I: pbuilder: network access will be disabled during build
I: Current time: Wed May 31 17:23:23 -12 2023
I: pbuilder-time-stamp: 1685597003
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/9251/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='armhf'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 '
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='armhf'
IFS='
'
INVOCATION_ID='307c780c21f247a2b7991bfed70f0975'
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='9251'
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.917SVKqy/pbuilderrc_6Vwf --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.917SVKqy/b1 --logfile b1/build.log mrbayes_3.2.7a-6.dsc'
SUDO_GID='113'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://10.0.0.15:3142/'
I: uname -a
Linux cbxi4pro0 5.10.0-23-armmp #1 SMP Debian 5.10.179-1 (2023-05-12) armv7l GNU/Linux
I: ls -l /bin
total 5072
-rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash
-rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2
-rwxr-xr-x 3 root root 67144 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 67144 Sep 18 2022 bzip2
-rwxr-xr-x 1 root root 67112 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 67632 Sep 20 2022 cat
-rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 67684 Sep 20 2022 chown
-rwxr-xr-x 1 root root 133532 Sep 20 2022 cp
-rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash
-rwxr-xr-x 1 root root 133220 Sep 20 2022 date
-rwxr-xr-x 1 root root 67732 Sep 20 2022 dd
-rwxr-xr-x 1 root root 68104 Sep 20 2022 df
-rwxr-xr-x 1 root root 133632 Sep 20 2022 dir
-rwxr-xr-x 1 root root 59128 Mar 22 21:02 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 67560 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep
-rwxr-xr-x 1 root root 67548 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep
-rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt
-rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount
-rwxr-xr-x 1 root root 128608 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 64220 Apr 9 2022 gzip
-rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname
-rwxr-xr-x 1 root root 67720 Sep 20 2022 ln
-rwxr-xr-x 1 root root 35132 Mar 22 21:51 login
-rwxr-xr-x 1 root root 133632 Sep 20 2022 ls
-rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk
-rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 38504 Mar 22 21:02 more
-rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount
-rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint
-rwxr-xr-x 1 root root 133532 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 67608 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash
-rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 67672 Sep 20 2022 rm
-rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts
-rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed
lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash
-rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 67644 Sep 20 2022 stty
-rwsr-xr-x 1 root root 50800 Mar 22 21:02 su
-rwxr-xr-x 1 root root 67584 Sep 20 2022 sync
-rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar
-rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile
-rwxr-xr-x 1 root root 133224 Sep 20 2022 touch
-rwxr-xr-x 1 root root 67548 Sep 20 2022 true
-rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server
-rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount
-rwxr-xr-x 1 root root 67572 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
-rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 42608 Mar 22 21:02 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/9251/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: armhf
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
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 ... 19324 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} libarchive-zip-perl{a} libbsd0{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} librdmacm1{a} libreadline-dev{a} libreadline8{a} libsensors-config{a} libsensors5{a} libsub-override-perl{a} libtool{a} libuchardet0{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, 108 newly installed, 0 to remove and 0 not upgraded.
Need to get 101 MB of archives. After unpacking 487 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main armhf autoconf-archive all 20220903-3 [775 kB]
Get: 2 http://deb.debian.org/debian bookworm/main armhf readline-common all 8.2-1.3 [69.0 kB]
Get: 3 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 4 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB]
Get: 5 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB]
Get: 6 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB]
Get: 7 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB]
Get: 8 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get: 9 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB]
Get: 10 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB]
Get: 11 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB]
Get: 12 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB]
Get: 13 http://deb.debian.org/debian bookworm/main armhf libbsd0 armhf 0.11.7-2 [113 kB]
Get: 14 http://deb.debian.org/debian bookworm/main armhf libedit2 armhf 3.1-20221030-2 [77.0 kB]
Get: 15 http://deb.debian.org/debian bookworm/main armhf libcbor0.8 armhf 0.8.0-2+b1 [23.1 kB]
Get: 16 http://deb.debian.org/debian bookworm/main armhf libfido2-1 armhf 1.12.0-2+b1 [69.3 kB]
Get: 17 http://deb.debian.org/debian bookworm/main armhf openssh-client armhf 1:9.2p1-2 [893 kB]
Get: 18 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB]
Get: 19 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB]
Get: 20 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get: 21 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get: 22 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB]
Get: 23 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 24 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB]
Get: 25 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 26 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 27 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get: 28 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 29 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 30 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB]
Get: 31 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB]
Get: 32 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB]
Get: 33 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB]
Get: 34 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB]
Get: 35 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 36 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 37 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB]
Get: 38 http://deb.debian.org/debian bookworm/main armhf libgfortran5 armhf 12.2.0-14 [246 kB]
Get: 39 http://deb.debian.org/debian bookworm/main armhf libgfortran-12-dev armhf 12.2.0-14 [298 kB]
Get: 40 http://deb.debian.org/debian bookworm/main armhf gfortran-12 armhf 12.2.0-14 [7633 kB]
Get: 41 http://deb.debian.org/debian bookworm/main armhf libnl-3-200 armhf 3.7.0-0.2+b1 [55.8 kB]
Get: 42 http://deb.debian.org/debian bookworm/main armhf libnl-route-3-200 armhf 3.7.0-0.2+b1 [156 kB]
Get: 43 http://deb.debian.org/debian bookworm/main armhf libibverbs1 armhf 44.0-2 [53.6 kB]
Get: 44 http://deb.debian.org/debian bookworm/main armhf ibverbs-providers armhf 44.0-2 [28.4 kB]
Get: 45 http://deb.debian.org/debian bookworm/main armhf libz3-4 armhf 4.8.12-3.1 [6061 kB]
Get: 46 http://deb.debian.org/debian bookworm/main armhf libllvm15 armhf 1:15.0.6-4+b1 [20.5 MB]
Get: 47 http://deb.debian.org/debian bookworm/main armhf libclang-common-15-dev armhf 1:15.0.6-4+b1 [3481 kB]
Get: 48 http://deb.debian.org/debian bookworm/main armhf libclang-cpp15 armhf 1:15.0.6-4+b1 [9846 kB]
Get: 49 http://deb.debian.org/debian bookworm/main armhf libclc-15-dev all 1:15.0.6-4 [53.6 kB]
Get: 50 http://deb.debian.org/debian bookworm/main armhf libclc-15 all 1:15.0.6-4 [10.1 MB]
Get: 51 http://deb.debian.org/debian bookworm/main armhf libdrm-common all 2.4.114-1 [7112 B]
Get: 52 http://deb.debian.org/debian bookworm/main armhf libdrm2 armhf 2.4.114-1+b1 [33.0 kB]
Get: 53 http://deb.debian.org/debian bookworm/main armhf libdrm-amdgpu1 armhf 2.4.114-1+b1 [19.3 kB]
Get: 54 http://deb.debian.org/debian bookworm/main armhf libdrm-nouveau2 armhf 2.4.114-1+b1 [16.7 kB]
Get: 55 http://deb.debian.org/debian bookworm/main armhf libdrm-radeon1 armhf 2.4.114-1+b1 [19.3 kB]
Get: 56 http://deb.debian.org/debian bookworm/main armhf libevent-2.1-7 armhf 2.1.12-stable-8 [161 kB]
Get: 57 http://deb.debian.org/debian bookworm/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-8 [120 kB]
Get: 58 http://deb.debian.org/debian bookworm/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-8 [97.5 kB]
Get: 59 http://deb.debian.org/debian bookworm/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-8 [53.2 kB]
Get: 60 http://deb.debian.org/debian bookworm/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-8 [58.3 kB]
Get: 61 http://deb.debian.org/debian bookworm/main armhf libevent-dev armhf 2.1.12-stable-8 [290 kB]
Get: 62 http://deb.debian.org/debian bookworm/main armhf libexpat1 armhf 2.5.0-1 [79.9 kB]
Get: 63 http://deb.debian.org/debian bookworm/main armhf librdmacm1 armhf 44.0-2 [60.6 kB]
Get: 64 http://deb.debian.org/debian bookworm/main armhf libfabric1 armhf 1.17.0-3 [385 kB]
Get: 65 http://deb.debian.org/debian bookworm/main armhf ocl-icd-libopencl1 armhf 2.3.1-1 [40.1 kB]
Get: 66 http://deb.debian.org/debian bookworm/main armhf libllvmspirvlib15 armhf 15.0.0-2 [619 kB]
Get: 67 http://deb.debian.org/debian bookworm/main armhf libsensors-config all 1:3.6.0-7.1 [14.3 kB]
Get: 68 http://deb.debian.org/debian bookworm/main armhf libsensors5 armhf 1:3.6.0-7.1 [31.6 kB]
Get: 69 http://deb.debian.org/debian bookworm/main armhf mesa-opencl-icd armhf 22.3.6-1+deb12u1 [10.5 MB]
Get: 70 http://deb.debian.org/debian bookworm/main armhf libhmsbeagle1v5 armhf 3.1.2+dfsg-13 [86.8 kB]
Get: 71 http://deb.debian.org/debian bookworm/main armhf libhmsbeagle-dev armhf 3.1.2+dfsg-13 [227 kB]
Get: 72 http://deb.debian.org/debian bookworm/main armhf libhwloc15 armhf 2.9.0-1 [127 kB]
Get: 73 http://deb.debian.org/debian bookworm/main armhf libnuma1 armhf 2.0.16-1 [17.8 kB]
Get: 74 http://deb.debian.org/debian bookworm/main armhf libnuma-dev armhf 2.0.16-1 [33.0 kB]
Get: 75 http://deb.debian.org/debian bookworm/main armhf libltdl7 armhf 2.4.7-5 [390 kB]
Get: 76 http://deb.debian.org/debian bookworm/main armhf libltdl-dev armhf 2.4.7-5 [162 kB]
Get: 77 http://deb.debian.org/debian bookworm/main armhf libhwloc-dev armhf 2.9.0-1 [214 kB]
Get: 78 http://deb.debian.org/debian bookworm/main armhf libpciaccess0 armhf 0.17-2 [48.7 kB]
Get: 79 http://deb.debian.org/debian bookworm/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB]
Get: 80 http://deb.debian.org/debian bookworm/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB]
Get: 81 http://deb.debian.org/debian bookworm/main armhf libxcb1 armhf 1.15-1 [140 kB]
Get: 82 http://deb.debian.org/debian bookworm/main armhf libx11-data all 2:1.8.4-2 [292 kB]
Get: 83 http://deb.debian.org/debian bookworm/main armhf libx11-6 armhf 2:1.8.4-2 [695 kB]
Get: 84 http://deb.debian.org/debian bookworm/main armhf libxext6 armhf 2:1.3.4-1+b1 [47.8 kB]
Get: 85 http://deb.debian.org/debian bookworm/main armhf libxnvctrl0 armhf 525.85.05-1 [12.2 kB]
Get: 86 http://deb.debian.org/debian bookworm/main armhf libhwloc-plugins armhf 2.9.0-1 [15.9 kB]
Get: 87 http://deb.debian.org/debian bookworm/main armhf libnl-3-dev armhf 3.7.0-0.2+b1 [98.4 kB]
Get: 88 http://deb.debian.org/debian bookworm/main armhf libnl-route-3-dev armhf 3.7.0-0.2+b1 [183 kB]
Get: 89 http://deb.debian.org/debian bookworm/main armhf libibverbs-dev armhf 44.0-2 [195 kB]
Get: 90 http://deb.debian.org/debian bookworm/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 91 http://deb.debian.org/debian bookworm/main armhf libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get: 92 http://deb.debian.org/debian bookworm/main armhf libmunge2 armhf 0.5.15-2 [15.7 kB]
Get: 93 http://deb.debian.org/debian bookworm/main armhf libncurses6 armhf 6.4-4 [81.1 kB]
Get: 94 http://deb.debian.org/debian bookworm/main armhf libncurses-dev armhf 6.4-4 [311 kB]
Get: 95 http://deb.debian.org/debian bookworm/main armhf libpmix2 armhf 4.2.2-1+b1 [553 kB]
Get: 96 http://deb.debian.org/debian bookworm/main armhf libopenmpi3 armhf 4.1.4-3+b1 [1849 kB]
Get: 97 http://deb.debian.org/debian bookworm/main armhf openmpi-common all 4.1.4-3 [167 kB]
Get: 98 http://deb.debian.org/debian bookworm/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [902 kB]
Get: 99 http://deb.debian.org/debian bookworm/main armhf libpmix-dev armhf 4.2.2-1+b1 [864 kB]
Get: 100 http://deb.debian.org/debian bookworm/main armhf openmpi-bin armhf 4.1.4-3+b1 [194 kB]
Get: 101 http://deb.debian.org/debian bookworm/main armhf libopenmpi-dev armhf 4.1.4-3+b1 [920 kB]
Get: 102 http://deb.debian.org/debian bookworm/main armhf libpkgconf3 armhf 1.8.1-1 [31.3 kB]
Get: 103 http://deb.debian.org/debian bookworm/main armhf libreadline8 armhf 8.2-1.3 [144 kB]
Get: 104 http://deb.debian.org/debian bookworm/main armhf libreadline-dev armhf 8.2-1.3 [136 kB]
Get: 105 http://deb.debian.org/debian bookworm/main armhf mpi-default-dev armhf 1.14 [5548 B]
Get: 106 http://deb.debian.org/debian bookworm/main armhf pkgconf-bin armhf 1.8.1-1 [28.5 kB]
Get: 107 http://deb.debian.org/debian bookworm/main armhf pkgconf armhf 1.8.1-1 [25.9 kB]
Get: 108 http://deb.debian.org/debian bookworm/main armhf pkg-config armhf 1.8.1-1 [13.7 kB]
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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
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Reading package lists...
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-> 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 <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
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=arm-linux-gnueabihf --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/arm-linux-gnueabihf --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... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
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 -j3
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
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;
| ^~~~~~~
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
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/arm-linux-gnueabihf/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);
| ^
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
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/arm-linux-gnueabihf/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 ());
| ~~~~~~~~~~~~~~~~~
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
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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 ());
| ~~~~~~~~~~~~~~~~~
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
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/arm-linux-gnueabihf/bits/string_fortified.h:95:10: warning: '__builtin_strncpy' accessing 0 or more bytes at offsets [-1073741824, 1073741823] and 0 may overlap up to 1073741824 bytes at offset [0, 1073741823] [-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/arm-linux-gnueabihf/bits/string_fortified.h:95:10: warning: '__builtin_strncpy' accessing 0 or more bytes at offsets [-1073741824, 1073741823] and 0 may overlap up to 1073741824 bytes at offset [0, 1073741823] [-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/arm-linux-gnueabihf/bits/string_fortified.h:95:10: warning: '__builtin_strncpy' accessing 0 or more bytes at offsets [-1073741824, 1073741823] and 0 may overlap up to 1073741824 bytes at offset [0, 1073741823] [-Wrestrict]
95 | return __builtin___strncpy_chk (__dest, __src, __len,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
96 | __glibc_objsize (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
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/arm-linux-gnueabihf/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=arm-linux-gnueabihf --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/arm-linux-gnueabihf --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... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
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 -j3
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
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;
| ^~~~~~~
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
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/arm-linux-gnueabihf/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);
| ^
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
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/arm-linux-gnueabihf/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 ());
| ~~~~~~~~~~~~~~~~~
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
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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 ());
| ~~~~~~~~~~~~~~~~~
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
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/arm-linux-gnueabihf/bits/string_fortified.h:95:10: warning: '__builtin_strncpy' accessing 0 or more bytes at offsets [-1073741824, 1073741823] and 0 may overlap up to 1073741824 bytes at offset [0, 1073741823] [-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/arm-linux-gnueabihf/bits/string_fortified.h:95:10: warning: '__builtin_strncpy' accessing 0 or more bytes at offsets [-1073741824, 1073741823] and 0 may overlap up to 1073741824 bytes at offset [0, 1073741823] [-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/arm-linux-gnueabihf/bits/string_fortified.h:95:10: warning: '__builtin_strncpy' accessing 0 or more bytes at offsets [-1073741824, 1073741823] and 0 may overlap up to 1073741824 bytes at offset [0, 1073741823] [-Wrestrict]
95 | return __builtin___strncpy_chk (__dest, __src, __len,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
96 | __glibc_objsize (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
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/arm-linux-gnueabihf/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 -j3 check "TESTSUITEFLAGS=-j3 --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 -j3 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'
make[3]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/build/mrbayes-3.2.7a/debian/tmp/usr/bin'
/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' in '../mrbayes_3.2.7a-6_armhf.deb'.
dpkg-deb: building package 'mrbayes-mpi' in '../mrbayes-mpi_3.2.7a-6_armhf.deb'.
dpkg-deb: building package 'mrbayes-doc' in '../mrbayes-doc_3.2.7a-6_all.deb'.
dpkg-deb: building package 'mrbayes-mpi-dbgsym' in '../mrbayes-mpi-dbgsym_3.2.7a-6_armhf.deb'.
dpkg-deb: building package 'mrbayes-dbgsym' in '../mrbayes-dbgsym_3.2.7a-6_armhf.deb'.
dpkg-genbuildinfo --build=binary -O../mrbayes_3.2.7a-6_armhf.buildinfo
dpkg-genchanges --build=binary -O../mrbayes_3.2.7a-6_armhf.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/9251 and its subdirectories
I: Current time: Wed May 31 18:35:51 -12 2023
I: pbuilder-time-stamp: 1685601351