Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/p/phast/phast_1.6+dfsg-3_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/phast-1.6+dfsg-3te_e8oo3/phast_1.6+dfsg-3_amd64.buildinfo Get source package info: phast=1.6+dfsg-3 Source URL: http://snapshot.notset.fr/mr/package/phast/1.6+dfsg-3/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.5-1.1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-3.1 binutils=2.37-9 binutils-common=2.37-9 binutils-x86-64-linux-gnu=2.37-9 bsdextrautils=2.37.2-4 bsdutils=1:2.37.2-4 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-12 dash=0.5.11+git20210903+057cd650a4ed-3 debconf=1.5.79 debhelper=13.5.2 debianutils=5.5-1 dh-autoreconf=20 dh-strip-nondeterminism=1.12.0-2 diffutils=1:3.7-5 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 file=1:5.39-3 findutils=4.8.0-1 g++=4:11.2.0-2 g++-11=11.2.0-12 gcc=4:11.2.0-2 gcc-11=11.2.0-12 gcc-11-base=11.2.0-12 gettext=0.21-4 gettext-base=0.21-4 grep=3.7-1 groff-base=1.22.4-7 gzip=1.10-4 help2man=1.48.5 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libasan6=11.2.0-12 libatlas-base-dev=3.10.3-11 libatlas3-base=3.10.3-11 libatomic1=11.2.0-12 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1 libbinutils=2.37-9 libblas-dev=3.10.0-1 libblas3=3.10.0-1 libblkid1=2.37.2-4 libbz2-1.0=1.0.8-4 libc-bin=2.32-4 libc-dev-bin=2.32-4 libc6=2.32-4 libc6-dev=2.32-4 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=11.2.0-12 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.26-1 libcrypt1=1:4.4.26-1 libctf-nobfd0=2.37-9 libctf0=2.37-9 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.261 libdebhelper-perl=13.5.2 libdpkg-perl=1.20.9 libelf1=0.186-1 libf2c2=20140711-1 libf2c2-dev=20140711-1 libfile-stripnondeterminism-perl=1.12.0-2 libgcc-11-dev=11.2.0-12 libgcc-s1=11.2.0-12 libgcrypt20=1.9.4-3+b1 libgdbm-compat4=1.22-1 libgdbm6=1.22-1 libgfortran5=11.2.0-12 libgmp10=2:6.2.1+dfsg-3 libgomp1=11.2.0-12 libgpg-error0=1.42-3 libgssapi-krb5-2=1.18.3-7 libicu67=67.1-7 libisl23=0.24-2 libitm1=11.2.0-12 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 liblapack-dev=3.10.0-1 liblapack3=3.10.0-1 liblocale-gettext-perl=1.07-4+b1 liblsan0=11.2.0-12 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.37.2-4 libmpc3=1.2.1-1 libmpfr6=4.1.0-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.4.0-10 libpam-modules-bin=1.4.0-10 libpam-runtime=1.4.0-10 libpam0g=1.4.0-10 libpcre2-16-0=10.39-3 libpcre2-32-0=10.39-3 libpcre2-8-0=10.39-3 libpcre2-dev=10.39-3 libpcre2-posix3=10.39-3 libpcre3=2:8.39-13 libperl5.32=5.32.1-6 libpipeline1=1.5.4-1 libquadmath0=11.2.0-12 libseccomp2=2.5.2-2 libselinux1=3.3-1 libsigsegv2=2.13-1 libsmartcols1=2.37.2-4 libssl1.1=1.1.1l-1 libstdc++-11-dev=11.2.0-12 libstdc++6=11.2.0-12 libsub-override-perl=0.09-2 libsystemd0=249.6-2 libtinfo6=6.3-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtmglib-dev=3.10.0-1 libtmglib3=3.10.0-1 libtool=2.4.6-15 libtsan0=11.2.0-12 libubsan1=11.2.0-12 libuchardet0=0.0.7-1 libudev1=249.6-2 libunistring2=0.9.10-6 libuuid1=2.37.2-4 libxml2=2.9.12+dfsg-5+b1 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.14.16-1 login=1:4.8.1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 ncurses-base=6.3-1 ncurses-bin=6.3-1 patch=2.7.6-7 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 po-debconf=1.0.21+nmu1 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.00-1 tar=1.34+dfsg-1 util-linux=2.37.2-4 xz-utils=5.2.5-2 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/20211121T025700Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211121T025700Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211216T085418Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211118T084946Z/ 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=1.6+dfsg-3 && mkdir -p /build/phast-BoRzJ4 && dpkg-source --no-check -x /*.dsc /build/phast-BoRzJ4/phast-1.6+dfsg && chown -R builduser:builduser /build/phast-BoRzJ4" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/phast-BoRzJ4/phast-1.6+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1637324274" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/phast-BoRzJ4 /tmp/phast-1.6+dfsg-3te_e8oo3 bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211118T084946Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.0dWin1p01R 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.0dWin1p01R Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-4). 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/20211118T084946Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211118T084946Z unstable/main amd64 fakeroot amd64 1.26-1 [87.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1017 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 ... 4669 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.26-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.26-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.26-1_amd64.deb ... Unpacking fakeroot (1.26-1) ... Setting up libfakeroot:amd64 (1.26-1) ... Setting up fakeroot (1.26-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.32-4) ... 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/20211121T025700Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211121T025700Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211216T085418Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211118T084946Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.0dWin1p01R Get:1 http://snapshot.notset.fr/archive/debian/20211121T025700Z bookworm InRelease [129 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211216T085418Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20211118T084946Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20211121T025700Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211121T025700Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211121T025700Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211121T025700Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211121T025700Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211121T025700Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20211121T025700Z bookworm/main Sources [11.7 MB] Get:5 http://snapshot.notset.fr/archive/debian/20211121T025700Z bookworm/main amd64 Packages [11.2 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20211216T085418Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20211216T085418Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20211216T085418Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20211216T085418Z unstable/main amd64 Packages [12.0 MB] Fetched 35.2 MB in 29s (1219 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.0dWin1p01R I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d phast=1.6+dfsg-3 && mkdir -p /build/phast-BoRzJ4 && dpkg-source --no-check -x /*.dsc /build/phast-BoRzJ4/phast-1.6+dfsg && chown -R builduser:builduser /build/phast-BoRzJ4"' exec /tmp/mmdebstrap.0dWin1p01R 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 1869 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20211121T025700Z bookworm/main phast 1.6+dfsg-3 (dsc) [2048 B] Get:2 http://snapshot.notset.fr/archive/debian/20211121T025700Z bookworm/main phast 1.6+dfsg-3 (tar) [1809 kB] Get:3 http://snapshot.notset.fr/archive/debian/20211121T025700Z bookworm/main phast 1.6+dfsg-3 (diff) [57.7 kB] Fetched 1869 kB in 2s (1235 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'phast_1.6+dfsg-3.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting phast in /build/phast-BoRzJ4/phast-1.6+dfsg dpkg-source: info: unpacking phast_1.6+dfsg.orig.tar.xz dpkg-source: info: unpacking phast_1.6+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying clapack.patch dpkg-source: info: applying do_not_install_to_opt.patch dpkg-source: info: applying use_debian_packaged_libpcre.patch dpkg-source: info: applying use_debian_packaged_help2man.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying fix_test_makefile.patch dpkg-source: info: applying pcre2.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/phast-BoRzJ4/phast-1.6+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1637324274" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.0dWin1p01R dpkg-buildpackage: info: source package phast dpkg-buildpackage: info: source version 1.6+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg' dh_auto_clean cd src && make clean make[2]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src' make[3]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/$dir && make clean ; done make[4]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base' rm -f *.o make[4]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base' make[4]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/msa' rm -f *.o make[4]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/msa' make[4]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/feature' rm -f *.o make[4]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/feature' make[4]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/hmm' rm -f *.o make[4]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/hmm' make[4]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo' rm -f *.o make[4]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo' make[4]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo_hmm' rm -f *.o make[4]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/motif' rm -f *.o make[4]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/motif' rm -f /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../lib/* make[3]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib' make[3]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/dless' rm -f *.o dless.help dlessP.help /build/phast-BoRzJ4/phast-1.6+dfsg/src/dless/../../bin/dless /build/phast-BoRzJ4/phast-1.6+dfsg/src/dless/../../bin/dlessP make[3]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/dless' make[3]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/exoniphy' rm -f *.o *.help /build/phast-BoRzJ4/phast-1.6+dfsg/src/exoniphy/../../bin/exoniphy make[3]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/exoniphy' make[3]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/phastCons' rm -f *.o /build/phast-BoRzJ4/phast-1.6+dfsg/src/phastCons/../../bin/phastCons phastCons.help make[3]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/phastCons' make[3]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/phastOdds' rm -f *.o *.help /build/phast-BoRzJ4/phast-1.6+dfsg/src/phastOdds/../../bin/phastOdds make[3]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/phastOdds' make[3]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/phastMotif' rm -f *.o /build/phast-BoRzJ4/phast-1.6+dfsg/src/phastMotif/../../bin/phastMotif make[3]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/phastMotif' make[3]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloFit' rm -f *.o /build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.help make[3]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloFit' make[3]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloBoot' rm -f *.o *.help /build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloBoot/../../bin/phyloBoot make[3]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloBoot' make[3]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloP' rm -f *.o /build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloP/../../bin/phyloP phyloP.help make[3]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloP' make[3]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/prequel' rm -f *.o /build/phast-BoRzJ4/phast-1.6+dfsg/src/prequel/../../bin/pbsDecode /build/phast-BoRzJ4/phast-1.6+dfsg/src/prequel/../../bin/pbsEncode /build/phast-BoRzJ4/phast-1.6+dfsg/src/prequel/../../bin/pbsScoreMatrix /build/phast-BoRzJ4/phast-1.6+dfsg/src/prequel/../../bin/pbsTrain /build/phast-BoRzJ4/phast-1.6+dfsg/src/prequel/../../bin/prequel pbsDecode.help pbsEncode.help pbsScoreMatrix.help pbsTrain.help prequel.help make[3]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/prequel' make[3]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/util' rm -f *.o *.help /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/all_dists /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/base_evolve /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/chooseLines /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/clean_genes /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/consEntropy /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/convert_coords /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/display_rate_matrix /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/draw_tree /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/eval_predictions /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/hmm_train /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/hmm_tweak /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/hmm_view /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/indelFit /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/indelHistory /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/maf_parse /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/makeHKY /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/modFreqs /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/msa_diff /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/msa_split /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/msa_view /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/phast /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/phastBias /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/refeature /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/stringiphy /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/treeGen /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/tree_doctor make[3]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/util' rm -rf ../bin ../lib ../doc make[2]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src' make[1]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+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 -j10 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg' Type "make package" to create a tarball reflecting the current state of the CVS tree. (cd src; make DESTDIR= CLAPACKPATH=/usr/lib ) make[2]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mkdir -p ../bin ../lib for dir in lib dless exoniphy phastCons phastOdds phastMotif phyloFit phyloBoot phyloP prequel util ; do cd /build/phast-BoRzJ4/phast-1.6+dfsg/src/$dir && make ; done make[3]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/$dir && make ; done make[4]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base' gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_complex_matrix.c -o phast_complex_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_complex_vector.c -o phast_complex_vector.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_eigen.c -o phast_eigen.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_eigen.c: In function ‘mat_diagonalize’: phast_eigen.c:62:3: warning: implicit declaration of function ‘dgeev_’ [-Wimplicit-function-declaration] 62 | dgeev_(&jobvl, &jobvr, &n, tmp, &n, wr, wi, vl, | ^~~~~~ gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_hashtable.c -o phast_hashtable.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_list_of_lists.c -o phast_list_of_lists.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_lists.c -o phast_lists.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_markov_matrix.c -o phast_markov_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_markov_matrix.c: In function ‘mm_exp_higham’: phast_markov_matrix.c:288:5: warning: implicit declaration of function ‘dgebal_’ [-Wimplicit-function-declaration] 288 | dgebal_(&job, &ln, mat, &ln, &ilo, &ihi, scale, &info); | ^~~~~~~ phast_markov_matrix.c:403:3: warning: implicit declaration of function ‘dgesv_’ [-Wimplicit-function-declaration] 403 | dgesv_(&ln, &ln, matU, &ln, ipiv, matV, &ln, &info); | ^~~~~~ phast_markov_matrix.c:428:5: warning: implicit declaration of function ‘dgebak_’ [-Wimplicit-function-declaration] 428 | dgebak_(&job, &side, &ln, &ilo, &ihi, scale, &ln, mat, &ln, &info); | ^~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_matrix.c -o phast_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_matrix.c: In function ‘mat_invert’: phast_matrix.c:263:3: warning: implicit declaration of function ‘dgetrf_’ [-Wimplicit-function-declaration] 263 | dgetrf_(&n, &n, (LAPACK_DOUBLE*)tmp, &n, ipiv, &info); | ^~~~~~~ phast_matrix.c:273:3: warning: implicit declaration of function ‘dgetri_’ [-Wimplicit-function-declaration] 273 | dgetri_(&n, (LAPACK_DOUBLE*)tmp, &n, ipiv, work, &lwork, &info); | ^~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_memory_handler.c -o phast_memory_handler.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_misc.c -o phast_misc.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_misc.c: In function ‘make_name_hash’: phast_misc.c:672:46: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 672 | pcre2_compile_context *map_re = str_re_new("^[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*(->|=)[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from phast_misc.c:16: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_misc.c:672:35: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 672 | pcre2_compile_context *map_re = str_re_new("^[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*(->|=)[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*"); | ^~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_numerical_opt.c -o phast_numerical_opt.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_prob_matrix.c -o phast_prob_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_prob_vector.c -o phast_prob_vector.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_stringsplus.c -o phast_stringsplus.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_stringsplus.c: In function ‘str_re_match_sub’: phast_stringsplus.c:501:25: warning: pointer targets in passing argument 2 of ‘pcre2_match_8’ differ in signedness [-Wpointer-sign] 501 | rc = pcre2_match(re, s->chars, s->length, offset, 0, match_data, NULL); | ~^~~~~~~ | | | char * In file included from phast_stringsplus.c:16: /usr/include/pcre2.h:935:1: note: expected ‘PCRE2_SPTR8’ {aka ‘const unsigned char *’} but argument is of type ‘char *’ 935 | PCRE2_TYPES_STRUCTURES_AND_FUNCTIONS | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ phast_stringsplus.c: In function ‘str_re_match’: phast_stringsplus.c:532:30: warning: passing argument 2 of ‘str_re_match_sub’ from incompatible pointer type [-Wincompatible-pointer-types] 532 | return str_re_match_sub(s, re, l, 0, nsubexp, NULL); | ^~ | | | pcre2_compile_context_8 * {aka struct pcre2_real_compile_context_8 *} phast_stringsplus.c:488:45: note: expected ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} but argument is of type ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} 488 | int str_re_match_sub(String *s, pcre2_code *re, List *l, int offset, int nsubexp, | ^ phast_stringsplus.c: In function ‘str_re_search’: phast_stringsplus.c:538:28: warning: passing argument 2 of ‘str_re_match_sub’ from incompatible pointer type [-Wincompatible-pointer-types] 538 | rc = str_re_match_sub(s, re, l, start_offset, nsubexp, &first_match_idx); | ^~ | | | pcre2_compile_context_8 * {aka struct pcre2_real_compile_context_8 *} phast_stringsplus.c:488:45: note: expected ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} but argument is of type ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} 488 | int str_re_match_sub(String *s, pcre2_code *re, List *l, int offset, int nsubexp, | ^ phast_stringsplus.c: In function ‘str_re_match_sub’: phast_stringsplus.c:504:52: warning: ‘ovector’ may be used uninitialized [-Wmaybe-uninitialized] 504 | if (first_match != NULL) (*first_match) = ovector[0]; | ~~~~~~~^~~ gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_vector.c -o phast_vector.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar: creating /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o make[4]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/base' make[4]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/msa' gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_local_alignment.c -o phast_local_alignment.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_local_alignment.c: In function ‘la_read_lav’: phast_local_alignment.c:50:55: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 50 | pcre2_compile_context *stanza_start_re = str_re_new("^([dshaxm])[[:space:]]*{"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/local_alignment.h:36, from phast_local_alignment.c:32: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_local_alignment.c:50:44: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 50 | pcre2_compile_context *stanza_start_re = str_re_new("^([dshaxm])[[:space:]]*{"); | ^~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_maf.c -o phast_maf.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_maf.c: In function ‘maf_read_cats_subset’: phast_maf.c:29:41: warning: variable ‘block_no’ set but not used [-Wunused-but-set-variable] 29 | int i, start_idx, length, max_tuples, block_no, | ^~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_maf_block.c -o phast_maf_block.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_msa.c -o phast_msa.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_msa.c: In function ‘msa_read_fasta’: phast_msa.c:264:29: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 264 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*([^[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_msa.c:39: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:264:16: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 264 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*([^[:space:]]+)"); | ^ phast_msa.c:257:40: warning: variable ‘line_no’ set but not used [-Wunused-but-set-variable] 257 | int maxlen, i, nseqs, j, do_toupper, line_no; | ^~~~~~~ phast_msa.c: In function ‘msa_read_seq_fasta’: phast_msa.c:1929:29: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 1929 | descrip_re = str_re_new("^[[:space:]]*>"); | ^~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_msa.c:39: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:1929:16: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 1929 | descrip_re = str_re_new("^[[:space:]]*>"); | ^ phast_msa.c: In function ‘msa_format_for_content’: phast_msa.c:2590:22: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 2590 | ss_re = str_re_new("^NSEQS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_msa.c:39: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2590:9: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 2590 | ss_re = str_re_new("^NSEQS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ phast_msa.c:2591:26: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 2591 | phylip_re = str_re_new("^([[:space:]]*([0-9]+))[[:space:]]*[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_msa.c:39: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2591:13: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 2591 | phylip_re = str_re_new("^([[:space:]]*([0-9]+))[[:space:]]*[[:space:]]*([0-9]+)"); | ^ phast_msa.c:2592:25: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 2592 | fasta_re = str_re_new("^>.*"); | ^~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_msa.c:39: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2592:12: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 2592 | fasta_re = str_re_new("^>.*"); | ^ phast_msa.c:2593:23: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 2593 | lav_re = str_re_new("^#:lav.*"); | ^~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_msa.c:39: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2593:10: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 2593 | lav_re = str_re_new("^#:lav.*"); | ^ phast_msa.c:2594:23: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 2594 | maf_re = str_re_new("^##maf"); | ^~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_msa.c:39: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2594:10: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 2594 | maf_re = str_re_new("^##maf"); | ^ gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_multi_msa.c -o phast_multi_msa.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_multi_msa.c: In function ‘multimsa_new_from_files’: phast_multi_msa.c:54:49: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 54 | pcre2_compile_context *blocks_re = str_re_new("#[[:space:]]*BLOCKS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_multi_msa.c:37: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_multi_msa.c:54:38: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 54 | pcre2_compile_context *blocks_re = str_re_new("#[[:space:]]*BLOCKS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~ phast_multi_msa.c:55:47: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 55 | pcre2_compile_context *alph_re = str_re_new("#[[:space:]]*ALPHABET[[:space:]]*=[[:space:]]*([A-Z]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_multi_msa.c:37: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_multi_msa.c:55:36: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 55 | pcre2_compile_context *alph_re = str_re_new("#[[:space:]]*ALPHABET[[:space:]]*=[[:space:]]*([A-Z]+)"); | ^~~~~~~~~~ phast_multi_msa.c:56:49: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 56 | pcre2_compile_context *format_re = str_re_new("#[[:space:]]*FORMAT[[:space:]]*=[[:space:]]*([A-Z]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_multi_msa.c:37: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_multi_msa.c:56:38: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 56 | pcre2_compile_context *format_re = str_re_new("#[[:space:]]*FORMAT[[:space:]]*=[[:space:]]*([A-Z]+)"); | ^~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_sufficient_stats.c -o phast_sufficient_stats.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_sufficient_stats.c: In function ‘ss_from_msas’: phast_sufficient_stats.c:140:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 140 | else | ^~~~ phast_sufficient_stats.c:142:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 142 | max_tuples = pow_bounded(strlen(msa->alphabet) + (int)strlen(msa->missing) + 1, | ^~~~~~~~~~ phast_sufficient_stats.c: In function ‘ss_read’: phast_sufficient_stats.c:661:25: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 661 | nseqs_re = str_re_new("NSEQS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/sufficient_stats.h:20, from phast_sufficient_stats.c:11: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:661:12: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 661 | nseqs_re = str_re_new("NSEQS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ phast_sufficient_stats.c:662:26: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 662 | length_re = str_re_new("LENGTH[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/sufficient_stats.h:20, from phast_sufficient_stats.c:11: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:662:13: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 662 | length_re = str_re_new("LENGTH[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ phast_sufficient_stats.c:663:30: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 663 | tuple_size_re = str_re_new("TUPLE_SIZE[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/sufficient_stats.h:20, from phast_sufficient_stats.c:11: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:663:17: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 663 | tuple_size_re = str_re_new("TUPLE_SIZE[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ phast_sufficient_stats.c:664:27: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 664 | ntuples_re = str_re_new("NTUPLES[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/sufficient_stats.h:20, from phast_sufficient_stats.c:11: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:664:14: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 664 | ntuples_re = str_re_new("NTUPLES[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ phast_sufficient_stats.c:665:25: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 665 | names_re = str_re_new("NAMES[[:space:]]*=[[:space:]]*(.*)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/sufficient_stats.h:20, from phast_sufficient_stats.c:11: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:665:12: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 665 | names_re = str_re_new("NAMES[[:space:]]*=[[:space:]]*(.*)"); | ^ phast_sufficient_stats.c:666:24: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 666 | alph_re = str_re_new("ALPHABET[[:space:]]*=[[:space:]]*([-.^A-Za-z ]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/sufficient_stats.h:20, from phast_sufficient_stats.c:11: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:666:11: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 666 | alph_re = str_re_new("ALPHABET[[:space:]]*=[[:space:]]*([-.^A-Za-z ]+)"); | ^ phast_sufficient_stats.c:667:25: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 667 | ncats_re = str_re_new("NCATS[[:space:]]*=[[:space:]]*([-0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/sufficient_stats.h:20, from phast_sufficient_stats.c:11: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:667:12: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 667 | ncats_re = str_re_new("NCATS[[:space:]]*=[[:space:]]*([-0-9]+)"); | ^ phast_sufficient_stats.c:668:26: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 668 | offset_re = str_re_new("IDX_OFFSET[[:space:]]*=[[:space:]]*([-0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/sufficient_stats.h:20, from phast_sufficient_stats.c:11: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:668:13: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 668 | offset_re = str_re_new("IDX_OFFSET[[:space:]]*=[[:space:]]*([-0-9]+)"); | ^ phast_sufficient_stats.c:669:25: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 669 | tuple_re = str_re_new("^([0-9]+)[[:space:]]+([-.^A-Za-z ]+)[[:space:]]+([0-9.[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/sufficient_stats.h:20, from phast_sufficient_stats.c:11: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:669:12: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 669 | tuple_re = str_re_new("^([0-9]+)[[:space:]]+([-.^A-Za-z ]+)[[:space:]]+([0-9.[:space:]]+)"); | ^ phast_sufficient_stats.c:670:25: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 670 | order_re = str_re_new("TUPLE_IDX_ORDER:"); | ^~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/sufficient_stats.h:20, from phast_sufficient_stats.c:11: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:670:12: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 670 | order_re = str_re_new("TUPLE_IDX_ORDER:"); | ^ ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o make[4]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/msa' make[4]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/feature' gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_bed.c -o phast_bed.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_bed.c: In function ‘gff_print_bed’: phast_bed.c:143:52: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 143 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from phast_bed.c:15: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_bed.c:143:41: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 143 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)"); | ^~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_category_map.c -o phast_category_map.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_category_map.c: In function ‘cm_read’: phast_category_map.c:39:31: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 39 | cat_range_re = str_re_new("^[[:space:]]*([^[:space:]]+)[[:space:]]+([[:digit:]]+)(-([[:digit:]]+))?([[:space:]]+([[:digit:]].*))?"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/category_map.h:92, from phast_category_map.c:10: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:39:18: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 39 | cat_range_re = str_re_new("^[[:space:]]*([^[:space:]]+)[[:space:]]+([[:digit:]]+)(-([[:digit:]]+))?([[:space:]]+([[:digit:]].*))?"); | ^ phast_category_map.c:40:27: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 40 | ncats_re = str_re_new("^[[:space:]]*NCATS[[:space:]]*=[[:space:]]*([[:digit:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/category_map.h:92, from phast_category_map.c:10: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:40:14: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 40 | ncats_re = str_re_new("^[[:space:]]*NCATS[[:space:]]*=[[:space:]]*([[:digit:]]+)"); | ^ phast_category_map.c:41:26: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 41 | fill_re = str_re_new("^[[:space:]]*FILL_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/category_map.h:92, from phast_category_map.c:10: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:41:13: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 41 | fill_re = str_re_new("^[[:space:]]*FILL_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$"); | ^ phast_category_map.c:42:27: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 42 | label_re = str_re_new("^[[:space:]]*LABELLING_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/category_map.h:92, from phast_category_map.c:10: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:42:14: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 42 | label_re = str_re_new("^[[:space:]]*LABELLING_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$"); | ^ phast_category_map.c:43:28: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 43 | extend_re = str_re_new("^[[:space:]]*FEATURE_EXTEND[[:space:]]*:[[:space:]]*(.+)[[:space:]]*\\((.+)\\)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/category_map.h:92, from phast_category_map.c:10: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:43:15: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 43 | extend_re = str_re_new("^[[:space:]]*FEATURE_EXTEND[[:space:]]*:[[:space:]]*(.+)[[:space:]]*\\((.+)\\)$"); | ^ gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_genepred.c -o phast_genepred.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_gff.c -o phast_gff.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_gff.c: In function ‘gff_read_set’: phast_gff.c:56:38: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 56 | spec_comment_re = str_re_new("^[[:space:]]*##[[:space:]]*([^[:space:]]+)[[:space:]]+([^[:space:]]+)([[:space:]]+([^[:space:]]+))?"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from phast_gff.c:13: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_gff.c:56:25: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 56 | spec_comment_re = str_re_new("^[[:space:]]*##[[:space:]]*([^[:space:]]+)[[:space:]]+([^[:space:]]+)([[:space:]]+([^[:space:]]+))?"); | ^ phast_gff.c: In function ‘gff_new_feature_genomic_pos’: phast_gff.c:272:24: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 272 | posre = str_re_new("(chr[_a-zA-Z0-9]+):([0-9]+)-([0-9]+)([-+])?"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from phast_gff.c:13: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_gff.c:272:11: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 272 | posre = str_re_new("(chr[_a-zA-Z0-9]+):([0-9]+)-([0-9]+)([-+])?"); | ^ phast_gff.c: In function ‘gff_group’: phast_gff.c:688:23: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 688 | tag_re = str_re_new(tmpstr); | ^~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from phast_gff.c:13: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_gff.c:688:10: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 688 | tag_re = str_re_new(tmpstr); | ^ gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_wig.c -o phast_wig.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o make[4]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/feature' make[4]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/hmm' gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/hmm/../../..\" -fno-strict-aliasing -c phast_em.c -o phast_em.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/hmm/../../..\" -fno-strict-aliasing -c phast_hmm.c -o phast_hmm.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o make[4]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/hmm' make[4]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo' gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_bgc_hmm.c -o phast_bgc_hmm.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_cons.c -o phast_cons.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_dgamma.c -o phast_dgamma.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_column.c -o phast_fit_column.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_em.c -o phast_fit_em.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_feature.c -o phast_fit_feature.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_indel_history.c -o phast_indel_history.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_indel_mod.c -o phast_indel_mod.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_fit.c -o phast_phylo_fit.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_p.c -o phast_phylo_p.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_p_print.c -o phast_phylo_p_print.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_phylo_p_print.c: In function ‘print_feats_generic’: phast_phylo_p_print.c:752:50: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 752 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_phylo_p_print.c:17: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_phylo_p_print.c:752:39: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 752 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)"); | ^~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_subst_distrib.c -o phast_subst_distrib.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_subst_mods.c -o phast_subst_mods.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_tree_likelihoods.c -o phast_tree_likelihoods.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_tree_model.c -o phast_tree_model.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_trees.c -o phast_trees.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o make[4]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo' make[4]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo_hmm' gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c phast_gap_patterns.c -o phast_gap_patterns.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c phast_phylo_hmm.c -o phast_phylo_hmm.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o make[4]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/motif' gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/motif/../../..\" -fno-strict-aliasing -c phast_motif.c -o phast_motif.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_motif.c: In function ‘mtf_print’: phast_motif.c:1411:7: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 1411 | fprintf(F, "\t%s\n", (char*)lst_get_ptr(notfound, i)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ phast_motif.c: In function ‘mtf_print_html’: phast_motif.c:1604:7: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 1604 | fprintf(F, "
  • %s\n", (char*)lst_get_ptr(notfound, i)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/motif/../../..\" -fno-strict-aliasing -c phast_tfbs.c -o phast_tfbs.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_tfbs.c: In function ‘pwm_read’: phast_tfbs.c:147:24: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 147 | pssm_re = str_re_new("^letter-probability matrix: alength= ([0-9]+) w= ([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_tfbs.c:16: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_tfbs.c:147:11: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 147 | pssm_re = str_re_new("^letter-probability matrix: alength= ([0-9]+) w= ([0-9]+)"); | ^ phast_tfbs.c:148:30: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 148 | motif_name_re = str_re_new("^MOTIF[[:space:]]+(.+?)[[:space:]].*"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_tfbs.c:16: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_tfbs.c:148:17: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 148 | motif_name_re = str_re_new("^MOTIF[[:space:]]+(.+?)[[:space:]].*"); | ^ phast_tfbs.c: In function ‘ms_read’: phast_tfbs.c:229:29: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 229 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*(.+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from phast_tfbs.c:16: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_tfbs.c:229:16: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 229 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*(.+)"); | ^ phast_tfbs.c:219:32: warning: variable ‘line_no’ set but not used [-Wunused-but-set-variable] 219 | int i, nseqs, j, do_toupper, line_no; | ^~~~~~~ ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o ar rs /build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o make[4]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib/motif' make[3]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/lib' make[3]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/dless' ../munge-help.sh dless.help_src > dless.help ../munge-help.sh dlessP.help_src > dlessP.help gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/dless/../..\" -fno-strict-aliasing -c dless.c -o dless.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition make[3]: *** No rule to make target 'bd_phylo_hmm.o', needed by '/build/phast-BoRzJ4/phast-1.6+dfsg/src/dless/../../bin/dless'. Stop. make[3]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/dless' make[3]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/exoniphy' ../munge-help.sh exoniphy.help_src > exoniphy.help gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/exoniphy/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/exoniphy/../..\" -fno-strict-aliasing -c exoniphy.c -o exoniphy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/exoniphy/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/exoniphy/../../bin/exoniphy exoniphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/exoniphy' make[3]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/phastCons' ../munge-help.sh phastCons.help_src > phastCons.help gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/phastCons/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/phastCons/../..\" -fno-strict-aliasing -c phastCons.c -o phastCons.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/phastCons/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/phastCons/../../bin/phastCons phastCons.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/phastCons' make[3]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/phastOdds' ../munge-help.sh phastOdds.help_src > phastOdds.help gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/phastOdds/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/phastOdds/../..\" -fno-strict-aliasing -c phastOdds.c -o phastOdds.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/phastOdds/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/phastOdds/../../bin/phastOdds phastOdds.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/phastOdds' make[3]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/phastMotif' gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/phastMotif/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/phastMotif/../..\" -fno-strict-aliasing -c phastMotif.c -o phastMotif.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phastMotif.c: In function ‘main’: phastMotif.c:131:13: warning: variable ‘separate_backgd’ set but not used [-Wunused-but-set-variable] 131 | int i, j, separate_backgd = 0, | ^~~~~~~~~~~~~~~ gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/phastMotif/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/phastMotif/../../bin/phastMotif phastMotif.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/phastMotif' make[3]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloFit' ../munge-help.sh phyloFit.help_src > phyloFit.help gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloFit/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloFit/../..\" -fno-strict-aliasing -c phyloFit.c -o phyloFit.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloFit/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloFit' make[3]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloBoot' ../munge-help.sh phyloBoot.help_src > phyloBoot.help gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloBoot/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloBoot/../..\" -fno-strict-aliasing -c phyloBoot.c -o phyloBoot.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloBoot/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloBoot/../../bin/phyloBoot phyloBoot.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloBoot' make[3]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloP' ../munge-help.sh phyloP.help_src > phyloP.help gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloP/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloP/../..\" -fno-strict-aliasing -c phyloP.c -o phyloP.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloP/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloP/../../bin/phyloP phyloP.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/phyloP' make[3]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/prequel' ../munge-help.sh pbsDecode.help_src > pbsDecode.help ../munge-help.sh pbsEncode.help_src > pbsEncode.help ../munge-help.sh pbsScoreMatrix.help_src > pbsScoreMatrix.help ../munge-help.sh pbsTrain.help_src > pbsTrain.help ../munge-help.sh prequel.help_src > prequel.help gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsDecode.c -o pbsDecode.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition make[3]: *** No rule to make target 'simplex_grid.o', needed by '/build/phast-BoRzJ4/phast-1.6+dfsg/src/prequel/../../bin/pbsDecode'. Stop. make[3]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/prequel' make[3]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/util' ../munge-help.sh base_evolve.help_src > base_evolve.help ../munge-help.sh clean_genes.help_src > clean_genes.help ../munge-help.sh consEntropy.help_src > consEntropy.help ../munge-help.sh indelFit.help_src > indelFit.help ../munge-help.sh indelHistory.help_src > indelHistory.help ../munge-help.sh makeHKY.help_src > makeHKY.help ../munge-help.sh modFreqs.help_src > modFreqs.help ../munge-help.sh msa_diff.help_src > msa_diff.help ../munge-help.sh phast.help_src > phast.help ../munge-help.sh phastBias.help_src > phastBias.help ../munge-help.sh treeGen.help_src > treeGen.help gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c all_dists.c -o all_dists.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/all_dists all_dists.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c base_evolve.c -o base_evolve.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/base_evolve base_evolve.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c chooseLines.c -o chooseLines.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c clean_genes.c -o clean_genes.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/clean_genes clean_genes.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c consEntropy.c -o consEntropy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/consEntropy consEntropy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c convert_coords.c -o convert_coords.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/convert_coords convert_coords.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c display_rate_matrix.c -o display_rate_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition display_rate_matrix.c: In function ‘do_context_dependent_ti_tv’: display_rate_matrix.c:204:8: warning: variable ‘tuple_i’ set but not used [-Wunused-but-set-variable] 204 | char tuple_i[mod->order+2], tuple_j[mod->order+2]; | ^~~~~~~ gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/display_rate_matrix display_rate_matrix.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c draw_tree.c -o draw_tree.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/draw_tree draw_tree.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c eval_predictions.c -o eval_predictions.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/eval_predictions eval_predictions.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_train.c -o hmm_train.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/hmm_train hmm_train.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_tweak.c -o hmm_tweak.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/hmm_tweak hmm_tweak.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_view.c -o hmm_view.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/hmm_view hmm_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c indelFit.c -o indelFit.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/indelFit indelFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c indelHistory.c -o indelHistory.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/indelHistory indelHistory.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c maf_parse.c -o maf_parse.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/maf_parse maf_parse.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c makeHKY.c -o makeHKY.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/makeHKY makeHKY.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c modFreqs.c -o modFreqs.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_diff.c -o msa_diff.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/msa_diff msa_diff.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_split.c -o msa_split.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/msa_split msa_split.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_view.c -o msa_view.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition msa_view.c: In function ‘fill_with_Ns’: msa_view.c:361:49: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 361 | pcre2_compile_context* fill_N_re = str_re_new("([[:digit:]]+):([[:digit:]]+)-([[:digit:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/gff.h:21, from /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/msa.h:19, from msa_view.c:14: /build/phast-BoRzJ4/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ msa_view.c:361:38: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 361 | pcre2_compile_context* fill_N_re = str_re_new("([[:digit:]]+):([[:digit:]]+)-([[:digit:]]+)"); | ^~~~~~~~~~ gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/msa_view msa_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c phast.c -o phast.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c phastBias.c -o phastBias.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/phastBias phastBias.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c refeature.c -o refeature.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/refeature refeature.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c stringiphy.c -o stringiphy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/stringiphy stringiphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c treeGen.c -o treeGen.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/treeGen treeGen.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-BoRzJ4/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c tree_doctor.c -o tree_doctor.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../lib -o /build/phast-BoRzJ4/phast-1.6+dfsg/src/util/../../bin/tree_doctor tree_doctor.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src/util' mkdir -p ../doc/man/ Generating man pages... USAGE: convert_coords -m -f [-s ] [-d ] [-p] [-n] [-i PHYLIP|FASTA|MPM] DESCRIPTION: Converts coordinates of features in a GFF file according to a multiple alignment. Will map from the coordinate system of any sequence to any other sequence; can also map to or from the coordinate system of the entire alignment. In addition, supports translation of coordinates by specified offset. OPTIONS: -m (required) Name of file in which alignment is defined. -f (required) Name of file in which features are defined (GFF). -s Index of frame of reference for feature coordinates, as defined in the GFF file. Use an integer 1-N (if N seqs) or 0 to indicate the coordinate system of the alignment as a whole. Default behavior is to match features with alignment sequences by name (feature by feature). -d Index of destination frame of reference. Default is 0 (whole MSA). -p Positive coordinate offset. This value will be added to all coordinates. Useful when the alignment (or sequence) for which the coordinates are specified is a sub-alignment of yours. -n Negative coordinate offset. This value will be subtracted from all coordinates. Useful when your alignment is a sub-alignment of the alignment (or sequence) for which the coordinates are specified. -i FASTA|PHYLIP|MPM|SS Alignment format. Default is to guess format from file contents PROGRAM: draw_tree DESCRIPTION: Produces a simple postscript rendering of a tree. USAGE: draw_tree [-dbvs] | OPTIONS: (Required) File name of tree (expected to be in Newick format, unless filename ends with '.mod', in which case expected to be a tree model file). -d Print "diagonal" branches, instead of "right-angle" or "square" ones (produces a "cladogram", as opposed to a "phenogram"). This option implies -s. -b Suppress branch lengths. -v Vertical layout. -s Don't draw branches to scale. Done. make[2]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src' make[1]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg' create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install --destdir=debian/phast/ -a make -j10 install DESTDIR=/build/phast-BoRzJ4/phast-1.6\+dfsg/debian/phast AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg' (cd src; make install DESTDIR=/build/phast-BoRzJ4/phast-1.6+dfsg/debian/phast ) make[2]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mkdir -p /build/phast-BoRzJ4/phast-1.6+dfsg/debian/phast/usr/bin/ mkdir -p /build/phast-BoRzJ4/phast-1.6+dfsg/debian/phast/usr/share/phast/data/ mkdir -p /build/phast-BoRzJ4/phast-1.6+dfsg/debian/phast/usr/share/man/man1/ cp ../bin/* /build/phast-BoRzJ4/phast-1.6+dfsg/debian/phast/usr/bin/ cp -R ../data/* /build/phast-BoRzJ4/phast-1.6+dfsg/debian/phast/usr/share/phast/data/ cp -R ../doc/man/* /build/phast-BoRzJ4/phast-1.6+dfsg/debian/phast/usr/share/man/man1/ make[2]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg/src' make[1]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installexamples make[1]: Entering directory '/build/phast-BoRzJ4/phast-1.6+dfsg' dh_installexamples find debian/*/usr/share/doc/*/examples -type f -size +1k -exec xz \{\} \; make[1]: Leaving directory '/build/phast-BoRzJ4/phast-1.6+dfsg' 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 dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'phast' in '../phast_1.6+dfsg-3_amd64.deb'. dpkg-deb: building package 'phast-dbgsym' in '../phast-dbgsym_1.6+dfsg-3_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../phast_1.6+dfsg-3_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-BoRzJ4 /tmp/phast-1.6+dfsg-3te_e8oo3 I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.0dWin1p01R... I: success in 473.6945 seconds md5: phast-dbgsym_1.6+dfsg-3_amd64.deb: OK md5: phast_1.6+dfsg-3_amd64.deb: OK sha1: phast-dbgsym_1.6+dfsg-3_amd64.deb: OK sha1: phast_1.6+dfsg-3_amd64.deb: OK sha256: phast-dbgsym_1.6+dfsg-3_amd64.deb: OK sha256: phast_1.6+dfsg-3_amd64.deb: OK Checksums: OK