I: pbuilder: network access will be disabled during build I: Current time: Tue Jul 13 05:38:36 +14 2021 I: pbuilder-time-stamp: 1626104316 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration 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_3.2.6+dfsg-2.dsc] I: copying [./mrbayes_3.2.6+dfsg.orig.tar.xz] I: copying [./mrbayes_3.2.6+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Jul 21 18:39:37 2017 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./mrbayes_3.2.6+dfsg-2.dsc dpkg-source: info: extracting mrbayes in mrbayes-3.2.6+dfsg dpkg-source: info: unpacking mrbayes_3.2.6+dfsg.orig.tar.xz dpkg-source: info: unpacking mrbayes_3.2.6+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying as-needed.patch dpkg-source: info: applying ldlibs.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/41622/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/41622/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/41622/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.0.3(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=9b6497db4abf4be79521963f39d7e159 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=41622 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.zMH4xeA4t0/pbuilderrc_EPmw --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.zMH4xeA4t0/b2 --logfile b2/build.log mrbayes_3.2.6+dfsg-2.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 4.19.0-17-amd64 #1 SMP Debian 4.19.194-2 (2021-06-21) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash -rwxr-xr-x 1 root root 109408 Mar 1 2019 date -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd -rwxr-xr-x 1 root root 93744 Mar 1 2019 df -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 35424 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln -rwxr-xr-x 1 root root 56760 Jul 27 2018 login -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 10 2019 more -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jul 13 05:38 sh -> bash lrwxrwxrwx 1 root root 4 Jul 7 22:24 sh.distrib -> dash -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty -rwsr-xr-x 1 root root 63568 Jan 10 2019 su -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch -rwxr-xr-x 1 root root 35424 Mar 1 2019 true -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/41622/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 (>= 9), libreadline-dev, mpi-default-dev, libhmsbeagle-dev (<< 2.1-1) | libhmsbeagle-dev (>= 2.1-2), autoconf, automake dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 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 (>= 9); however: Package debhelper 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 (<< 2.1-1) | libhmsbeagle-dev (>= 2.1-2); however: Package libhmsbeagle-dev is not installed. Package libhmsbeagle-dev is not installed. pbuilder-satisfydepends-dummy depends on autoconf; however: Package autoconf is not installed. pbuilder-satisfydepends-dummy depends on automake; however: Package automake 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} automake{a} autopoint{a} autotools-dev{a} beignet-opencl-icd{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libegl-mesa0{a} libegl1{a} libelf1{a} libevent-2.1-6{a} libevent-core-2.1-6{a} libevent-pthreads-2.1-6{a} libexpat1{a} libfabric1{a} libfile-stripnondeterminism-perl{a} libgbm1{a} libgfortran5{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgssapi-krb5-2{a} libhmsbeagle-dev{a} libhmsbeagle1v5{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc5{a} libibverbs-dev{a} libibverbs1{a} libicu63{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libllvm7{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{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} libpmix2{a} libpsm-infinipath1{a} libpsm2-2{a} librdmacm1{a} libreadline-dev{a} libreadline7{a} libsensors-config{a} libsensors5{a} libsigsegv2{a} libssl1.1{a} libtool{a} libuchardet0{a} libwayland-client0{a} libwayland-server0{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxdamage1{a} libxdmcp6{a} libxext6{a} libxfixes3{a} libxml2{a} libxshmfence1{a} libxxf86vm1{a} m4{a} man-db{a} mpi-default-dev{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} po-debconf{a} readline-common{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libglib2.0-data libgpm2 libmail-sendmail-perl lynx shared-mime-info wget xauth xdg-user-dirs 0 packages upgraded, 116 newly installed, 0 to remove and 0 not upgraded. Need to get 68.7 MB of archives. After unpacking 397 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libedit2 amd64 3.1-20181209-1 [94.0 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u1 [65.8 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u1 [122 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u6 [1539 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u1 [369 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u1 [158 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 openssh-client amd64 1:7.9p1-10+deb10u2 [782 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 libdrm-common all 2.4.97-1 [13.8 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libdrm2 amd64 2.4.97-1 [39.7 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 libpciaccess0 amd64 0.14-1 [53.5 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 libdrm-intel1 amd64 2.4.97-1 [69.8 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 libglvnd0 amd64 1.1.0-1 [48.6 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 libwayland-server0 amd64 1.16.0-1 [32.5 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 libgbm1 amd64 18.3.6-2+deb10u1 [67.8 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libglapi-mesa amd64 18.3.6-2+deb10u1 [66.3 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libwayland-client0 amd64 1.16.0-1 [26.4 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 libx11-xcb1 amd64 2:1.6.7-1+deb10u2 [191 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 libxcb-dri2-0 amd64 1.13.1-2 [101 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libxcb-dri3-0 amd64 1.13.1-2 [100 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libxcb-present0 amd64 1.13.1-2 [99.1 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libxcb-sync1 amd64 1.13.1-2 [103 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libxcb-xfixes0 amd64 1.13.1-2 [103 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get: 47 http://deb.debian.org/debian buster/main amd64 libegl-mesa0 amd64 18.3.6-2+deb10u1 [135 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 libegl1 amd64 1.1.0-1 [33.6 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libx11-data all 2:1.6.7-1+deb10u2 [299 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 libx11-6 amd64 2:1.6.7-1+deb10u2 [757 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libxcb-glx0 amd64 1.13.1-2 [116 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libxfixes3 amd64 1:5.0.3-1 [21.9 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libxdamage1 amd64 1:1.1.4-3+b3 [14.9 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 libdrm-amdgpu1 amd64 2.4.97-1 [27.3 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 libdrm-nouveau2 amd64 2.4.97-1 [26.3 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 libdrm-radeon1 amd64 2.4.97-1 [31.1 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 libllvm7 amd64 1:7.0.1-8+deb10u2 [13.1 MB] Get: 61 http://deb.debian.org/debian buster/main amd64 libsensors-config all 1:3.5.0-3 [31.6 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 libsensors5 amd64 1:3.5.0-3 [52.6 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 libgl1-mesa-dri amd64 18.3.6-2+deb10u1 [6685 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 libglx-mesa0 amd64 18.3.6-2+deb10u1 [180 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libglx0 amd64 1.1.0-1 [30.0 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libgl1 amd64 1.1.0-1 [91.1 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 beignet-opencl-icd amd64 1.3.2-6+b10 [14.5 MB] Get: 68 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 libnl-3-200 amd64 3.4.0-1 [63.0 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 libnl-route-3-200 amd64 3.4.0-1 [162 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 libibverbs1 amd64 22.1-1 [51.2 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 ibverbs-providers amd64 22.1-1 [187 kB] Get: 87 http://deb.debian.org/debian buster/main amd64 libevent-2.1-6 amd64 2.1.8-stable-4 [177 kB] Get: 88 http://deb.debian.org/debian buster/main amd64 libevent-core-2.1-6 amd64 2.1.8-stable-4 [129 kB] Get: 89 http://deb.debian.org/debian buster/main amd64 libevent-pthreads-2.1-6 amd64 2.1.8-stable-4 [47.9 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6 [168 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 libnuma1 amd64 2.0.12-1 [26.2 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 libpsm2-2 amd64 11.2.78-1 [177 kB] Get: 93 http://deb.debian.org/debian buster/main amd64 librdmacm1 amd64 22.1-1 [65.3 kB] Get: 94 http://deb.debian.org/debian buster/main amd64 libfabric1 amd64 1.6.2-3 [396 kB] Get: 95 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get: 96 http://deb.debian.org/debian buster/main amd64 ocl-icd-libopencl1 amd64 2.2.12-2 [37.5 kB] Get: 97 http://deb.debian.org/debian buster/main amd64 libhmsbeagle1v5 amd64 3.1.2+dfsg-6 [195 kB] Get: 98 http://deb.debian.org/debian buster/main amd64 libhmsbeagle-dev amd64 3.1.2+dfsg-6 [250 kB] Get: 99 http://deb.debian.org/debian buster/main amd64 libltdl7 amd64 2.4.6-9 [390 kB] Get: 100 http://deb.debian.org/debian buster/main amd64 libhwloc5 amd64 1.11.12-3 [111 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 libnuma-dev amd64 2.0.12-1 [39.2 kB] Get: 102 http://deb.debian.org/debian buster/main amd64 libltdl-dev amd64 2.4.6-9 [162 kB] Get: 103 http://deb.debian.org/debian buster/main amd64 libhwloc-dev amd64 1.11.12-3 [175 kB] Get: 104 http://deb.debian.org/debian buster/main amd64 libhwloc-plugins amd64 1.11.12-3 [17.4 kB] Get: 105 http://deb.debian.org/debian buster/main amd64 libnl-3-dev amd64 3.4.0-1 [102 kB] Get: 106 http://deb.debian.org/debian buster/main amd64 libnl-route-3-dev amd64 3.4.0-1 [177 kB] Get: 107 http://deb.debian.org/debian buster/main amd64 libibverbs-dev amd64 22.1-1 [362 kB] Get: 108 http://deb.debian.org/debian buster/main amd64 libncurses-dev amd64 6.1+20181013-2+deb10u2 [333 kB] Get: 109 http://deb.debian.org/debian buster/main amd64 libpmix2 amd64 3.1.2-3 [498 kB] Get: 110 http://deb.debian.org/debian buster/main amd64 libopenmpi3 amd64 3.1.3-11 [2191 kB] Get: 111 http://deb.debian.org/debian buster/main amd64 openmpi-common all 3.1.3-11 [165 kB] Get: 112 http://deb.debian.org/debian buster/main amd64 openmpi-bin amd64 3.1.3-11 [200 kB] Get: 113 http://deb.debian.org/debian buster/main amd64 libopenmpi-dev amd64 3.1.3-11 [974 kB] Get: 114 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 115 http://deb.debian.org/debian buster/main amd64 libreadline-dev amd64 7.0-5 [133 kB] Get: 116 http://deb.debian.org/debian buster/main amd64 mpi-default-dev amd64 1.13 [5476 B] Fetched 68.7 MB in 1s (60.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. 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Unpacking libxau6:amd64 (1:1.0.8-1+b2) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../038-libxdmcp6_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../039-libxcb1_1.13.1-2_amd64.deb ... Unpacking libxcb1:amd64 (1.13.1-2) ... Selecting previously unselected package libxcb-dri2-0:amd64. Preparing to unpack .../040-libxcb-dri2-0_1.13.1-2_amd64.deb ... Unpacking libxcb-dri2-0:amd64 (1.13.1-2) ... Selecting previously unselected package libxcb-dri3-0:amd64. Preparing to unpack .../041-libxcb-dri3-0_1.13.1-2_amd64.deb ... Unpacking libxcb-dri3-0:amd64 (1.13.1-2) ... Selecting previously unselected package libxcb-present0:amd64. Preparing to unpack .../042-libxcb-present0_1.13.1-2_amd64.deb ... Unpacking libxcb-present0:amd64 (1.13.1-2) ... Selecting previously unselected package libxcb-sync1:amd64. 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Unpacking libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Selecting previously unselected package libdrm-amdgpu1:amd64. Preparing to unpack .../055-libdrm-amdgpu1_2.4.97-1_amd64.deb ... Unpacking libdrm-amdgpu1:amd64 (2.4.97-1) ... Selecting previously unselected package libdrm-nouveau2:amd64. Preparing to unpack .../056-libdrm-nouveau2_2.4.97-1_amd64.deb ... Unpacking libdrm-nouveau2:amd64 (2.4.97-1) ... Selecting previously unselected package libdrm-radeon1:amd64. Preparing to unpack .../057-libdrm-radeon1_2.4.97-1_amd64.deb ... Unpacking libdrm-radeon1:amd64 (2.4.97-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../058-libelf1_0.176-1.1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1.1) ... Selecting previously unselected package libllvm7:amd64. Preparing to unpack .../059-libllvm7_1%3a7.0.1-8+deb10u2_amd64.deb ... Unpacking libllvm7:amd64 (1:7.0.1-8+deb10u2) ... Selecting previously unselected package libsensors-config. 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Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u1) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up libxcb-dri2-0:amd64 (1.13.1-2) ... Setting up libdrm2:amd64 (2.4.97-1) ... Setting up dwz (0.12-3) ... Setting up libnl-3-dev:amd64 (3.4.0-1) ... Setting up groff-base (1.22.4-3+deb10u1) ... Setting up libllvm7:amd64 (1:7.0.1-8+deb10u2) ... Setting up libx11-6:amd64 (2:1.6.7-1+deb10u2) ... Setting up libdrm-amdgpu1:amd64 (2.4.97-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libxcb-dri3-0:amd64 (1.13.1-2) ... Setting up libibverbs1:amd64 (22.1-1) ... Setting up libdrm-nouveau2:amd64 (2.4.97-1) ... 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Setting up po-debconf (1.0.21) ... Setting up libibverbs-dev:amd64 (22.1-1) ... Setting up libfabric1 (1.6.2-3) ... Setting up libglx-mesa0:amd64 (18.3.6-2+deb10u1) ... Setting up libglx0:amd64 (1.1.0-1) ... Setting up libopenmpi3:amd64 (3.1.3-11) ... Setting up libgl1:amd64 (1.1.0-1) ... Setting up openmpi-bin (3.1.3-11) ... 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 beignet-opencl-icd:amd64 (1.3.2-6+b10) ... Setting up libopenmpi-dev:amd64 (3.1.3-11) ... 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 libhmsbeagle1v5 (3.1.2+dfsg-6) ... Setting up mpi-default-dev (1.13) ... Setting up libhmsbeagle-dev (3.1.2+dfsg-6) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/mrbayes-3.2.6+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package mrbayes dpkg-buildpackage: info: source version 3.2.6+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nadiya Sitdykova dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --sourcedirectory=src debian/rules override_dh_auto_clean make[1]: Entering directory '/build/mrbayes-3.2.6+dfsg' ( cd src ; /usr/bin/make -f Makefile.in distclean ) make[2]: Entering directory '/build/mrbayes-3.2.6+dfsg/src' rm -f *.o *~ mb rm -rf Makefile config.log config.status config.h *.cache make[2]: Leaving directory '/build/mrbayes-3.2.6+dfsg/src' rm -f src/configure rm -f mb mb-mpi src/mb make[1]: Leaving directory '/build/mrbayes-3.2.6+dfsg' dh_clean -O--sourcedirectory=src debian/rules build dh build --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src debian/rules override_dh_auto_configure make[1]: Entering directory '/build/mrbayes-3.2.6+dfsg' #Configure for MPI at first ( cd src ; autoconf ) dh_auto_configure -- --with-beagle=/usr --enable-mpi=yes --enable-debug=yes cd src && ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --with-beagle=/usr --enable-mpi=yes --enable-debug=yes configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking configure: NOTICE: Because the variable $CFLAGS is defined in your shell, the default MrBayes flags will be overridden. To ensure optimal performance, please check that your $CFLAGS variable is set correctly. Alternatively, unset the $CFLAGS variable in your shell in order to use the default MrBayes compiler options. 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 we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for exp in -lm... yes checking for a BSD-compatible install... /usr/bin/install -c checking for mpicc... yes checking for SSE support... yes checking for /usr/include/libhmsbeagle/libhmsbeagle/beagle.h... yes checking for /usr/include/libhmsbeagle/libhmsbeagle/platform.h... yes checking for /usr/lib... yes checking for readline in -lreadline... yes checking for rl_completion_matches function... yes checking for 32 or 64 bits cpu... 64 configure: creating ./config.status config.status: creating Makefile config.status: creating config.h configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking make[1]: Leaving directory '/build/mrbayes-3.2.6+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/mrbayes-3.2.6+dfsg' # build mb-mpi (from initial config) LIBS="-Wl,--as-needed" dh_auto_build cd src && make -j1 make[2]: Entering directory '/build/mrbayes-3.2.6+dfsg/src' mpicc -g -O2 -ffile-prefix-map=/build/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bayes.o bayes.c mpicc -g -O2 -ffile-prefix-map=/build/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o command.o command.c mpicc -g -O2 -ffile-prefix-map=/build/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o model.o model.c model.c: In function 'SetModelParams': model.c:18739:48: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] sprintf (tempMult, "g_m{%d}", i+1); ^ In file included from /usr/include/stdio.h:873, from bayes.h:10, from model.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 15 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mpicc -g -O2 -ffile-prefix-map=/build/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcmc.o mcmc.c mcmc.c: In function 'ReusePreviousResults.part.15': mcmc.c:15811:52: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 3 and 210 [-Wformat-overflow=] sprintf (fileName, "%s%s.tree%d.run%d.t", workingDir, localFileName, i+1, n+1); ^~ mcmc.c:15811:36: note: directive argument in the range [1, 2147483647] sprintf (fileName, "%s%s.tree%d.run%d.t", workingDir, localFileName, i+1, n+1); ^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from mcmc.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 14 and 230 bytes into a destination of size 220 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmc.c: In function 'ReopenMBPrintFiles': mcmc.c:15265:50: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 2 and 110 [-Wformat-overflow=] sprintf (fileName, "%s.tree%d.run%d.t", localFileName, i+1, n+1); ^~ mcmc.c:15265:36: note: directive argument in the range [1, 2147483647] sprintf (fileName, "%s.tree%d.run%d.t", localFileName, i+1, n+1); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from mcmc.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 14 and 131 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmc.c: In function 'RunChain': mcmc.c:17251:46: warning: '.ss' directive writing 3 bytes into a region of size between 1 and 220 [-Wformat-overflow=] sprintf (bkupFileName,"%s.ss%d", ckpFileName,chainParams.numStepsSS-stepIndexSS); ^~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from mcmc.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 5 and 234 bytes into a destination of size 220 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mpicc -g -O2 -ffile-prefix-map=/build/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o likelihood.o likelihood.c mpicc -g -O2 -ffile-prefix-map=/build/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o proposal.o proposal.c mpicc -g -O2 -ffile-prefix-map=/build/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sumpt.o sumpt.c sumpt.c: In function 'OpenSumtFiles': sumpt.c:7101:40: warning: '.parts' directive writing 6 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (pFilename, "%s.parts", sumtParams.sumtOutfile); ^~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 126 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7102:40: warning: '.tstat' directive writing 6 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (sFilename, "%s.tstat", sumtParams.sumtOutfile); ^~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 126 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7103:40: warning: '.vstat' directive writing 6 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (vFilename, "%s.vstat", sumtParams.sumtOutfile); ^~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 126 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7104:40: warning: '.con.tre' directive writing 8 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (cFilename, "%s.con.tre", sumtParams.sumtOutfile); ^~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 9 and 128 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7105:40: warning: '.trprobs' directive writing 8 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (tFilename, "%s.trprobs", sumtParams.sumtOutfile); ^~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 9 and 128 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7093:40: warning: '.tree' directive writing 5 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (pFilename, "%s.tree%d.parts", sumtParams.sumtOutfile, i+1); ^~~~~ sumpt.c:7093:37: note: directive argument in the range [1, 2147483647] sprintf (pFilename, "%s.tree%d.parts", sumtParams.sumtOutfile, i+1); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 13 and 141 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7094:40: warning: '.tree' directive writing 5 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (sFilename, "%s.tree%d.tstat", sumtParams.sumtOutfile, i+1); ^~~~~ sumpt.c:7094:37: note: directive argument in the range [1, 2147483647] sprintf (sFilename, "%s.tree%d.tstat", sumtParams.sumtOutfile, i+1); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 13 and 141 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7095:40: warning: '.tree' directive writing 5 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (vFilename, "%s.tree%d.vstat", sumtParams.sumtOutfile, i+1); ^~~~~ sumpt.c:7095:37: note: directive argument in the range [1, 2147483647] sprintf (vFilename, "%s.tree%d.vstat", sumtParams.sumtOutfile, i+1); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 13 and 141 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7096:40: warning: '.tree' directive writing 5 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (cFilename, "%s.tree%d.con.tre", sumtParams.sumtOutfile, i+1); ^~~~~ sumpt.c:7096:37: note: directive argument in the range [1, 2147483647] sprintf (cFilename, "%s.tree%d.con.tre", sumtParams.sumtOutfile, i+1); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 15 and 143 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7097:40: warning: '.tree' directive writing 5 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (tFilename, "%s.tree%d.trprobs", sumtParams.sumtOutfile, i+1); ^~~~~ sumpt.c:7097:37: note: directive argument in the range [1, 2147483647] sprintf (tFilename, "%s.tree%d.trprobs", sumtParams.sumtOutfile, i+1); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 15 and 143 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7165:32: warning: '.parts' directive writing 6 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (pFilename, "%s.parts", sumtParams.sumtOutfile); ^~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 126 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7166:32: warning: '.tstat' directive writing 6 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (sFilename, "%s.tstat", sumtParams.sumtOutfile); ^~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 126 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7167:32: warning: '.vstat' directive writing 6 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (vFilename, "%s.vstat", sumtParams.sumtOutfile); ^~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 126 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7168:32: warning: '.con.tre' directive writing 8 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (cFilename, "%s.con.tre", sumtParams.sumtOutfile); ^~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 9 and 128 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7169:32: warning: '.trprobs' directive writing 8 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (tFilename, "%s.trprobs", sumtParams.sumtOutfile); ^~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 9 and 128 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7157:32: warning: '.tree' directive writing 5 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (pFilename, "%s.tree%d.parts", sumtParams.sumtOutfile, treeNo+1); ^~~~~ sumpt.c:7157:29: note: directive argument in the range [-2147483647, 2147483647] sprintf (pFilename, "%s.tree%d.parts", sumtParams.sumtOutfile, treeNo+1); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 13 and 142 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7158:32: warning: '.tree' directive writing 5 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (sFilename, "%s.tree%d.tstat", sumtParams.sumtOutfile, treeNo+1); ^~~~~ sumpt.c:7158:29: note: directive argument in the range [-2147483647, 2147483647] sprintf (sFilename, "%s.tree%d.tstat", sumtParams.sumtOutfile, treeNo+1); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 13 and 142 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7159:32: warning: '.tree' directive writing 5 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (vFilename, "%s.tree%d.vstat", sumtParams.sumtOutfile, treeNo+1); ^~~~~ sumpt.c:7159:29: note: directive argument in the range [-2147483647, 2147483647] sprintf (vFilename, "%s.tree%d.vstat", sumtParams.sumtOutfile, treeNo+1); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 13 and 142 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7160:32: warning: '.tree' directive writing 5 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (cFilename, "%s.tree%d.con.tre", sumtParams.sumtOutfile, treeNo+1); ^~~~~ sumpt.c:7160:29: note: directive argument in the range [-2147483647, 2147483647] sprintf (cFilename, "%s.tree%d.con.tre", sumtParams.sumtOutfile, treeNo+1); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 15 and 144 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7161:32: warning: '.tree' directive writing 5 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (tFilename, "%s.tree%d.trprobs", sumtParams.sumtOutfile, treeNo+1); ^~~~~ sumpt.c:7161:29: note: directive argument in the range [-2147483647, 2147483647] sprintf (tFilename, "%s.tree%d.trprobs", sumtParams.sumtOutfile, treeNo+1); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 15 and 144 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c: In function 'PrintBrlensToFile': sumpt.c:7257:29: warning: '%s' directive writing up to 119 bytes into a region of size 100 [-Wformat-overflow=] sprintf (filename, "%s.brlens", sumtParams.sumtOutfile); ^~ ~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 8 and 127 bytes into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7255:29: warning: '%s' directive writing up to 119 bytes into a region of size 100 [-Wformat-overflow=] sprintf (filename, "%s.tree%d.brlens", sumtParams.sumtOutfile, treeNo+1); ^~ ~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7255:28: note: directive argument in the range [-2147483647, 2147483647] sprintf (filename, "%s.tree%d.brlens", sumtParams.sumtOutfile, treeNo+1); ^~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 14 and 143 bytes into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c: In function 'DoSumt': sumpt.c:4953:39: warning: '.run' directive writing 4 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1); ^~~~ sumpt.c:4953:36: note: directive argument in the range [-2147483647, 2147483647] sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1); ^~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 8 and 137 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:4951:39: warning: '.t' directive writing 2 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (tempName, "%s.t", fileName); ^~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 3 and 122 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mpicc -g -O2 -ffile-prefix-map=/build/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o utils.o utils.c mpicc -g -O2 -ffile-prefix-map=/build/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mbbeagle.o mbbeagle.c mpicc -g -O2 -ffile-prefix-map=/build/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o best.o best.c mpicc -g -O2 -ffile-prefix-map=/build/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -o mb bayes.o command.o model.o mcmc.o likelihood.o proposal.o sumpt.o utils.o mbbeagle.o best.o -Wl,-z,relro -L/usr/lib -lhmsbeagle -lreadline -lm make[2]: Leaving directory '/build/mrbayes-3.2.6+dfsg/src' mv src/mb ./mb-mpi # Now - build mb ( cd src ; make clean ) make[2]: Entering directory '/build/mrbayes-3.2.6+dfsg/src' rm -f *.o *~ mb make[2]: Leaving directory '/build/mrbayes-3.2.6+dfsg/src' dh_auto_configure -- --with-beagle=/usr --enable-mpi=no --enable-debug=yes cd src && ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --with-beagle=/usr --enable-mpi=no --enable-debug=yes configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking configure: NOTICE: Because the variable $CFLAGS is defined in your shell, the default MrBayes flags will be overridden. To ensure optimal performance, please check that your $CFLAGS variable is set correctly. Alternatively, unset the $CFLAGS variable in your shell in order to use the default MrBayes compiler options. 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 we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for exp in -lm... yes checking for a BSD-compatible install... /usr/bin/install -c checking for SSE support... yes checking for /usr/include/libhmsbeagle/libhmsbeagle/beagle.h... yes checking for /usr/include/libhmsbeagle/libhmsbeagle/platform.h... yes checking for /usr/lib... yes checking for readline in -lreadline... yes checking for rl_completion_matches function... yes checking for 32 or 64 bits cpu... 64 configure: creating ./config.status config.status: creating Makefile config.status: creating config.h configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking LIBS="-Wl,--as-needed" dh_auto_build cd src && make -j1 make[2]: Entering directory '/build/mrbayes-3.2.6+dfsg/src' gcc -g -O2 -ffile-prefix-map=/build/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bayes.o bayes.c gcc -g -O2 -ffile-prefix-map=/build/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o command.o command.c gcc -g -O2 -ffile-prefix-map=/build/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o model.o model.c model.c: In function 'SetModelParams': model.c:18739:48: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] sprintf (tempMult, "g_m{%d}", i+1); ^ In file included from /usr/include/stdio.h:873, from bayes.h:10, from model.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 15 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcmc.o mcmc.c mcmc.c: In function 'ReusePreviousResults.part.12': mcmc.c:15811:52: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 3 and 210 [-Wformat-overflow=] sprintf (fileName, "%s%s.tree%d.run%d.t", workingDir, localFileName, i+1, n+1); ^~ mcmc.c:15811:36: note: directive argument in the range [1, 2147483647] sprintf (fileName, "%s%s.tree%d.run%d.t", workingDir, localFileName, i+1, n+1); ^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from mcmc.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 14 and 230 bytes into a destination of size 220 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmc.c: In function 'ReopenMBPrintFiles': mcmc.c:15265:50: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 2 and 110 [-Wformat-overflow=] sprintf (fileName, "%s.tree%d.run%d.t", localFileName, i+1, n+1); ^~ mcmc.c:15265:36: note: directive argument in the range [1, 2147483647] sprintf (fileName, "%s.tree%d.run%d.t", localFileName, i+1, n+1); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from mcmc.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 14 and 131 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmc.c: In function 'RunChain': mcmc.c:17251:46: warning: '.ss' directive writing 3 bytes into a region of size between 1 and 220 [-Wformat-overflow=] sprintf (bkupFileName,"%s.ss%d", ckpFileName,chainParams.numStepsSS-stepIndexSS); ^~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from mcmc.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 5 and 234 bytes into a destination of size 220 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o likelihood.o likelihood.c gcc -g -O2 -ffile-prefix-map=/build/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o proposal.o proposal.c gcc -g -O2 -ffile-prefix-map=/build/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sumpt.o sumpt.c sumpt.c: In function 'OpenSumtFiles': sumpt.c:7101:40: warning: '.parts' directive writing 6 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (pFilename, "%s.parts", sumtParams.sumtOutfile); ^~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 126 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7102:40: warning: '.tstat' directive writing 6 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (sFilename, "%s.tstat", sumtParams.sumtOutfile); ^~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 126 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7103:40: warning: '.vstat' directive writing 6 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (vFilename, "%s.vstat", sumtParams.sumtOutfile); ^~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 126 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7104:40: warning: '.con.tre' directive writing 8 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (cFilename, "%s.con.tre", sumtParams.sumtOutfile); ^~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 9 and 128 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7105:40: warning: '.trprobs' directive writing 8 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (tFilename, "%s.trprobs", sumtParams.sumtOutfile); ^~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 9 and 128 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7093:40: warning: '.tree' directive writing 5 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (pFilename, "%s.tree%d.parts", sumtParams.sumtOutfile, i+1); ^~~~~ sumpt.c:7093:37: note: directive argument in the range [1, 2147483647] sprintf (pFilename, "%s.tree%d.parts", sumtParams.sumtOutfile, i+1); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 13 and 141 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7094:40: warning: '.tree' directive writing 5 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (sFilename, "%s.tree%d.tstat", sumtParams.sumtOutfile, i+1); ^~~~~ sumpt.c:7094:37: note: directive argument in the range [1, 2147483647] sprintf (sFilename, "%s.tree%d.tstat", sumtParams.sumtOutfile, i+1); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 13 and 141 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7095:40: warning: '.tree' directive writing 5 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (vFilename, "%s.tree%d.vstat", sumtParams.sumtOutfile, i+1); ^~~~~ sumpt.c:7095:37: note: directive argument in the range [1, 2147483647] sprintf (vFilename, "%s.tree%d.vstat", sumtParams.sumtOutfile, i+1); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 13 and 141 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7096:40: warning: '.tree' directive writing 5 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (cFilename, "%s.tree%d.con.tre", sumtParams.sumtOutfile, i+1); ^~~~~ sumpt.c:7096:37: note: directive argument in the range [1, 2147483647] sprintf (cFilename, "%s.tree%d.con.tre", sumtParams.sumtOutfile, i+1); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 15 and 143 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7097:40: warning: '.tree' directive writing 5 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (tFilename, "%s.tree%d.trprobs", sumtParams.sumtOutfile, i+1); ^~~~~ sumpt.c:7097:37: note: directive argument in the range [1, 2147483647] sprintf (tFilename, "%s.tree%d.trprobs", sumtParams.sumtOutfile, i+1); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 15 and 143 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7165:32: warning: '.parts' directive writing 6 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (pFilename, "%s.parts", sumtParams.sumtOutfile); ^~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 126 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7166:32: warning: '.tstat' directive writing 6 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (sFilename, "%s.tstat", sumtParams.sumtOutfile); ^~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 126 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7167:32: warning: '.vstat' directive writing 6 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (vFilename, "%s.vstat", sumtParams.sumtOutfile); ^~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 126 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7168:32: warning: '.con.tre' directive writing 8 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (cFilename, "%s.con.tre", sumtParams.sumtOutfile); ^~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 9 and 128 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7169:32: warning: '.trprobs' directive writing 8 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (tFilename, "%s.trprobs", sumtParams.sumtOutfile); ^~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 9 and 128 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7157:32: warning: '.tree' directive writing 5 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (pFilename, "%s.tree%d.parts", sumtParams.sumtOutfile, treeNo+1); ^~~~~ sumpt.c:7157:29: note: directive argument in the range [-2147483647, 2147483647] sprintf (pFilename, "%s.tree%d.parts", sumtParams.sumtOutfile, treeNo+1); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 13 and 142 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7158:32: warning: '.tree' directive writing 5 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (sFilename, "%s.tree%d.tstat", sumtParams.sumtOutfile, treeNo+1); ^~~~~ sumpt.c:7158:29: note: directive argument in the range [-2147483647, 2147483647] sprintf (sFilename, "%s.tree%d.tstat", sumtParams.sumtOutfile, treeNo+1); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 13 and 142 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7159:32: warning: '.tree' directive writing 5 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (vFilename, "%s.tree%d.vstat", sumtParams.sumtOutfile, treeNo+1); ^~~~~ sumpt.c:7159:29: note: directive argument in the range [-2147483647, 2147483647] sprintf (vFilename, "%s.tree%d.vstat", sumtParams.sumtOutfile, treeNo+1); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 13 and 142 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7160:32: warning: '.tree' directive writing 5 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (cFilename, "%s.tree%d.con.tre", sumtParams.sumtOutfile, treeNo+1); ^~~~~ sumpt.c:7160:29: note: directive argument in the range [-2147483647, 2147483647] sprintf (cFilename, "%s.tree%d.con.tre", sumtParams.sumtOutfile, treeNo+1); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 15 and 144 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7161:32: warning: '.tree' directive writing 5 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (tFilename, "%s.tree%d.trprobs", sumtParams.sumtOutfile, treeNo+1); ^~~~~ sumpt.c:7161:29: note: directive argument in the range [-2147483647, 2147483647] sprintf (tFilename, "%s.tree%d.trprobs", sumtParams.sumtOutfile, treeNo+1); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 15 and 144 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c: In function 'PrintBrlensToFile': sumpt.c:7257:29: warning: '%s' directive writing up to 119 bytes into a region of size 100 [-Wformat-overflow=] sprintf (filename, "%s.brlens", sumtParams.sumtOutfile); ^~ ~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 8 and 127 bytes into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7255:29: warning: '%s' directive writing up to 119 bytes into a region of size 100 [-Wformat-overflow=] sprintf (filename, "%s.tree%d.brlens", sumtParams.sumtOutfile, treeNo+1); ^~ ~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:7255:28: note: directive argument in the range [-2147483647, 2147483647] sprintf (filename, "%s.tree%d.brlens", sumtParams.sumtOutfile, treeNo+1); ^~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 14 and 143 bytes into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c: In function 'DoSumt': sumpt.c:4953:39: warning: '.run' directive writing 4 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1); ^~~~ sumpt.c:4953:36: note: directive argument in the range [-2147483647, 2147483647] sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1); ^~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 8 and 137 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c:4951:39: warning: '.t' directive writing 2 bytes into a region of size between 1 and 120 [-Wformat-overflow=] sprintf (tempName, "%s.t", fileName); ^~ In file included from /usr/include/stdio.h:873, from bayes.h:10, from sumpt.c:37: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 3 and 122 bytes into a destination of size 120 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o utils.o utils.c gcc -g -O2 -ffile-prefix-map=/build/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mbbeagle.o mbbeagle.c gcc -g -O2 -ffile-prefix-map=/build/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o best.o best.c gcc -g -O2 -ffile-prefix-map=/build/mrbayes-3.2.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -o mb bayes.o command.o model.o mcmc.o likelihood.o proposal.o sumpt.o utils.o mbbeagle.o best.o -Wl,-z,relro -L/usr/lib -lhmsbeagle -lreadline -lm make[2]: Leaving directory '/build/mrbayes-3.2.6+dfsg/src' mv src/mb . make[1]: Leaving directory '/build/mrbayes-3.2.6+dfsg' dh_auto_test -O--sourcedirectory=src fakeroot debian/rules binary dh binary --sourcedirectory=src dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src debian/rules override_dh_auto_install make[1]: Entering directory '/build/mrbayes-3.2.6+dfsg' echo "Do not try to install to /usr/local/bin" Do not try to install to /usr/local/bin make[1]: Leaving directory '/build/mrbayes-3.2.6+dfsg' dh_install -O--sourcedirectory=src dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src dh_installman -O--sourcedirectory=src dh_installinit -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src debian/rules override_dh_compress make[1]: Entering directory '/build/mrbayes-3.2.6+dfsg' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/mrbayes-3.2.6+dfsg' dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_strip -O--sourcedirectory=src dh_makeshlibs -O--sourcedirectory=src dh_shlibdeps -O--sourcedirectory=src dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/mrbayes-mpi/usr/lib/mrbayes-mpi/mb-mpi was not linked against libpthread.so.0 (it uses none of the library's symbols) dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'mrbayes' in '../mrbayes_3.2.6+dfsg-2_amd64.deb'. dpkg-deb: building package 'mrbayes-dbgsym' in '../mrbayes-dbgsym_3.2.6+dfsg-2_amd64.deb'. dpkg-deb: building package 'mrbayes-mpi' in '../mrbayes-mpi_3.2.6+dfsg-2_amd64.deb'. dpkg-deb: building package 'mrbayes-mpi-dbgsym' in '../mrbayes-mpi-dbgsym_3.2.6+dfsg-2_amd64.deb'. dpkg-deb: building package 'mrbayes-doc' in '../mrbayes-doc_3.2.6+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../mrbayes_3.2.6+dfsg-2_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) I: copying local configuration I: user script /srv/workspace/pbuilder/41622/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/41622/tmp/hooks/B01_cleanup finished 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/41622 and its subdirectories I: Current time: Tue Jul 13 05:41:49 +14 2021 I: pbuilder-time-stamp: 1626104509