I: pbuilder: network access will be disabled during build I: Current time: Thu May 4 09:39:33 -12 2023 I: pbuilder-time-stamp: 1683236373 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [mrbayes_3.2.7a-6.dsc] I: copying [./mrbayes_3.2.7a.orig.tar.gz] I: copying [./mrbayes_3.2.7a-6.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Nov 24 00:00:25 2022 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./mrbayes_3.2.7a-6.dsc: no acceptable signature found dpkg-source: info: extracting mrbayes in mrbayes-3.2.7a dpkg-source: info: unpacking mrbayes_3.2.7a.orig.tar.gz dpkg-source: info: unpacking mrbayes_3.2.7a-6.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: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2931846/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='1cdebdf9914744dca15d32ef52de6c4f' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2931846' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.xfsfOO0i/pbuilderrc_Nmqu --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xfsfOO0i/b1 --logfile b1/build.log mrbayes_3.2.7a-6.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 09:23 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:23 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/2931846/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libreadline-dev, mpi-default-dev, libhmsbeagle-dev, autoconf-archive, pkg-config dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libreadline-dev; however: Package libreadline-dev is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-dev; however: Package mpi-default-dev is not installed. pbuilder-satisfydepends-dummy depends on libhmsbeagle-dev; however: Package libhmsbeagle-dev is not installed. pbuilder-satisfydepends-dummy depends on autoconf-archive; however: Package autoconf-archive is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} autoconf-archive{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran-12{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} lib32gcc-s1{a} lib32stdc++6{a} libarchive-zip-perl{a} libbsd0{a} libc6-i386{a} libcbor0.8{a} libclang-common-15-dev{a} libclang-cpp15{a} libclc-15{a} libclc-15-dev{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libelf1{a} libevent-2.1-7{a} libevent-core-2.1-7{a} libevent-dev{a} libevent-extra-2.1-7{a} libevent-openssl-2.1-7{a} libevent-pthreads-2.1-7{a} libexpat1{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-12-dev{a} libgfortran5{a} libhmsbeagle-dev{a} libhmsbeagle1v5{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libicu72{a} libjs-jquery{a} libjs-jquery-ui{a} libllvm15{a} libllvmspirvlib15{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libmunge2{a} libncurses-dev{a} libncurses6{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi3{a} libpciaccess0{a} libpipeline1{a} libpkgconf3{a} libpmix-dev{a} libpmix2{a} libpsm-infinipath1{a} libpsm2-2{a} librdmacm1{a} libreadline-dev{a} libreadline8{a} libsensors-config{a} libsensors5{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libucx0{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} libz3-4{a} m4{a} man-db{a} mesa-opencl-icd{a} mpi-default-dev{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common libarchive-cpio-perl libcoarrays-openmpi-dev libgpm2 libmail-sendmail-perl lynx wget xauth 0 packages upgraded, 114 newly installed, 0 to remove and 0 not upgraded. Need to get 125 MB of archives. After unpacking 646 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 libcbor0.8 amd64 0.8.0-2+b1 [27.4 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libfido2-1 amd64 1.12.0-2+b1 [77.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 openssh-client amd64 1:9.2p1-2 [988 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 28 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libgfortran-12-dev amd64 12.2.0-14 [834 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 gfortran-12 amd64 12.2.0-14 [10.2 MB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libnl-3-200 amd64 3.7.0-0.2+b1 [63.1 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libnl-route-3-200 amd64 3.7.0-0.2+b1 [185 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libibverbs1 amd64 44.0-2 [60.7 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 ibverbs-providers amd64 44.0-2 [335 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 libc6-i386 amd64 2.36-9 [2456 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 lib32gcc-s1 amd64 12.2.0-14 [59.7 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 lib32stdc++6 amd64 12.2.0-14 [644 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libz3-4 amd64 4.8.12-3.1 [7216 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 libllvm15 amd64 1:15.0.6-4+b1 [23.1 MB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libclang-common-15-dev amd64 1:15.0.6-4+b1 [5855 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libclang-cpp15 amd64 1:15.0.6-4+b1 [11.6 MB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libclc-15-dev all 1:15.0.6-4 [53.6 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libclc-15 all 1:15.0.6-4 [10.1 MB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libdrm-common all 2.4.114-1 [7112 B] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libdrm2 amd64 2.4.114-1+b1 [37.5 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libdrm-amdgpu1 amd64 2.4.114-1+b1 [20.9 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libdrm-nouveau2 amd64 2.4.114-1+b1 [19.1 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libdrm-radeon1 amd64 2.4.114-1+b1 [21.8 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libevent-2.1-7 amd64 2.1.12-stable-8 [180 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-8 [131 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libevent-extra-2.1-7 amd64 2.1.12-stable-8 [107 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-8 [53.6 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libevent-openssl-2.1-7 amd64 2.1.12-stable-8 [60.6 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libevent-dev amd64 2.1.12-stable-8 [305 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.2 [168 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libnuma1 amd64 2.0.16-1 [21.0 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 librdmacm1 amd64 44.0-2 [68.6 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 libfabric1 amd64 1.17.0-3 [627 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 ocl-icd-libopencl1 amd64 2.3.1-1 [43.0 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 libllvmspirvlib15 amd64 15.0.0-1+b2 [828 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libsensors5 amd64 1:3.6.0-7.1 [34.2 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 mesa-opencl-icd amd64 22.3.6-1+deb12u1 [15.5 MB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libhmsbeagle1v5 amd64 3.1.2+dfsg-13 [135 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libhmsbeagle-dev amd64 3.1.2+dfsg-13 [261 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libhwloc15 amd64 2.9.0-1 [154 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 libnuma-dev amd64 2.0.16-1 [35.0 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 libltdl7 amd64 2.4.7-5 [393 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libltdl-dev amd64 2.4.7-5 [164 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 libhwloc-dev amd64 2.9.0-1 [241 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2 [292 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2 [759 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 libxnvctrl0 amd64 525.85.05-1 [13.3 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libhwloc-plugins amd64 2.9.0-1 [17.5 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 libnl-3-dev amd64 3.7.0-0.2+b1 [104 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libnl-route-3-dev amd64 3.7.0-0.2+b1 [203 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 libibverbs-dev amd64 44.0-2 [633 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 libmunge2 amd64 0.5.15-2 [19.5 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-2 [103 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 libncurses-dev amd64 6.4-2 [348 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 libpmix2 amd64 4.2.2-1+b1 [622 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 libucx0 amd64 1.13.1-1 [860 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 libopenmpi3 amd64 4.1.4-3+b1 [2422 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 openmpi-common all 4.1.4-3 [167 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 libpmix-dev amd64 4.2.2-1+b1 [902 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 openmpi-bin amd64 4.1.4-3+b1 [226 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 libopenmpi-dev amd64 4.1.4-3+b1 [970 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 libpkgconf3 amd64 1.8.1-1 [36.1 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 libreadline-dev amd64 8.2-1.3 [151 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 mpi-default-dev amd64 1.14 [5548 B] Get: 112 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB] Fetched 125 MB in 5s (27.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package autoconf-archive. (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 ... 19596 files and directories currently installed.) Preparing to unpack .../000-autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Selecting previously unselected package readline-common. Preparing to unpack .../001-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package sensible-utils. 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Preparing to unpack .../027-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../028-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../029-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../030-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../031-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../032-libxml2_2.9.14+dfsg-1.2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../033-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../034-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../035-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../036-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../037-libgfortran5_12.2.0-14_amd64.deb ... Unpacking libgfortran5:amd64 (12.2.0-14) ... Selecting previously unselected package libgfortran-12-dev:amd64. Preparing to unpack .../038-libgfortran-12-dev_12.2.0-14_amd64.deb ... Unpacking libgfortran-12-dev:amd64 (12.2.0-14) ... Selecting previously unselected package gfortran-12. Preparing to unpack .../039-gfortran-12_12.2.0-14_amd64.deb ... Unpacking gfortran-12 (12.2.0-14) ... Selecting previously unselected package libnl-3-200:amd64. Preparing to unpack .../040-libnl-3-200_3.7.0-0.2+b1_amd64.deb ... Unpacking libnl-3-200:amd64 (3.7.0-0.2+b1) ... Selecting previously unselected package libnl-route-3-200:amd64. Preparing to unpack .../041-libnl-route-3-200_3.7.0-0.2+b1_amd64.deb ... Unpacking libnl-route-3-200:amd64 (3.7.0-0.2+b1) ... Selecting previously unselected package libibverbs1:amd64. Preparing to unpack .../042-libibverbs1_44.0-2_amd64.deb ... Unpacking libibverbs1:amd64 (44.0-2) ... Selecting previously unselected package ibverbs-providers:amd64. Preparing to unpack .../043-ibverbs-providers_44.0-2_amd64.deb ... Unpacking ibverbs-providers:amd64 (44.0-2) ... Selecting previously unselected package libc6-i386. Preparing to unpack .../044-libc6-i386_2.36-9_amd64.deb ... Unpacking libc6-i386 (2.36-9) ... 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Unpacking libclang-cpp15 (1:15.0.6-4+b1) ... Selecting previously unselected package libclc-15-dev. Preparing to unpack .../051-libclc-15-dev_1%3a15.0.6-4_all.deb ... Unpacking libclc-15-dev (1:15.0.6-4) ... Selecting previously unselected package libclc-15. Preparing to unpack .../052-libclc-15_1%3a15.0.6-4_all.deb ... Unpacking libclc-15 (1:15.0.6-4) ... Selecting previously unselected package libdrm-common. Preparing to unpack .../053-libdrm-common_2.4.114-1_all.deb ... Unpacking libdrm-common (2.4.114-1) ... Selecting previously unselected package libdrm2:amd64. Preparing to unpack .../054-libdrm2_2.4.114-1+b1_amd64.deb ... Unpacking libdrm2:amd64 (2.4.114-1+b1) ... Selecting previously unselected package libdrm-amdgpu1:amd64. Preparing to unpack .../055-libdrm-amdgpu1_2.4.114-1+b1_amd64.deb ... Unpacking libdrm-amdgpu1:amd64 (2.4.114-1+b1) ... Selecting previously unselected package libdrm-nouveau2:amd64. Preparing to unpack .../056-libdrm-nouveau2_2.4.114-1+b1_amd64.deb ... Unpacking libdrm-nouveau2:amd64 (2.4.114-1+b1) ... Selecting previously unselected package libdrm-radeon1:amd64. Preparing to unpack .../057-libdrm-radeon1_2.4.114-1+b1_amd64.deb ... Unpacking libdrm-radeon1:amd64 (2.4.114-1+b1) ... Selecting previously unselected package libevent-2.1-7:amd64. Preparing to unpack .../058-libevent-2.1-7_2.1.12-stable-8_amd64.deb ... Unpacking libevent-2.1-7:amd64 (2.1.12-stable-8) ... Selecting previously unselected package libevent-core-2.1-7:amd64. Preparing to unpack .../059-libevent-core-2.1-7_2.1.12-stable-8_amd64.deb ... Unpacking libevent-core-2.1-7:amd64 (2.1.12-stable-8) ... Selecting previously unselected package libevent-extra-2.1-7:amd64. Preparing to unpack .../060-libevent-extra-2.1-7_2.1.12-stable-8_amd64.deb ... Unpacking libevent-extra-2.1-7:amd64 (2.1.12-stable-8) ... Selecting previously unselected package libevent-pthreads-2.1-7:amd64. Preparing to unpack .../061-libevent-pthreads-2.1-7_2.1.12-stable-8_amd64.deb ... Unpacking libevent-pthreads-2.1-7:amd64 (2.1.12-stable-8) ... Selecting previously unselected package libevent-openssl-2.1-7:amd64. Preparing to unpack .../062-libevent-openssl-2.1-7_2.1.12-stable-8_amd64.deb ... Unpacking libevent-openssl-2.1-7:amd64 (2.1.12-stable-8) ... Selecting previously unselected package libevent-dev. Preparing to unpack .../063-libevent-dev_2.1.12-stable-8_amd64.deb ... Unpacking libevent-dev (2.1.12-stable-8) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../064-libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package libpsm-infinipath1. Preparing to unpack .../065-libpsm-infinipath1_3.3+20.604758e7-6.2_amd64.deb ... Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.2) ... Selecting previously unselected package libnuma1:amd64. Preparing to unpack .../066-libnuma1_2.0.16-1_amd64.deb ... Unpacking libnuma1:amd64 (2.0.16-1) ... Selecting previously unselected package libpsm2-2. Preparing to unpack .../067-libpsm2-2_11.2.185-2_amd64.deb ... Unpacking libpsm2-2 (11.2.185-2) ... Selecting previously unselected package librdmacm1:amd64. Preparing to unpack .../068-librdmacm1_44.0-2_amd64.deb ... Unpacking librdmacm1:amd64 (44.0-2) ... Selecting previously unselected package libfabric1:amd64. Preparing to unpack .../069-libfabric1_1.17.0-3_amd64.deb ... Unpacking libfabric1:amd64 (1.17.0-3) ... Selecting previously unselected package ocl-icd-libopencl1:amd64. Preparing to unpack .../070-ocl-icd-libopencl1_2.3.1-1_amd64.deb ... Unpacking ocl-icd-libopencl1:amd64 (2.3.1-1) ... Selecting previously unselected package libllvmspirvlib15:amd64. Preparing to unpack .../071-libllvmspirvlib15_15.0.0-1+b2_amd64.deb ... Unpacking libllvmspirvlib15:amd64 (15.0.0-1+b2) ... Selecting previously unselected package libsensors-config. Preparing to unpack .../072-libsensors-config_1%3a3.6.0-7.1_all.deb ... Unpacking libsensors-config (1:3.6.0-7.1) ... Selecting previously unselected package libsensors5:amd64. Preparing to unpack .../073-libsensors5_1%3a3.6.0-7.1_amd64.deb ... Unpacking libsensors5:amd64 (1:3.6.0-7.1) ... Selecting previously unselected package mesa-opencl-icd:amd64. Preparing to unpack .../074-mesa-opencl-icd_22.3.6-1+deb12u1_amd64.deb ... Unpacking mesa-opencl-icd:amd64 (22.3.6-1+deb12u1) ... Selecting previously unselected package libhmsbeagle1v5:amd64. Preparing to unpack .../075-libhmsbeagle1v5_3.1.2+dfsg-13_amd64.deb ... Unpacking libhmsbeagle1v5:amd64 (3.1.2+dfsg-13) ... Selecting previously unselected package libhmsbeagle-dev. Preparing to unpack .../076-libhmsbeagle-dev_3.1.2+dfsg-13_amd64.deb ... Unpacking libhmsbeagle-dev (3.1.2+dfsg-13) ... Selecting previously unselected package libhwloc15:amd64. Preparing to unpack .../077-libhwloc15_2.9.0-1_amd64.deb ... Unpacking libhwloc15:amd64 (2.9.0-1) ... Selecting previously unselected package libnuma-dev:amd64. 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Unpacking pkg-config:amd64 (1.8.1-1) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libpciaccess0:amd64 (0.17-2) ... Setting up libclc-15-dev (1:15.0.6-4) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libicu72:amd64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libcbor0.8:amd64 (0.8.0-2+b1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libsensors-config (1:3.6.0-7.1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up autoconf-archive (20220903-3) ... Setting up file (1:5.44-3) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.8.12-3.1) ... Setting up libpkgconf3:amd64 (1.8.1-1) ... Setting up libmunge2 (0.5.15-2) ... Setting up libx11-data (2:1.8.4-2) ... Setting up libncurses6:amd64 (6.4-2) ... 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Setting up openmpi-bin (4.1.4-3+b1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:amd64 (4.1.4-3+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up mpi-default-dev (1.14) ... Processing triggers for libc-bin (2.36-9) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/mrbayes-3.2.7a/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../mrbayes_3.2.7a-6_source.changes dpkg-buildpackage: info: source package mrbayes dpkg-buildpackage: info: source version 3.2.7a-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/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... 12.2.0 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-3.2.7a' debian/rules override_dh_auto_build make[1]: Entering directory '/build/mrbayes-3.2.7a' # build mb-mpi (from initial config) LIBS="-Wl,--as-needed" dh_auto_build make -j15 make[2]: Entering directory '/build/mrbayes-3.2.7a' Making all in src make[3]: Entering directory '/build/mrbayes-3.2.7a/src' make all-am make[4]: Entering directory '/build/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-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-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-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-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-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-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-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-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-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-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-utils.o `test -f 'utils.c' || echo './'`utils.c mbbeagle.c: In function 'TreeLikelihood_BeagleMultiPartition': mbbeagle.c:2618:33: warning: 'nStates' may be used uninitialized [-Wmaybe-uninitialized] 2618 | int i, j, d, c = 0, nStates, beagleReturn, site, dIndex, divisionOffset; | ^~~~~~~ In file included from /usr/include/string.h:535, 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:95:10: 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] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'strncpy', inlined from 'CopyProcessSsFile' at utils.c:350:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: 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] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'strncpy', inlined from 'CopyTreeResults' at utils.c:422:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: 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] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c: In function 'DoSump': sumpt.c:335:5: warning: '__builtin_strncpy' output may be truncated copying 90 bytes from a string of length 119 [-Wstringop-truncation] 335 | strncpy (temp, sumpParams.sumpOutfile, 90); | ^ 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:906, from bayes.h:32, from sumpt.c:38: In function 'sprintf', inlined from 'DoCompRefTree' at sumpt.c:4612:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 8 and 136 bytes into a destination of size 130 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function 'sprintf', inlined from 'ShowConTree' at sumpt.c:8173:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: '__builtin_sprintf' argument 3 may overlap destination object 'printLine' [-Wrestrict] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __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 function 'sprintf', inlined from 'DoSumt' at sumpt.c:4958:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 8 and 137 bytes into a destination of size 120 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sumpt.c: In function 'DoSumt': 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 function 'sprintf', inlined from 'DoSumt' at sumpt.c:4956:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 3 and 122 bytes into a destination of size 120 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __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:906, from bayes.h:32, from mcmc.c:45: In function 'sprintf', inlined from 'ReopenMBPrintFiles' at mcmc.c:15467:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 14 and 131 bytes into a destination of size 120 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command.c: In function 'DoExecute': command.c:3560:5: warning: '__builtin_strncpy' output may be truncated copying 98 bytes from a string of length 99 [-Wstringop-truncation] 3560 | strncpy (exeFileName, inputFileName, 98); | ^ 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 function 'sprintf', inlined from 'RunChain' at mcmc.c:17362:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 5 and 234 bytes into a destination of size 220 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __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:906, from bayes.h:32, from model.c:38: In function 'sprintf', inlined from 'SetModelParams' at model.c:19111:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 15 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/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-3.2.7a/src' make[3]: Leaving directory '/build/mrbayes-3.2.7a/src' Making all in doc make[3]: Entering directory '/build/mrbayes-3.2.7a/doc' Making all in manual make[4]: Entering directory '/build/mrbayes-3.2.7a/doc/manual' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/mrbayes-3.2.7a/doc/manual' Making all in tutorial make[4]: Entering directory '/build/mrbayes-3.2.7a/doc/tutorial' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/mrbayes-3.2.7a/doc/tutorial' make[4]: Entering directory '/build/mrbayes-3.2.7a/doc' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/mrbayes-3.2.7a/doc' make[3]: Leaving directory '/build/mrbayes-3.2.7a/doc' Making all in examples make[3]: Entering directory '/build/mrbayes-3.2.7a/examples' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/mrbayes-3.2.7a/examples' make[3]: Entering directory '/build/mrbayes-3.2.7a' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/mrbayes-3.2.7a' make[2]: Leaving directory '/build/mrbayes-3.2.7a' mv src/mb ./mb-mpi # Now - build mb ( cd src ; make clean ) make[2]: Entering directory '/build/mrbayes-3.2.7a/src' test -z "mb" || rm -f mb rm -f *.o make[2]: Leaving directory '/build/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... 12.2.0 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 -j15 make[2]: Entering directory '/build/mrbayes-3.2.7a' Making all in src make[3]: Entering directory '/build/mrbayes-3.2.7a/src' make all-am make[4]: Entering directory '/build/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-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-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-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-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-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-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-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-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-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-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-utils.o `test -f 'utils.c' || echo './'`utils.c mbbeagle.c: In function 'TreeLikelihood_BeagleMultiPartition': mbbeagle.c:2618:33: warning: 'nStates' may be used uninitialized [-Wmaybe-uninitialized] 2618 | int i, j, d, c = 0, nStates, beagleReturn, site, dIndex, divisionOffset; | ^~~~~~~ In file included from /usr/include/string.h:535, 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:95:10: 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] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'strncpy', inlined from 'CopyProcessSsFile' at utils.c:350:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: 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] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'strncpy', inlined from 'CopyTreeResults' at utils.c:422:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: 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] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c: In function 'DoSump': sumpt.c:335:5: warning: '__builtin_strncpy' output may be truncated copying 90 bytes from a string of length 119 [-Wstringop-truncation] 335 | strncpy (temp, sumpParams.sumpOutfile, 90); | ^ 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:906, from bayes.h:32, from sumpt.c:38: In function 'sprintf', inlined from 'DoCompRefTree' at sumpt.c:4612:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 8 and 136 bytes into a destination of size 130 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function 'sprintf', inlined from 'ShowConTree' at sumpt.c:8173:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: '__builtin_sprintf' argument 3 may overlap destination object 'printLine' [-Wrestrict] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __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 function 'sprintf', inlined from 'DoSumt' at sumpt.c:4958:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 8 and 137 bytes into a destination of size 120 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sumpt.c: In function 'DoSumt': 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 function 'sprintf', inlined from 'DoSumt' at sumpt.c:4956:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 3 and 122 bytes into a destination of size 120 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __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:906, from bayes.h:32, from mcmc.c:45: In function 'sprintf', inlined from 'ReopenMBPrintFiles' at mcmc.c:15467:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 14 and 131 bytes into a destination of size 120 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command.c: In function 'DoExecute': command.c:3560:5: warning: '__builtin_strncpy' output may be truncated copying 98 bytes from a string of length 99 [-Wstringop-truncation] 3560 | strncpy (exeFileName, inputFileName, 98); | ^ 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 function 'sprintf', inlined from 'RunChain' at mcmc.c:17362:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 5 and 234 bytes into a destination of size 220 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __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:906, from bayes.h:32, from model.c:38: In function 'sprintf', inlined from 'SetModelParams' at model.c:19111:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 15 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/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-3.2.7a/src' make[3]: Leaving directory '/build/mrbayes-3.2.7a/src' Making all in doc make[3]: Entering directory '/build/mrbayes-3.2.7a/doc' Making all in manual make[4]: Entering directory '/build/mrbayes-3.2.7a/doc/manual' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/mrbayes-3.2.7a/doc/manual' Making all in tutorial make[4]: Entering directory '/build/mrbayes-3.2.7a/doc/tutorial' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/mrbayes-3.2.7a/doc/tutorial' make[4]: Entering directory '/build/mrbayes-3.2.7a/doc' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/mrbayes-3.2.7a/doc' make[3]: Leaving directory '/build/mrbayes-3.2.7a/doc' Making all in examples make[3]: Entering directory '/build/mrbayes-3.2.7a/examples' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/mrbayes-3.2.7a/examples' make[3]: Entering directory '/build/mrbayes-3.2.7a' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/mrbayes-3.2.7a' make[2]: Leaving directory '/build/mrbayes-3.2.7a' mv src/mb . make[1]: Leaving directory '/build/mrbayes-3.2.7a' dh_auto_test make -j15 check "TESTSUITEFLAGS=-j15 --verbose" VERBOSE=1 make[1]: Entering directory '/build/mrbayes-3.2.7a' Making check in src make[2]: Entering directory '/build/mrbayes-3.2.7a/src' gcc -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/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[2]: Leaving directory '/build/mrbayes-3.2.7a/src' Making check in doc make[2]: Entering directory '/build/mrbayes-3.2.7a/doc' Making check in manual make[3]: Entering directory '/build/mrbayes-3.2.7a/doc/manual' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/mrbayes-3.2.7a/doc/manual' Making check in tutorial make[3]: Entering directory '/build/mrbayes-3.2.7a/doc/tutorial' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/mrbayes-3.2.7a/doc/tutorial' make[3]: Entering directory '/build/mrbayes-3.2.7a/doc' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/mrbayes-3.2.7a/doc' make[2]: Leaving directory '/build/mrbayes-3.2.7a/doc' Making check in examples make[2]: Entering directory '/build/mrbayes-3.2.7a/examples' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/mrbayes-3.2.7a/examples' make[2]: Entering directory '/build/mrbayes-3.2.7a' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/build/mrbayes-3.2.7a' make[1]: Leaving directory '/build/mrbayes-3.2.7a' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j15 install DESTDIR=/build/mrbayes-3.2.7a/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/mrbayes-3.2.7a' Making install in src make[2]: Entering directory '/build/mrbayes-3.2.7a/src' make[3]: Entering directory '/build/mrbayes-3.2.7a/src' /bin/mkdir -p '/build/mrbayes-3.2.7a/debian/tmp/usr/bin' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/install -c mb '/build/mrbayes-3.2.7a/debian/tmp/usr/bin' make[3]: Leaving directory '/build/mrbayes-3.2.7a/src' make[2]: Leaving directory '/build/mrbayes-3.2.7a/src' Making install in doc make[2]: Entering directory '/build/mrbayes-3.2.7a/doc' Making install in manual make[3]: Entering directory '/build/mrbayes-3.2.7a/doc/manual' make[4]: Entering directory '/build/mrbayes-3.2.7a/doc/manual' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' /usr/bin/install -c -m 644 Manual_MrBayes_v3.2.pdf '/build/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' make[4]: Leaving directory '/build/mrbayes-3.2.7a/doc/manual' make[3]: Leaving directory '/build/mrbayes-3.2.7a/doc/manual' Making install in tutorial make[3]: Entering directory '/build/mrbayes-3.2.7a/doc/tutorial' make[4]: Entering directory '/build/mrbayes-3.2.7a/doc/tutorial' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' /bin/mkdir -p '/build/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' /usr/bin/install -c -m 644 hym.nex '/build/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' /usr/bin/install -c -m 644 MBDating.pdf '/build/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' make[4]: Leaving directory '/build/mrbayes-3.2.7a/doc/tutorial' make[3]: Leaving directory '/build/mrbayes-3.2.7a/doc/tutorial' make[3]: Entering directory '/build/mrbayes-3.2.7a/doc' make[4]: Entering directory '/build/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-3.2.7a/doc' make[3]: Leaving directory '/build/mrbayes-3.2.7a/doc' make[2]: Leaving directory '/build/mrbayes-3.2.7a/doc' Making install in examples make[2]: Entering directory '/build/mrbayes-3.2.7a/examples' make[3]: Entering directory '/build/mrbayes-3.2.7a/examples' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/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-3.2.7a/debian/tmp/usr/share/examples/mrbayes' make[3]: Leaving directory '/build/mrbayes-3.2.7a/examples' make[2]: Leaving directory '/build/mrbayes-3.2.7a/examples' make[2]: Entering directory '/build/mrbayes-3.2.7a' make[3]: Entering directory '/build/mrbayes-3.2.7a' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' /usr/bin/install -c -m 644 COPYING README NEWS '/build/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' make[3]: Leaving directory '/build/mrbayes-3.2.7a' make[2]: Leaving directory '/build/mrbayes-3.2.7a' make[1]: Leaving directory '/build/mrbayes-3.2.7a' dh_install dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/mrbayes-3.2.7a' dh_installexamples find debian -name "Makefile*" -delete make[1]: Leaving directory '/build/mrbayes-3.2.7a' dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/mrbayes-3.2.7a' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/mrbayes-3.2.7a' dh_fixperms debian/rules override_dh_missing make[1]: Entering directory '/build/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-3.2.7a' dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a debian/rules override_dh_installdeb make[1]: Entering directory '/build/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-3.2.7a' dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'mrbayes-dbgsym' in '../mrbayes-dbgsym_3.2.7a-6_amd64.deb'. dpkg-deb: building package 'mrbayes-doc' in '../mrbayes-doc_3.2.7a-6_all.deb'. dpkg-deb: building package 'mrbayes-mpi' in '../mrbayes-mpi_3.2.7a-6_amd64.deb'. dpkg-deb: building package 'mrbayes' in '../mrbayes_3.2.7a-6_amd64.deb'. dpkg-deb: building package 'mrbayes-mpi-dbgsym' in '../mrbayes-mpi-dbgsym_3.2.7a-6_amd64.deb'. dpkg-genbuildinfo --build=binary -O../mrbayes_3.2.7a-6_amd64.buildinfo dpkg-genchanges --build=binary -O../mrbayes_3.2.7a-6_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2931846 and its subdirectories I: Current time: Thu May 4 09:44:54 -12 2023 I: pbuilder-time-stamp: 1683236694