Tue May 9 14:32:59 UTC 2023 I: starting to build phast/bookworm/armhf on jenkins on '2023-05-09 14:32' Tue May 9 14:32:59 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_16/9331/console.log Tue May 9 14:32:59 UTC 2023 I: Downloading source for bookworm/phast=1.6+dfsg-3 --2023-05-09 14:32:59-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/phast/phast_1.6%2bdfsg-3.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2048 (2.0K) [text/prs.lines.tag] Saving to: ‘phast_1.6+dfsg-3.dsc’ 0K .. 100% 116M=0s 2023-05-09 14:33:00 (116 MB/s) - ‘phast_1.6+dfsg-3.dsc’ saved [2048/2048] Tue May 9 14:33:00 UTC 2023 I: phast_1.6+dfsg-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: phast Binary: phast Architecture: any Version: 1.6+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://compgen.cshl.edu/phast/ Standards-Version: 4.6.0 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, libblas-dev, libtmglib-dev, libpcre2-dev, libf2c2-dev, libatlas-base-dev, help2man Package-List: phast deb science optional arch=any Checksums-Sha1: 5bf657d4f4556f8848c6e4f362b407ec998cf10a 1808800 phast_1.6+dfsg.orig.tar.xz b59881c299836be37bc9e5852454d786998b1e55 57668 phast_1.6+dfsg-3.debian.tar.xz Checksums-Sha256: 7deae15e8bd8ce8e11b251b42795e0595dd86271360b08d15e6ba107ae66863f 1808800 phast_1.6+dfsg.orig.tar.xz 95f5073ace91794c2f9bffcc725a73c4e1c7f8d754080ae5df622192c378b8b6 57668 phast_1.6+dfsg-3.debian.tar.xz Files: b625b9d3abbe0fdc31468820121b30e9 1808800 phast_1.6+dfsg.orig.tar.xz 38cf28b61182cc39d4f63c4e951b70bb 57668 phast_1.6+dfsg-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmGXntIRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHyThAAlXHzwYoS5ah85j8Dv6yi0Xehm+5Re01l egeOgBLS31DmypElUK+6zAd8nF4Tz2bUN9K4kuILBNyR+hnL3H5uj4hrn4OBBsja EYDiC+9H1r+AceeXHAbBoCobNjR5R3o27OwzXY73G6FCm5vC5f9VxkcdwF9MS6rB SLVpUK03MuQ8Rgf0Ys8ZWjCdXDP7A0b+XjvaGe1Lz86+NmsdnWSRFw+/OGPFwjyz 1sZIc/2ikyCml3X9Uu/eVIFEqk6kPQFhuSbWlkGv/O/HiaJNuVlAtgRrOQgX7k8R R1jA1Q1xY643LA4t8HpIqi8k9GRuUvnkzHmtTnAmoyhWFRnXi8SeNza4mC9KyWif jVk2bvozbxt4IzjnZDJHNL7lpthj3iNBo/0+v5Gx4DYEOMwkRtlXbynxEPFEUZ9m BBelrqOuXZfOGWLtMQsOygMbX/dzpns4XU3Plr7h2XKmDnGQ5+rafhzhyZpGs/cI AbXvCtw4+TZN6HlI7SYh7zZclv/ItOD0i+Fj27fmD9AHJDL25cpPE9T1XxNLSaqo oFvRko0lK71A9M2ViruOTCbUZiR5mz94pEKYTxMLGoN/MqOzoCOUTRCQBX7ckSGt +I4R2gcANUgfqwK5k5b+RkqDWl/rl/2bZr7OrSf23NTLgi+RtG5stt+X1YnHhOa4 0SUyYl1U8L0= =ODVQ -----END PGP SIGNATURE----- Tue May 9 14:33:00 UTC 2023 I: Checking whether the package is not for us Tue May 9 14:33:00 UTC 2023 I: Starting 1st build on remote node virt32b-armhf-rb.debian.net. Tue May 9 14:33:00 UTC 2023 I: Preparing to do remote build '1' on virt32b-armhf-rb.debian.net. Tue May 9 14:42:21 UTC 2023 I: Deleting $TMPDIR on virt32b-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue May 9 02:33:06 -12 2023 I: pbuilder-time-stamp: 1683642786 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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-3.dsc] I: copying [./phast_1.6+dfsg.orig.tar.xz] I: copying [./phast_1.6+dfsg-3.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Nov 19 00:55:46 2021 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./phast_1.6+dfsg-3.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-3.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/24491/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='3973b5a775e44e288cb03c90b534b993' 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='24491' 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.rVIc7mor/pbuilderrc_6QcL --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.rVIc7mor/b1 --logfile b1/build.log phast_1.6+dfsg-3.dsc' SUDO_GID='112' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt32b 5.10.0-22-armmp-lpae #1 SMP Debian 5.10.178-3 (2023-04-22) armv7l GNU/Linux I: ls -l /bin total 5072 -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash -rwxr-xr-x 1 root root 133220 Sep 20 2022 date -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd -rwxr-xr-x 1 root root 68104 Sep 20 2022 df -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 67548 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch -rwxr-xr-x 1 root root 67548 Sep 20 2022 true -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/24491/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: armhf 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, libblas-dev, libtmglib-dev, libpcre2-dev, libf2c2-dev, libatlas-base-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 ... 19329 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; however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev; however: Package libblas-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 libf2c2-dev; however: Package libf2c2-dev is not installed. pbuilder-satisfydepends-dummy depends on libatlas-base-dev; however: Package libatlas-base-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} libatlas-base-dev{a} libatlas3-base{a} libblas-dev{a} libblas3{a} libdebhelper-perl{a} libelf1{a} libf2c2{a} libf2c2-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libicu72{a} liblapack-dev{a} liblapack3{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpipeline1{a} libsub-override-perl{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, 47 newly installed, 0 to remove and 0 not upgraded. Need to get 28.7 MB of archives. After unpacking 113 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf liblocale-gettext-perl armhf 1.07-5 [14.9 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 11 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 12 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 22 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 23 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 24 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 25 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 26 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB] Get: 28 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 32 http://deb.debian.org/debian bookworm/main armhf help2man armhf 1.49.3 [198 kB] Get: 33 http://deb.debian.org/debian bookworm/main armhf libgfortran5 armhf 12.2.0-14 [246 kB] Get: 34 http://deb.debian.org/debian bookworm/main armhf libatlas3-base armhf 3.10.3-13 [2341 kB] Get: 35 http://deb.debian.org/debian bookworm/main armhf libatlas-base-dev armhf 3.10.3-13 [2508 kB] Get: 36 http://deb.debian.org/debian bookworm/main armhf libblas3 armhf 3.11.0-2 [105 kB] Get: 37 http://deb.debian.org/debian bookworm/main armhf libblas-dev armhf 3.11.0-2 [115 kB] Get: 38 http://deb.debian.org/debian bookworm/main armhf libf2c2 armhf 20140711-1 [113 kB] Get: 39 http://deb.debian.org/debian bookworm/main armhf libf2c2-dev armhf 20140711-1 [121 kB] Get: 40 http://deb.debian.org/debian bookworm/main armhf liblapack3 armhf 3.11.0-2 [1724 kB] Get: 41 http://deb.debian.org/debian bookworm/main armhf liblapack-dev armhf 3.11.0-2 [1798 kB] Get: 42 http://deb.debian.org/debian bookworm/main armhf libpcre2-16-0 armhf 10.42-1 [211 kB] Get: 43 http://deb.debian.org/debian bookworm/main armhf libpcre2-32-0 armhf 10.42-1 [203 kB] Get: 44 http://deb.debian.org/debian bookworm/main armhf libpcre2-posix3 armhf 10.42-1 [55.0 kB] Get: 45 http://deb.debian.org/debian bookworm/main armhf libpcre2-dev armhf 10.42-1 [666 kB] Get: 46 http://deb.debian.org/debian bookworm/main armhf libtmglib3 armhf 3.11.0-2 [92.3 kB] Get: 47 http://deb.debian.org/debian bookworm/main armhf libtmglib-dev armhf 3.11.0-2 [95.8 kB] Fetched 28.7 MB in 3s (9506 kB/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 ... 19329 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-5_armhf.deb ... Unpacking liblocale-gettext-perl (1.07-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.44-3_armhf.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../03-libmagic1_1%3a5.44-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.44-3_armhf.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-12_armhf.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../06-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.22.4-10_armhf.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.38.1-5+b1_armhf.deb ... 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Preparing to unpack .../45-libtmglib3_3.11.0-2_armhf.deb ... Unpacking libtmglib3:armhf (3.11.0-2) ... Selecting previously unselected package libtmglib-dev:armhf. Preparing to unpack .../46-libtmglib-dev_3.11.0-2_armhf.deb ... Unpacking libtmglib-dev:armhf (3.11.0-2) ... Setting up libpipeline1:armhf (1.5.7-1) ... Setting up libicu72:armhf (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libmagic1:armhf (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libpcre2-16-0:armhf (10.42-1) ... Setting up autotools-dev (20220109.1) ... Setting up libpcre2-32-0:armhf (10.42-1) ... Setting up libblas3:armhf (3.11.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up autopoint (0.21-12) ... Setting up libgfortran5:armhf (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up libpcre2-posix3:armhf (10.42-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libf2c2:armhf (20140711-1) ... Setting up libf2c2-dev:armhf (20140711-1) ... Setting up libelf1:armhf (0.188-2.1) ... Setting up libxml2:armhf (2.9.14+dfsg-1.2) ... Setting up liblocale-gettext-perl (1.07-5) ... Setting up libblas-dev:armhf (3.11.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) 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 (1.13.1-1) ... Setting up liblapack3:armhf (3.11.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up gettext (0.21-12) ... Setting up libatlas3-base:armhf (3.10.3-13) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/atlas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode update-alternatives: using /usr/lib/arm-linux-gnueabihf/atlas/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up libpcre2-dev:armhf (10.42-1) ... Setting up libtool (2.4.7-5) ... Setting up libatlas-base-dev:armhf (3.10.3-13) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/atlas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode update-alternatives: using /usr/lib/arm-linux-gnueabihf/atlas/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up libtmglib3:armhf (3.11.0-2) ... Setting up liblapack-dev:armhf (3.11.0-2) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up libtmglib-dev:armhf (3.11.0-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-9) ... 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/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-3_source.changes dpkg-buildpackage: info: source package phast dpkg-buildpackage: info: source version 1.6+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/phast-1.6+dfsg' dh_auto_clean cd src && make clean make[2]: Entering directory '/build/phast-1.6+dfsg/src' make[3]: Entering directory '/build/phast-1.6+dfsg/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/phast-1.6+dfsg/src/lib/$dir && make clean ; done make[4]: Entering directory '/build/phast-1.6+dfsg/src/lib/base' rm -f *.o make[4]: Leaving directory '/build/phast-1.6+dfsg/src/lib/base' make[4]: Entering directory '/build/phast-1.6+dfsg/src/lib/msa' rm -f *.o make[4]: Leaving directory '/build/phast-1.6+dfsg/src/lib/msa' make[4]: Entering directory '/build/phast-1.6+dfsg/src/lib/feature' rm -f *.o make[4]: Leaving directory '/build/phast-1.6+dfsg/src/lib/feature' make[4]: Entering directory '/build/phast-1.6+dfsg/src/lib/hmm' rm -f *.o make[4]: Leaving directory '/build/phast-1.6+dfsg/src/lib/hmm' make[4]: Entering directory '/build/phast-1.6+dfsg/src/lib/phylo' rm -f *.o make[4]: Leaving directory '/build/phast-1.6+dfsg/src/lib/phylo' make[4]: Entering directory '/build/phast-1.6+dfsg/src/lib/phylo_hmm' rm -f *.o make[4]: Leaving directory '/build/phast-1.6+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/build/phast-1.6+dfsg/src/lib/motif' rm -f *.o make[4]: Leaving directory '/build/phast-1.6+dfsg/src/lib/motif' rm -f /build/phast-1.6+dfsg/src/lib/../../lib/* make[3]: Leaving directory '/build/phast-1.6+dfsg/src/lib' make[3]: Entering directory '/build/phast-1.6+dfsg/src/dless' rm -f *.o dless.help dlessP.help /build/phast-1.6+dfsg/src/dless/../../bin/dless /build/phast-1.6+dfsg/src/dless/../../bin/dlessP make[3]: Leaving directory '/build/phast-1.6+dfsg/src/dless' make[3]: Entering directory '/build/phast-1.6+dfsg/src/exoniphy' rm -f *.o *.help /build/phast-1.6+dfsg/src/exoniphy/../../bin/exoniphy make[3]: Leaving directory '/build/phast-1.6+dfsg/src/exoniphy' make[3]: Entering directory '/build/phast-1.6+dfsg/src/phastCons' rm -f *.o /build/phast-1.6+dfsg/src/phastCons/../../bin/phastCons phastCons.help make[3]: Leaving directory '/build/phast-1.6+dfsg/src/phastCons' make[3]: Entering directory '/build/phast-1.6+dfsg/src/phastOdds' rm -f *.o *.help /build/phast-1.6+dfsg/src/phastOdds/../../bin/phastOdds make[3]: Leaving directory '/build/phast-1.6+dfsg/src/phastOdds' make[3]: Entering directory '/build/phast-1.6+dfsg/src/phastMotif' rm -f *.o /build/phast-1.6+dfsg/src/phastMotif/../../bin/phastMotif make[3]: Leaving directory '/build/phast-1.6+dfsg/src/phastMotif' make[3]: Entering directory '/build/phast-1.6+dfsg/src/phyloFit' rm -f *.o /build/phast-1.6+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.help make[3]: Leaving directory '/build/phast-1.6+dfsg/src/phyloFit' make[3]: Entering directory '/build/phast-1.6+dfsg/src/phyloBoot' rm -f *.o *.help /build/phast-1.6+dfsg/src/phyloBoot/../../bin/phyloBoot make[3]: Leaving directory '/build/phast-1.6+dfsg/src/phyloBoot' make[3]: Entering directory '/build/phast-1.6+dfsg/src/phyloP' rm -f *.o /build/phast-1.6+dfsg/src/phyloP/../../bin/phyloP phyloP.help make[3]: Leaving directory '/build/phast-1.6+dfsg/src/phyloP' make[3]: Entering directory '/build/phast-1.6+dfsg/src/prequel' rm -f *.o /build/phast-1.6+dfsg/src/prequel/../../bin/pbsDecode /build/phast-1.6+dfsg/src/prequel/../../bin/pbsEncode /build/phast-1.6+dfsg/src/prequel/../../bin/pbsScoreMatrix /build/phast-1.6+dfsg/src/prequel/../../bin/pbsTrain /build/phast-1.6+dfsg/src/prequel/../../bin/prequel pbsDecode.help pbsEncode.help pbsScoreMatrix.help pbsTrain.help prequel.help make[3]: Leaving directory '/build/phast-1.6+dfsg/src/prequel' make[3]: Entering directory '/build/phast-1.6+dfsg/src/util' rm -f *.o *.help /build/phast-1.6+dfsg/src/util/../../bin/all_dists /build/phast-1.6+dfsg/src/util/../../bin/base_evolve /build/phast-1.6+dfsg/src/util/../../bin/chooseLines /build/phast-1.6+dfsg/src/util/../../bin/clean_genes /build/phast-1.6+dfsg/src/util/../../bin/consEntropy /build/phast-1.6+dfsg/src/util/../../bin/convert_coords /build/phast-1.6+dfsg/src/util/../../bin/display_rate_matrix /build/phast-1.6+dfsg/src/util/../../bin/draw_tree /build/phast-1.6+dfsg/src/util/../../bin/eval_predictions /build/phast-1.6+dfsg/src/util/../../bin/hmm_train /build/phast-1.6+dfsg/src/util/../../bin/hmm_tweak /build/phast-1.6+dfsg/src/util/../../bin/hmm_view /build/phast-1.6+dfsg/src/util/../../bin/indelFit /build/phast-1.6+dfsg/src/util/../../bin/indelHistory /build/phast-1.6+dfsg/src/util/../../bin/maf_parse /build/phast-1.6+dfsg/src/util/../../bin/makeHKY /build/phast-1.6+dfsg/src/util/../../bin/modFreqs /build/phast-1.6+dfsg/src/util/../../bin/msa_diff /build/phast-1.6+dfsg/src/util/../../bin/msa_split /build/phast-1.6+dfsg/src/util/../../bin/msa_view /build/phast-1.6+dfsg/src/util/../../bin/phast /build/phast-1.6+dfsg/src/util/../../bin/phastBias /build/phast-1.6+dfsg/src/util/../../bin/refeature /build/phast-1.6+dfsg/src/util/../../bin/stringiphy /build/phast-1.6+dfsg/src/util/../../bin/treeGen /build/phast-1.6+dfsg/src/util/../../bin/tree_doctor make[3]: Leaving directory '/build/phast-1.6+dfsg/src/util' rm -rf ../bin ../lib ../doc make[2]: Leaving directory '/build/phast-1.6+dfsg/src' make[1]: Leaving directory '/build/phast-1.6+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j3 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/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/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/phast-1.6+dfsg/src/$dir && make ; done make[3]: Entering directory '/build/phast-1.6+dfsg/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/phast-1.6+dfsg/src/lib/$dir && make ; done make[4]: Entering directory '/build/phast-1.6+dfsg/src/lib/base' gcc -g -O2 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 phast_eigen.c: In function 'mat_diagonalize': phast_eigen.c:62:3: warning: implicit declaration of function 'dgeev_' [-Wimplicit-function-declaration] 62 | dgeev_(&jobvl, &jobvr, &n, tmp, &n, wr, wi, vl, | ^~~~~~ gcc -g -O2 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 phast_markov_matrix.c: In function 'mm_exp_higham': phast_markov_matrix.c:288:5: warning: implicit declaration of function 'dgebal_' [-Wimplicit-function-declaration] 288 | dgebal_(&job, &ln, mat, &ln, &ilo, &ihi, scale, &info); | ^~~~~~~ phast_markov_matrix.c:403:3: warning: implicit declaration of function 'dgesv_' [-Wimplicit-function-declaration] 403 | dgesv_(&ln, &ln, matU, &ln, ipiv, matV, &ln, &info); | ^~~~~~ phast_markov_matrix.c:428:5: warning: implicit declaration of function 'dgebak_' [-Wimplicit-function-declaration] 428 | dgebak_(&job, &side, &ln, &ilo, &ihi, scale, &ln, mat, &ln, &info); | ^~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 phast_matrix.c: In function 'mat_invert': phast_matrix.c:263:3: warning: implicit declaration of function 'dgetrf_' [-Wimplicit-function-declaration] 263 | dgetrf_(&n, &n, (LAPACK_DOUBLE*)tmp, &n, ipiv, &info); | ^~~~~~~ phast_matrix.c:273:3: warning: implicit declaration of function 'dgetri_' [-Wimplicit-function-declaration] 273 | dgetri_(&n, (LAPACK_DOUBLE*)tmp, &n, ipiv, work, &lwork, &info); | ^~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_misc.c:672:35: warning: initialization of 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 672 | pcre2_compile_context *map_re = str_re_new("^[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*(->|=)[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*"); | ^~~~~~~~~~ In function 'phast_fclose', inlined from 'phast_fclose' at phast_misc.c:298:6: 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); | ^~~~~~~~~ In function 'phast_fclose', inlined from 'phast_fclose' at phast_misc.c:298:6, inlined from 'get_arg_list' at phast_misc.c:371:5: phast_misc.c:301:5: warning: pointer 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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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: In function 'str_re_match': phast_stringsplus.c:532:30: warning: passing argument 2 of 'str_re_match_sub' from incompatible pointer type [-Wincompatible-pointer-types] 532 | return str_re_match_sub(s, re, l, 0, nsubexp, NULL); | ^~ | | | pcre2_compile_context_8 * {aka struct pcre2_real_compile_context_8 *} phast_stringsplus.c:488:45: note: expected 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} but argument is of type 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} 488 | int str_re_match_sub(String *s, pcre2_code *re, List *l, int offset, int nsubexp, | ^ phast_stringsplus.c: In function 'str_re_search': phast_stringsplus.c:538:28: warning: passing argument 2 of 'str_re_match_sub' from incompatible pointer type [-Wincompatible-pointer-types] 538 | rc = str_re_match_sub(s, re, l, start_offset, nsubexp, &first_match_idx); | ^~ | | | pcre2_compile_context_8 * {aka struct pcre2_real_compile_context_8 *} phast_stringsplus.c:488:45: note: expected 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} but argument is of type 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} 488 | int str_re_match_sub(String *s, pcre2_code *re, List *l, int offset, int nsubexp, | ^ phast_stringsplus.c: In function 'str_re_match_sub': 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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/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/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a ar rs /build/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/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/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/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/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/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/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/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/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/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/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/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/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/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/phast-1.6+dfsg/src/lib/base' make[4]: Entering directory '/build/phast-1.6+dfsg/src/lib/msa' gcc -g -O2 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/../include/phast/local_alignment.h:36, from phast_local_alignment.c:32: /build/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_local_alignment.c:50:44: warning: initialization of 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 50 | pcre2_compile_context *stanza_start_re = str_re_new("^([dshaxm])[[:space:]]*{"); | ^~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_msa.c:39: /build/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:264:16: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 264 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*([^[:space:]]+)"); | ^ 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/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:1929:16: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 1929 | descrip_re = str_re_new("^[[:space:]]*>"); | ^ 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/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2590:9: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 2590 | ss_re = str_re_new("^NSEQS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ 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/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2591:13: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 2591 | phylip_re = str_re_new("^([[:space:]]*([0-9]+))[[:space:]]*[[:space:]]*([0-9]+)"); | ^ 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/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2592:12: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 2592 | fasta_re = str_re_new("^>.*"); | ^ 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/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2593:10: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 2593 | lav_re = str_re_new("^#:lav.*"); | ^ 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/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2594:10: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 2594 | maf_re = str_re_new("^##maf"); | ^ gcc -g -O2 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_multi_msa.c:37: /build/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_multi_msa.c:54:38: warning: initialization of 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 54 | pcre2_compile_context *blocks_re = str_re_new("#[[:space:]]*BLOCKS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~ 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/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_multi_msa.c:55:36: warning: initialization of 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 55 | pcre2_compile_context *alph_re = str_re_new("#[[:space:]]*ALPHABET[[:space:]]*=[[:space:]]*([A-Z]+)"); | ^~~~~~~~~~ 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/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_multi_msa.c:56:38: warning: initialization of 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 56 | pcre2_compile_context *format_re = str_re_new("#[[:space:]]*FORMAT[[:space:]]*=[[:space:]]*([A-Z]+)"); | ^~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-1.6+dfsg/src/../include/phast/msa.h:19, from /build/phast-1.6+dfsg/src/../include/phast/sufficient_stats.h:20, from phast_sufficient_stats.c:11: /build/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:661:12: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 661 | nseqs_re = str_re_new("NSEQS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ 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/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:662:13: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 662 | length_re = str_re_new("LENGTH[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ 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/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:663:17: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 663 | tuple_size_re = str_re_new("TUPLE_SIZE[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ 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/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:664:14: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 664 | ntuples_re = str_re_new("NTUPLES[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ 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/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:665:12: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 665 | names_re = str_re_new("NAMES[[:space:]]*=[[:space:]]*(.*)"); | ^ 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/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:666:11: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 666 | alph_re = str_re_new("ALPHABET[[:space:]]*=[[:space:]]*([-.^A-Za-z ]+)"); | ^ 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/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:667:12: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 667 | ncats_re = str_re_new("NCATS[[:space:]]*=[[:space:]]*([-0-9]+)"); | ^ 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/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:668:13: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 668 | offset_re = str_re_new("IDX_OFFSET[[:space:]]*=[[:space:]]*([-0-9]+)"); | ^ 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/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:669:12: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 669 | tuple_re = str_re_new("^([0-9]+)[[:space:]]+([-.^A-Za-z ]+)[[:space:]]+([0-9.[:space:]]+)"); | ^ 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/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:670:12: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 670 | order_re = str_re_new("TUPLE_IDX_ORDER:"); | ^ ar rs /build/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/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/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/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/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/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/phast-1.6+dfsg/src/lib/msa' make[4]: Entering directory '/build/phast-1.6+dfsg/src/lib/feature' gcc -g -O2 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/../include/phast/gff.h:21, from phast_bed.c:15: /build/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_bed.c:143:41: warning: initialization of 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 143 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)"); | ^~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-1.6+dfsg/src/../include/phast/category_map.h:92, from phast_category_map.c:10: /build/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:39:18: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 39 | cat_range_re = str_re_new("^[[:space:]]*([^[:space:]]+)[[:space:]]+([[:digit:]]+)(-([[:digit:]]+))?([[:space:]]+([[:digit:]].*))?"); | ^ 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/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:40:14: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 40 | ncats_re = str_re_new("^[[:space:]]*NCATS[[:space:]]*=[[:space:]]*([[:digit:]]+)"); | ^ 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:]]*(.*)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /build/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:41:13: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 41 | fill_re = str_re_new("^[[:space:]]*FILL_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$"); | ^ 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:]]*(.*)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /build/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:42:14: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 42 | label_re = str_re_new("^[[:space:]]*LABELLING_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$"); | ^ 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:]]*\\((.+)\\)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /build/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:43:15: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 43 | extend_re = str_re_new("^[[:space:]]*FEATURE_EXTEND[[:space:]]*:[[:space:]]*(.+)[[:space:]]*\\((.+)\\)$"); | ^ gcc -g -O2 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/../include/phast/gff.h:21, from phast_gff.c:13: /build/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_gff.c:56:25: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 56 | spec_comment_re = str_re_new("^[[:space:]]*##[[:space:]]*([^[:space:]]+)[[:space:]]+([^[:space:]]+)([[:space:]]+([^[:space:]]+))?"); | ^ 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/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_gff.c:272:11: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 272 | posre = str_re_new("(chr[_a-zA-Z0-9]+):([0-9]+)-([0-9]+)([-+])?"); | ^ 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/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_gff.c:688:10: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 688 | tag_re = str_re_new(tmpstr); | ^ gcc -g -O2 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/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/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/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/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/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/phast-1.6+dfsg/src/lib/feature' make[4]: Entering directory '/build/phast-1.6+dfsg/src/lib/hmm' gcc -g -O2 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o ar rs /build/phast-1.6+dfsg/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o make[4]: Leaving directory '/build/phast-1.6+dfsg/src/lib/hmm' make[4]: Entering directory '/build/phast-1.6+dfsg/src/lib/phylo' gcc -g -O2 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_phylo_p_print.c:17: /build/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_phylo_p_print.c:752:39: warning: initialization of 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 752 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)"); | ^~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/phast-1.6+dfsg/src/lib/phylo' make[4]: Entering directory '/build/phast-1.6+dfsg/src/lib/phylo_hmm' gcc -g -O2 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o ar rs /build/phast-1.6+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o make[4]: Leaving directory '/build/phast-1.6+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/build/phast-1.6+dfsg/src/lib/motif' gcc -g -O2 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_tfbs.c:16: /build/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_tfbs.c:147:11: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 147 | pssm_re = str_re_new("^letter-probability matrix: alength= ([0-9]+) w= ([0-9]+)"); | ^ 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/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_tfbs.c:148:17: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 148 | motif_name_re = str_re_new("^MOTIF[[:space:]]+(.+?)[[:space:]].*"); | ^ 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/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_tfbs.c:229:16: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 229 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*(.+)"); | ^ 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/phast-1.6+dfsg/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o ar rs /build/phast-1.6+dfsg/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o make[4]: Leaving directory '/build/phast-1.6+dfsg/src/lib/motif' make[3]: Leaving directory '/build/phast-1.6+dfsg/src/lib' make[3]: Entering directory '/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/dless/../../bin/dless'. Stop. make[3]: Leaving directory '/build/phast-1.6+dfsg/src/dless' make[3]: Entering directory '/build/phast-1.6+dfsg/src/exoniphy' ../munge-help.sh exoniphy.help_src > exoniphy.help gcc -g -O2 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/exoniphy/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/exoniphy/../../lib -o /build/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/phast-1.6+dfsg/src/exoniphy' make[3]: Entering directory '/build/phast-1.6+dfsg/src/phastCons' ../munge-help.sh phastCons.help_src > phastCons.help gcc -g -O2 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/phastCons/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/phastCons/../../lib -o /build/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/phast-1.6+dfsg/src/phastCons' make[3]: Entering directory '/build/phast-1.6+dfsg/src/phastOdds' ../munge-help.sh phastOdds.help_src > phastOdds.help gcc -g -O2 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/phastOdds/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/phastOdds/../../lib -o /build/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/phast-1.6+dfsg/src/phastOdds' make[3]: Entering directory '/build/phast-1.6+dfsg/src/phastMotif' gcc -g -O2 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/phastMotif/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/phastMotif/../../lib -o /build/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/phast-1.6+dfsg/src/phastMotif' make[3]: Entering directory '/build/phast-1.6+dfsg/src/phyloFit' ../munge-help.sh phyloFit.help_src > phyloFit.help gcc -g -O2 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/phyloFit/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/phyloFit/../../lib -o /build/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/phast-1.6+dfsg/src/phyloFit' make[3]: Entering directory '/build/phast-1.6+dfsg/src/phyloBoot' ../munge-help.sh phyloBoot.help_src > phyloBoot.help gcc -g -O2 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/phyloBoot/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/phyloBoot/../../lib -o /build/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/phast-1.6+dfsg/src/phyloBoot' make[3]: Entering directory '/build/phast-1.6+dfsg/src/phyloP' ../munge-help.sh phyloP.help_src > phyloP.help gcc -g -O2 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/phyloP/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/phyloP/../../lib -o /build/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/phast-1.6+dfsg/src/phyloP' make[3]: Entering directory '/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/prequel/../../bin/pbsDecode'. Stop. make[3]: Leaving directory '/build/phast-1.6+dfsg/src/prequel' make[3]: Entering directory '/build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-1.6+dfsg/src/../include/phast/msa.h:19, from msa_view.c:14: /build/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *' 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ msa_view.c:361:38: warning: initialization of 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types] 361 | pcre2_compile_context* fill_N_re = str_re_new("([[:digit:]]+):([[:digit:]]+)-([[:digit:]]+)"); | ^~~~~~~~~~ gcc -L/build/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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 -ffile-prefix-map=/build/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/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/phast-1.6+dfsg/src/../include/phast/tree_model.h:26, from tree_doctor.c:14: /build/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/phast-1.6+dfsg/src/util/../../lib -o /build/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/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/phast-1.6+dfsg/src' make[1]: Leaving directory '/build/phast-1.6+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/phast-1.6+dfsg' cd test && PATH=/build/phast-1.6+dfsg/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games make msa_view make[2]: Entering directory '/build/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/phast-1.6+dfsg/test' make[1]: Leaving directory '/build/phast-1.6+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/phast/ make -j3 install DESTDIR=/build/phast-1.6\+dfsg/debian/phast AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/phast-1.6+dfsg' (cd src; make install DESTDIR=/build/phast-1.6+dfsg/debian/phast ) make[2]: Entering directory '/build/phast-1.6+dfsg/src' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mkdir -p /build/phast-1.6+dfsg/debian/phast/usr/bin/ mkdir -p /build/phast-1.6+dfsg/debian/phast/usr/share/phast/data/ mkdir -p /build/phast-1.6+dfsg/debian/phast/usr/share/man/man1/ cp ../bin/* /build/phast-1.6+dfsg/debian/phast/usr/bin/ cp -R ../data/* /build/phast-1.6+dfsg/debian/phast/usr/share/phast/data/ cp -R ../doc/man/* /build/phast-1.6+dfsg/debian/phast/usr/share/man/man1/ make[2]: Leaving directory '/build/phast-1.6+dfsg/src' make[1]: Leaving directory '/build/phast-1.6+dfsg' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/phast-1.6+dfsg' dh_installexamples find debian/*/usr/share/doc/*/examples -type f -size +1k -exec xz \{\} \; make[1]: Leaving directory '/build/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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'phast-dbgsym' in '../phast-dbgsym_1.6+dfsg-3_armhf.deb'. dpkg-deb: building package 'phast' in '../phast_1.6+dfsg-3_armhf.deb'. dpkg-genbuildinfo --build=binary -O../phast_1.6+dfsg-3_armhf.buildinfo dpkg-genchanges --build=binary -O../phast_1.6+dfsg-3_armhf.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/24491 and its subdirectories I: Current time: Tue May 9 02:38:44 -12 2023 I: pbuilder-time-stamp: 1683643124 Tue May 9 14:42:23 UTC 2023 I: 1st build successful. Starting 2nd build on remote node jtx1b-armhf-rb.debian.net. Tue May 9 14:42:23 UTC 2023 I: Preparing to do remote build '2' on jtx1b-armhf-rb.debian.net. Tue May 9 14:52:24 UTC 2023 I: Deleting $TMPDIR on jtx1b-armhf-rb.debian.net. Tue May 9 14:52:29 UTC 2023 I: phast_1.6+dfsg-3_armhf.changes: Format: 1.8 Date: Fri, 19 Nov 2021 13:17:54 +0100 Source: phast Binary: phast phast-dbgsym Architecture: armhf Version: 1.6+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: phast - phylogenetic analysis with space/time models Closes: 1000000 1000163 Changes: phast (1.6+dfsg-3) unstable; urgency=medium . * Port to pcre2 Closes: #1000000, #1000163 Checksums-Sha1: 798b1ccf61f2e5fe12fab84746699d73528bba3a 25363976 phast-dbgsym_1.6+dfsg-3_armhf.deb e2343ebdbb1df87953dab55c0e2057f93110235a 5458 phast_1.6+dfsg-3_armhf.buildinfo 6ee4440e709afd4332878da1a146dc05a74d0eb0 2531552 phast_1.6+dfsg-3_armhf.deb Checksums-Sha256: b1f47649b69f7496f7bf6e0c45e35d1dc1562dad4162a409518ffb1fe002d862 25363976 phast-dbgsym_1.6+dfsg-3_armhf.deb 58ebfe7d846ccdb28e91a746dfd95537faa6d9837ce253b5b8fa81c0b5ab05a7 5458 phast_1.6+dfsg-3_armhf.buildinfo 5ed7792e577f2d9305a0dee47aff905c6e12c34a31cfea0cada8b63000d84f40 2531552 phast_1.6+dfsg-3_armhf.deb Files: 280ac639295634525a7960f9e237f2f9 25363976 debug optional phast-dbgsym_1.6+dfsg-3_armhf.deb 1081c2ba0c8a133c2f52c277ef21ae51 5458 science optional phast_1.6+dfsg-3_armhf.buildinfo 639e7ea05f92af0467a06ca5fac1f493 2531552 science optional phast_1.6+dfsg-3_armhf.deb Tue May 9 14:52:30 UTC 2023 I: diffoscope 242 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.rVIc7mor/phast_1.6+dfsg-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.rVIc7mor/phast_1.6+dfsg-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.rVIc7mor/phast_1.6+dfsg-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.rVIc7mor/b1/phast_1.6+dfsg-3_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.rVIc7mor/b2/phast_1.6+dfsg-3_armhf.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: 0.315s) 0.314s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Tue May 9 14:52:31 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists. Tue May 9 14:52:31 UTC 2023 I: phast from bookworm built successfully and reproducibly on armhf. Tue May 9 14:52:32 UTC 2023 I: Submitting .buildinfo files to external archives: Tue May 9 14:52:32 UTC 2023 I: Submitting 8.0K b1/phast_1.6+dfsg-3_armhf.buildinfo.asc Tue May 9 14:52:33 UTC 2023 I: Submitting 8.0K b2/phast_1.6+dfsg-3_armhf.buildinfo.asc Tue May 9 14:52:34 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue May 9 14:52:34 UTC 2023 I: Done submitting .buildinfo files. Tue May 9 14:52:34 UTC 2023 I: Removing signed phast_1.6+dfsg-3_armhf.buildinfo.asc files: removed './b1/phast_1.6+dfsg-3_armhf.buildinfo.asc' removed './b2/phast_1.6+dfsg-3_armhf.buildinfo.asc'