I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 8 12:22:41 -12 2021 I: pbuilder-time-stamp: 1631146961 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration 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_1.4+dfsg-1.dsc] I: copying [./phast_1.4+dfsg.orig.tar.xz] I: copying [./phast_1.4+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sun Nov 5 11:09:40 2017 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./phast_1.4+dfsg-1.dsc dpkg-source: info: extracting phast in phast-1.4+dfsg dpkg-source: info: unpacking phast_1.4+dfsg.orig.tar.xz dpkg-source: info: unpacking phast_1.4+dfsg-1.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 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/24659/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='24659' 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/tmp.fgDz09jPQE/pbuilderrc_dDuo --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.fgDz09jPQE/b1 --logfile b1/build.log phast_1.4+dfsg-1.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink-sled11-arm64 4.4.0-186-generic #216-Ubuntu SMP Wed Jul 1 05:35:21 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14264 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 35576 Feb 28 2019 cat -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash -rwxr-xr-x 1 root root 97136 Feb 28 2019 date -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd -rwxr-xr-x 1 root root 93752 Feb 28 2019 df -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir -rwxr-xr-x 1 root root 75984 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 31368 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 27256 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 174304 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 89656 Jan 5 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln -rwxr-xr-x 1 root root 52544 Jul 26 2018 login -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 9 2019 more -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138736 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35560 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Sep 7 02:49 sh -> dash -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty -rwsr-xr-x 1 root root 59424 Jan 9 2019 su -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch -rwxr-xr-x 1 root root 27256 Feb 28 2019 true -rwxr-xr-x 1 root root 14264 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34824 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/24659/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 10), liblapack-dev, libblas-dev, libtmglib-dev, libpcre3-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 ... 19168 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 (>= 10); however: Package debhelper 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 libpcre3-dev; however: Package libpcre3-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} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libicu63{a} liblapack-dev{a} liblapack3{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpcre16-3{a} libpcre3-dev{a} libpcre32-3{a} libpcrecpp0v5{a} libpipeline1{a} libsigsegv2{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 libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 46 newly installed, 0 to remove and 0 not upgraded. Need to get 23.7 MB of archives. After unpacking 91.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 liblocale-gettext-perl arm64 1.07-3+b4 [18.8 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Get: 35 http://deb.debian.org/debian buster/main arm64 help2man arm64 1.47.8 [177 kB] Get: 36 http://deb.debian.org/debian buster/main arm64 libgfortran5 arm64 8.3.0-6 [298 kB] Get: 37 http://deb.debian.org/debian buster/main arm64 libblas3 arm64 3.8.0-2 [100 kB] Get: 38 http://deb.debian.org/debian buster/main arm64 libblas-dev arm64 3.8.0-2 [105 kB] Get: 39 http://deb.debian.org/debian buster/main arm64 liblapack3 arm64 3.8.0-2 [1489 kB] Get: 40 http://deb.debian.org/debian buster/main arm64 liblapack-dev arm64 3.8.0-2 [1524 kB] Get: 41 http://deb.debian.org/debian buster/main arm64 libpcre16-3 arm64 2:8.39-12 [236 kB] Get: 42 http://deb.debian.org/debian buster/main arm64 libpcre32-3 arm64 2:8.39-12 [230 kB] Get: 43 http://deb.debian.org/debian buster/main arm64 libpcrecpp0v5 arm64 2:8.39-12 [151 kB] Get: 44 http://deb.debian.org/debian buster/main arm64 libpcre3-dev arm64 2:8.39-12 [578 kB] Get: 45 http://deb.debian.org/debian buster/main arm64 libtmglib3 arm64 3.8.0-2 [93.6 kB] Get: 46 http://deb.debian.org/debian buster/main arm64 libtmglib-dev arm64 3.8.0-2 [94.9 kB] Fetched 23.7 MB in 2s (10.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (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 ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_arm64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../04-libpipeline1_1.5.1-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_arm64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../06-liblocale-gettext-perl_1.07-3+b4_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../07-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../08-libmagic-mgc_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../09-libmagic1_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../10-file_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../11-gettext-base_0.19.8.1-9_arm64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../12-libsigsegv2_2.12-2_arm64.deb ... Unpacking libsigsegv2:arm64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.18-2_arm64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../23-libelf1_0.176-1.1_arm64.deb ... Unpacking libelf1:arm64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.12-3_arm64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:arm64. Preparing to unpack .../25-libglib2.0-0_2.58.3-2+deb10u2_arm64.deb ... Unpacking libglib2.0-0:arm64 (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:arm64. Preparing to unpack .../26-libicu63_63.1-6+deb10u1_arm64.deb ... Unpacking libicu63:arm64 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../27-libxml2_2.9.4+dfsg1-7+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:arm64. Preparing to unpack .../28-libcroco3_0.6.12-3_arm64.deb ... Unpacking libcroco3:arm64 (0.6.12-3) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../29-libncurses6_6.1+20181013-2+deb10u2_arm64.deb ... Unpacking libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../30-gettext_0.19.8.1-9_arm64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../31-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../32-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... 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Selecting previously unselected package libtmglib-dev:arm64. Preparing to unpack .../45-libtmglib-dev_3.8.0-2_arm64.deb ... Unpacking libtmglib-dev:arm64 (3.8.0-2) ... Setting up libpcrecpp0v5:arm64 (2:8.39-12) ... Setting up libpipeline1:arm64 (1.5.1-2) ... Setting up libpcre16-3:arm64 (2:8.39-12) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:arm64 (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libmagic1:arm64 (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libicu63:arm64 (63.1-6+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:arm64 (2.12-2) ... Setting up libpcre32-3:arm64 (2:8.39-12) ... Setting up autopoint (0.19.8.1-9) ... Setting up libgfortran5:arm64 (8.3.0-6) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:arm64 (0.0.6-3) ... Setting up libbsd0:arm64 (0.9.1-2) ... Setting up libelf1:arm64 (0.176-1.1) ... Setting up libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libtool (2.4.6-9) ... Setting up libpcre3-dev:arm64 (2:8.39-12) ... Setting up m4 (1.4.18-2) ... Setting up help2man (1.47.8) ... Setting up libblas3:arm64 (3.8.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:arm64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libblas-dev:arm64 (3.8.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up liblapack3:arm64 (3.8.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libtmglib3:arm64 (3.8.0-2) ... Setting up liblapack-dev:arm64 (3.8.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up libtmglib-dev:arm64 (3.8.0-2) ... Setting up po-debconf (1.0.21) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/phast-1.4+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package phast dpkg-buildpackage: info: source version 1.4+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/phast-1.4+dfsg' dh_auto_clean cd src && make clean make[2]: Entering directory '/build/phast-1.4+dfsg/src' make[3]: Entering directory '/build/phast-1.4+dfsg/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/phast-1.4+dfsg/src/lib/$dir && make clean ; done make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/base' rm -f *.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/base' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/msa' rm -f *.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/msa' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/feature' rm -f *.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/feature' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/hmm' rm -f *.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/hmm' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/phylo' rm -f *.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/phylo' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/phylo_hmm' rm -f *.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/motif' rm -f *.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/motif' rm -f /build/phast-1.4+dfsg/src/lib/../../lib/* make[3]: Leaving directory '/build/phast-1.4+dfsg/src/lib' make[3]: Entering directory '/build/phast-1.4+dfsg/src/dless' rm -f *.o dless.help dlessP.help /build/phast-1.4+dfsg/src/dless/../../bin/dless /build/phast-1.4+dfsg/src/dless/../../bin/dlessP make[3]: Leaving directory '/build/phast-1.4+dfsg/src/dless' make[3]: Entering directory '/build/phast-1.4+dfsg/src/exoniphy' rm -f *.o *.help /build/phast-1.4+dfsg/src/exoniphy/../../bin/exoniphy make[3]: Leaving directory '/build/phast-1.4+dfsg/src/exoniphy' make[3]: Entering directory '/build/phast-1.4+dfsg/src/phastCons' rm -f *.o /build/phast-1.4+dfsg/src/phastCons/../../bin/phastCons phastCons.help make[3]: Leaving directory '/build/phast-1.4+dfsg/src/phastCons' make[3]: Entering directory '/build/phast-1.4+dfsg/src/phastOdds' rm -f *.o *.help /build/phast-1.4+dfsg/src/phastOdds/../../bin/phastOdds make[3]: Leaving directory '/build/phast-1.4+dfsg/src/phastOdds' make[3]: Entering directory '/build/phast-1.4+dfsg/src/phastMotif' rm -f *.o /build/phast-1.4+dfsg/src/phastMotif/../../bin/phastMotif make[3]: Leaving directory '/build/phast-1.4+dfsg/src/phastMotif' make[3]: Entering directory '/build/phast-1.4+dfsg/src/phyloFit' rm -f *.o /build/phast-1.4+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.help make[3]: Leaving directory '/build/phast-1.4+dfsg/src/phyloFit' make[3]: Entering directory '/build/phast-1.4+dfsg/src/phyloBoot' rm -f *.o *.help /build/phast-1.4+dfsg/src/phyloBoot/../../bin/phyloBoot make[3]: Leaving directory '/build/phast-1.4+dfsg/src/phyloBoot' make[3]: Entering directory '/build/phast-1.4+dfsg/src/phyloP' rm -f *.o /build/phast-1.4+dfsg/src/phyloP/../../bin/phyloP phyloP.help make[3]: Leaving directory '/build/phast-1.4+dfsg/src/phyloP' make[3]: Entering directory '/build/phast-1.4+dfsg/src/prequel' rm -f *.o /build/phast-1.4+dfsg/src/prequel/../../bin/pbsDecode /build/phast-1.4+dfsg/src/prequel/../../bin/pbsEncode /build/phast-1.4+dfsg/src/prequel/../../bin/pbsScoreMatrix /build/phast-1.4+dfsg/src/prequel/../../bin/pbsTrain /build/phast-1.4+dfsg/src/prequel/../../bin/prequel pbsTrain.help pbsDecode.help pbsEncode.help prequel.help pbsScoreMatrix.help make[3]: Leaving directory '/build/phast-1.4+dfsg/src/prequel' make[3]: Entering directory '/build/phast-1.4+dfsg/src/util' rm -f *.o *.help /build/phast-1.4+dfsg/src/util/../../bin/hmm_train /build/phast-1.4+dfsg/src/util/../../bin/chooseLines /build/phast-1.4+dfsg/src/util/../../bin/modFreqs /build/phast-1.4+dfsg/src/util/../../bin/indelHistory /build/phast-1.4+dfsg/src/util/../../bin/clean_genes /build/phast-1.4+dfsg/src/util/../../bin/treeGen /build/phast-1.4+dfsg/src/util/../../bin/base_evolve /build/phast-1.4+dfsg/src/util/../../bin/phast /build/phast-1.4+dfsg/src/util/../../bin/tree_doctor /build/phast-1.4+dfsg/src/util/../../bin/msa_diff /build/phast-1.4+dfsg/src/util/../../bin/indelFit /build/phast-1.4+dfsg/src/util/../../bin/hmm_tweak /build/phast-1.4+dfsg/src/util/../../bin/all_dists /build/phast-1.4+dfsg/src/util/../../bin/stringiphy /build/phast-1.4+dfsg/src/util/../../bin/convert_coords /build/phast-1.4+dfsg/src/util/../../bin/hmm_view /build/phast-1.4+dfsg/src/util/../../bin/consEntropy /build/phast-1.4+dfsg/src/util/../../bin/maf_parse /build/phast-1.4+dfsg/src/util/../../bin/msa_split /build/phast-1.4+dfsg/src/util/../../bin/eval_predictions /build/phast-1.4+dfsg/src/util/../../bin/display_rate_matrix /build/phast-1.4+dfsg/src/util/../../bin/draw_tree /build/phast-1.4+dfsg/src/util/../../bin/makeHKY /build/phast-1.4+dfsg/src/util/../../bin/msa_view /build/phast-1.4+dfsg/src/util/../../bin/phastBias /build/phast-1.4+dfsg/src/util/../../bin/refeature make[3]: Leaving directory '/build/phast-1.4+dfsg/src/util' rm -rf ../bin ../lib ../doc make[2]: Leaving directory '/build/phast-1.4+dfsg/src' make[1]: Leaving directory '/build/phast-1.4+dfsg' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j8 make[1]: Entering directory '/build/phast-1.4+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-1.4+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-1.4+dfsg/src/$dir && make ; done make[3]: Entering directory '/build/phast-1.4+dfsg/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/phast-1.4+dfsg/src/lib/$dir && make ; done make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/base' gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c complex_matrix.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c memory_handler.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c eigen.c -o eigen.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c lists.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c prob_vector.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c complex_vector.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c numerical_opt.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c misc.c -o 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 gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c markov_matrix.c -o markov_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c vector.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c stringsplus.c -o 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 gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c list_of_lists.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c hashtable.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c matrix.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c prob_matrix.c -o 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 ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar: creating /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/base' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/msa' gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c sufficient_stats.c -o 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 gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c maf.c -o 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 maf.c: In function 'maf_read_cats_subset': maf.c:29:41: warning: variable 'block_no' set but not used [-Wunused-but-set-variable] int i, start_idx, length, max_tuples, block_no, ^~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c maf_block.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c local_alignment.c -o 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 gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c msa.c -o 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 msa.c: In function 'msa_read_fasta': msa.c:257:40: warning: variable 'line_no' set but not used [-Wunused-but-set-variable] int maxlen, i, nseqs, j, do_toupper, line_no; ^~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c multi_msa.c -o 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 ar rs /build/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a sufficient_stats.o maf.o maf_block.o local_alignment.o msa.o multi_msa.o ar rs /build/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a sufficient_stats.o maf.o maf_block.o local_alignment.o msa.o multi_msa.o ar rs /build/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a sufficient_stats.o maf.o maf_block.o local_alignment.o msa.o multi_msa.o ar rs /build/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a sufficient_stats.o maf.o maf_block.o local_alignment.o msa.o multi_msa.o ar rs /build/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a sufficient_stats.o maf.o maf_block.o local_alignment.o msa.o multi_msa.o ar rs /build/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a sufficient_stats.o maf.o maf_block.o local_alignment.o msa.o multi_msa.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/msa' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/feature' gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c bed.c -o 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 gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c wig.c -o 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 gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c genepred.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c category_map.c -o 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 gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c gff.c -o 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 ar rs /build/phast-1.4+dfsg/src/lib/feature/../../../lib/libphast.a bed.o wig.o genepred.o category_map.o gff.o ar rs /build/phast-1.4+dfsg/src/lib/feature/../../../lib/libphast.a bed.o wig.o genepred.o category_map.o gff.o ar rs /build/phast-1.4+dfsg/src/lib/feature/../../../lib/libphast.a bed.o wig.o genepred.o category_map.o gff.o ar rs /build/phast-1.4+dfsg/src/lib/feature/../../../lib/libphast.a bed.o wig.o genepred.o category_map.o gff.o ar rs /build/phast-1.4+dfsg/src/lib/feature/../../../lib/libphast.a bed.o wig.o genepred.o category_map.o gff.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/feature' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/hmm' gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/hmm/../../..\" -fno-strict-aliasing -c hmm.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/hmm/../../..\" -fno-strict-aliasing -c em.c -o 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 ar rs /build/phast-1.4+dfsg/src/lib/hmm/../../../lib/libphast.a hmm.o em.o ar rs /build/phast-1.4+dfsg/src/lib/hmm/../../../lib/libphast.a hmm.o em.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/hmm' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/phylo' gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c dgamma.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c tree_model.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c indel_history.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phylo_fit.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c fit_column.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c subst_mods.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c fit_feature.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c tree_likelihoods.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c indel_mod.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phylo_p.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phylo_p_print.c -o 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 gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c trees.c -o 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 gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c subst_distrib.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c fit_em.c -o 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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c bgc_hmm.c -o 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 bgc_hmm.c: In function 'bgcHmm': bgc_hmm.c:241:15: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] sprintf(warning_str, "%s, %s", warning_str, ((String*)lst_get_ptr(pruned_names, j))->chars); ^~~~~~~~~~~ ~~~~~~~~~~~ bgc_hmm.c:242:13: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] sprintf(warning_str, "%s)\n", warning_str); ^~~~~~~~~~~ ~~~~~~~~~~~ bgc_hmm.c:241:31: warning: ', ' directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] sprintf(warning_str, "%s, %s", warning_str, ((String*)lst_get_ptr(pruned_names, j))->chars); ^~ bgc_hmm.c:241:7: note: 'sprintf' output 3 or more bytes (assuming 10002) into a destination of size 10000 sprintf(warning_str, "%s, %s", warning_str, ((String*)lst_get_ptr(pruned_names, j))->chars); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bgc_hmm.c:242:29: warning: ') ' directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] sprintf(warning_str, "%s)\n", warning_str); ^~~ bgc_hmm.c:242:5: note: 'sprintf' output between 3 and 10002 bytes into a destination of size 10000 sprintf(warning_str, "%s)\n", warning_str); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/phylo' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/phylo_hmm' gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c phylo_hmm.c -o 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 gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c gap_patterns.c -o 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 ar rs /build/phast-1.4+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phylo_hmm.o gap_patterns.o ar rs /build/phast-1.4+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phylo_hmm.o gap_patterns.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/motif' gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/motif/../../..\" -fno-strict-aliasing -c tfbs.c -o 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 tfbs.c: In function 'ms_read': tfbs.c:219:32: warning: variable 'line_no' set but not used [-Wunused-but-set-variable] int i, nseqs, j, do_toupper, line_no; ^~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/motif/../../..\" -fno-strict-aliasing -c motif.c -o 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 ar rs /build/phast-1.4+dfsg/src/lib/motif/../../../lib/libphast.a tfbs.o motif.o ar rs /build/phast-1.4+dfsg/src/lib/motif/../../../lib/libphast.a tfbs.o motif.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/motif' make[3]: Leaving directory '/build/phast-1.4+dfsg/src/lib' make[3]: Entering directory '/build/phast-1.4+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-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/dless/../..\" -fno-strict-aliasing -c bd_phylo_hmm.c -o bd_phylo_hmm.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.4+dfsg/src/dless/../../lib -o /build/phast-1.4+dfsg/src/dless/../../bin/dless dless.o bd_phylo_hmm.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/dless/../..\" -fno-strict-aliasing -c dlessP.c -o dlessP.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.4+dfsg/src/dless/../../lib -o /build/phast-1.4+dfsg/src/dless/../../bin/dlessP dlessP.o bd_phylo_hmm.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-1.4+dfsg/src/dless' make[3]: Entering directory '/build/phast-1.4+dfsg/src/exoniphy' ../munge-help.sh exoniphy.help_src > exoniphy.help gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/exoniphy/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/exoniphy/../../lib -o /build/phast-1.4+dfsg/src/exoniphy/../../bin/exoniphy exoniphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-1.4+dfsg/src/exoniphy' make[3]: Entering directory '/build/phast-1.4+dfsg/src/phastCons' ../munge-help.sh phastCons.help_src > phastCons.help gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/phastCons/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/phastCons/../../lib -o /build/phast-1.4+dfsg/src/phastCons/../../bin/phastCons phastCons.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-1.4+dfsg/src/phastCons' make[3]: Entering directory '/build/phast-1.4+dfsg/src/phastOdds' ../munge-help.sh phastOdds.help_src > phastOdds.help gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/phastOdds/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/phastOdds/../../lib -o /build/phast-1.4+dfsg/src/phastOdds/../../bin/phastOdds phastOdds.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-1.4+dfsg/src/phastOdds' make[3]: Entering directory '/build/phast-1.4+dfsg/src/phastMotif' gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/phastMotif/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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] int i, j, separate_backgd = 0, ^~~~~~~~~~~~~~~ gcc -L/build/phast-1.4+dfsg/src/phastMotif/../../lib -o /build/phast-1.4+dfsg/src/phastMotif/../../bin/phastMotif phastMotif.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-1.4+dfsg/src/phastMotif' make[3]: Entering directory '/build/phast-1.4+dfsg/src/phyloFit' ../munge-help.sh phyloFit.help_src > phyloFit.help gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/phyloFit/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/phyloFit/../../lib -o /build/phast-1.4+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-1.4+dfsg/src/phyloFit' make[3]: Entering directory '/build/phast-1.4+dfsg/src/phyloBoot' ../munge-help.sh phyloBoot.help_src > phyloBoot.help gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/phyloBoot/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/phyloBoot/../../lib -o /build/phast-1.4+dfsg/src/phyloBoot/../../bin/phyloBoot phyloBoot.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-1.4+dfsg/src/phyloBoot' make[3]: Entering directory '/build/phast-1.4+dfsg/src/phyloP' ../munge-help.sh phyloP.help_src > phyloP.help gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/phyloP/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/phyloP/../../lib -o /build/phast-1.4+dfsg/src/phyloP/../../bin/phyloP phyloP.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-1.4+dfsg/src/phyloP' make[3]: Entering directory '/build/phast-1.4+dfsg/src/prequel' ../munge-help.sh pbsTrain.help_src > pbsTrain.help ../munge-help.sh pbsDecode.help_src > pbsDecode.help ../munge-help.sh pbsEncode.help_src > pbsEncode.help ../munge-help.sh prequel.help_src > prequel.help ../munge-help.sh pbsScoreMatrix.help_src > pbsScoreMatrix.help gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/prequel/../..\" -fno-strict-aliasing -c simplex_grid.c -o simplex_grid.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbs_code.c -o pbs_code.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.4+dfsg/src/prequel/../../lib -o /build/phast-1.4+dfsg/src/prequel/../../bin/pbsDecode pbsDecode.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsEncode.c -o pbsEncode.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.4+dfsg/src/prequel/../../lib -o /build/phast-1.4+dfsg/src/prequel/../../bin/pbsEncode pbsEncode.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsScoreMatrix.c -o pbsScoreMatrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.4+dfsg/src/prequel/../../lib -o /build/phast-1.4+dfsg/src/prequel/../../bin/pbsScoreMatrix pbsScoreMatrix.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsTrain.c -o pbsTrain.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.4+dfsg/src/prequel/../../lib -o /build/phast-1.4+dfsg/src/prequel/../../bin/pbsTrain pbsTrain.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/prequel/../..\" -fno-strict-aliasing -c prequel.c -o prequel.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.4+dfsg/src/prequel/../../lib -o /build/phast-1.4+dfsg/src/prequel/../../bin/prequel prequel.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-1.4+dfsg/src/prequel' make[3]: Entering directory '/build/phast-1.4+dfsg/src/util' ../munge-help.sh phastBias.help_src > phastBias.help ../munge-help.sh modFreqs.help_src > modFreqs.help ../munge-help.sh indelHistory.help_src > indelHistory.help ../munge-help.sh clean_genes.help_src > clean_genes.help ../munge-help.sh treeGen.help_src > treeGen.help ../munge-help.sh base_evolve.help_src > base_evolve.help ../munge-help.sh phast.help_src > phast.help ../munge-help.sh msa_diff.help_src > msa_diff.help ../munge-help.sh makeHKY.help_src > makeHKY.help ../munge-help.sh indelFit.help_src > indelFit.help ../munge-help.sh consEntropy.help_src > consEntropy.help gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/hmm_train hmm_train.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/indelHistory indelHistory.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/clean_genes clean_genes.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/treeGen treeGen.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/base_evolve base_evolve.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c tree_doctor.c -o tree_doctor.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/tree_doctor tree_doctor.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/msa_diff msa_diff.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/indelFit indelFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/hmm_tweak hmm_tweak.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/all_dists all_dists.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/stringiphy stringiphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/convert_coords convert_coords.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/hmm_view hmm_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/consEntropy consEntropy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/maf_parse maf_parse.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/msa_split msa_split.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/eval_predictions eval_predictions.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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] char tuple_i[mod->order+2], tuple_j[mod->order+2]; ^~~~~~~ gcc -L/build/phast-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/display_rate_matrix display_rate_matrix.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/draw_tree draw_tree.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/makeHKY makeHKY.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_view.c -o msa_view.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/msa_view msa_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/phastBias phastBias.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/refeature refeature.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-1.4+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-1.4+dfsg/src' make[1]: Leaving directory '/build/phast-1.4+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install make -j8 install DESTDIR=/build/phast-1.4\+dfsg/debian/phast AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/phast-1.4+dfsg' (cd src; make install DESTDIR=/build/phast-1.4+dfsg/debian/phast ) make[2]: Entering directory '/build/phast-1.4+dfsg/src' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mkdir -p /build/phast-1.4+dfsg/debian/phast/usr/bin/ mkdir -p /build/phast-1.4+dfsg/debian/phast/usr/share/phast/data/ mkdir -p /build/phast-1.4+dfsg/debian/phast/usr/share/man/man1/ cp ../bin/* /build/phast-1.4+dfsg/debian/phast/usr/bin/ cp -R ../data/* /build/phast-1.4+dfsg/debian/phast/usr/share/phast/data/ cp -R ../doc/man/* /build/phast-1.4+dfsg/debian/phast/usr/share/man/man1/ make[2]: Leaving directory '/build/phast-1.4+dfsg/src' make[1]: Leaving directory '/build/phast-1.4+dfsg' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phast/usr/bin/phastCons debian/phast/usr/bin/display_rate_matrix debian/phast/usr/bin/draw_tree debian/phast/usr/bin/indelFit debian/phast/usr/bin/pbsDecode debian/phast/usr/bin/tree_doctor debian/phast/usr/bin/phast debian/phast/usr/bin/indelHistory debian/phast/usr/bin/hmm_tweak debian/phast/usr/bin/msa_view debian/phast/usr/bin/base_evolve debian/phast/usr/bin/phyloP debian/phast/usr/bin/dless debian/phast/usr/bin/refeature debian/phast/usr/bin/phyloFit debian/phast/usr/bin/convert_coords debian/phast/usr/bin/pbsEncode debian/phast/usr/bin/phastOdds debian/phast/usr/bin/all_dists debian/phast/usr/bin/phastBias debian/phast/usr/bin/pbsScoreMatrix debian/phast/usr/bin/clean_genes debian/phast/usr/bin/eval_predictions debian/phast/usr/bin/modFreqs debian/phast/usr/bin/hmm_train debian/phast/usr/bin/stringiphy debian/phast/usr/bin/exoniphy debian/phast/usr/bin/dlessP debian/phast/usr/bin/maf_parse debian/phast/usr/bin/chooseLines debian/phast/usr/bin/msa_split debian/phast/usr/bin/treeGen debian/phast/usr/bin/msa_diff debian/phast/usr/bin/prequel debian/phast/usr/bin/phyloBoot debian/phast/usr/bin/pbsTrain debian/phast/usr/bin/hmm_view debian/phast/usr/bin/phastMotif debian/phast/usr/bin/makeHKY debian/phast/usr/bin/consEntropy were not linked against libblas.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phast/usr/bin/phastCons debian/phast/usr/bin/display_rate_matrix debian/phast/usr/bin/draw_tree debian/phast/usr/bin/indelFit debian/phast/usr/bin/pbsDecode debian/phast/usr/bin/tree_doctor debian/phast/usr/bin/phast debian/phast/usr/bin/indelHistory debian/phast/usr/bin/hmm_tweak debian/phast/usr/bin/msa_view debian/phast/usr/bin/base_evolve debian/phast/usr/bin/phyloP debian/phast/usr/bin/dless debian/phast/usr/bin/refeature debian/phast/usr/bin/phyloFit debian/phast/usr/bin/convert_coords debian/phast/usr/bin/pbsEncode debian/phast/usr/bin/phastOdds debian/phast/usr/bin/all_dists debian/phast/usr/bin/phastBias debian/phast/usr/bin/pbsScoreMatrix debian/phast/usr/bin/clean_genes debian/phast/usr/bin/eval_predictions debian/phast/usr/bin/modFreqs debian/phast/usr/bin/hmm_train debian/phast/usr/bin/stringiphy debian/phast/usr/bin/exoniphy debian/phast/usr/bin/dlessP debian/phast/usr/bin/maf_parse debian/phast/usr/bin/chooseLines debian/phast/usr/bin/msa_split debian/phast/usr/bin/treeGen debian/phast/usr/bin/msa_diff debian/phast/usr/bin/prequel debian/phast/usr/bin/phyloBoot debian/phast/usr/bin/pbsTrain debian/phast/usr/bin/hmm_view debian/phast/usr/bin/phastMotif debian/phast/usr/bin/makeHKY debian/phast/usr/bin/consEntropy were not linked against libtmglib.so.3 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'phast' in '../phast_1.4+dfsg-1_arm64.deb'. dpkg-deb: building package 'phast-dbgsym' in '../phast-dbgsym_1.4+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../phast_1.4+dfsg-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/24659 and its subdirectories I: Current time: Wed Sep 8 12:27:41 -12 2021 I: pbuilder-time-stamp: 1631147261