsg' dh_installexamples find debian/*/usr/share/doc/*/examples -type f -size +1k -exec xz \{\} \; make[1]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg' dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'phast' in '../phast_1.6+dfsg-6_arm64.deb'. dpkg-deb: building package 'phast-dbgsym' in '../phast-dbgsym_1.6+dfsg-6_arm64.deb'. dpkg-genbuildinfo --build=binary -O../phast_1.6+dfsg-6_arm64.buildinfo dpkg-genchanges --build=binary -O../phast_1.6+dfsg-6_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: 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/4111687 and its subdirectories I: Current time: Tue Dec 23 20:50:35 -12 2025 I: pbuilder-time-stamp: 1766566235 Wed Dec 24 08:50:35 UTC 2025 I: Signing ./b1/phast_1.6+dfsg-6_arm64.buildinfo as phast_1.6+dfsg-6_arm64.buildinfo.asc Wed Dec 24 08:50:35 UTC 2025 I: Signed ./b1/phast_1.6+dfsg-6_arm64.buildinfo as ./b1/phast_1.6+dfsg-6_arm64.buildinfo.asc Wed Dec 24 08:50:35 UTC 2025 - build #1 for phast/trixie/arm64 on codethink01-arm64 done. Starting cleanup. All cleanup done. Wed Dec 24 08:50:35 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-jGQ24daR, removing. /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 02:27 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 02:25 b2 -rw-r--r-- 1 jenkins jenkins 2218 Jul 31 20:37 phast_1.6+dfsg-6.dsc -rw------- 1 jenkins jenkins 3327 Nov 21 02:25 rbuildlog.NplgiYB /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/b1: total 29204 -rw-r--r-- 1 jenkins jenkins 174601 Nov 21 02:27 build.log -rw-r--r-- 1 jenkins jenkins 26719824 Nov 21 02:27 phast-dbgsym_1.6+dfsg-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 59204 Nov 21 02:27 phast_1.6+dfsg-6.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2218 Nov 21 02:27 phast_1.6+dfsg-6.dsc -rw-r--r-- 1 jenkins jenkins 5408 Nov 21 02:27 phast_1.6+dfsg-6_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6290 Nov 21 02:27 phast_1.6+dfsg-6_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1538 Nov 21 02:27 phast_1.6+dfsg-6_arm64.changes -rw-r--r-- 1 jenkins jenkins 2884204 Nov 21 02:27 phast_1.6+dfsg-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 1397 Nov 21 02:27 phast_1.6+dfsg-6_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/b2: total 0 Thu Nov 21 02:27:37 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Dec 23 20:48:34 -12 2025 I: pbuilder-time-stamp: 1766566114 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] tar: ./dev/shm: time stamp 2027-01-26 00:52:16 is 34401821.609963636 s in the future tar: ./etc/resolv.conf: time stamp 2027-01-26 00:52:16 is 34401821.609490316 s in the future tar: ./etc/mailname: time stamp 2027-01-26 00:52:16 is 34401821.609435716 s in the future tar: ./etc/hostname: time stamp 2027-01-26 00:52:16 is 34401821.609397076 s in the future tar: ./etc/hosts: time stamp 2027-01-26 00:52:16 is 34401821.609359876 s in the future tar: ./tmp: time stamp 2027-01-26 00:52:21 is 34401826.603924956 s in the future tar: ./var/cache/apt: time stamp 2027-01-26 00:52:21 is 34401821.425953076 s in the future tar: ./var/lib/apt/lists/partial: time stamp 2027-01-26 00:52:17 is 34401817.395332076 s in the future tar: ./run/shm: time stamp 2027-01-26 00:52:16 is 34401816.015226876 s in the future tar: ./run: time stamp 2027-01-26 00:52:16 is 34401816.006278396 s in the future tar: ./etc: time stamp 2027-01-26 00:52:16 is 34401816.006202476 s in the future tar: ./dev: time stamp 2027-01-26 00:52:16 is 34401816.006191916 s in the future 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_1.6+dfsg-6.dsc] I: copying [./phast_1.6+dfsg.orig.tar.xz] I: copying [./phast_1.6+dfsg-6.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Jul 31 20:28:57 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./phast_1.6+dfsg-6.dsc: no acceptable signature found dpkg-source: info: extracting phast in phast-1.6+dfsg dpkg-source: info: unpacking phast_1.6+dfsg.orig.tar.xz dpkg-source: info: unpacking phast_1.6+dfsg-6.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 fix_test_makefile.patch dpkg-source: info: applying pcre2.patch dpkg-source: info: applying gcc-14.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4111687/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='7cefe57d4f8b4a118db06f539197c79d' 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='4111687' 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.eewESGYn/pbuilderrc_mrRd --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/b1 --logfile b1/build.log phast_1.6+dfsg-6.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink01-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4111687/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team 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 ... 20087 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} libicu72{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} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 44 newly installed, 0 to remove and 0 not upgraded. Need to get 27.7 MB of archives. After unpacking 126 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-8 [517 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 23 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-3+b1 [98.9 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libblas-dev arm64 3.12.0-3+b1 [106 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-8 [361 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-3+b1 [1812 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 liblapack-dev arm64 3.12.0-3+b1 [3709 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libtmglib3 arm64 3.12.0-3+b1 [98.8 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 liblapacke arm64 3.12.0-3+b1 [336 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libtmglib-dev arm64 3.12.0-3+b1 [103 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 liblapacke-dev arm64 3.12.0-3+b1 [322 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libpcre2-16-0 arm64 10.42-4+b2 [220 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libpcre2-32-0 arm64 10.42-4+b2 [211 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libpcre2-posix3 arm64 10.42-4+b2 [55.9 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libpcre2-dev arm64 10.42-4+b2 [683 kB] Fetched 27.7 MB in 0s (166 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 20087 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../09-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... 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_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../22-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package help2man. Preparing to unpack .../30-help2man_1.49.3+b1_arm64.deb ... Unpacking help2man (1.49.3+b1) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../31-libblas3_3.12.0-3+b1_arm64.deb ... Unpacking libblas3:arm64 (3.12.0-3+b1) ... Selecting previously unselected package libblas-dev:arm64. Preparing to unpack .../32-libblas-dev_3.12.0-3+b1_arm64.deb ... Unpacking libblas-dev:arm64 (3.12.0-3+b1) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../33-libgfortran5_14.2.0-8_arm64.deb ... Unpacking libgfortran5:arm64 (14.2.0-8) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../34-liblapack3_3.12.0-3+b1_arm64.deb ... Unpacking liblapack3:arm64 (3.12.0-3+b1) ... Selecting previously unselected package liblapack-dev:arm64. Preparing to unpack .../35-liblapack-dev_3.12.0-3+b1_arm64.deb ... Unpacking liblapack-dev:arm64 (3.12.0-3+b1) ... Selecting previously unselected package libtmglib3:arm64. Preparing to unpack .../36-libtmglib3_3.12.0-3+b1_arm64.deb ... Unpacking libtmglib3:arm64 (3.12.0-3+b1) ... Selecting previously unselected package liblapacke:arm64. Preparing to unpack .../37-liblapacke_3.12.0-3+b1_arm64.deb ... Unpacking liblapacke:arm64 (3.12.0-3+b1) ... Selecting previously unselected package libtmglib-dev:arm64. Preparing to unpack .../38-libtmglib-dev_3.12.0-3+b1_arm64.deb ... Unpacking libtmglib-dev:arm64 (3.12.0-3+b1) ... Selecting previously unselected package liblapacke-dev:arm64. Preparing to unpack .../39-liblapacke-dev_3.12.0-3+b1_arm64.deb ... Unpacking liblapacke-dev:arm64 (3.12.0-3+b1) ... Selecting previously unselected package libpcre2-16-0:arm64. Preparing to unpack .../40-libpcre2-16-0_10.42-4+b2_arm64.deb ... Unpacking libpcre2-16-0:arm64 (10.42-4+b2) ... Selecting previously unselected package libpcre2-32-0:arm64. Preparing to unpack .../41-libpcre2-32-0_10.42-4+b2_arm64.deb ... Unpacking libpcre2-32-0:arm64 (10.42-4+b2) ... Selecting previously unselected package libpcre2-posix3:arm64. Preparing to unpack .../42-libpcre2-posix3_10.42-4+b2_arm64.deb ... Unpacking libpcre2-posix3:arm64 (10.42-4+b2) ... Selecting previously unselected package libpcre2-dev:arm64. Preparing to unpack .../43-libpcre2-dev_10.42-4+b2_arm64.deb ... Unpacking libpcre2-dev:arm64 (10.42-4+b2) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libpcre2-16-0:arm64 (10.42-4+b2) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up libpcre2-32-0:arm64 (10.42-4+b2) ... Setting up libblas3:arm64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up autopoint (0.22.5-2) ... Setting up libgfortran5:arm64 (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up libpcre2-posix3:arm64 (10.42-4+b2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up libblas-dev:arm64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:arm64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libpcre2-dev:arm64 (10.42-4+b2) ... Setting up libtool (2.4.7-8) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3+b1) ... Setting up dh-autoreconf (20) ... Setting up libtmglib3:arm64 (3.12.0-3+b1) ... Setting up liblapack-dev:arm64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up liblapacke:arm64 (3.12.0-3+b1) ... Setting up libtmglib-dev:arm64 (3.12.0-3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up liblapacke-dev:arm64 (3.12.0-3+b1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... 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-1.6+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_1.6+dfsg-6_source.changes dpkg-buildpackage: info: source package phast dpkg-buildpackage: info: source version 1.6+dfsg-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/phast-1.6+dfsg' dh_auto_clean cd src && make clean make[2]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/reproducible-path/phast-1.6+dfsg/src/lib/$dir && make clean ; done make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/base' rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/base' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/msa' rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/msa' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/feature' rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/feature' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/hmm' rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/hmm' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo' rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo_hmm' rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/motif' rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/motif' rm -f /build/reproducible-path/phast-1.6+dfsg/src/lib/../../lib/* make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/dless' rm -f *.o dless.help dlessP.help /build/reproducible-path/phast-1.6+dfsg/src/dless/../../bin/dless /build/reproducible-path/phast-1.6+dfsg/src/dless/../../bin/dlessP make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/dless' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/exoniphy' rm -f *.o *.help /build/reproducible-path/phast-1.6+dfsg/src/exoniphy/../../bin/exoniphy make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/exoniphy' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/phastCons' rm -f *.o /build/reproducible-path/phast-1.6+dfsg/src/phastCons/../../bin/phastCons phastCons.help make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phastCons' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/phastOdds' rm -f *.o *.help /build/reproducible-path/phast-1.6+dfsg/src/phastOdds/../../bin/phastOdds make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phastOdds' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/phastMotif' rm -f *.o /build/reproducible-path/phast-1.6+dfsg/src/phastMotif/../../bin/phastMotif make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phastMotif' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloFit' rm -f *.o /build/reproducible-path/phast-1.6+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.help make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloFit' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloBoot' rm -f *.o *.help /build/reproducible-path/phast-1.6+dfsg/src/phyloBoot/../../bin/phyloBoot make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloBoot' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloP' rm -f *.o /build/reproducible-path/phast-1.6+dfsg/src/phyloP/../../bin/phyloP phyloP.help make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloP' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/prequel' rm -f *.o /build/reproducible-path/phast-1.6+dfsg/src/prequel/../../bin/pbsDecode /build/reproducible-path/phast-1.6+dfsg/src/prequel/../../bin/pbsEncode /build/reproducible-path/phast-1.6+dfsg/src/prequel/../../bin/pbsScoreMatrix /build/reproducible-path/phast-1.6+dfsg/src/prequel/../../bin/pbsTrain /build/reproducible-path/phast-1.6+dfsg/src/prequel/../../bin/prequel pbsDecode.help pbsEncode.help pbsScoreMatrix.help pbsTrain.help prequel.help make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/prequel' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/util' rm -f *.o *.help /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/all_dists /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/base_evolve /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/chooseLines /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/clean_genes /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/consEntropy /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/convert_coords /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/display_rate_matrix /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/draw_tree /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/eval_predictions /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/hmm_train /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/hmm_tweak /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/hmm_view /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/indelFit /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/indelHistory /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/maf_parse /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/makeHKY /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/modFreqs /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/msa_diff /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/msa_split /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/msa_view /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/phast /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/phastBias /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/refeature /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/stringiphy /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/treeGen /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/tree_doctor make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/util' rm -rf ../bin ../lib ../doc make[2]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg/src' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mkdir -p ../bin ../lib for dir in lib dless exoniphy phastCons phastOdds phastMotif phyloFit phyloBoot phyloP prequel util ; do cd /build/reproducible-path/phast-1.6+dfsg/src/$dir && make ; done make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/reproducible-path/phast-1.6+dfsg/src/lib/$dir && make ; done make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/base' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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:672:46: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 672 | 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-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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:935:1: note: expected 'PCRE2_SPTR8' {aka 'const unsigned char *'} but argument is of type 'char *' 935 | 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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+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-1.6+dfsg/src/lib/base/../../../lib/libphast.a ar rs /build/reproducible-path/phast-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+dfsg/src/lib/base' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/msa' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/../include/phast/local_alignment.h:36, from phast_local_alignment.c:32: /build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_msa.c:39: /build/reproducible-path/phast-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_multi_msa.c:37: /build/reproducible-path/phast-1.6+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-1.6+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-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/msa.h:19, from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/sufficient_stats.h:20, from phast_sufficient_stats.c:11: /build/reproducible-path/phast-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+dfsg/src/lib/msa' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/feature' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/../include/phast/gff.h:21, from phast_bed.c:15: /build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/category_map.h:92, from phast_category_map.c:10: /build/reproducible-path/phast-1.6+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-1.6+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:]]*(.*)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:42:27: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 42 | label_re = str_re_new("^[[:space:]]*LABELLING_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /build/reproducible-path/phast-1.6+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-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/../include/phast/gff.h:21, from phast_gff.c:13: /build/reproducible-path/phast-1.6+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-1.6+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-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+dfsg/src/lib/feature' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/hmm' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/hmm' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_p.c -o phast_phylo_p.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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_p_print.c -o phast_phylo_p_print.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_p_print.c: In function 'print_feats_generic': phast_phylo_p_print.c:752:50: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 752 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_phylo_p_print.c:17: /build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_subst_distrib.c -o phast_subst_distrib.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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_subst_mods.c -o phast_subst_mods.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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_tree_likelihoods.c -o phast_tree_likelihoods.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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_tree_model.c -o phast_tree_model.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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_trees.c -o phast_trees.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-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo_hmm' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/motif' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_tfbs.c:16: /build/reproducible-path/phast-1.6+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-1.6+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-1.6+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-1.6+dfsg/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/motif' make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/dless/../..\" -fno-strict-aliasing -c dless.c -o dless.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition make[3]: *** No rule to make target 'bd_phylo_hmm.o', needed by '/build/reproducible-path/phast-1.6+dfsg/src/dless/../../bin/dless'. Stop. make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/dless' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/exoniphy/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/exoniphy/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/exoniphy/../../bin/exoniphy exoniphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/exoniphy' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/phastCons/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/phastCons/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/phastCons/../../bin/phastCons phastCons.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phastCons' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/phastOdds/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/phastOdds/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/phastOdds/../../bin/phastOdds phastOdds.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phastOdds' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/phastMotif' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/phastMotif/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/phastMotif/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/phastMotif/../../bin/phastMotif phastMotif.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phastMotif' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/phyloFit/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 gcc -L/build/reproducible-path/phast-1.6+dfsg/src/phyloFit/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloFit' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/phyloBoot/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/phyloBoot/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/phyloBoot/../../bin/phyloBoot phyloBoot.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloBoot' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/phyloP/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/phyloP/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/phyloP/../../bin/phyloP phyloP.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloP' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsDecode.c -o pbsDecode.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition make[3]: *** No rule to make target 'simplex_grid.o', needed by '/build/reproducible-path/phast-1.6+dfsg/src/prequel/../../bin/pbsDecode'. Stop. make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/prequel' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c all_dists.c -o all_dists.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/all_dists all_dists.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c base_evolve.c -o base_evolve.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/base_evolve base_evolve.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c chooseLines.c -o chooseLines.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c clean_genes.c -o clean_genes.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/clean_genes clean_genes.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/consEntropy consEntropy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/convert_coords convert_coords.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 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]; | ^~~~~~~ gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/display_rate_matrix display_rate_matrix.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/draw_tree draw_tree.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c eval_predictions.c -o eval_predictions.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/eval_predictions eval_predictions.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/hmm_train hmm_train.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_tweak.c -o hmm_tweak.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/hmm_tweak hmm_tweak.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_view.c -o hmm_view.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/hmm_view hmm_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c indelFit.c -o indelFit.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/indelFit indelFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/indelHistory indelHistory.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/maf_parse maf_parse.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/makeHKY makeHKY.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/msa_diff msa_diff.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/msa_split msa_split.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 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-1.6+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/msa.h:19, from msa_view.c:14: /build/reproducible-path/phast-1.6+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-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/msa_view msa_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c phast.c -o phast.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c phastBias.c -o phastBias.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/phastBias phastBias.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c refeature.c -o refeature.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/refeature refeature.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c stringiphy.c -o stringiphy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/stringiphy stringiphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c treeGen.c -o treeGen.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/treeGen treeGen.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c tree_doctor.c -o tree_doctor.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition 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-1.6+dfsg/src/../include/phast/tree_model.h:26, from tree_doctor.c:14: /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/trees.h:47:8: note: 'name' declared here 47 | char name [STR_MED_LEN]; /**< Name of this node i.e. 'Drosophila 23' usually one of the sequence names */ | ^~~~ gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/tree_doctor tree_doctor.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/util' mkdir -p ../doc/man/ Generating man pages... USAGE: convert_coords -m -f [-s ] [-d ] [-p] [-n] [-i PHYLIP|FASTA|MPM] DESCRIPTION: Converts coordinates of features in a GFF file according to a multiple alignment. Will map from the coordinate system of any sequence to any other sequence; can also map to or from the coordinate system of the entire alignment. In addition, supports translation of coordinates by specified offset. OPTIONS: -m (required) Name of file in which alignment is defined. -f (required) Name of file in which features are defined (GFF). -s Index of frame of reference for feature coordinates, as defined in the GFF file. Use an integer 1-N (if N seqs) or 0 to indicate the coordinate system of the alignment as a whole. Default behavior is to match features with alignment sequences by name (feature by feature). -d Index of destination frame of reference. Default is 0 (whole MSA). -p Positive coordinate offset. This value will be added to all coordinates. Useful when the alignment (or sequence) for which the coordinates are specified is a sub-alignment of yours. -n Negative coordinate offset. This value will be subtracted from all coordinates. Useful when your alignment is a sub-alignment of the alignment (or sequence) for which the coordinates are specified. -i FASTA|PHYLIP|MPM|SS Alignment format. Default is to guess format from file contents PROGRAM: draw_tree DESCRIPTION: Produces a simple postscript rendering of a tree. USAGE: draw_tree [-dbvs] | OPTIONS: (Required) File name of tree (expected to be in Newick format, unless filename ends with '.mod', in which case expected to be a tree model file). -d Print "diagonal" branches, instead of "right-angle" or "square" ones (produces a "cladogram", as opposed to a "phenogram"). This option implies -s. -b Suppress branch lengths. -v Vertical layout. -s Don't draw branches to scale. Done. make[2]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/phast-1.6+dfsg' cd test && PATH=/build/reproducible-path/phast-1.6+dfsg/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games make msa_view make[2]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/test' *** Testing msa_view *** msa_view hmrc.ss -i SS --end 10000 > hmrc.fa if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.fa -o PHYLIP > hmrc.ph msa_view hmrc.ph -i PHYLIP > hmrc.fa if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ph --out-format MPM --in-format PHYLIP > hmrc.mpm msa_view hmrc.mpm --in-format MPM > hmrc.fa if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.fa -o SS > hmrc_short_a.ss msa_view hmrc.ss --end 10000 -i SS -o SS > hmrc_short_b.ss if ! diff --brief hmrc_short_[ab].ss ; then echo "ERROR" ; exit 1 ; fi msa_view --seqs human,cow hmrc_short_a.ss -i SS -o SS | msa_view - -i SS > hm_a.fa msa_view --seqs human,cow hmrc.fa > hm_b.fa if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --gap-strip ANY -i SS -o SS | msa_view - -i SS > hmrc_nogaps_a.fa msa_view hmrc.ss -i SS | msa_view - --gap-strip ANY > hmrc_nogaps_b.fa if ! diff --brief hmrc_nogaps_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.fa --seqs human,cow --gap-strip ALL > hm_a.fa msa_view hmrc_short_a.ss --seqs human,cow -i SS --gap-strip ALL > hm_b.fa if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --start 10000 --end 20000 -i SS > hmrc_sub_a.fa msa_view hmrc.ss -i SS | msa_view - --start 10000 --end 20000 > hmrc_sub_b.fa if ! diff --brief hmrc_sub_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --summary -i SS > hmrc_summary if ! diff --brief -b hmrc_summary hmrc_summary_correct ; then echo "ERROR" ; exit 1 ; fi -e Passed all tests. make[2]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/test' make[1]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/phast/ make -j12 install DESTDIR=/build/reproducible-path/phast-1.6\+dfsg/debian/phast AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/phast-1.6+dfsg' (cd src; make install DESTDIR=/build/reproducible-path/phast-1.6+dfsg/debian/phast ) make[2]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mkdir -p /build/reproducible-path/phast-1.6+dfsg/debian/phast/usr/bin/ mkdir -p /build/reproducible-path/phast-1.6+dfsg/debian/phast/usr/share/phast/data/ mkdir -p /build/reproducible-path/phast-1.6+dfsg/debian/phast/usr/share/man/man1/ cp ../bin/* /build/reproducible-path/phast-1.6+dfsg/debian/phast/usr/bin/ cp -R ../data/* /build/reproducible-path/phast-1.6+dfsg/debian/phast/usr/share/phast/data/ cp -R ../doc/man/* /build/reproducible-path/phast-1.6+dfsg/debian/phast/usr/share/man/man1/ make[2]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/phast-1.6+dfsg' dh_installexamples find debian/*/usr/share/doc/*/examples -type f -size +1k -exec xz \{\} \; make[1]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg' dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'phast' in '../phast_1.6+dfsg-6_arm64.deb'. dpkg-deb: building package 'phast-dbgsym' in '../phast-dbgsym_1.6+dfsg-6_arm64.deb'. dpkg-genbuildinfo --build=binary -O../phast_1.6+dfsg-6_arm64.buildinfo dpkg-genchanges --build=binary -O../phast_1.6+dfsg-6_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: 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/4111687 and its subdirectories I: Current time: Tue Dec 23 20:50:35 -12 2025 I: pbuilder-time-stamp: 1766566235 Thu Nov 21 02:27:38 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Thu Nov 21 02:27:38 UTC 2024 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Thu Nov 21 02:27:38 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Thu Nov 21 02:27:38 UTC 2024 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-OKXuxJ' ==================================================================================== Thu Nov 21 02:27:39 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "2 phast trixie /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn 1.6+dfsg-6" as arguments. Thu Nov 21 02:27:39 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-FwUgQFcz" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Nov 21 02:27:39 UTC 2024 I: Downloading source for trixie/phast=1.6+dfsg-6 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 1870 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main phast 1.6+dfsg-6 (dsc) [2218 B] Get:2 http://deb.debian.org/debian trixie/main phast 1.6+dfsg-6 (tar) [1809 kB] Get:3 http://deb.debian.org/debian trixie/main phast 1.6+dfsg-6 (diff) [59.2 kB] Fetched 1870 kB in 0s (102 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 1870 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main phast 1.6+dfsg-6 (dsc) [2218 B] Get:2 http://deb.debian.org/debian trixie/main phast 1.6+dfsg-6 (tar) [1809 kB] Get:3 http://deb.debian.org/debian trixie/main phast 1.6+dfsg-6 (diff) [59.2 kB] Fetched 1870 kB in 0s (102 MB/s) Download complete and in download only mode ============================================================================= Re-Building phast in trixie on arm64 on codethink04-arm64 now. Date: Thu Nov 21 02:27:40 GMT 2024 Date UTC: Thu Nov 21 02:27:40 UTC 2024 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/pbuilderrc_Cm5M + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' phast = debian-installer -o phast = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' phast = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/pbuilderrc_Cm5M --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/b2 --logfile b2/build.log phast_1.6+dfsg-6.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Nov 21 16:27:40 +14 2024 I: pbuilder-time-stamp: 1732156060 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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_1.6+dfsg-6.dsc] I: copying [./phast_1.6+dfsg.orig.tar.xz] I: copying [./phast_1.6+dfsg-6.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Jul 31 20:28:57 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./phast_1.6+dfsg-6.dsc: no acceptable signature found dpkg-source: info: extracting phast in phast-1.6+dfsg dpkg-source: info: unpacking phast_1.6+dfsg.orig.tar.xz dpkg-source: info: unpacking phast_1.6+dfsg-6.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 fix_test_makefile.patch dpkg-source: info: applying pcre2.patch dpkg-source: info: applying gcc-14.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2229366/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Nov 21 02:27 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2229366/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2229366/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=78adefd9ae7c44108f473606a56a0276 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2229366 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/pbuilderrc_Cm5M --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/b2 --logfile b2/build.log phast_1.6+dfsg-6.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2229366/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team 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 ... 20087 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} libicu72{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} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 44 newly installed, 0 to remove and 0 not upgraded. Need to get 27.7 MB of archives. After unpacking 126 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-8 [517 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 23 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-3+b1 [98.9 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libblas-dev arm64 3.12.0-3+b1 [106 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-8 [361 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-3+b1 [1812 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 liblapack-dev arm64 3.12.0-3+b1 [3709 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libtmglib3 arm64 3.12.0-3+b1 [98.8 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 liblapacke arm64 3.12.0-3+b1 [336 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libtmglib-dev arm64 3.12.0-3+b1 [103 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 liblapacke-dev arm64 3.12.0-3+b1 [322 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libpcre2-16-0 arm64 10.42-4+b2 [220 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libpcre2-32-0 arm64 10.42-4+b2 [211 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libpcre2-posix3 arm64 10.42-4+b2 [55.9 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libpcre2-dev arm64 10.42-4+b2 [683 kB] Fetched 27.7 MB in 0s (155 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 20087 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../09-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... 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_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../22-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package help2man. Preparing to unpack .../30-help2man_1.49.3+b1_arm64.deb ... Unpacking help2man (1.49.3+b1) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../31-libblas3_3.12.0-3+b1_arm64.deb ... Unpacking libblas3:arm64 (3.12.0-3+b1) ... Selecting previously unselected package libblas-dev:arm64. Preparing to unpack .../32-libblas-dev_3.12.0-3+b1_arm64.deb ... Unpacking libblas-dev:arm64 (3.12.0-3+b1) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../33-libgfortran5_14.2.0-8_arm64.deb ... Unpacking libgfortran5:arm64 (14.2.0-8) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../34-liblapack3_3.12.0-3+b1_arm64.deb ... Unpacking liblapack3:arm64 (3.12.0-3+b1) ... Selecting previously unselected package liblapack-dev:arm64. Preparing to unpack .../35-liblapack-dev_3.12.0-3+b1_arm64.deb ... Unpacking liblapack-dev:arm64 (3.12.0-3+b1) ... Selecting previously unselected package libtmglib3:arm64. Preparing to unpack .../36-libtmglib3_3.12.0-3+b1_arm64.deb ... Unpacking libtmglib3:arm64 (3.12.0-3+b1) ... Selecting previously unselected package liblapacke:arm64. Preparing to unpack .../37-liblapacke_3.12.0-3+b1_arm64.deb ... Unpacking liblapacke:arm64 (3.12.0-3+b1) ... Selecting previously unselected package libtmglib-dev:arm64. Preparing to unpack .../38-libtmglib-dev_3.12.0-3+b1_arm64.deb ... Unpacking libtmglib-dev:arm64 (3.12.0-3+b1) ... Selecting previously unselected package liblapacke-dev:arm64. Preparing to unpack .../39-liblapacke-dev_3.12.0-3+b1_arm64.deb ... Unpacking liblapacke-dev:arm64 (3.12.0-3+b1) ... Selecting previously unselected package libpcre2-16-0:arm64. Preparing to unpack .../40-libpcre2-16-0_10.42-4+b2_arm64.deb ... Unpacking libpcre2-16-0:arm64 (10.42-4+b2) ... Selecting previously unselected package libpcre2-32-0:arm64. Preparing to unpack .../41-libpcre2-32-0_10.42-4+b2_arm64.deb ... Unpacking libpcre2-32-0:arm64 (10.42-4+b2) ... Selecting previously unselected package libpcre2-posix3:arm64. Preparing to unpack .../42-libpcre2-posix3_10.42-4+b2_arm64.deb ... Unpacking libpcre2-posix3:arm64 (10.42-4+b2) ... Selecting previously unselected package libpcre2-dev:arm64. Preparing to unpack .../43-libpcre2-dev_10.42-4+b2_arm64.deb ... Unpacking libpcre2-dev:arm64 (10.42-4+b2) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libpcre2-16-0:arm64 (10.42-4+b2) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up libpcre2-32-0:arm64 (10.42-4+b2) ... Setting up libblas3:arm64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up autopoint (0.22.5-2) ... Setting up libgfortran5:arm64 (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up libpcre2-posix3:arm64 (10.42-4+b2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up libblas-dev:arm64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:arm64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libpcre2-dev:arm64 (10.42-4+b2) ... Setting up libtool (2.4.7-8) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3+b1) ... Setting up dh-autoreconf (20) ... Setting up libtmglib3:arm64 (3.12.0-3+b1) ... Setting up liblapack-dev:arm64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up liblapacke:arm64 (3.12.0-3+b1) ... Setting up libtmglib-dev:arm64 (3.12.0-3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up liblapacke-dev:arm64 (3.12.0-3+b1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2229366/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2229366/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/phast-1.6+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../phast_1.6+dfsg-6_source.changes dpkg-buildpackage: info: source package phast dpkg-buildpackage: info: source version 1.6+dfsg-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/phast-1.6+dfsg' dh_auto_clean cd src && make clean make[2]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/reproducible-path/phast-1.6+dfsg/src/lib/$dir && make clean ; done make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/base' rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/base' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/msa' rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/msa' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/feature' rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/feature' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/hmm' rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/hmm' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo' rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo_hmm' rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/motif' rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/motif' rm -f /build/reproducible-path/phast-1.6+dfsg/src/lib/../../lib/* make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/dless' rm -f *.o dless.help dlessP.help /build/reproducible-path/phast-1.6+dfsg/src/dless/../../bin/dless /build/reproducible-path/phast-1.6+dfsg/src/dless/../../bin/dlessP make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/dless' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/exoniphy' rm -f *.o *.help /build/reproducible-path/phast-1.6+dfsg/src/exoniphy/../../bin/exoniphy make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/exoniphy' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/phastCons' rm -f *.o /build/reproducible-path/phast-1.6+dfsg/src/phastCons/../../bin/phastCons phastCons.help make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phastCons' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/phastOdds' rm -f *.o *.help /build/reproducible-path/phast-1.6+dfsg/src/phastOdds/../../bin/phastOdds make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phastOdds' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/phastMotif' rm -f *.o /build/reproducible-path/phast-1.6+dfsg/src/phastMotif/../../bin/phastMotif make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phastMotif' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloFit' rm -f *.o /build/reproducible-path/phast-1.6+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.help make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloFit' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloBoot' rm -f *.o *.help /build/reproducible-path/phast-1.6+dfsg/src/phyloBoot/../../bin/phyloBoot make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloBoot' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloP' rm -f *.o /build/reproducible-path/phast-1.6+dfsg/src/phyloP/../../bin/phyloP phyloP.help make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloP' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/prequel' rm -f *.o /build/reproducible-path/phast-1.6+dfsg/src/prequel/../../bin/pbsDecode /build/reproducible-path/phast-1.6+dfsg/src/prequel/../../bin/pbsEncode /build/reproducible-path/phast-1.6+dfsg/src/prequel/../../bin/pbsScoreMatrix /build/reproducible-path/phast-1.6+dfsg/src/prequel/../../bin/pbsTrain /build/reproducible-path/phast-1.6+dfsg/src/prequel/../../bin/prequel pbsDecode.help pbsEncode.help pbsScoreMatrix.help pbsTrain.help prequel.help make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/prequel' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/util' rm -f *.o *.help /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/all_dists /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/base_evolve /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/chooseLines /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/clean_genes /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/consEntropy /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/convert_coords /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/display_rate_matrix /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/draw_tree /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/eval_predictions /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/hmm_train /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/hmm_tweak /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/hmm_view /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/indelFit /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/indelHistory /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/maf_parse /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/makeHKY /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/modFreqs /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/msa_diff /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/msa_split /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/msa_view /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/phast /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/phastBias /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/refeature /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/stringiphy /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/treeGen /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/tree_doctor make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/util' rm -rf ../bin ../lib ../doc make[2]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg/src' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mkdir -p ../bin ../lib for dir in lib dless exoniphy phastCons phastOdds phastMotif phyloFit phyloBoot phyloP prequel util ; do cd /build/reproducible-path/phast-1.6+dfsg/src/$dir && make ; done make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/reproducible-path/phast-1.6+dfsg/src/lib/$dir && make ; done make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/base' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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:672:46: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 672 | 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-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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:935:1: note: expected 'PCRE2_SPTR8' {aka 'const unsigned char *'} but argument is of type 'char *' 935 | 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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+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-1.6+dfsg/src/lib/base/../../../lib/libphast.a ar rs /build/reproducible-path/phast-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+dfsg/src/lib/base' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/msa' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/../include/phast/local_alignment.h:36, from phast_local_alignment.c:32: /build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_msa.c:39: /build/reproducible-path/phast-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_multi_msa.c:37: /build/reproducible-path/phast-1.6+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-1.6+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-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/msa.h:19, from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/sufficient_stats.h:20, from phast_sufficient_stats.c:11: /build/reproducible-path/phast-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+dfsg/src/lib/msa' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/feature' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/../include/phast/gff.h:21, from phast_bed.c:15: /build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/category_map.h:92, from phast_category_map.c:10: /build/reproducible-path/phast-1.6+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-1.6+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-1.6+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:]]*(.*)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:43:28: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 43 | extend_re = str_re_new("^[[:space:]]*FEATURE_EXTEND[[:space:]]*:[[:space:]]*(.+)[[:space:]]*\\((.+)\\)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/../include/phast/gff.h:21, from phast_gff.c:13: /build/reproducible-path/phast-1.6+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-1.6+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-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+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-1.6+dfsg/src/lib/feature' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/hmm' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/hmm' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_p.c -o phast_phylo_p.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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_p_print.c -o phast_phylo_p_print.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_p_print.c: In function 'print_feats_generic': phast_phylo_p_print.c:752:50: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign] 752 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_phylo_p_print.c:17: /build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_subst_distrib.c -o phast_subst_distrib.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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_subst_mods.c -o phast_subst_mods.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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_tree_likelihoods.c -o phast_tree_likelihoods.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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_tree_model.c -o phast_tree_model.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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_trees.c -o phast_trees.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-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo_hmm' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/motif' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_tfbs.c:16: /build/reproducible-path/phast-1.6+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-1.6+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-1.6+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-1.6+dfsg/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o ar rs /build/reproducible-path/phast-1.6+dfsg/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o make[4]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib/motif' make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/lib' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/dless/../..\" -fno-strict-aliasing -c dless.c -o dless.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition make[3]: *** No rule to make target 'bd_phylo_hmm.o', needed by '/build/reproducible-path/phast-1.6+dfsg/src/dless/../../bin/dless'. Stop. make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/dless' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/exoniphy/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/exoniphy/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/exoniphy/../../bin/exoniphy exoniphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/exoniphy' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/phastCons/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/phastCons/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/phastCons/../../bin/phastCons phastCons.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phastCons' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/phastOdds/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/phastOdds/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/phastOdds/../../bin/phastOdds phastOdds.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phastOdds' make[3]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src/phastMotif' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/phastMotif/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/phastMotif/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/phastMotif/../../bin/phastMotif phastMotif.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phastMotif' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/phyloFit/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 gcc -L/build/reproducible-path/phast-1.6+dfsg/src/phyloFit/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloFit' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/phyloBoot/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/phyloBoot/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/phyloBoot/../../bin/phyloBoot phyloBoot.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloBoot' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/phyloP/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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-1.6+dfsg/src/phyloP/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/phyloP/../../bin/phyloP phyloP.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/phyloP' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsDecode.c -o pbsDecode.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition make[3]: *** No rule to make target 'simplex_grid.o', needed by '/build/reproducible-path/phast-1.6+dfsg/src/prequel/../../bin/pbsDecode'. Stop. make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/prequel' make[3]: Entering directory '/build/reproducible-path/phast-1.6+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-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c all_dists.c -o all_dists.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/all_dists all_dists.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c base_evolve.c -o base_evolve.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/base_evolve base_evolve.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c chooseLines.c -o chooseLines.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c clean_genes.c -o clean_genes.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/clean_genes clean_genes.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/consEntropy consEntropy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/convert_coords convert_coords.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 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]; | ^~~~~~~ gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/display_rate_matrix display_rate_matrix.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/draw_tree draw_tree.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c eval_predictions.c -o eval_predictions.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/eval_predictions eval_predictions.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/hmm_train hmm_train.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_tweak.c -o hmm_tweak.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/hmm_tweak hmm_tweak.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_view.c -o hmm_view.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/hmm_view hmm_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c indelFit.c -o indelFit.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/indelFit indelFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/indelHistory indelHistory.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/maf_parse maf_parse.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/makeHKY makeHKY.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/msa_diff msa_diff.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/msa_split msa_split.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+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 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-1.6+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/msa.h:19, from msa_view.c:14: /build/reproducible-path/phast-1.6+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-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/msa_view msa_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c phast.c -o phast.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c phastBias.c -o phastBias.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/phastBias phastBias.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c refeature.c -o refeature.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/refeature refeature.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c stringiphy.c -o stringiphy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/stringiphy stringiphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c treeGen.c -o treeGen.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/treeGen treeGen.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/reproducible-path/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c tree_doctor.c -o tree_doctor.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition 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-1.6+dfsg/src/../include/phast/tree_model.h:26, from tree_doctor.c:14: /build/reproducible-path/phast-1.6+dfsg/src/../include/phast/trees.h:47:8: note: 'name' declared here 47 | char name [STR_MED_LEN]; /**< Name of this node i.e. 'Drosophila 23' usually one of the sequence names */ | ^~~~ gcc -L/build/reproducible-path/phast-1.6+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.6+dfsg/src/util/../../bin/tree_doctor tree_doctor.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src/util' mkdir -p ../doc/man/ Generating man pages... USAGE: convert_coords -m -f [-s ] [-d ] [-p] [-n] [-i PHYLIP|FASTA|MPM] DESCRIPTION: Converts coordinates of features in a GFF file according to a multiple alignment. Will map from the coordinate system of any sequence to any other sequence; can also map to or from the coordinate system of the entire alignment. In addition, supports translation of coordinates by specified offset. OPTIONS: -m (required) Name of file in which alignment is defined. -f (required) Name of file in which features are defined (GFF). -s Index of frame of reference for feature coordinates, as defined in the GFF file. Use an integer 1-N (if N seqs) or 0 to indicate the coordinate system of the alignment as a whole. Default behavior is to match features with alignment sequences by name (feature by feature). -d Index of destination frame of reference. Default is 0 (whole MSA). -p Positive coordinate offset. This value will be added to all coordinates. Useful when the alignment (or sequence) for which the coordinates are specified is a sub-alignment of yours. -n Negative coordinate offset. This value will be subtracted from all coordinates. Useful when your alignment is a sub-alignment of the alignment (or sequence) for which the coordinates are specified. -i FASTA|PHYLIP|MPM|SS Alignment format. Default is to guess format from file contents PROGRAM: draw_tree DESCRIPTION: Produces a simple postscript rendering of a tree. USAGE: draw_tree [-dbvs] | OPTIONS: (Required) File name of tree (expected to be in Newick format, unless filename ends with '.mod', in which case expected to be a tree model file). -d Print "diagonal" branches, instead of "right-angle" or "square" ones (produces a "cladogram", as opposed to a "phenogram"). This option implies -s. -b Suppress branch lengths. -v Vertical layout. -s Don't draw branches to scale. Done. make[2]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/phast-1.6+dfsg' cd test && PATH=/build/reproducible-path/phast-1.6+dfsg/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path make msa_view make[2]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/test' *** Testing msa_view *** msa_view hmrc.ss -i SS --end 10000 > hmrc.fa if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.fa -o PHYLIP > hmrc.ph msa_view hmrc.ph -i PHYLIP > hmrc.fa if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ph --out-format MPM --in-format PHYLIP > hmrc.mpm msa_view hmrc.mpm --in-format MPM > hmrc.fa if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.fa -o SS > hmrc_short_a.ss msa_view hmrc.ss --end 10000 -i SS -o SS > hmrc_short_b.ss if ! diff --brief hmrc_short_[ab].ss ; then echo "ERROR" ; exit 1 ; fi msa_view --seqs human,cow hmrc_short_a.ss -i SS -o SS | msa_view - -i SS > hm_a.fa msa_view --seqs human,cow hmrc.fa > hm_b.fa if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --gap-strip ANY -i SS -o SS | msa_view - -i SS > hmrc_nogaps_a.fa msa_view hmrc.ss -i SS | msa_view - --gap-strip ANY > hmrc_nogaps_b.fa if ! diff --brief hmrc_nogaps_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.fa --seqs human,cow --gap-strip ALL > hm_a.fa msa_view hmrc_short_a.ss --seqs human,cow -i SS --gap-strip ALL > hm_b.fa if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --start 10000 --end 20000 -i SS > hmrc_sub_a.fa msa_view hmrc.ss -i SS | msa_view - --start 10000 --end 20000 > hmrc_sub_b.fa if ! diff --brief hmrc_sub_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --summary -i SS > hmrc_summary if ! diff --brief -b hmrc_summary hmrc_summary_correct ; then echo "ERROR" ; exit 1 ; fi Passed all tests. make[2]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/test' make[1]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/phast/ make -j12 install DESTDIR=/build/reproducible-path/phast-1.6\+dfsg/debian/phast AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/phast-1.6+dfsg' (cd src; make install DESTDIR=/build/reproducible-path/phast-1.6+dfsg/debian/phast ) make[2]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/src' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mkdir -p /build/reproducible-path/phast-1.6+dfsg/debian/phast/usr/bin/ mkdir -p /build/reproducible-path/phast-1.6+dfsg/debian/phast/usr/share/phast/data/ mkdir -p /build/reproducible-path/phast-1.6+dfsg/debian/phast/usr/share/man/man1/ cp ../bin/* /build/reproducible-path/phast-1.6+dfsg/debian/phast/usr/bin/ cp -R ../data/* /build/reproducible-path/phast-1.6+dfsg/debian/phast/usr/share/phast/data/ cp -R ../doc/man/* /build/reproducible-path/phast-1.6+dfsg/debian/phast/usr/share/man/man1/ make[2]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/phast-1.6+dfsg' dh_installexamples find debian/*/usr/share/doc/*/examples -type f -size +1k -exec xz \{\} \; make[1]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg' dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'phast-dbgsym' in '../phast-dbgsym_1.6+dfsg-6_arm64.deb'. dpkg-deb: building package 'phast' in '../phast_1.6+dfsg-6_arm64.deb'. dpkg-genbuildinfo --build=binary -O../phast_1.6+dfsg-6_arm64.buildinfo dpkg-genchanges --build=binary -O../phast_1.6+dfsg-6_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2229366/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2229366/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2229366 and its subdirectories I: Current time: Thu Nov 21 16:30:51 +14 2024 I: pbuilder-time-stamp: 1732156251 + false + set +x Thu Nov 21 02:30:51 UTC 2024 I: Signing ./b2/phast_1.6+dfsg-6_arm64.buildinfo as phast_1.6+dfsg-6_arm64.buildinfo.asc Thu Nov 21 02:30:51 UTC 2024 I: Signed ./b2/phast_1.6+dfsg-6_arm64.buildinfo as ./b2/phast_1.6+dfsg-6_arm64.buildinfo.asc Thu Nov 21 02:30:51 UTC 2024 - build #2 for phast/trixie/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Thu Nov 21 02:30:51 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-FwUgQFcz, removing. /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn: total 192 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 02:27 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 02:30 b2 -rw-r--r-- 1 jenkins jenkins 2218 Jul 31 20:37 phast_1.6+dfsg-6.dsc -rw------- 1 jenkins jenkins 178229 Nov 21 02:27 rbuildlog.NplgiYB /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/b1: total 29220 -rw-r--r-- 1 jenkins jenkins 174601 Nov 21 02:27 build.log -rw-r--r-- 1 jenkins jenkins 26719824 Nov 21 02:27 phast-dbgsym_1.6+dfsg-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 59204 Nov 21 02:27 phast_1.6+dfsg-6.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2218 Nov 21 02:27 phast_1.6+dfsg-6.dsc -rw-r--r-- 1 jenkins jenkins 5408 Nov 21 02:27 phast_1.6+dfsg-6_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6290 Nov 21 02:27 phast_1.6+dfsg-6_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1538 Nov 21 02:27 phast_1.6+dfsg-6_arm64.changes -rw-r--r-- 1 jenkins jenkins 2884204 Nov 21 02:27 phast_1.6+dfsg-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 1397 Nov 21 02:27 phast_1.6+dfsg-6_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/b2: total 29176 -rw-r--r-- 1 jenkins jenkins 175513 Nov 21 02:30 build.log -rw-r--r-- 1 jenkins jenkins 26719824 Nov 21 02:30 phast-dbgsym_1.6+dfsg-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 59204 Nov 21 02:30 phast_1.6+dfsg-6.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2218 Nov 21 02:30 phast_1.6+dfsg-6.dsc -rw-r--r-- 1 jenkins jenkins 5408 Nov 21 02:30 phast_1.6+dfsg-6_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6290 Nov 21 02:30 phast_1.6+dfsg-6_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1538 Nov 21 02:30 phast_1.6+dfsg-6_arm64.changes -rw-r--r-- 1 jenkins jenkins 2884204 Nov 21 02:30 phast_1.6+dfsg-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 1397 Nov 21 02:30 phast_1.6+dfsg-6_source.changes Thu Nov 21 02:30:53 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Thu Nov 21 02:30:54 UTC 2024 I: phast_1.6+dfsg-6_arm64.changes: Format: 1.8 Date: Wed, 31 Jul 2024 22:24:23 +0200 Source: phast Binary: phast phast-dbgsym Architecture: arm64 Version: 1.6+dfsg-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: phast - phylogenetic analysis with space/time models Closes: 1075383 Changes: phast (1.6+dfsg-6) unstable; urgency=medium . * gcc-14.patch: fix build failure with gcc 14. (Closes: #1075383) * d/control: add myself to uploaders. * d/control: declare compliance to standards version 4.7.0. * d/p/clapack.patch: convert e acute to UTF-8. Checksums-Sha1: 35b30656bec3b2c6a1dc6e00f85fcce0ce8bcce6 26719824 phast-dbgsym_1.6+dfsg-6_arm64.deb 6d1a726be0f6e648c0cb037cfd9d779a278b521a 5408 phast_1.6+dfsg-6_arm64.buildinfo 26a2fe078ec51a58b9434ad166ceee864b1216cd 2884204 phast_1.6+dfsg-6_arm64.deb Checksums-Sha256: cd37264c0c5acb88c18af26f98d634ff7a04acd67f54226261c5f7e273d7aee3 26719824 phast-dbgsym_1.6+dfsg-6_arm64.deb 02bf407c91af6a9a2b1c3b9abaf9b714cf16c21d93591cc3b6f23123ff0f4106 5408 phast_1.6+dfsg-6_arm64.buildinfo 7ebdcc55ab0ccb7b4d5724b72207602fd6483acbfab11ffead8457ca7d4b265d 2884204 phast_1.6+dfsg-6_arm64.deb Files: 92483d8f98e31c56b8124850f88c3263 26719824 debug optional phast-dbgsym_1.6+dfsg-6_arm64.deb 2f61cd825180cfe5232a17560b1906f2 5408 science optional phast_1.6+dfsg-6_arm64.buildinfo 20a67424ded2f0733509cbc593294827 2884204 science optional phast_1.6+dfsg-6_arm64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/phast_1.6+dfsg-6.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/phast_1.6+dfsg-6.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/phast_1.6+dfsg-6.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/phast_1.6+dfsg-6.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/arm64/phast_1.6+dfsg-6_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/phast_1.6+dfsg-6.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-11-21 02:27:36.531924444 +0000 +++ b2/build.log 2024-11-21 02:30:52.679066370 +0000 @@ -1,20 +1,8 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Dec 23 20:48:34 -12 2025 -I: pbuilder-time-stamp: 1766566114 +I: Current time: Thu Nov 21 16:27:40 +14 2024 +I: pbuilder-time-stamp: 1732156060 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] -tar: ./dev/shm: time stamp 2027-01-26 00:52:16 is 34401821.609963636 s in the future -tar: ./etc/resolv.conf: time stamp 2027-01-26 00:52:16 is 34401821.609490316 s in the future -tar: ./etc/mailname: time stamp 2027-01-26 00:52:16 is 34401821.609435716 s in the future -tar: ./etc/hostname: time stamp 2027-01-26 00:52:16 is 34401821.609397076 s in the future -tar: ./etc/hosts: time stamp 2027-01-26 00:52:16 is 34401821.609359876 s in the future -tar: ./tmp: time stamp 2027-01-26 00:52:21 is 34401826.603924956 s in the future -tar: ./var/cache/apt: time stamp 2027-01-26 00:52:21 is 34401821.425953076 s in the future -tar: ./var/lib/apt/lists/partial: time stamp 2027-01-26 00:52:17 is 34401817.395332076 s in the future -tar: ./run/shm: time stamp 2027-01-26 00:52:16 is 34401816.015226876 s in the future -tar: ./run: time stamp 2027-01-26 00:52:16 is 34401816.006278396 s in the future -tar: ./etc: time stamp 2027-01-26 00:52:16 is 34401816.006202476 s in the future -tar: ./dev: time stamp 2027-01-26 00:52:16 is 34401816.006191916 s in the future I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem @@ -47,52 +35,84 @@ dpkg-source: info: applying gcc-14.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4111687/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2229366/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 21 02:27 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2229366/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2229366/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='7cefe57d4f8b4a118db06f539197c79d' - 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='4111687' - PS1='# ' - PS2='> ' + INVOCATION_ID=78adefd9ae7c44108f473606a56a0276 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2229366 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.eewESGYn/pbuilderrc_mrRd --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/b1 --logfile b1/build.log phast_1.6+dfsg-6.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/pbuilderrc_Cm5M --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/b2 --logfile b2/build.log phast_1.6+dfsg-6.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink01-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4111687/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2229366/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -186,7 +206,7 @@ Get: 42 http://deb.debian.org/debian trixie/main arm64 libpcre2-32-0 arm64 10.42-4+b2 [211 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libpcre2-posix3 arm64 10.42-4+b2 [55.9 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libpcre2-dev arm64 10.42-4+b2 [683 kB] -Fetched 27.7 MB in 0s (166 MB/s) +Fetched 27.7 MB in 0s (155 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 20087 files and directories currently installed.) @@ -381,7 +401,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/phast-1.6+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_1.6+dfsg-6_source.changes +I: user script /srv/workspace/pbuilder/2229366/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2229366/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/phast-1.6+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../phast_1.6+dfsg-6_source.changes dpkg-buildpackage: info: source package phast dpkg-buildpackage: info: source version 1.6+dfsg-6 dpkg-buildpackage: info: source distribution unstable @@ -1410,7 +1434,7 @@ make[1]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/phast-1.6+dfsg' -cd test && PATH=/build/reproducible-path/phast-1.6+dfsg/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games make msa_view +cd test && PATH=/build/reproducible-path/phast-1.6+dfsg/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path make msa_view make[2]: Entering directory '/build/reproducible-path/phast-1.6+dfsg/test' *** Testing msa_view *** msa_view hmrc.ss -i SS --end 10000 > hmrc.fa @@ -1438,7 +1462,7 @@ if ! diff --brief hmrc_sub_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --summary -i SS > hmrc_summary if ! diff --brief -b hmrc_summary hmrc_summary_correct ; then echo "ERROR" ; exit 1 ; fi --e Passed all tests. +Passed all tests. make[2]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg/test' make[1]: Leaving directory '/build/reproducible-path/phast-1.6+dfsg' @@ -1484,8 +1508,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'phast' in '../phast_1.6+dfsg-6_arm64.deb'. dpkg-deb: building package 'phast-dbgsym' in '../phast-dbgsym_1.6+dfsg-6_arm64.deb'. +dpkg-deb: building package 'phast' in '../phast_1.6+dfsg-6_arm64.deb'. dpkg-genbuildinfo --build=binary -O../phast_1.6+dfsg-6_arm64.buildinfo dpkg-genchanges --build=binary -O../phast_1.6+dfsg-6_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1493,12 +1517,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2229366/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2229366/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/4111687 and its subdirectories -I: Current time: Tue Dec 23 20:50:35 -12 2025 -I: pbuilder-time-stamp: 1766566235 +I: removing directory /srv/workspace/pbuilder/2229366 and its subdirectories +I: Current time: Thu Nov 21 16:30:51 +14 2024 +I: pbuilder-time-stamp: 1732156251 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/phast_1.6+dfsg-6.diff: 68.9% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/phast_1.6+dfsg-6.diff.gz b2/build.log: 91.1% -- replaced with stdout Compressing the 1st log... b1/build.log: 91.4% -- replaced with stdout Thu Nov 21 02:30:55 UTC 2024 I: diffoscope 283 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_phast_trixie_arm64_1732156255 + touch /var/log/reproducible-builds/diffoscope_stamp_phast_trixie_arm64_1732156255 + RESULT=0 + systemd-run '--description=diffoscope on phast/1.6+dfsg-6 in trixie/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_15-71323 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn --run-session -c jenkins-reproducible-trixie-diffoscope-3497fd79-8274-44b5-bc3c-2478bfb20e21 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/dbd-tmp-NS6JABv ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/phast_1.6+dfsg-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/phast_1.6+dfsg-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/phast_1.6+dfsg-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/b1/phast_1.6+dfsg-6_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/b2/phast_1.6+dfsg-6_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_15-71323.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/phast_1.6+dfsg-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/phast_1.6+dfsg-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/phast_1.6+dfsg-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/b1/phast_1.6+dfsg-6_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.eewESGYn/b2/phast_1.6+dfsg-6_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.603s) 0.603s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.266s) 0.266s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 916ms CPU time consumed: 911ms _ _ _ __ | |__ __ _ ___| |_ | '_ \| '_ \ / _` / __| __| | |_) | | | | (_| \__ \ |_ | .__/|_| |_|\__,_|___/\__| |_| Thu Nov 21 02:30:56 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Thu Nov 21 02:30:56 UTC 2024 I: phast from trixie built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-11-21 02:30:56] INFO: Starting at 2024-11-21 02:30:56.969107 [2024-11-21 02:30:57] INFO: Generating the pages of 1 package(s) [2024-11-21 02:30:57] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/arm64/phast didn't produce a buildlog, even though it has been built. [2024-11-21 02:30:57] INFO: Finished at 2024-11-21 02:30:57.396863, took: 0:00:00.427762 Thu Nov 21 02:30:57 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/arm64/phast.html Thu Nov 21 02:30:57 UTC 2024 I: Submitting .buildinfo files to external archives: Thu Nov 21 02:30:57 UTC 2024 I: Submitting 8.0K b1/phast_1.6+dfsg-6_arm64.buildinfo.asc https://buildinfo.debian.net/6d1a726be0f6e648c0cb037cfd9d779a278b521a/phast_1.6+dfsg-6_arm64 Thu Nov 21 02:30:59 UTC 2024 I: Submitting 8.0K b2/phast_1.6+dfsg-6_arm64.buildinfo.asc https://buildinfo.debian.net/22dce182976a7e21bf24dc5a9049560c227c4daf/phast_1.6+dfsg-6_arm64 Thu Nov 21 02:31:00 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Nov 21 02:31:00 UTC 2024 I: Done submitting .buildinfo files. Thu Nov 21 02:31:00 UTC 2024 I: Removing signed phast_1.6+dfsg-6_arm64.buildinfo.asc files: removed './b1/phast_1.6+dfsg-6_arm64.buildinfo.asc' removed './b2/phast_1.6+dfsg-6_arm64.buildinfo.asc' 1732156260 arm64 trixie phast Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/phast_1.6+dfsg-6.rbuild.log: 89.9% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/phast_1.6+dfsg-6.rbuild.log.gz [2024-11-21 02:31:00] INFO: Starting at 2024-11-21 02:31:00.594349 [2024-11-21 02:31:00] INFO: Generating the pages of 1 package(s) [2024-11-21 02:31:00] INFO: Finished at 2024-11-21 02:31:00.997983, took: 0:00:00.403643 All cleanup done. Thu Nov 21 02:31:01 UTC 2024 - total duration: 0h 5m 38s. Thu Nov 21 02:31:01 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-0Y5UFKSf, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 5min 42.842s CPU time consumed: 8.115s