Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/p/phast/phast_1.5+dfsg-2_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/phast-1.5+dfsg-25i5x1e0r/phast_1.5+dfsg-2_amd64.buildinfo Get source package info: phast=1.5+dfsg-2 Source URL: http://snapshot.notset.fr/mr/package/phast/1.5+dfsg-2/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11.1 automake=1:1.16.2-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.47 bash=5.0-7 binutils=2.35.1-1 binutils-common=2.35.1-1 binutils-x86-64-linux-gnu=2.35.1-1 bsdextrautils=2.36-3+b1 bsdutils=1:2.36-3+b1 build-essential=12.8 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.0-13 dash=0.5.10.2-7 debconf=1.5.74 debhelper=13.2.1 debianutils=4.11.2 dh-autoreconf=19 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13-5 file=1:5.38-5 findutils=4.7.0-1 g++=4:10.2.0-1 g++-10=10.2.0-13 gcc=4:10.2.0-1 gcc-10=10.2.0-13 gcc-10-base=10.2.0-13 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.4-1 groff-base=1.22.4-5 gzip=1.10-2 help2man=1.47.16 hostname=3.23 init-system-helpers=1.58 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libarchive-zip-perl=1.68-1 libasan6=10.2.0-13 libatomic1=10.2.0-13 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3 libaudit1=1:2.8.5-3+b1 libbinutils=2.35.1-1 libblas-dev=3.9.0-3 libblas3=3.9.0-3 libblkid1=2.36-3+b1 libbz2-1.0=1.0.8-4 libc-bin=2.31-3 libc-dev-bin=2.31-3 libc6=2.31-3 libc6-dev=2.31-3 libcap-ng0=0.7.9-2.2 libcc1-0=10.2.0-13 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-1 libctf0=2.35.1-1 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.254 libdebhelper-perl=13.2.1 libdpkg-perl=1.20.5 libelf1=0.181-1 libffi7=3.3-4 libfile-stripnondeterminism-perl=1.9.0-1 libgcc-10-dev=10.2.0-13 libgcc-s1=10.2.0-13 libgcrypt20=1.8.6-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libgfortran5=10.2.0-13 libglib2.0-0=2.66.0-2 libgmp10=2:6.2.0+dfsg-6 libgomp1=10.2.0-13 libgpg-error0=1.38-2 libicu67=67.1-4 libisl22=0.22.1-1 libitm1=10.2.0-13 liblapack-dev=3.9.0-3 liblapack3=3.9.0-3 liblocale-gettext-perl=1.07-4 liblsan0=10.2.0-13 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-5 libmagic1=1:5.38-5 libmount1=2.36-3+b1 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpcre16-3=2:8.39-13 libpcre2-8-0=10.34-7 libpcre3=2:8.39-13 libpcre3-dev=2:8.39-13 libpcre32-3=2:8.39-13 libpcrecpp0v5=2:8.39-13 libperl5.30=5.30.3-4 libpipeline1=1.5.3-1 libquadmath0=10.2.0-13 libseccomp2=2.4.4-1 libselinux1=3.1-2 libsigsegv2=2.12-2 libsmartcols1=2.36-3+b1 libstdc++-10-dev=10.2.0-13 libstdc++6=10.2.0-13 libsub-override-perl=0.09-2 libsystemd0=246.6-1 libtinfo6=6.2+20200918-1 libtmglib-dev=3.9.0-3 libtmglib3=3.9.0-3 libtool=2.4.6-14 libtsan0=10.2.0-13 libubsan1=10.2.0-13 libuchardet0=0.0.7-1 libudev1=246.6-1 libunistring2=0.9.10-4 libuuid1=2.36-3+b1 libxml2=2.9.10+dfsg-6 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.8.10-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20200918-1 ncurses-bin=6.2+20200918-1 patch=2.7.6-6 perl=5.30.3-4 perl-base=5.30.3-4 perl-modules-5.30=5.30.3-4 po-debconf=1.0.21 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-5 tar=1.30+dfsg-7 util-linux=2.36-3+b1 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201009T150112Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d phast=1.5+dfsg-2 && mkdir -p /build/phast-HKLvMS && dpkg-source --no-check -x /*.dsc /build/phast-HKLvMS/phast-1.5+dfsg && chown -R builduser:builduser /build/phast-HKLvMS" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/phast-HKLvMS/phast-1.5+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1601709690" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/phast-HKLvMS /tmp/phast-1.5+dfsg-25i5x1e0r bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201009T150112Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.eOSw4p6CWN as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.eOSw4p6CWN Reading package lists... Building dependency tree... util-linux is already the newest version (2.36-3+b1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20201009T150112Z unstable/main amd64 libfakeroot amd64 1.25.3-1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201009T150112Z unstable/main amd64 fakeroot amd64 1.25.3-1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (910 kB/s) Selecting previously unselected package libfakeroot:amd64. (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 ... 4582 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1_amd64.deb ... Unpacking fakeroot (1.25.3-1) ... Setting up libfakeroot:amd64 (1.25.3-1) ... Setting up fakeroot (1.25.3-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-3) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201009T150112Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.eOSw4p6CWN Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20201009T150112Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 19s (1167 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.eOSw4p6CWN I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d phast=1.5+dfsg-2 && mkdir -p /build/phast-HKLvMS && dpkg-source --no-check -x /*.dsc /build/phast-HKLvMS/phast-1.5+dfsg && chown -R builduser:builduser /build/phast-HKLvMS"' exec /tmp/mmdebstrap.eOSw4p6CWN Reading package lists... NOTICE: 'phast' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/phast.git Please use: git clone https://salsa.debian.org/med-team/phast.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1871 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main phast 1.5+dfsg-2 (dsc) [1997 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main phast 1.5+dfsg-2 (tar) [1811 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main phast 1.5+dfsg-2 (diff) [57.9 kB] Fetched 1871 kB in 2s (1242 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'phast_1.5+dfsg-2.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting phast in /build/phast-HKLvMS/phast-1.5+dfsg dpkg-source: info: unpacking phast_1.5+dfsg.orig.tar.xz dpkg-source: info: unpacking phast_1.5+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying clapack.patch dpkg-source: info: applying do_not_install_to_opt.patch dpkg-source: info: applying use_debian_packaged_libpcre.patch dpkg-source: info: applying use_debian_packaged_help2man.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying fix_test_makefile.patch dpkg-source: info: applying arm64.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/phast-HKLvMS/phast-1.5+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1601709690" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.eOSw4p6CWN dpkg-buildpackage: info: source package phast dpkg-buildpackage: info: source version 1.5+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg' dh_auto_clean cd src && make clean make[2]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src' make[3]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/$dir && make clean ; done make[4]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base' rm -f *.o make[4]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base' make[4]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/msa' rm -f *.o make[4]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/msa' make[4]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/feature' rm -f *.o make[4]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/feature' make[4]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/hmm' rm -f *.o make[4]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/hmm' make[4]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo' rm -f *.o make[4]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo' make[4]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo_hmm' rm -f *.o make[4]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/motif' rm -f *.o make[4]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/motif' rm -f /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../lib/* make[3]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib' make[3]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/dless' rm -f *.o dless.help dlessP.help /build/phast-HKLvMS/phast-1.5+dfsg/src/dless/../../bin/dless /build/phast-HKLvMS/phast-1.5+dfsg/src/dless/../../bin/dlessP make[3]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/dless' make[3]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/exoniphy' rm -f *.o *.help /build/phast-HKLvMS/phast-1.5+dfsg/src/exoniphy/../../bin/exoniphy make[3]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/exoniphy' make[3]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/phastCons' rm -f *.o /build/phast-HKLvMS/phast-1.5+dfsg/src/phastCons/../../bin/phastCons phastCons.help make[3]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/phastCons' make[3]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/phastOdds' rm -f *.o *.help /build/phast-HKLvMS/phast-1.5+dfsg/src/phastOdds/../../bin/phastOdds make[3]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/phastOdds' make[3]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/phastMotif' rm -f *.o /build/phast-HKLvMS/phast-1.5+dfsg/src/phastMotif/../../bin/phastMotif make[3]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/phastMotif' make[3]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/phyloFit' rm -f *.o /build/phast-HKLvMS/phast-1.5+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.help make[3]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/phyloFit' make[3]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/phyloBoot' rm -f *.o *.help /build/phast-HKLvMS/phast-1.5+dfsg/src/phyloBoot/../../bin/phyloBoot make[3]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/phyloBoot' make[3]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/phyloP' rm -f *.o /build/phast-HKLvMS/phast-1.5+dfsg/src/phyloP/../../bin/phyloP phyloP.help make[3]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/phyloP' make[3]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/prequel' rm -f *.o /build/phast-HKLvMS/phast-1.5+dfsg/src/prequel/../../bin/pbsDecode /build/phast-HKLvMS/phast-1.5+dfsg/src/prequel/../../bin/pbsEncode /build/phast-HKLvMS/phast-1.5+dfsg/src/prequel/../../bin/pbsScoreMatrix /build/phast-HKLvMS/phast-1.5+dfsg/src/prequel/../../bin/pbsTrain /build/phast-HKLvMS/phast-1.5+dfsg/src/prequel/../../bin/prequel pbsDecode.help pbsEncode.help pbsScoreMatrix.help pbsTrain.help prequel.help make[3]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/prequel' make[3]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/util' rm -f *.o *.help /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/all_dists /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/base_evolve /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/chooseLines /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/clean_genes /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/consEntropy /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/convert_coords /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/display_rate_matrix /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/draw_tree /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/eval_predictions /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/hmm_train /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/hmm_tweak /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/hmm_view /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/indelFit /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/indelHistory /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/maf_parse /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/makeHKY /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/modFreqs /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/msa_diff /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/msa_split /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/msa_view /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/phast /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/phastBias /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/refeature /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/stringiphy /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/treeGen /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/tree_doctor make[3]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/util' rm -rf ../bin ../lib ../doc make[2]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src' make[1]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/$dir && make ; done make[3]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/$dir && make ; done make[4]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base' gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar: creating /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o make[4]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/base' make[4]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/msa' gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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] 29 | int i, start_idx, length, max_tuples, block_no, | ^~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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] 257 | int maxlen, i, nseqs, j, do_toupper, line_no; | ^~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 sufficient_stats.c: In function ‘ss_from_msas’: sufficient_stats.c:140:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 140 | else | ^~~~ sufficient_stats.c:142:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 142 | max_tuples = pow_bounded(strlen(msa->alphabet) + (int)strlen(msa->missing) + 1, | ^~~~~~~~~~ ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/msa/../../../lib/libphast.a local_alignment.o maf.o maf_block.o msa.o multi_msa.o sufficient_stats.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/msa/../../../lib/libphast.a local_alignment.o maf.o maf_block.o msa.o multi_msa.o sufficient_stats.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/msa/../../../lib/libphast.a local_alignment.o maf.o maf_block.o msa.o multi_msa.o sufficient_stats.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/msa/../../../lib/libphast.a local_alignment.o maf.o maf_block.o msa.o multi_msa.o sufficient_stats.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/msa/../../../lib/libphast.a local_alignment.o maf.o maf_block.o msa.o multi_msa.o sufficient_stats.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/msa/../../../lib/libphast.a local_alignment.o maf.o maf_block.o msa.o multi_msa.o sufficient_stats.o make[4]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/msa' make[4]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/feature' gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/feature/../../../lib/libphast.a bed.o category_map.o genepred.o gff.o wig.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/feature/../../../lib/libphast.a bed.o category_map.o genepred.o gff.o wig.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/feature/../../../lib/libphast.a bed.o category_map.o genepred.o gff.o wig.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/feature/../../../lib/libphast.a bed.o category_map.o genepred.o gff.o wig.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/feature/../../../lib/libphast.a bed.o category_map.o genepred.o gff.o wig.o make[4]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/feature' make[4]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/hmm' gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/hmm/../../../lib/libphast.a em.o hmm.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/hmm/../../../lib/libphast.a em.o hmm.o make[4]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/hmm' make[4]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo' gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 241 | 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 241 | sprintf(warning_str, "%s, %s", warning_str, ((String*)lst_get_ptr(pruned_names, j))->chars); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bgc_hmm.c:241:7: warning: ‘sprintf’ argument 3 overlaps destination object ‘warning_str’ [-Wrestrict] bgc_hmm.c:235:10: note: destination object referenced by ‘restrict’-qualified argument 1 was declared here 235 | char warning_str[10000]; | ^~~~~~~~~~~ bgc_hmm.c:242:29: warning: ‘) ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 242 | 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 242 | sprintf(warning_str, "%s)\n", warning_str); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bgc_hmm.c:242:5: warning: ‘sprintf’ argument 3 overlaps destination object ‘warning_str’ [-Wrestrict] bgc_hmm.c:235:10: note: destination object referenced by ‘restrict’-qualified argument 1 was declared here 235 | char warning_str[10000]; | ^~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o make[4]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo' make[4]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo_hmm' gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a gap_patterns.o phylo_hmm.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a gap_patterns.o phylo_hmm.o make[4]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/motif' gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 motif.c: In function ‘mtf_print’: motif.c:1411:7: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 1411 | fprintf(F, "\t%s\n", (char*)lst_get_ptr(notfound, i)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ motif.c: In function ‘mtf_print_html’: motif.c:1604:7: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 1604 | fprintf(F, "
  • %s\n", (char*)lst_get_ptr(notfound, i)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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] 219 | int i, nseqs, j, do_toupper, line_no; | ^~~~~~~ ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/motif/../../../lib/libphast.a motif.o tfbs.o ar rs /build/phast-HKLvMS/phast-1.5+dfsg/src/lib/motif/../../../lib/libphast.a motif.o tfbs.o make[4]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib/motif' make[3]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/lib' make[3]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/dless' ../munge-help.sh dless.help_src > dless.help ../munge-help.sh dlessP.help_src > dlessP.help gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/dless/../../lib -o /build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/dless/../../lib -o /build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/dless' make[3]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/exoniphy' ../munge-help.sh exoniphy.help_src > exoniphy.help gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/exoniphy/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/exoniphy/../../lib -o /build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/exoniphy' make[3]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/phastCons' ../munge-help.sh phastCons.help_src > phastCons.help gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/phastCons/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/phastCons/../../lib -o /build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/phastCons' make[3]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/phastOdds' ../munge-help.sh phastOdds.help_src > phastOdds.help gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/phastOdds/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/phastOdds/../../lib -o /build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/phastOdds' make[3]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/phastMotif' gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/phastMotif/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/phastMotif/../..\" -fno-strict-aliasing -c phastMotif.c -o phastMotif.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phastMotif.c: In function ‘main’: phastMotif.c:131:13: warning: variable ‘separate_backgd’ set but not used [-Wunused-but-set-variable] 131 | int i, j, separate_backgd = 0, | ^~~~~~~~~~~~~~~ gcc -L/build/phast-HKLvMS/phast-1.5+dfsg/src/phastMotif/../../lib -o /build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/phastMotif' make[3]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/phyloFit' ../munge-help.sh phyloFit.help_src > phyloFit.help gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/phyloFit/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/phyloFit/../../lib -o /build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/phyloFit' make[3]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/phyloBoot' ../munge-help.sh phyloBoot.help_src > phyloBoot.help gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/phyloBoot/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/phyloBoot/../../lib -o /build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/phyloBoot' make[3]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/phyloP' ../munge-help.sh phyloP.help_src > phyloP.help gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/phyloP/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/phyloP/../../lib -o /build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/phyloP' make[3]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/prequel' ../munge-help.sh pbsDecode.help_src > pbsDecode.help ../munge-help.sh pbsEncode.help_src > pbsEncode.help ../munge-help.sh pbsScoreMatrix.help_src > pbsScoreMatrix.help ../munge-help.sh pbsTrain.help_src > pbsTrain.help ../munge-help.sh prequel.help_src > prequel.help gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/prequel/../../lib -o /build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/prequel/../../lib -o /build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/prequel/../../lib -o /build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/prequel/../../lib -o /build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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 prequel.c: In function ‘main’: prequel.c:285:32: warning: ‘.bin’ directive writing 4 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 285 | sprintf(out_fname, "%s.%s.bin", out_root, n->name); | ^~~~ prequel.c:285:7: note: ‘sprintf’ output 6 or more bytes (assuming 261) into a destination of size 256 285 | sprintf(out_fname, "%s.%s.bin", out_root, n->name); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prequel.c:253:32: warning: ‘.fa’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 253 | sprintf(out_fname, "%s.%s.fa", out_root, n->name); | ^~~ prequel.c:253:7: note: ‘sprintf’ output 5 or more bytes (assuming 260) into a destination of size 256 253 | sprintf(out_fname, "%s.%s.fa", out_root, n->name); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prequel.c:203:32: warning: ‘.probs’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 203 | sprintf(out_fname, "%s.%s.probs", out_root, n->name); | ^~~~~~ prequel.c:203:7: note: ‘sprintf’ output 8 or more bytes (assuming 263) into a destination of size 256 203 | sprintf(out_fname, "%s.%s.probs", out_root, n->name); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -L/build/phast-HKLvMS/phast-1.5+dfsg/src/prequel/../../lib -o /build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/prequel' make[3]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src/util' ../munge-help.sh base_evolve.help_src > base_evolve.help ../munge-help.sh clean_genes.help_src > clean_genes.help ../munge-help.sh consEntropy.help_src > consEntropy.help ../munge-help.sh indelFit.help_src > indelFit.help ../munge-help.sh indelHistory.help_src > indelHistory.help ../munge-help.sh makeHKY.help_src > makeHKY.help ../munge-help.sh modFreqs.help_src > modFreqs.help ../munge-help.sh msa_diff.help_src > msa_diff.help ../munge-help.sh phast.help_src > phast.help ../munge-help.sh phastBias.help_src > phastBias.help ../munge-help.sh treeGen.help_src > treeGen.help gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/consEntropy consEntropy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c display_rate_matrix.c -o display_rate_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition display_rate_matrix.c: In function ‘do_context_dependent_ti_tv’: display_rate_matrix.c:204:8: warning: variable ‘tuple_i’ set but not used [-Wunused-but-set-variable] 204 | char tuple_i[mod->order+2], tuple_j[mod->order+2]; | ^~~~~~~ gcc -L/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/indelFit indelFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/indelHistory indelHistory.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/makeHKY makeHKY.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+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 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/phastBias phastBias.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/refeature refeature.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/stringiphy stringiphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/treeGen treeGen.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-HKLvMS/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src/util/../../lib -o /build/phast-HKLvMS/phast-1.5+dfsg/src/util/../../bin/tree_doctor tree_doctor.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-HKLvMS/phast-1.5+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-HKLvMS/phast-1.5+dfsg/src' make[1]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg' cd test && PATH=/build/phast-HKLvMS/phast-1.5+dfsg/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin make msa_view make[2]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/test' *** Testing msa_view *** msa_view hmrc.ss -i SS --end 10000 > hmrc.fa if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.fa -o PHYLIP > hmrc.ph msa_view hmrc.ph -i PHYLIP > hmrc.fa if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ph --out-format MPM --in-format PHYLIP > hmrc.mpm msa_view hmrc.mpm --in-format MPM > hmrc.fa if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.fa -o SS > hmrc_short_a.ss msa_view hmrc.ss --end 10000 -i SS -o SS > hmrc_short_b.ss if ! diff --brief hmrc_short_[ab].ss ; then echo "ERROR" ; exit 1 ; fi msa_view --seqs human,cow hmrc_short_a.ss -i SS -o SS | msa_view - -i SS > hm_a.fa msa_view --seqs human,cow hmrc.fa > hm_b.fa if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --gap-strip ANY -i SS -o SS | msa_view - -i SS > hmrc_nogaps_a.fa msa_view hmrc.ss -i SS | msa_view - --gap-strip ANY > hmrc_nogaps_b.fa if ! diff --brief hmrc_nogaps_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.fa --seqs human,cow --gap-strip ALL > hm_a.fa msa_view hmrc_short_a.ss --seqs human,cow -i SS --gap-strip ALL > hm_b.fa if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --start 10000 --end 20000 -i SS > hmrc_sub_a.fa msa_view hmrc.ss -i SS | msa_view - --start 10000 --end 20000 > hmrc_sub_b.fa if ! diff --brief hmrc_sub_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --summary -i SS > hmrc_summary if ! diff --brief -b hmrc_summary hmrc_summary_correct ; then echo "ERROR" ; exit 1 ; fi -e Passed all tests. make[2]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/test' make[1]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -a dh_prep -a dh_auto_install -a make -j4 install DESTDIR=/build/phast-HKLvMS/phast-1.5\+dfsg/debian/phast AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg' (cd src; make install DESTDIR=/build/phast-HKLvMS/phast-1.5+dfsg/debian/phast ) make[2]: Entering directory '/build/phast-HKLvMS/phast-1.5+dfsg/src' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mkdir -p /build/phast-HKLvMS/phast-1.5+dfsg/debian/phast/usr/bin/ mkdir -p /build/phast-HKLvMS/phast-1.5+dfsg/debian/phast/usr/share/phast/data/ mkdir -p /build/phast-HKLvMS/phast-1.5+dfsg/debian/phast/usr/share/man/man1/ cp ../bin/* /build/phast-HKLvMS/phast-1.5+dfsg/debian/phast/usr/bin/ cp -R ../data/* /build/phast-HKLvMS/phast-1.5+dfsg/debian/phast/usr/share/phast/data/ cp -R ../doc/man/* /build/phast-HKLvMS/phast-1.5+dfsg/debian/phast/usr/share/man/man1/ make[2]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg/src' make[1]: Leaving directory '/build/phast-HKLvMS/phast-1.5+dfsg' dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a -a dh_strip -a -a dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'phast' in '../phast_1.5+dfsg-2_amd64.deb'. dpkg-deb: building package 'phast-dbgsym' in '../phast-dbgsym_1.5+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../phast_1.5+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/phast-HKLvMS /tmp/phast-1.5+dfsg-25i5x1e0r I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.eOSw4p6CWN... I: success in 529.9850 seconds md5: phast-dbgsym_1.5+dfsg-2_amd64.deb: OK md5: phast_1.5+dfsg-2_amd64.deb: OK sha1: phast-dbgsym_1.5+dfsg-2_amd64.deb: OK sha1: phast_1.5+dfsg-2_amd64.deb: OK sha256: phast-dbgsym_1.5+dfsg-2_amd64.deb: OK sha256: phast_1.5+dfsg-2_amd64.deb: OK Checksums: OK