Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/m/mrbayes/mrbayes_3.2.7a-5_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/mrbayes-3.2.7a-5htc4ex_s/mrbayes_3.2.7a-5_all.buildinfo Get source package info: mrbayes=3.2.7a-5 Source URL: http://snapshot.notset.fr/mr/package/mrbayes/3.2.7a-5/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.118 autoconf=2.71-2 autoconf-archive=20210219-2 automake=1:1.16.4-2 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-3+b1 beignet-opencl-icd=1.3.2-8 binutils=2.37-7 binutils-common=2.37-7 binutils-x86-64-linux-gnu=2.37-7 bsdextrautils=2.37.2-3 bsdutils=1:2.37.2-3 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.3.0-11 dash=0.5.11+git20210120+802ebd4-1 debconf=1.5.77 debhelper=13.5.2 debianutils=5.5-1 dh-autoreconf=20 dh-strip-nondeterminism=1.12.0-1 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++=4:10.2.1-1 g++-10=10.3.0-11 gcc=4:10.2.1-1 gcc-10=10.3.0-11 gcc-10-base=10.3.0-11 gcc-11-base=11.2.0-8 gettext=0.21-4 gettext-base=0.21-4 gfortran-10=10.3.0-11 grep=3.7-1 groff-base=1.22.4-7 gzip=1.10-4 hostname=3.23 ibverbs-providers=36.0-1 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libasan6=11.2.0-8 libatomic1=11.2.0-8 libattr1=1:2.5.1-1 libaudit-common=1:3.0.5-1 libaudit1=1:3.0.5-1 libbinutils=2.37-7 libblkid1=2.37.2-3 libbsd0=0.11.3-1 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 libcbor0=0.5.0+dfsg-2 libcc1-0=11.2.0-8 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.25-2 libcrypt1=1:4.4.25-2 libctf-nobfd0=2.37-7 libctf0=2.37-7 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.260 libdebhelper-perl=13.5.2 libdpkg-perl=1.20.9 libdrm-common=2.4.107-8 libdrm-intel1=2.4.107-8 libdrm2=2.4.107-8 libedit2=3.1-20210910-1 libelf1=0.185-2 libevent-2.1-7=2.1.12-stable-1 libevent-core-2.1-7=2.1.12-stable-1 libevent-dev=2.1.12-stable-1 libevent-extra-2.1-7=2.1.12-stable-1 libevent-openssl-2.1-7=2.1.12-stable-1 libevent-pthreads-2.1-7=2.1.12-stable-1 libfabric1=1.11.0-2 libffi8=3.4.2-2 libfido2-1=1.8.0-1 libfile-stripnondeterminism-perl=1.12.0-1 libgcc-10-dev=10.3.0-11 libgcc-s1=11.2.0-8 libgcrypt20=1.9.4-3+b1 libgdbm-compat4=1.21-1 libgdbm6=1.21-1 libgfortran-10-dev=10.3.0-11 libgfortran5=11.2.0-8 libglib2.0-0=2.70.0-1+b1 libgmp10=2:6.2.1+dfsg-2 libgomp1=11.2.0-8 libgpg-error0=1.42-3 libgssapi-krb5-2=1.18.3-7 libhmsbeagle-dev=3.1.2+dfsg-11 libhmsbeagle1v5=3.1.2+dfsg-11 libhwloc-dev=2.5.0+dfsg-2 libhwloc-plugins=2.5.0+dfsg-2 libhwloc15=2.5.0+dfsg-2 libibverbs-dev=36.0-1 libibverbs1=36.0-1 libicu67=67.1-7 libisl23=0.23-1 libitm1=11.2.0-8 libjs-jquery=3.5.1+dfsg+~3.5.5-7 libjs-jquery-ui=1.12.1+dfsg-8 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 liblsan0=11.2.0-8 libltdl-dev=2.4.6-15 libltdl7=2.4.6-15 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmd0=1.0.3-3 libmount1=2.37.2-3 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libncurses-dev=6.2+20210905-1 libncurses6=6.2+20210905-1 libncursesw6=6.2+20210905-1 libnl-3-200=3.4.0-1+b1 libnl-3-dev=3.4.0-1+b1 libnl-route-3-200=3.4.0-1+b1 libnl-route-3-dev=3.4.0-1+b1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnuma-dev=2.0.14-3 libnuma1=2.0.14-3 libopenmpi-dev=4.1.2~rc1-4 libopenmpi3=4.1.2~rc1-4 libpam-modules=1.4.0-10 libpam-modules-bin=1.4.0-10 libpam-runtime=1.4.0-10 libpam0g=1.4.0-10 libpciaccess0=0.16-1 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.1-6 libpipeline1=1.5.3-1 libpmix-dev=4.1.1~rc2-1 libpmix2=4.1.1~rc2-1 libpsm-infinipath1=3.3+20.604758e7-6.1 libpsm2-2=11.2.185-1 libquadmath0=11.2.0-8 librdmacm1=36.0-1 libreadline-dev=8.1-2 libreadline8=8.1-2 libseccomp2=2.5.2-1 libselinux1=3.1-3 libsemanage-common=3.1-1 libsemanage1=3.1-1+b2 libsepol1=3.1-1 libsigsegv2=2.13-1 libsmartcols1=2.37.2-3 libssl1.1=1.1.1l-1 libstdc++-10-dev=10.3.0-11 libstdc++6=11.2.0-8 libsub-override-perl=0.09-2 libsystemd0=247.9-3 libtinfo6=6.2+20210905-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-8 libubsan1=11.2.0-8 libuchardet0=0.0.7-1 libucx0=1.11.2~rc1-2 libudev1=247.9-3 libunistring2=0.9.10-6 libuuid1=2.37.2-3 libx11-6=2:1.7.2-2+b1 libx11-data=2:1.7.2-2 libxau6=1:1.0.9-1 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.4-1 libxfixes3=1:5.0.3-2 libxml2=2.9.12+dfsg-5 libxnvctrl0=470.57.02-2 libzstd1=1.4.8+dfsg-2.1 linux-libc-dev=5.14.6-3 login=1:4.8.1-1 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 mpi-default-dev=1.14 ncurses-base=6.2+20210905-1 ncurses-bin=6.2+20210905-1 ocl-icd-libopencl1=2.2.14-3 openmpi-bin=4.1.2~rc1-4 openmpi-common=4.1.2~rc1-4 openssh-client=1:8.4p1-6 passwd=1:4.8.1-1 patch=2.7.6-7 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 readline-common=8.1-2 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=2.37.2-3 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=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/20211004T210045Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211004T210045Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211001T101807Z/ 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 mrbayes=3.2.7a-5 && mkdir -p /build/mrbayes-kohYDz && dpkg-source --no-check -x /*.dsc /build/mrbayes-kohYDz/mrbayes-3.2.7a && chown -R builduser:builduser /build/mrbayes-kohYDz" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/mrbayes-kohYDz/mrbayes-3.2.7a && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1633093220" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/mrbayes-kohYDz /tmp/mrbayes-3.2.7a-5htc4ex_s bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211001T101807Z 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._njCIz0Svv 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._njCIz0Svv Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-3). 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/20211001T101807Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211001T101807Z 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 (536 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 ... 4668 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/20211004T210045Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211004T210045Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211001T101807Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap._njCIz0Svv Get:1 http://snapshot.notset.fr/archive/debian/20211004T210045Z bookworm InRelease [128 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20211001T101807Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20211004T210045Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211004T210045Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20211004T210045Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211004T210045Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20211004T210045Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211004T210045Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20211004T210045Z bookworm/main Sources [11.7 MB] Get:4 http://snapshot.notset.fr/archive/debian/20211004T210045Z bookworm/main amd64 Packages [11.2 MB] Fetched 23.0 MB in 19s (1200 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._njCIz0Svv I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d mrbayes=3.2.7a-5 && mkdir -p /build/mrbayes-kohYDz && dpkg-source --no-check -x /*.dsc /build/mrbayes-kohYDz/mrbayes-3.2.7a && chown -R builduser:builduser /build/mrbayes-kohYDz"' exec /tmp/mmdebstrap._njCIz0Svv Reading package lists... NOTICE: 'mrbayes' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/mrbayes.git Please use: git clone https://salsa.debian.org/med-team/mrbayes.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 9829 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20211004T210045Z bookworm/main mrbayes 3.2.7a-5 (dsc) [2184 B] Get:2 http://snapshot.notset.fr/archive/debian/20211004T210045Z bookworm/main mrbayes 3.2.7a-5 (tar) [9819 kB] Get:3 http://snapshot.notset.fr/archive/debian/20211004T210045Z bookworm/main mrbayes 3.2.7a-5 (diff) [7216 B] Fetched 9829 kB in 8s (1283 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'mrbayes_3.2.7a-5.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting mrbayes in /build/mrbayes-kohYDz/mrbayes-3.2.7a dpkg-source: info: unpacking mrbayes_3.2.7a.orig.tar.gz dpkg-source: info: unpacking mrbayes_3.2.7a-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_rpath.patch dpkg-source: info: applying autoreconf.patch dpkg-source: info: applying no_baseline_violation.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/mrbayes-kohYDz/mrbayes-3.2.7a && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1633093220" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap._njCIz0Svv dpkg-buildpackage: info: source package mrbayes dpkg-buildpackage: info: source version 3.2.7a-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . debian/rules clean dh clean dh_clean debian/rules binary-indep dh binary-indep dh_update_autotools_config -i dh_autoreconf -i debian/rules override_dh_auto_configure make[1]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' dh_auto_configure -- --with-beagle=/usr --enable-mpi=yes --enable-debug=yes ./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 --with-beagle=/usr --enable-mpi=yes --enable-debug=yes 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 whether to enable maintainer-specific portions of Makefiles... no checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for pdflatex... no checking for bibtex... no configure: WARNING: pdflatex or bibtex is missing, documentation will not be rebuilt checking whether make supports the include directive... yes (GNU style) checking whether to compile using MPI... no 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... unsupported checking for gcc option to enable C99 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for sqrt 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 configure: Trying to locate Beagle (hmsbeagle-1) in '/usr' checking for libhmsbeagle/beagle.h... yes checking for beagleCreateInstance in -lhmsbeagle... yes configure: Found Beagle in '/usr' checking for beagleSetCPUThreadCount in -lhmsbeagle... yes configure: Using BEAGLE_CFLAGS="-I/usr/include/libhmsbeagle-1 -pthread" configure: Using BEAGLE_LIBS="-L/usr/lib -lhmsbeagle" checking for a readline compatible library... -lreadline checking for readline.h... no checking for readline/readline.h... yes checking whether readline supports history... yes checking for history.h... no checking for readline/history.h... yes checking for float.h... yes checking for limits.h... yes checking for memory.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for size_t... yes checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for C compiler vendor... gnu checking for a sed that does not truncate output... /bin/sed checking for C compiler version... 10.3.0 checking CFLAGS for most reasonable warnings... -Wall checking for floor... yes checking for memset... yes checking for pow... yes checking for sqrt... yes checking for strchr... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/manual/Makefile config.status: creating doc/tutorial/Makefile config.status: creating examples/Makefile config.status: creating src/Makefile config.status: creating src/config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' debian/rules override_dh_auto_build make[1]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' # build mb-mpi (from initial config) LIBS="-Wl,--as-needed" dh_auto_build make -j10 make[2]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' Making all in src make[3]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/src' make all-am make[4]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/src' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/mrbayes-kohYDz/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-bayes.o `test -f 'bayes.c' || echo './'`bayes.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/mrbayes-kohYDz/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-best.o `test -f 'best.c' || echo './'`best.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/mrbayes-kohYDz/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-command.o `test -f 'command.c' || echo './'`command.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/mrbayes-kohYDz/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-likelihood.o `test -f 'likelihood.c' || echo './'`likelihood.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/mrbayes-kohYDz/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-mbbeagle.o `test -f 'mbbeagle.c' || echo './'`mbbeagle.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/mrbayes-kohYDz/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-mcmc.o `test -f 'mcmc.c' || echo './'`mcmc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/mrbayes-kohYDz/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-model.o `test -f 'model.c' || echo './'`model.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/mrbayes-kohYDz/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-proposal.o `test -f 'proposal.c' || echo './'`proposal.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/mrbayes-kohYDz/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-sumpt.o `test -f 'sumpt.c' || echo './'`sumpt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/mrbayes-kohYDz/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-utils.o `test -f 'utils.c' || echo './'`utils.c In file included from /usr/include/string.h:519, from /usr/include/memory.h:29, from bayes.h:31, from sumpt.c:38: In function ‘strncpy’, inlined from ‘DoSump’ at sumpt.c:335:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:91:10: warning: ‘__builtin_strncpy’ output may be truncated copying 90 bytes from a string of length 119 [-Wstringop-truncation] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:519, from /usr/include/memory.h:29, from bayes.h:31, from utils.c:38: In function ‘strncpy’, inlined from ‘CopyResults’ at utils.c:311:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:91:10: warning: ‘__builtin_strncpy’ accessing between 0 and 2147483647 bytes at offsets [-2147483636, 2147483649] and 0 may overlap up to 11 bytes at offset [0, 10] [-Wrestrict] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncpy’, inlined from ‘CopyProcessSsFile’ at utils.c:350:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:91:10: warning: ‘__builtin_strncpy’ accessing between 0 and 2147483647 bytes at offsets [-2147483636, 2147483649] and 0 may overlap up to 11 bytes at offset [0, 10] [-Wrestrict] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncpy’, inlined from ‘CopyTreeResults’ at utils.c:422:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:91:10: warning: ‘__builtin_strncpy’ accessing between 0 and 2147483647 bytes at offsets [-2147483636, 2147483649] and 0 may overlap up to 11 bytes at offset [0, 10] [-Wrestrict] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c: In function ‘DoCompRefTree’: sumpt.c:4612:40: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 7 and 126 [-Wformat-overflow=] 4612 | sprintf (inRefName, "%s.run%d.t", comptreeParams.comptFileName2, n+1); | ^~ sumpt.c:4612:33: note: directive argument in the range [1, 2147483647] 4612 | sprintf (inRefName, "%s.run%d.t", comptreeParams.comptFileName2, n+1); | ^~~~~~~~~~~~ In file included from /usr/include/stdio.h:866, from bayes.h:32, from sumpt.c:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 8 and 136 bytes into a destination of size 130 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmc.c: In function ‘ReopenMBPrintFiles’: mcmc.c:15467:50: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 2 and 110 [-Wformat-overflow=] 15467 | sprintf (fileName, "%s.tree%d.run%d.t", localFileName, i+1, n+1); | ^~ mcmc.c:15467:36: note: directive argument in the range [1, 2147483647] 15467 | sprintf (fileName, "%s.tree%d.run%d.t", localFileName, i+1, n+1); | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:866, from bayes.h:32, from mcmc.c:45: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 14 and 131 bytes into a destination of size 120 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c: In function ‘DoSumt’: sumpt.c:4958:39: warning: ‘.run’ directive writing 4 bytes into a region of size between 1 and 120 [-Wformat-overflow=] 4958 | sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1); | ^~~~ sumpt.c:4958:36: note: directive argument in the range [-2147483647, 2147483647] 4958 | sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1); | ^~~~~~~~~~~~ In file included from /usr/include/stdio.h:866, from bayes.h:32, from sumpt.c:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 8 and 137 bytes into a destination of size 120 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:4956:39: warning: ‘.t’ directive writing 2 bytes into a region of size between 1 and 120 [-Wformat-overflow=] 4956 | sprintf (tempName, "%s.t", fileName); | ^~ In file included from /usr/include/stdio.h:866, from bayes.h:32, from sumpt.c:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 3 and 122 bytes into a destination of size 120 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:519, from /usr/include/memory.h:29, from bayes.h:31, from command.c:38: In function ‘strncpy’, inlined from ‘DoExecute’ at command.c:3560:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:91:10: warning: ‘__builtin_strncpy’ output may be truncated copying 98 bytes from a string of length 99 [-Wstringop-truncation] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmc.c: In function ‘RunChain’: mcmc.c:17362:46: warning: ‘.ss’ directive writing 3 bytes into a region of size between 1 and 220 [-Wformat-overflow=] 17362 | sprintf (bkupFileName,"%s.ss%d", ckpFileName,chainParams.numStepsSS-stepIndexSS); | ^~~ In file included from /usr/include/stdio.h:866, from bayes.h:32, from mcmc.c:45: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 5 and 234 bytes into a destination of size 220 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.c: In function ‘SetModelParams’: model.c:19111:48: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 19111 | sprintf (tempMult, "g_m{%d}", i+1); | ^ In file included from /usr/include/stdio.h:866, from bayes.h:32, from model.c:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 7 and 16 bytes into a destination of size 15 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/mrbayes-kohYDz/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o mb mb-bayes.o mb-best.o mb-command.o mb-likelihood.o mb-mbbeagle.o mb-mcmc.o mb-model.o mb-proposal.o mb-sumpt.o mb-utils.o -L/usr/lib -lhmsbeagle -lm -lreadline make[4]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/src' make[3]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/src' Making all in doc make[3]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc' Making all in manual make[4]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc/manual' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc/manual' Making all in tutorial make[4]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc/tutorial' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc/tutorial' make[4]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc' make[3]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc' Making all in examples make[3]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/examples' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/examples' make[3]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' make[2]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' mv src/mb ./mb-mpi # Now - build mb ( cd src ; make clean ) make[2]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/src' test -z "mb" || rm -f mb rm -f *.o make[2]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/src' dh_auto_configure -- --with-beagle=/usr --enable-mpi=no --enable-debug=yes ./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 --with-beagle=/usr --enable-mpi=no --enable-debug=yes 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 whether to enable maintainer-specific portions of Makefiles... no checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for pdflatex... no checking for bibtex... no configure: WARNING: pdflatex or bibtex is missing, documentation will not be rebuilt checking whether make supports the include directive... yes (GNU style) checking whether to compile using MPI... no 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... unsupported checking for gcc option to enable C99 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for sqrt 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 configure: Trying to locate Beagle (hmsbeagle-1) in '/usr' checking for libhmsbeagle/beagle.h... yes checking for beagleCreateInstance in -lhmsbeagle... yes configure: Found Beagle in '/usr' checking for beagleSetCPUThreadCount in -lhmsbeagle... yes configure: Using BEAGLE_CFLAGS="-I/usr/include/libhmsbeagle-1 -pthread" configure: Using BEAGLE_LIBS="-L/usr/lib -lhmsbeagle" checking for a readline compatible library... -lreadline checking for readline.h... no checking for readline/readline.h... yes checking whether readline supports history... yes checking for history.h... no checking for readline/history.h... yes checking for float.h... yes checking for limits.h... yes checking for memory.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for size_t... yes checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for C compiler vendor... gnu checking for a sed that does not truncate output... /bin/sed checking for C compiler version... 10.3.0 checking CFLAGS for most reasonable warnings... -Wall checking for floor... yes checking for memset... yes checking for pow... yes checking for sqrt... yes checking for strchr... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/manual/Makefile config.status: creating doc/tutorial/Makefile config.status: creating examples/Makefile config.status: creating src/Makefile config.status: creating src/config.h config.status: src/config.h is unchanged config.status: executing depfiles commands LIBS="-Wl,--as-needed" dh_auto_build make -j10 make[2]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' Making all in src make[3]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/src' make all-am make[4]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/src' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/mrbayes-kohYDz/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-bayes.o `test -f 'bayes.c' || echo './'`bayes.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/mrbayes-kohYDz/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-best.o `test -f 'best.c' || echo './'`best.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/mrbayes-kohYDz/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-command.o `test -f 'command.c' || echo './'`command.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/mrbayes-kohYDz/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-likelihood.o `test -f 'likelihood.c' || echo './'`likelihood.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/mrbayes-kohYDz/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-mbbeagle.o `test -f 'mbbeagle.c' || echo './'`mbbeagle.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/mrbayes-kohYDz/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-mcmc.o `test -f 'mcmc.c' || echo './'`mcmc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/mrbayes-kohYDz/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-model.o `test -f 'model.c' || echo './'`model.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/mrbayes-kohYDz/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-proposal.o `test -f 'proposal.c' || echo './'`proposal.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/mrbayes-kohYDz/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-sumpt.o `test -f 'sumpt.c' || echo './'`sumpt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/mrbayes-kohYDz/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-utils.o `test -f 'utils.c' || echo './'`utils.c In file included from /usr/include/string.h:519, from /usr/include/memory.h:29, from bayes.h:31, from utils.c:38: In function ‘strncpy’, inlined from ‘CopyResults’ at utils.c:311:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:91:10: warning: ‘__builtin_strncpy’ accessing between 0 and 2147483647 bytes at offsets [-2147483636, 2147483649] and 0 may overlap up to 11 bytes at offset [0, 10] [-Wrestrict] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncpy’, inlined from ‘CopyProcessSsFile’ at utils.c:350:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:91:10: warning: ‘__builtin_strncpy’ accessing between 0 and 2147483647 bytes at offsets [-2147483636, 2147483649] and 0 may overlap up to 11 bytes at offset [0, 10] [-Wrestrict] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncpy’, inlined from ‘CopyTreeResults’ at utils.c:422:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:91:10: warning: ‘__builtin_strncpy’ accessing between 0 and 2147483647 bytes at offsets [-2147483636, 2147483649] and 0 may overlap up to 11 bytes at offset [0, 10] [-Wrestrict] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:519, from /usr/include/memory.h:29, from bayes.h:31, from sumpt.c:38: In function ‘strncpy’, inlined from ‘DoSump’ at sumpt.c:335:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:91:10: warning: ‘__builtin_strncpy’ output may be truncated copying 90 bytes from a string of length 119 [-Wstringop-truncation] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c: In function ‘DoCompRefTree’: sumpt.c:4612:40: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 7 and 126 [-Wformat-overflow=] 4612 | sprintf (inRefName, "%s.run%d.t", comptreeParams.comptFileName2, n+1); | ^~ sumpt.c:4612:33: note: directive argument in the range [1, 2147483647] 4612 | sprintf (inRefName, "%s.run%d.t", comptreeParams.comptFileName2, n+1); | ^~~~~~~~~~~~ In file included from /usr/include/stdio.h:866, from bayes.h:32, from sumpt.c:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 8 and 136 bytes into a destination of size 130 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c: In function ‘DoSumt’: sumpt.c:4958:39: warning: ‘.run’ directive writing 4 bytes into a region of size between 1 and 120 [-Wformat-overflow=] 4958 | sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1); | ^~~~ sumpt.c:4958:36: note: directive argument in the range [-2147483647, 2147483647] 4958 | sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1); | ^~~~~~~~~~~~ In file included from /usr/include/stdio.h:866, from bayes.h:32, from sumpt.c:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 8 and 137 bytes into a destination of size 120 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:4956:39: warning: ‘.t’ directive writing 2 bytes into a region of size between 1 and 120 [-Wformat-overflow=] 4956 | sprintf (tempName, "%s.t", fileName); | ^~ In file included from /usr/include/stdio.h:866, from bayes.h:32, from sumpt.c:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 3 and 122 bytes into a destination of size 120 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmc.c: In function ‘ReopenMBPrintFiles’: mcmc.c:15467:50: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 2 and 110 [-Wformat-overflow=] 15467 | sprintf (fileName, "%s.tree%d.run%d.t", localFileName, i+1, n+1); | ^~ mcmc.c:15467:36: note: directive argument in the range [1, 2147483647] 15467 | sprintf (fileName, "%s.tree%d.run%d.t", localFileName, i+1, n+1); | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:866, from bayes.h:32, from mcmc.c:45: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 14 and 131 bytes into a destination of size 120 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:519, from /usr/include/memory.h:29, from bayes.h:31, from command.c:38: In function ‘strncpy’, inlined from ‘DoExecute’ at command.c:3560:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:91:10: warning: ‘__builtin_strncpy’ output may be truncated copying 98 bytes from a string of length 99 [-Wstringop-truncation] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmc.c: In function ‘RunChain’: mcmc.c:17362:46: warning: ‘.ss’ directive writing 3 bytes into a region of size between 1 and 220 [-Wformat-overflow=] 17362 | sprintf (bkupFileName,"%s.ss%d", ckpFileName,chainParams.numStepsSS-stepIndexSS); | ^~~ In file included from /usr/include/stdio.h:866, from bayes.h:32, from mcmc.c:45: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 5 and 234 bytes into a destination of size 220 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ model.c: In function ‘SetModelParams’: model.c:19111:48: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 19111 | sprintf (tempMult, "g_m{%d}", i+1); | ^ In file included from /usr/include/stdio.h:866, from bayes.h:32, from model.c:38: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 7 and 16 bytes into a destination of size 15 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/mrbayes-kohYDz/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o mb mb-bayes.o mb-best.o mb-command.o mb-likelihood.o mb-mbbeagle.o mb-mcmc.o mb-model.o mb-proposal.o mb-sumpt.o mb-utils.o -L/usr/lib -lhmsbeagle -lm -lreadline make[4]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/src' make[3]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/src' Making all in doc make[3]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc' Making all in manual make[4]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc/manual' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc/manual' Making all in tutorial make[4]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc/tutorial' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc/tutorial' make[4]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc' make[3]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc' Making all in examples make[3]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/examples' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/examples' make[3]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' make[2]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' mv src/mb . make[1]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' dh: command-omitted: The call to "dh_auto_test -i" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep -i dh_auto_install -i make -j10 install DESTDIR=/build/mrbayes-kohYDz/mrbayes-3.2.7a/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' Making install in src make[2]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/src' gcc -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/mrbayes-kohYDz/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o mb mb-bayes.o mb-best.o mb-command.o mb-likelihood.o mb-mbbeagle.o mb-mcmc.o mb-model.o mb-proposal.o mb-sumpt.o mb-utils.o -L/usr/lib -lhmsbeagle -lm -lreadline make[3]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/src' make[3]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/mrbayes-kohYDz/mrbayes-3.2.7a/debian/tmp/usr/bin' /usr/bin/install -c mb '/build/mrbayes-kohYDz/mrbayes-3.2.7a/debian/tmp/usr/bin' make[3]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/src' make[2]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/src' Making install in doc make[2]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc' Making install in manual make[3]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc/manual' make[4]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc/manual' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/mrbayes-kohYDz/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' /usr/bin/install -c -m 644 Manual_MrBayes_v3.2.pdf '/build/mrbayes-kohYDz/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' make[4]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc/manual' make[3]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc/manual' Making install in tutorial make[3]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc/tutorial' make[4]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc/tutorial' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/mrbayes-kohYDz/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' /bin/mkdir -p '/build/mrbayes-kohYDz/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' /usr/bin/install -c -m 644 hym.nex '/build/mrbayes-kohYDz/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' /usr/bin/install -c -m 644 MBDating.pdf '/build/mrbayes-kohYDz/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' make[4]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc/tutorial' make[3]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc/tutorial' make[3]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc' make[4]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc' 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/mrbayes-kohYDz/mrbayes-3.2.7a/doc' make[3]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc' make[2]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/doc' Making install in examples make[2]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/examples' make[3]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/examples' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/mrbayes-kohYDz/mrbayes-3.2.7a/debian/tmp/usr/share/examples/mrbayes' /usr/bin/install -c -m 644 avian_ovomucoids.nex codon.nex cynmix.nex finch.nex hymfossil.nex primates.nex replicase.nex sceloporus.nex '/build/mrbayes-kohYDz/mrbayes-3.2.7a/debian/tmp/usr/share/examples/mrbayes' make[3]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/examples' make[2]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a/examples' make[2]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' make[3]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/mrbayes-kohYDz/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' /usr/bin/install -c -m 644 COPYING README NEWS '/build/mrbayes-kohYDz/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' make[3]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' make[2]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' make[1]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' dh_install -i dh_installdocs -i dh_installchangelogs -i debian/rules override_dh_installexamples make[1]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' dh_installexamples find debian -name "Makefile*" -delete make[1]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' dh_installman -i dh_perl -i dh_link -i dh_strip_nondeterminism -i debian/rules override_dh_compress make[1]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' dh_fixperms -i debian/rules override_dh_missing make[1]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' dh_missing --list-missing dh_missing: warning: usr/bin/mb exists in debian/tmp but is not installed to anywhere (related file: "mb") dh_missing: warning: usr/share/doc/mrbayes/COPYING exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/doc/mrbayes/MBDating.pdf exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/doc/mrbayes/Manual_MrBayes_v3.2.pdf exists in debian/tmp but is not installed to anywhere (related file: "doc/manual/Manual_MrBayes_v3.2.pdf") dh_missing: warning: usr/share/doc/mrbayes/NEWS exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/doc/mrbayes/README exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/doc/mrbayes/hym.nex exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/examples/mrbayes/avian_ovomucoids.nex exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/examples/mrbayes/codon.nex exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/examples/mrbayes/cynmix.nex exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/examples/mrbayes/finch.nex exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/examples/mrbayes/hymfossil.nex exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/examples/mrbayes/primates.nex exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/examples/mrbayes/replicase.nex exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/examples/mrbayes/sceloporus.nex exists in debian/tmp but is not installed to anywhere While detecting missing files, dh_missing noted some files with a similar name to those that were missing. This warning /might/ be resolved by replacing references to the missing files with the similarly named ones that dh_missing found - assuming the content is identical. As an example, you might want to replace: * mb with: * usr/bin/mb in a file in debian/ or as argument to one of the dh_* tools called from debian/rules. (Note it is possible the paths are not used verbatim but instead directories containing or globs matching them are used instead) Alternatively, add the missing file to debian/not-installed if it cannot and should not be used. The following debhelper tools have reported what they installed (with files per package) * dh_install: mrbayes (1), mrbayes-doc (1), mrbayes-mpi (2) * dh_installdocs: mrbayes (3), mrbayes-doc (0), mrbayes-mpi (0) * dh_installexamples: mrbayes (0), mrbayes-doc (0), mrbayes-mpi (0) * dh_installman: mrbayes (1), mrbayes-doc (0), mrbayes-mpi (1) If the missing files are installed by another tool, please file a bug against it. When filing the report, if the tool is not part of debhelper itself, please reference the "Logging helpers and dh_missing" section from the "PROGRAMMING" guide for debhelper (10.6.3+). (in the debhelper package: /usr/share/doc/debhelper/PROGRAMMING.gz) Be sure to test with dpkg-buildpackage -A/-B as the results may vary when only a subset is built If the omission is intentional or no other helper can take care of this consider adding the paths to debian/not-installed. make[1]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' debian/rules override_dh_installdeb make[1]: Entering directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' # FIXME: That's a dirty hack by simply removing debug information in mrbayes-mpi-dbgsym # Due to the duplicated build above this is just a duplicate of mrbayes-dbgsym and creates a file conflict if [ -d debian/.debhelper/mrbayes-mpi/dbgsym-root/usr/lib/debug ] ; then \ find debian/.debhelper/mrbayes-mpi/dbgsym-root/usr/lib/debug -name "*.debug" -delete ; \ fi dh_installdeb make[1]: Leaving directory '/build/mrbayes-kohYDz/mrbayes-3.2.7a' dh_gencontrol -i dh_md5sums -i dh_builddeb -i dpkg-deb: building package 'mrbayes-doc' in '../mrbayes-doc_3.2.7a-5_all.deb'. dpkg-genbuildinfo --build=all dpkg-genchanges --build=all >../mrbayes_3.2.7a-5_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/mrbayes-kohYDz /tmp/mrbayes-3.2.7a-5htc4ex_s I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap._njCIz0Svv... I: success in 521.1349 seconds md5: mrbayes-doc_3.2.7a-5_all.deb: OK sha1: mrbayes-doc_3.2.7a-5_all.deb: OK sha256: mrbayes-doc_3.2.7a-5_all.deb: OK Checksums: OK