Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/p/phyml/phyml_3.3.20220408-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/phyml-3.3.20220408-1v_t8440c/phyml_3.3.20220408-1_amd64.buildinfo Get source package info: phyml=3:3.3.20220408-1 Source URL: http://snapshot.notset.fr/mr/package/phyml/3:3.3.20220408-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.121 autoconf=2.71-2 automake=1:1.16.5-1.3 autopoint=0.21-6 autotools-dev=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6+b1 binutils=2.38-4 binutils-common=2.38-4 binutils-x86-64-linux-gnu=2.38-4 bsdextrautils=2.38-4 bsdutils=1:2.38-4 build-essential=12.9 bzip2=1.0.8-5 chrpath=0.16-2+b1 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.3.0-1 dash=0.5.11+git20210903+057cd650a4ed-8 debconf=1.5.79 debhelper=13.7.1 debianutils=5.7-0.2 dh-autoreconf=20 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 dpkg=1.21.7 dpkg-dev=1.21.7 dwz=0.14-1 file=1:5.41-4 findutils=4.9.0-3 g++=4:11.2.0-2 g++-11=11.3.0-1 gcc=4:11.2.0-2 gcc-11=11.3.0-1 gcc-11-base=11.3.0-1 gcc-12-base=12-20220428-1 gettext=0.21-6 gettext-base=0.21-6 gfortran-11=11.3.0-1 grep=3.7-1 groff-base=1.22.4-8 gzip=1.12-1 hostname=3.23 ibverbs-providers=39.0-1+b1 init-system-helpers=1.62 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libasan6=11.3.0-1 libatomic1=12-20220428-1 libattr1=1:2.5.1-1 libaudit-common=1:3.0.7-1 libaudit1=1:3.0.7-1+b1 libbinutils=2.38-4 libblkid1=2.38-4 libbrotli1=1.0.9-2+b3 libbsd0=0.11.6-1 libbz2-1.0=1.0.8-5 libc-bin=2.33-7 libc-dev-bin=2.33-7 libc6=2.33-7 libc6-dev=2.33-7 libcap-ng0=0.7.9-2.2+b2 libcap2=1:2.44-1 libcbor0.8=0.8.0-2 libcc1-0=12-20220428-1 libcom-err2=1.46.5-2 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.38-4 libctf0=2.38-4 libcurl3-gnutls=7.83.0-1 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.262 libdebhelper-perl=13.7.1 libdpkg-perl=1.21.7 libedit2=3.1-20210910-1 libelf1=0.187-1 libevent-2.1-7=2.1.12-stable-5 libevent-core-2.1-7=2.1.12-stable-5 libevent-dev=2.1.12-stable-5 libevent-extra-2.1-7=2.1.12-stable-5 libevent-openssl-2.1-7=2.1.12-stable-5 libevent-pthreads-2.1-7=2.1.12-stable-5 libfabric1=1.11.0-3 libffi8=3.4.2-4 libfido2-1=1.10.0-1 libfile-stripnondeterminism-perl=1.13.0-1 libgcc-11-dev=11.3.0-1 libgcc-s1=12-20220428-1 libgcrypt20=1.10.1-2 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libgfortran-11-dev=11.3.0-1 libgfortran5=12-20220428-1 libglib2.0-0=2.72.1-1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.4-2 libgomp1=12-20220428-1 libgpg-error0=1.45-2 libgssapi-krb5-2=1.19.2-2+b1 libhogweed6=3.7.3-1 libhwloc-dev=2.7.1-1 libhwloc-plugins=2.7.1-1 libhwloc15=2.7.1-1 libibverbs-dev=39.0-1+b1 libibverbs1=39.0-1+b1 libicu71=71.1-2 libidn2-0=2.3.2-2 libisl23=0.24-2 libitm1=12-20220428-1 libjs-jquery=3.6.0+dfsg+~3.5.13-1 libjs-jquery-ui=1.13.1+dfsg-1 libk5crypto3=1.19.2-2+b1 libkeyutils1=1.6.1-3 libkrb5-3=1.19.2-2+b1 libkrb5support0=1.19.2-2+b1 libldap-2.5-0=2.5.12+dfsg-1 liblsan0=12-20220428-1 libltdl-dev=2.4.7-4 libltdl7=2.4.7-4 liblz4-1=1.9.3-2 liblzma5=5.2.5-2.1 libmagic-mgc=1:5.41-4 libmagic1=1:5.41-4 libmd0=1.0.4-1 libmount1=2.38-4 libmpc3=1.2.1-2 libmpfr6=4.1.0-3 libnettle8=3.7.3-1 libnghttp2-14=1.47.0-1 libnl-3-200=3.5.0-0.1 libnl-3-dev=3.5.0-0.1 libnl-route-3-200=3.5.0-0.1 libnl-route-3-dev=3.5.0-0.1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnuma-dev=2.0.14-3 libnuma1=2.0.14-3 libopenmpi-dev=4.1.3-2 libopenmpi3=4.1.3-2 libp11-kit0=0.24.1-1 libpam-modules=1.4.0-13 libpam-modules-bin=1.4.0-13 libpam-runtime=1.4.0-13 libpam0g=1.4.0-13 libpciaccess0=0.16-3 libpcre2-8-0=10.40-1 libpcre3=2:8.39-14 libperl5.34=5.34.0-4 libpipeline1=1.5.6-1 libpmix-dev=4.1.2-2 libpmix2=4.1.2-2 libpsl5=0.21.0-1.2 libpsm-infinipath1=3.3+20.604758e7-6.1 libpsm2-2=11.2.185-1 libquadmath0=12-20220428-1 librdmacm1=39.0-1+b1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.28+dfsg-4 libsasl2-modules-db=2.1.28+dfsg-4 libseccomp2=2.5.4-1 libselinux1=3.3-1+b2 libsemanage-common=3.3-1 libsemanage2=3.3-1+b2 libsepol2=3.3-1 libsigsegv2=2.14-1 libsmartcols1=2.38-4 libssh2-1=1.10.0-3 libssl1.1=1.1.1n-1 libstdc++-11-dev=11.3.0-1 libstdc++6=12-20220428-1 libsub-override-perl=0.09-2 libsystemd0=250.4-1 libtasn1-6=4.18.0-4 libtinfo6=6.3+20220423-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.7-4 libtsan0=11.3.0-1 libubsan1=12-20220428-1 libuchardet0=0.0.7-1 libucx0=1.12.1-1 libudev1=250.4-1 libunistring2=1.0-1 libuuid1=2.38-4 libx11-6=2:1.7.5-1 libx11-data=2:1.7.5-1 libxau6=1:1.0.9-1 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.4-1 libxml2=2.9.14+dfsg-1 libxnvctrl0=470.103.01-2 libzstd1=1.5.2+dfsg-1 linux-libc-dev=5.17.3-1 login=1:4.11.1+dfsg1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.2-1 mawk=1.3.4.20200120-3+b1 ncurses-base=6.3+20220423-1 ncurses-bin=6.3+20220423-1 ocl-icd-libopencl1=2.2.14-3 openmpi-bin=4.1.3-2 openmpi-common=4.1.3-2 openssh-client=1:9.0p1-1 passwd=1:4.11.1+dfsg1-2 patch=2.7.6-7 perl=5.34.0-4 perl-base=5.34.0-4 perl-modules-5.34=5.34.0-4 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.03-1 tar=1.34+dfsg-1 util-linux=2.38-4 util-linux-extra=2.38-4 xz-utils=5.2.5-2.1 zlib1g=1:1.2.11.dfsg-4 zlib1g-dev=1:1.2.11.dfsg-4 --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/20220511T030041Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220511T030041Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220505T152452Z/ 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 phyml=3:3.3.20220408-1 && mkdir -p /build/phyml-n91Atr && dpkg-source --no-check -x /*.dsc /build/phyml-n91Atr/phyml-3.3.20220408 && chown -R builduser:builduser /build/phyml-n91Atr" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/phyml-n91Atr/phyml-3.3.20220408 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1652020867" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/phyml-n91Atr /tmp/phyml-3.3.20220408-1v_t8440c bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220505T152452Z 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.qhh3AJvxUn 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.qhh3AJvxUn Reading package lists... Building dependency tree... util-linux is already the newest version (2.38-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 135 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220505T152452Z unstable/main amd64 libfakeroot amd64 1.28-1 [48.2 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220505T152452Z unstable/main amd64 fakeroot amd64 1.28-1 [87.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 135 kB in 0s (1031 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 ... 4628 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.28-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.28-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.28-1_amd64.deb ... Unpacking fakeroot (1.28-1) ... Setting up libfakeroot:amd64 (1.28-1) ... Setting up fakeroot (1.28-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-7) ... 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/20220511T030041Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220511T030041Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220505T152452Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.qhh3AJvxUn Get:1 http://snapshot.notset.fr/archive/debian/20220511T030041Z bookworm InRelease [130 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20220505T152452Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20220511T030041Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220511T030041Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220511T030041Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220511T030041Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220511T030041Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220511T030041Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20220511T030041Z bookworm/main Sources [11.9 MB] Get:4 http://snapshot.notset.fr/archive/debian/20220511T030041Z bookworm/main amd64 Packages [11.4 MB] Fetched 23.5 MB in 20s (1188 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.qhh3AJvxUn I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d phyml=3:3.3.20220408-1 && mkdir -p /build/phyml-n91Atr && dpkg-source --no-check -x /*.dsc /build/phyml-n91Atr/phyml-3.3.20220408 && chown -R builduser:builduser /build/phyml-n91Atr"' exec /tmp/mmdebstrap.qhh3AJvxUn Reading package lists... NOTICE: 'phyml' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/phyml.git Please use: git clone https://salsa.debian.org/med-team/phyml.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1833 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220511T030041Z bookworm/main phyml 3:3.3.20220408-1 (dsc) [2258 B] Get:2 http://snapshot.notset.fr/archive/debian/20220511T030041Z bookworm/main phyml 3:3.3.20220408-1 (tar) [1804 kB] Get:3 http://snapshot.notset.fr/archive/debian/20220511T030041Z bookworm/main phyml 3:3.3.20220408-1 (diff) [26.7 kB] Fetched 1833 kB in 1s (1246 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'phyml_3.3.20220408-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting phyml in /build/phyml-n91Atr/phyml-3.3.20220408 dpkg-source: info: unpacking phyml_3.3.20220408.orig.tar.gz dpkg-source: info: unpacking phyml_3.3.20220408-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying sse_only_if_supported.patch dpkg-source: info: applying no-configure-ac-date.patch dpkg-source: info: applying fix_declaration_of_temp.patch dpkg-source: info: applying fix_wrong_initialisation_of_array.patch dpkg-source: info: applying no-march-native.patch dpkg-source: info: applying cross.patch dpkg-source: info: applying apply-cflags.patch dpkg-source: info: applying filter-sse3-intrinsics.patch dpkg-source: info: applying apply-ldflags.patch dpkg-source: info: applying typos.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/phyml-n91Atr/phyml-3.3.20220408 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1652020867" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.qhh3AJvxUn dpkg-buildpackage: info: source package phyml dpkg-buildpackage: info: source version 3:3.3.20220408-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier 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/phyml-n91Atr/phyml-3.3.20220408' # save pdf from cleaning mv doc/phyml-manual.pdf . dh_auto_clean mv phyml-manual.pdf doc # remove temporary bin dir for phyml (see above hack) rm -rf debian/bin rm -rf doc/Makefile make[1]: Leaving directory '/build/phyml-n91Atr/phyml-3.3.20220408' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a debian/rules override_dh_autoreconf make[1]: Entering directory '/build/phyml-n91Atr/phyml-3.3.20220408' dh_autoreconf --as-needed configure.ac:31: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:31: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:31: the top level configure.ac:52: warning: The macro `AC_FUNC_SETVBUF_REVERSED' is obsolete. Remove it and all references to SETVBUF_REVERSED. ./lib/autoconf/functions.m4:1766: AC_FUNC_SETVBUF_REVERSED is expanded from... configure.ac:52: the top level configure.ac:14: installing './compile' configure.ac:12: installing './config.guess' configure.ac:12: installing './config.sub' configure.ac:5: installing './install-sh' configure.ac:5: installing './missing' src/Makefile.am: installing './depcomp' make[1]: Leaving directory '/build/phyml-n91Atr/phyml-3.3.20220408' debian/rules override_dh_auto_build make[1]: Entering directory '/build/phyml-n91Atr/phyml-3.3.20220408' # According to README you need different configure options to get different executables # Here we hack in a full build process for phyml executable # The hack includes saving the documentation from beeing cleaned up mv doc/phyml-manual.pdf . dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none configure: "On arch x86_64-pc-linux-gnu use MSSE = -msse" checking for log in -lm... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for float.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking for pdflatex... no checking for latex... no configure: WARNING: Documentation will not be built! checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking for vprintf... yes checking for floor... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for strchr... yes checking for strstr... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating doc/Makefile config.status: creating config.h config.status: executing depfiles commands dh_auto_build -- LDFLAGS="-Wl,-z,relro -Wl,-z,now" make -j10 "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/phyml-n91Atr/phyml-3.3.20220408' make all-recursive make[3]: Entering directory '/build/phyml-n91Atr/phyml-3.3.20220408' Making all in src make[4]: Entering directory '/build/phyml-n91Atr/phyml-3.3.20220408/src' gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.c .: Building [phyml]. Version 3.3.3:3.3.20220408-1 :. gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utilities.o utilities.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o optimiz.o optimiz.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o lk.o lk.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bionj.o bionj.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o models.o models.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o free.o free.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o help.o help.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o simu.o simu.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o eigen.o eigen.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pars.o pars.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alrt.o alrt.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o interface.o interface.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cl.o cl.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o spr.o spr.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o draw.o draw.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stats.o stats.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o io.o io.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o make.o make.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o nexus.o nexus.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o init.o init.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o xml.o xml.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sse.o sse.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o avx.o avx.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o tbe.o tbe.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ancestral.o ancestral.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mixt.o mixt.c io.c: In function ‘Sub_Trees’: io.c:511:25: warning: ‘subs’ may be used uninitialized in this function [-Wmaybe-uninitialized] 511 | subs = (char **)mRealloc(subs,*degree+1,sizeof(char *)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o phyml main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o io.o make.o nexus.o init.o xml.o sse.o avx.o tbe.o ancestral.o mixt.o -lm -lm Done. make[4]: Leaving directory '/build/phyml-n91Atr/phyml-3.3.20220408/src' make[4]: Entering directory '/build/phyml-n91Atr/phyml-3.3.20220408' make[4]: Leaving directory '/build/phyml-n91Atr/phyml-3.3.20220408' make[3]: Leaving directory '/build/phyml-n91Atr/phyml-3.3.20220408' make[2]: Leaving directory '/build/phyml-n91Atr/phyml-3.3.20220408' # move phyml binary to temporary dir inside debian/ mkdir -p /build/phyml-n91Atr/phyml-3.3.20220408/debian/bin mv src/phyml /build/phyml-n91Atr/phyml-3.3.20220408/debian/bin/phyml /usr/bin/make distclean make[2]: Entering directory '/build/phyml-n91Atr/phyml-3.3.20220408' Making distclean in src make[3]: Entering directory '/build/phyml-n91Atr/phyml-3.3.20220408/src' test -z "phyml" || rm -f phyml rm -f *.o rm -f *.tab.c test -z "" || rm -f test . = "." || test -z "" || rm -f rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags rm -f ./.deps/alrt.Po rm -f ./.deps/ancestral.Po rm -f ./.deps/avx.Po rm -f ./.deps/bionj.Po rm -f ./.deps/cl.Po rm -f ./.deps/date.Po rm -f ./.deps/draw.Po rm -f ./.deps/eigen.Po rm -f ./.deps/free.Po rm -f ./.deps/help.Po rm -f ./.deps/init.Po rm -f ./.deps/interface.Po rm -f ./.deps/io.Po rm -f ./.deps/lk.Po rm -f ./.deps/location.Po rm -f ./.deps/main.Po rm -f ./.deps/make.Po rm -f ./.deps/mcmc.Po rm -f ./.deps/mg.Po rm -f ./.deps/mixt.Po rm -f ./.deps/models.Po rm -f ./.deps/nexus.Po rm -f ./.deps/optimiz.Po rm -f ./.deps/pars.Po rm -f ./.deps/phyml_mpi-alrt.Po rm -f ./.deps/phyml_mpi-ancestral.Po rm -f ./.deps/phyml_mpi-avx.Po rm -f ./.deps/phyml_mpi-bionj.Po rm -f ./.deps/phyml_mpi-cl.Po rm -f ./.deps/phyml_mpi-draw.Po rm -f ./.deps/phyml_mpi-eigen.Po rm -f ./.deps/phyml_mpi-free.Po rm -f ./.deps/phyml_mpi-help.Po rm -f ./.deps/phyml_mpi-init.Po rm -f ./.deps/phyml_mpi-interface.Po rm -f ./.deps/phyml_mpi-io.Po rm -f ./.deps/phyml_mpi-lk.Po rm -f ./.deps/phyml_mpi-main.Po rm -f ./.deps/phyml_mpi-make.Po rm -f ./.deps/phyml_mpi-mixt.Po rm -f ./.deps/phyml_mpi-models.Po rm -f ./.deps/phyml_mpi-mpi_boot.Po rm -f ./.deps/phyml_mpi-nexus.Po rm -f ./.deps/phyml_mpi-optimiz.Po rm -f ./.deps/phyml_mpi-pars.Po rm -f ./.deps/phyml_mpi-simu.Po rm -f ./.deps/phyml_mpi-spr.Po rm -f ./.deps/phyml_mpi-sse.Po rm -f ./.deps/phyml_mpi-stats.Po rm -f ./.deps/phyml_mpi-tbe.Po rm -f ./.deps/phyml_mpi-utilities.Po rm -f ./.deps/phyml_mpi-xml.Po rm -f ./.deps/phyrex.Po rm -f ./.deps/rates.Po rm -f ./.deps/rrw.Po rm -f ./.deps/rw.Po rm -f ./.deps/simu.Po rm -f ./.deps/slfv.Po rm -f ./.deps/spr.Po rm -f ./.deps/sse.Po rm -f ./.deps/stats.Po rm -f ./.deps/tbe.Po rm -f ./.deps/times.Po rm -f ./.deps/utilities.Po rm -f ./.deps/xml.Po rm -f Makefile make[3]: Leaving directory '/build/phyml-n91Atr/phyml-3.3.20220408/src' make[3]: Entering directory '/build/phyml-n91Atr/phyml-3.3.20220408' test -z "" || rm -f test . = "." || test -z "" || rm -f rm -f config.h stamp-h1 rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags rm -f cscope.out cscope.in.out cscope.po.out cscope.files make[3]: Leaving directory '/build/phyml-n91Atr/phyml-3.3.20220408' rm -f config.status config.cache config.log configure.lineno config.status.lineno rm -f Makefile make[2]: Leaving directory '/build/phyml-n91Atr/phyml-3.3.20220408' dh_auto_configure -- --enable-phyml-mpi ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-phyml-mpi checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none configure: "On arch x86_64-pc-linux-gnu use MSSE = -msse" checking for log in -lm... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for float.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking for pdflatex... no checking for latex... no configure: WARNING: Documentation will not be built! checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking for vprintf... yes checking for floor... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for strchr... yes checking for strstr... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for mpi-c... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating doc/Makefile config.status: creating config.h config.status: executing depfiles commands dh_auto_build -- LDFLAGS="-Wl,-z,relro -Wl,-z,now" make -j10 "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/phyml-n91Atr/phyml-3.3.20220408' make all-recursive make[3]: Entering directory '/build/phyml-n91Atr/phyml-3.3.20220408' Making all in src make[4]: Entering directory '/build/phyml-n91Atr/phyml-3.3.20220408/src' gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-main.o `test -f 'main.c' || echo './'`main.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-utilities.o `test -f 'utilities.c' || echo './'`utilities.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-optimiz.o `test -f 'optimiz.c' || echo './'`optimiz.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-lk.o `test -f 'lk.c' || echo './'`lk.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-bionj.o `test -f 'bionj.c' || echo './'`bionj.c .: Building [phyml-mpi]. Version 3.3.3:3.3.20220408-1 :. gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-models.o `test -f 'models.c' || echo './'`models.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-free.o `test -f 'free.c' || echo './'`free.c In file included from lk.h:18, from lk.c:14: utilities.h:18: warning: "_POSIX_C_SOURCE" redefined 18 | #define _POSIX_C_SOURCE 200112L | In file included from /usr/include/assert.h:35, from lk.c:13: /usr/include/features.h:310: note: this is the location of the previous definition 310 | # define _POSIX_C_SOURCE 199506L | gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-help.o `test -f 'help.c' || echo './'`help.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-simu.o `test -f 'simu.c' || echo './'`simu.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-eigen.o `test -f 'eigen.c' || echo './'`eigen.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-pars.o `test -f 'pars.c' || echo './'`pars.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-alrt.o `test -f 'alrt.c' || echo './'`alrt.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-interface.o `test -f 'interface.c' || echo './'`interface.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-cl.o `test -f 'cl.c' || echo './'`cl.c In file included from cl.h:21, from cl.c:13: utilities.h:18: warning: "_POSIX_C_SOURCE" redefined 18 | #define _POSIX_C_SOURCE 200112L | In file included from /usr/include/unistd.h:25, from cl.h:19, from cl.c:13: /usr/include/features.h:310: note: this is the location of the previous definition 310 | # define _POSIX_C_SOURCE 199506L | gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-spr.o `test -f 'spr.c' || echo './'`spr.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-draw.o `test -f 'draw.c' || echo './'`draw.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-stats.o `test -f 'stats.c' || echo './'`stats.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-io.o `test -f 'io.c' || echo './'`io.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-make.o `test -f 'make.c' || echo './'`make.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-nexus.o `test -f 'nexus.c' || echo './'`nexus.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-init.o `test -f 'init.c' || echo './'`init.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-xml.o `test -f 'xml.c' || echo './'`xml.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-mixt.o `test -f 'mixt.c' || echo './'`mixt.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-tbe.o `test -f 'tbe.c' || echo './'`tbe.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-sse.o `test -f 'sse.c' || echo './'`sse.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-avx.o `test -f 'avx.c' || echo './'`avx.c In file included from sse.h:18, from sse.c:14: utilities.h:18: warning: "_POSIX_C_SOURCE" redefined 18 | #define _POSIX_C_SOURCE 200112L | In file included from /usr/include/assert.h:35, from sse.c:13: /usr/include/features.h:310: note: this is the location of the previous definition 310 | # define _POSIX_C_SOURCE 199506L | In file included from avx.h:18, from avx.c:14: utilities.h:18: warning: "_POSIX_C_SOURCE" redefined 18 | #define _POSIX_C_SOURCE 200112L | In file included from /usr/include/assert.h:35, from avx.c:13: /usr/include/features.h:310: note: this is the location of the previous definition 310 | # define _POSIX_C_SOURCE 199506L | gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-ancestral.o `test -f 'ancestral.c' || echo './'`ancestral.c io.c: In function ‘Sub_Trees’: io.c:511:25: warning: ‘subs’ may be used uninitialized in this function [-Wmaybe-uninitialized] 511 | subs = (char **)mRealloc(subs,*degree+1,sizeof(char *)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phyml_mpi-mpi_boot.o `test -f 'mpi_boot.c' || echo './'`mpi_boot.c gcc -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o phyml-mpi phyml_mpi-main.o phyml_mpi-utilities.o phyml_mpi-optimiz.o phyml_mpi-lk.o phyml_mpi-bionj.o phyml_mpi-models.o phyml_mpi-free.o phyml_mpi-help.o phyml_mpi-simu.o phyml_mpi-eigen.o phyml_mpi-pars.o phyml_mpi-alrt.o phyml_mpi-interface.o phyml_mpi-cl.o phyml_mpi-spr.o phyml_mpi-draw.o phyml_mpi-stats.o phyml_mpi-io.o phyml_mpi-make.o phyml_mpi-nexus.o phyml_mpi-init.o phyml_mpi-xml.o phyml_mpi-mixt.o phyml_mpi-tbe.o phyml_mpi-sse.o phyml_mpi-avx.o phyml_mpi-ancestral.o phyml_mpi-mpi_boot.o -lm -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi -lm Done. make[4]: Leaving directory '/build/phyml-n91Atr/phyml-3.3.20220408/src' make[4]: Entering directory '/build/phyml-n91Atr/phyml-3.3.20220408' make[4]: Leaving directory '/build/phyml-n91Atr/phyml-3.3.20220408' make[3]: Leaving directory '/build/phyml-n91Atr/phyml-3.3.20220408' make[2]: Leaving directory '/build/phyml-n91Atr/phyml-3.3.20220408' # move phyml binary to temporary dir inside debian/ # mkdir -p /build/phyml-n91Atr/phyml-3.3.20220408/debian/bin mv src/phyml-mpi /build/phyml-n91Atr/phyml-3.3.20220408/debian/bin/phyml-mpi mv phyml-manual.pdf doc make[1]: Leaving directory '/build/phyml-n91Atr/phyml-3.3.20220408' dh: command-omitted: The call to "dh_auto_test -a" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/phyml-n91Atr/phyml-3.3.20220408' dh_auto_install make -j10 install DESTDIR=/build/phyml-n91Atr/phyml-3.3.20220408/debian/phyml AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/phyml-n91Atr/phyml-3.3.20220408' Making install in src make[3]: Entering directory '/build/phyml-n91Atr/phyml-3.3.20220408/src' .: Building [phyml-mpi]. Version 3.3.3:3.3.20220408-1 :. gcc -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -ffile-prefix-map=/build/phyml-n91Atr/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o phyml-mpi phyml_mpi-main.o phyml_mpi-utilities.o phyml_mpi-optimiz.o phyml_mpi-lk.o phyml_mpi-bionj.o phyml_mpi-models.o phyml_mpi-free.o phyml_mpi-help.o phyml_mpi-simu.o phyml_mpi-eigen.o phyml_mpi-pars.o phyml_mpi-alrt.o phyml_mpi-interface.o phyml_mpi-cl.o phyml_mpi-spr.o phyml_mpi-draw.o phyml_mpi-stats.o phyml_mpi-io.o phyml_mpi-make.o phyml_mpi-nexus.o phyml_mpi-init.o phyml_mpi-xml.o phyml_mpi-mixt.o phyml_mpi-tbe.o phyml_mpi-sse.o phyml_mpi-avx.o phyml_mpi-ancestral.o phyml_mpi-mpi_boot.o -lm -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi -lm Done. make[4]: Entering directory '/build/phyml-n91Atr/phyml-3.3.20220408/src' /bin/mkdir -p '/build/phyml-n91Atr/phyml-3.3.20220408/debian/phyml/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c phyml-mpi '/build/phyml-n91Atr/phyml-3.3.20220408/debian/phyml/usr/bin' make[4]: Leaving directory '/build/phyml-n91Atr/phyml-3.3.20220408/src' make[3]: Leaving directory '/build/phyml-n91Atr/phyml-3.3.20220408/src' make[3]: Entering directory '/build/phyml-n91Atr/phyml-3.3.20220408' make[4]: Entering directory '/build/phyml-n91Atr/phyml-3.3.20220408' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/phyml-n91Atr/phyml-3.3.20220408' make[3]: Leaving directory '/build/phyml-n91Atr/phyml-3.3.20220408' make[2]: Leaving directory '/build/phyml-n91Atr/phyml-3.3.20220408' # install phyml binary we have kept safe above mkdir -p /build/phyml-n91Atr/phyml-3.3.20220408/debian/phyml/usr/lib/phyml/bin mv /build/phyml-n91Atr/phyml-3.3.20220408/debian/bin/* /build/phyml-n91Atr/phyml-3.3.20220408/debian/phyml/usr/lib/phyml/bin chrpath --delete debian/phyml/usr/lib/phyml/bin/phyml* make[1]: Leaving directory '/build/phyml-n91Atr/phyml-3.3.20220408' dh_install -a debian/rules override_dh_installdocs make[1]: Entering directory '/build/phyml-n91Atr/phyml-3.3.20220408' dh_installdocs mv /build/phyml-n91Atr/phyml-3.3.20220408/debian/phyml/usr/share/doc/phyml/phyml-manual.pdf /build/phyml-n91Atr/phyml-3.3.20220408/debian/phyml/usr/share/doc/phyml/phyml_manual.pdf make[1]: Leaving directory '/build/phyml-n91Atr/phyml-3.3.20220408' dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a debian/rules override_dh_compress make[1]: Entering directory '/build/phyml-n91Atr/phyml-3.3.20220408' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/phyml-n91Atr/phyml-3.3.20220408' debian/rules override_dh_fixperms make[1]: Entering directory '/build/phyml-n91Atr/phyml-3.3.20220408' dh_fixperms find debian/*/usr/share/doc -name "*.nxs" -exec chmod -x \{\} \; find debian/*/usr/share/doc -name "*.xml" -exec chmod -x \{\} \; find debian/*/usr/share/doc -name "*.mat" -exec chmod -x \{\} \; find debian/*/usr/share/doc -name "*.txt" -exec chmod -x \{\} \; chmod -x debian/*/usr/share/doc/phyml/examples/nucleic chmod -x debian/*/usr/share/doc/phyml/examples/proteic make[1]: Leaving directory '/build/phyml-n91Atr/phyml-3.3.20220408' dh_missing -a debian/rules override_dh_dwz make[1]: Entering directory '/build/phyml-n91Atr/phyml-3.3.20220408' echo "Do not run dh_dwz" Do not run dh_dwz make[1]: Leaving directory '/build/phyml-n91Atr/phyml-3.3.20220408' 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 'phyml-dbgsym' in '../phyml-dbgsym_3.3.20220408-1_amd64.deb'. dpkg-deb: building package 'phyml' in '../phyml_3.3.20220408-1_amd64.deb'. dpkg-genbuildinfo --build=any -O../phyml_3.3.20220408-1_amd64.buildinfo dpkg-genchanges --build=any -O../phyml_3.3.20220408-1_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/phyml-n91Atr /tmp/phyml-3.3.20220408-1v_t8440c I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.qhh3AJvxUn... I: success in 324.8381 seconds md5: phyml-dbgsym_3.3.20220408-1_amd64.deb: OK md5: phyml_3.3.20220408-1_amd64.deb: OK sha1: phyml-dbgsym_3.3.20220408-1_amd64.deb: OK sha1: phyml_3.3.20220408-1_amd64.deb: OK sha256: phyml-dbgsym_3.3.20220408-1_amd64.deb: OK sha256: phyml_3.3.20220408-1_amd64.deb: OK Checksums: OK