mrbayes →
3.2.7a-7+b1 →
armhf → 2024-01-20 12:00:53
sbuild (Debian sbuild) 0.85.0 (04 January 2023) on test2023
+==============================================================================+
| mrbayes 3.2.7a-7+b1 (armhf) Sat, 20 Jan 2024 11:56:52 +0000 |
+==============================================================================+
Package: mrbayes
Version: 3.2.7a-7+b1
Source Version: 3.2.7a-7
Distribution: trixie-staging
Machine Architecture: arm64
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/trixie-staging-armhf-sbuild-9eed0b91-6fdb-412f-9e42-f13ce240b15c' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/mrbayes-Yllye9/resolver-PSeyYL' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.4 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [15.0 MB]
Fetched 29.4 MB in 5s (5466 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/trixie-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'mrbayes' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/mrbayes.git
Please use:
git clone https://salsa.debian.org/med-team/mrbayes.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 9829 kB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main mrbayes 3.2.7a-7 (dsc) [2184 B]
Get:2 http://172.17.4.1/private trixie-staging/main mrbayes 3.2.7a-7 (tar) [9819 kB]
Get:3 http://172.17.4.1/private trixie-staging/main mrbayes 3.2.7a-7 (diff) [7380 B]
Fetched 9829 kB in 1s (8249 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/mrbayes-Yllye9/mrbayes-3.2.7a' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/mrbayes-Yllye9' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libreadline-dev, mpi-default-dev, libhmsbeagle-dev, autoconf-archive, pkg-config, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), libreadline-dev, mpi-default-dev, libhmsbeagle-dev, autoconf-archive, pkg-config, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [699 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [731 B]
Fetched 2039 B in 0s (0 B/s)
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf autoconf-archive automake autopoint autotools-dev bsdextrautils
bsdutils cpp-13 debhelper dh-autoreconf dh-strip-nondeterminism dwz file
g++-13 gcc-13 gcc-13-base gettext gettext-base gfortran-13 groff-base
ibverbs-providers intltool-debian libarchive-zip-perl libasan8 libatomic1
libblkid1 libbsd0 libcbor0.10 libcc1-0 libclang-common-15-dev libclang-cpp15
libclc-15 libclc-15-dev libdebhelper-perl libdrm-amdgpu1 libdrm-common
libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libevent-2.1-7
libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7
libevent-pthreads-2.1-7 libexpat1 libfabric1 libfido2-1
libfile-stripnondeterminism-perl libgcc-13-dev libgcc-s1 libgfortran-13-dev
libgfortran5 libgomp1 libhmsbeagle-dev libhmsbeagle1v5 libhwloc-dev
libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu72 libjs-jquery
libjs-jquery-ui libllvm15 libllvmspirvlib15 libltdl-dev libltdl7
libmagic-mgc libmagic1 libmount1 libmunge2 libncurses-dev libncurses6
libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev
libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpkgconf3
libpmix-dev libpmix2 librdmacm1 libreadline-dev libsensors-config
libsensors5 libsmartcols1 libstdc++-13-dev libstdc++6 libsub-override-perl
libtool libubsan1 libuchardet0 libuuid1 libx11-6 libx11-data libxau6 libxcb1
libxdmcp6 libxext6 libxml2 libxnvctrl0 libz3-4 m4 man-db mesa-opencl-icd
mount mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common
openssh-client pkg-config pkgconf pkgconf-bin po-debconf sensible-utils
util-linux zlib1g zlib1g-dev
Suggested packages:
gnu-standards autoconf-doc gcc-13-locales cpp-13-doc dh-make gcc-13-doc
gettext-doc libasprintf-dev libgettextpo-dev gfortran-13-doc libcoarrays-dev
groff libjs-jquery-ui-docs libtool-doc cryptsetup-bin ncurses-doc
openmpi-doc pciutils readline-doc lm-sensors libstdc++-13-doc gcj-jdk m4-doc
apparmor less www-browser nfs-common gfortran | fortran-compiler keychain
libpam-ssh monkeysphere ssh-askpass libmail-box-perl dosfstools kbd
util-linux-extra util-linux-locales
Recommended packages:
curl | wget | lynx libclang-rt-15-dev libarchive-cpio-perl javascript-common
libgpm2 libcoarrays-openmpi-dev uuid-runtime xauth libmail-sendmail-perl
The following NEW packages will be installed:
autoconf autoconf-archive automake autopoint autotools-dev bsdextrautils
debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext
gettext-base gfortran-13 groff-base ibverbs-providers intltool-debian
libarchive-zip-perl libbsd0 libcbor0.10 libclang-common-15-dev
libclang-cpp15 libclc-15 libclc-15-dev libdebhelper-perl libdrm-amdgpu1
libdrm-common libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1
libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7
libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libexpat1 libfabric1
libfido2-1 libfile-stripnondeterminism-perl libgfortran-13-dev libgfortran5
libhmsbeagle-dev libhmsbeagle1v5 libhwloc-dev libhwloc-plugins libhwloc15
libibverbs-dev libibverbs1 libicu72 libjs-jquery libjs-jquery-ui libllvm15
libllvmspirvlib15 libltdl-dev libltdl7 libmagic-mgc libmagic1 libmunge2
libncurses-dev libncurses6 libnl-3-200 libnl-3-dev libnl-route-3-200
libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3
libpciaccess0 libpipeline1 libpkgconf3 libpmix-dev libpmix2 librdmacm1
libreadline-dev libsensors-config libsensors5 libsub-override-perl libtool
libuchardet0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2
libxnvctrl0 libz3-4 m4 man-db mesa-opencl-icd mpi-default-dev
ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config
pkgconf pkgconf-bin po-debconf sbuild-build-depends-main-dummy
sensible-utils zlib1g-dev
The following packages will be upgraded:
bsdutils cpp-13 g++-13 gcc-13 gcc-13-base libasan8 libatomic1 libblkid1
libcc1-0 libgcc-13-dev libgcc-s1 libgomp1 libmount1 libsmartcols1
libstdc++-13-dev libstdc++6 libubsan1 libuuid1 mount util-linux zlib1g
21 upgraded, 107 newly installed, 0 to remove and 32 not upgraded.
Need to get 141 MB of archives.
After this operation, 504 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [924 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf bsdutils armhf 1:2.39.3-6 [87.1 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf util-linux armhf 2.39.3-6 [1113 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf mount armhf 2.39.3-6 [134 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf autoconf-archive all 20220903-3 [775 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf zlib1g armhf 1:1.3.dfsg-3 [74.3 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf libcc1-0 armhf 13.2.0-9+rpi1 [35.4 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf libgomp1 armhf 13.2.0-9+rpi1 [104 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf gcc-13-base armhf 13.2.0-9+rpi1 [41.7 kB]
Get:10 http://172.17.4.1/private trixie-staging/main armhf libatomic1 armhf 13.2.0-9+rpi1 [8448 B]
Get:11 http://172.17.4.1/private trixie-staging/main armhf libasan8 armhf 13.2.0-9+rpi1 [2391 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf libubsan1 armhf 13.2.0-9+rpi1 [964 kB]
Get:13 http://172.17.4.1/private trixie-staging/main armhf libstdc++6 armhf 13.2.0-9+rpi1 [578 kB]
Get:14 http://172.17.4.1/private trixie-staging/main armhf g++-13 armhf 13.2.0-9+rpi1 [8138 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf libstdc++-13-dev armhf 13.2.0-9+rpi1 [2209 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf libgcc-13-dev armhf 13.2.0-9+rpi1 [763 kB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf gcc-13 armhf 13.2.0-9+rpi1 [14.7 MB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf cpp-13 armhf 13.2.0-9+rpi1 [7372 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf libgcc-s1 armhf 13.2.0-9+rpi1 [36.2 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf libblkid1 armhf 2.39.3-6 [145 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf libmount1 armhf 2.39.3-6 [168 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf libsmartcols1 armhf 2.39.3-6 [102 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf libuuid1 armhf 2.39.3-6 [28.3 kB]
Get:24 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.8-1 [65.5 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.23.0-3 [1033 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.3-6 [81.4 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.12.0-3 [1358 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf sensible-utils all 0.0.20 [19.3 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf libmagic1 armhf 1:5.45-2 [96.1 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-14 [157 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf libbsd0 armhf 0.11.8-1 [120 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf libedit2 armhf 3.1-20230828-1 [76.0 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf libcbor0.10 armhf 0.10.2-1.1 [23.8 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf libfido2-1 armhf 1.14.0-1 [67.7 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf openssh-client armhf 1:9.6p1-2 [801 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-4 [256 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-14 [496 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.9 [82.3 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:47 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:48 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.10-1 [10.6 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:50 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:51 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:52 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:53 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-4 [9009 kB]
Get:54 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:55 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-14 [1203 kB]
Get:56 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:57 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:58 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.9 [956 kB]
Get:59 http://172.17.4.1/private trixie-staging/main armhf libgfortran5 armhf 13.2.0-9+rpi1 [247 kB]
Get:60 http://172.17.4.1/private trixie-staging/main armhf libgfortran-13-dev armhf 13.2.0-9+rpi1 [293 kB]
Get:61 http://172.17.4.1/private trixie-staging/main armhf gfortran-13 armhf 13.2.0-9+rpi1 [7837 kB]
Get:62 http://172.17.4.1/private trixie-staging/main armhf libnl-3-200 armhf 3.7.0-0.2 [55.0 kB]
Get:63 http://172.17.4.1/private trixie-staging/main armhf libnl-route-3-200 armhf 3.7.0-0.2 [152 kB]
Get:64 http://172.17.4.1/private trixie-staging/main armhf libibverbs1 armhf 48.0-1 [52.6 kB]
Get:65 http://172.17.4.1/private trixie-staging/main armhf ibverbs-providers armhf 48.0-1 [28.0 kB]
Get:66 http://172.17.4.1/private trixie-staging/main armhf libz3-4 armhf 4.8.12-3.1 [5797 kB]
Get:67 http://172.17.4.1/private trixie-staging/main armhf libllvm15 armhf 1:15.0.7-10+rpi1 [20.7 MB]
Get:68 http://172.17.4.1/private trixie-staging/main armhf libclang-common-15-dev all 1:15.0.7-10+rpi1 [647 kB]
Get:69 http://172.17.4.1/private trixie-staging/main armhf libclang-cpp15 armhf 1:15.0.7-10+rpi1 [9906 kB]
Get:70 http://172.17.4.1/private trixie-staging/main armhf libclc-15-dev all 1:15.0.7-10+rpi1 [57.3 kB]
Get:71 http://172.17.4.1/private trixie-staging/main armhf libclc-15 all 1:15.0.7-10+rpi1 [8513 kB]
Get:72 http://172.17.4.1/private trixie-staging/main armhf libdrm-common all 2.4.117-1+rpi1 [7468 B]
Get:73 http://172.17.4.1/private trixie-staging/main armhf libdrm2 armhf 2.4.117-1+rpi1 [33.3 kB]
Get:74 http://172.17.4.1/private trixie-staging/main armhf libdrm-amdgpu1 armhf 2.4.117-1+rpi1 [19.8 kB]
Get:75 http://172.17.4.1/private trixie-staging/main armhf libdrm-nouveau2 armhf 2.4.117-1+rpi1 [17.1 kB]
Get:76 http://172.17.4.1/private trixie-staging/main armhf libdrm-radeon1 armhf 2.4.117-1+rpi1 [20.8 kB]
Get:77 http://172.17.4.1/private trixie-staging/main armhf libevent-2.1-7 armhf 2.1.12-stable-8 [160 kB]
Get:78 http://172.17.4.1/private trixie-staging/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-8 [119 kB]
Get:79 http://172.17.4.1/private trixie-staging/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-8 [97.3 kB]
Get:80 http://172.17.4.1/private trixie-staging/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-8 [53.2 kB]
Get:81 http://172.17.4.1/private trixie-staging/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-8 [58.3 kB]
Get:82 http://172.17.4.1/private trixie-staging/main armhf libevent-dev armhf 2.1.12-stable-8 [274 kB]
Get:83 http://172.17.4.1/private trixie-staging/main armhf libexpat1 armhf 2.5.0-2 [76.8 kB]
Get:84 http://172.17.4.1/private trixie-staging/main armhf librdmacm1 armhf 48.0-1 [59.2 kB]
Get:85 http://172.17.4.1/private trixie-staging/main armhf libfabric1 armhf 1.17.0-3 [376 kB]
Get:86 http://172.17.4.1/private trixie-staging/main armhf ocl-icd-libopencl1 armhf 2.3.2-1 [36.8 kB]
Get:87 http://172.17.4.1/private trixie-staging/main armhf libllvmspirvlib15 armhf 15.0.0-2+rpi1 [598 kB]
Get:88 http://172.17.4.1/private trixie-staging/main armhf libsensors-config all 1:3.6.0-8 [14.4 kB]
Get:89 http://172.17.4.1/private trixie-staging/main armhf libsensors5 armhf 1:3.6.0-8 [31.7 kB]
Get:90 http://172.17.4.1/private trixie-staging/main armhf mesa-opencl-icd armhf 23.1.7-1+rpi1 [12.4 MB]
Get:91 http://172.17.4.1/private trixie-staging/main armhf libhmsbeagle1v5 armhf 3.1.2+dfsg-13 [86.7 kB]
Get:92 http://172.17.4.1/private trixie-staging/main armhf libhmsbeagle-dev armhf 3.1.2+dfsg-13 [225 kB]
Get:93 http://172.17.4.1/private trixie-staging/main armhf libhwloc15 armhf 2.10.0-1 [131 kB]
Get:94 http://172.17.4.1/private trixie-staging/main armhf libnuma1 armhf 2.0.16-1 [18.4 kB]
Get:95 http://172.17.4.1/private trixie-staging/main armhf libnuma-dev armhf 2.0.16-1 [31.5 kB]
Get:96 http://172.17.4.1/private trixie-staging/main armhf libltdl7 armhf 2.4.7-7 [390 kB]
Get:97 http://172.17.4.1/private trixie-staging/main armhf libltdl-dev armhf 2.4.7-7 [161 kB]
Get:98 http://172.17.4.1/private trixie-staging/main armhf libhwloc-dev armhf 2.10.0-1 [204 kB]
Get:99 http://172.17.4.1/private trixie-staging/main armhf libpciaccess0 armhf 0.17-3 [49.1 kB]
Get:100 http://172.17.4.1/private trixie-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:101 http://172.17.4.1/private trixie-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:102 http://172.17.4.1/private trixie-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
Get:103 http://172.17.4.1/private trixie-staging/main armhf libx11-data all 2:1.8.7-1 [328 kB]
Get:104 http://172.17.4.1/private trixie-staging/main armhf libx11-6 armhf 2:1.8.7-1 [729 kB]
Get:105 http://172.17.4.1/private trixie-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:106 http://172.17.4.1/private trixie-staging/main armhf libxnvctrl0 armhf 525.125.06-1 [12.3 kB]
Get:107 http://172.17.4.1/private trixie-staging/main armhf libhwloc-plugins armhf 2.10.0-1 [16.1 kB]
Get:108 http://172.17.4.1/private trixie-staging/main armhf libnl-3-dev armhf 3.7.0-0.2 [93.4 kB]
Get:109 http://172.17.4.1/private trixie-staging/main armhf libnl-route-3-dev armhf 3.7.0-0.2 [163 kB]
Get:110 http://172.17.4.1/private trixie-staging/main armhf libibverbs-dev armhf 48.0-1 [192 kB]
Get:111 http://172.17.4.1/private trixie-staging/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:112 http://172.17.4.1/private trixie-staging/main armhf libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get:113 http://172.17.4.1/private trixie-staging/main armhf libmunge2 armhf 0.5.15-3 [15.8 kB]
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Get:115 http://172.17.4.1/private trixie-staging/main armhf libncurses-dev armhf 6.4+20231209-1 [290 kB]
Get:116 http://172.17.4.1/private trixie-staging/main armhf libpmix2 armhf 5.0.1-4 [528 kB]
Get:117 http://172.17.4.1/private trixie-staging/main armhf libopenmpi3 armhf 4.1.6-5+rpi1 [1792 kB]
Get:118 http://172.17.4.1/private trixie-staging/main armhf openmpi-common all 4.1.6-5+rpi1 [166 kB]
Get:119 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.3.dfsg-3 [903 kB]
Get:120 http://172.17.4.1/private trixie-staging/main armhf libpmix-dev armhf 5.0.1-4 [3831 kB]
Get:121 http://172.17.4.1/private trixie-staging/main armhf openmpi-bin armhf 4.1.6-5+rpi1 [193 kB]
Get:122 http://172.17.4.1/private trixie-staging/main armhf libopenmpi-dev armhf 4.1.6-5+rpi1 [923 kB]
Get:123 http://172.17.4.1/private trixie-staging/main armhf libpkgconf3 armhf 1.8.1-1 [31.3 kB]
Get:124 http://172.17.4.1/private trixie-staging/main armhf libreadline-dev armhf 8.2-3 [124 kB]
Get:125 http://172.17.4.1/private trixie-staging/main armhf mpi-default-dev armhf 1.15 [3152 B]
Get:126 http://172.17.4.1/private trixie-staging/main armhf pkgconf-bin armhf 1.8.1-1 [27.8 kB]
Get:127 http://172.17.4.1/private trixie-staging/main armhf pkgconf armhf 1.8.1-1 [25.9 kB]
Get:128 http://172.17.4.1/private trixie-staging/main armhf pkg-config armhf 1.8.1-1 [13.7 kB]
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Setting up libexpat1:armhf (2.5.0-2) ...
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Setting up libpciaccess0:armhf (0.17-3) ...
Setting up libclc-15-dev (1:15.0.7-10+rpi1) ...
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Setting up libpkgconf3:armhf (1.8.1-1) ...
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Setting up zlib1g-dev:armhf (1:1.3.dfsg-3) ...
Setting up libnuma1:armhf (2.0.16-1) ...
Setting up mount (2.39.3-6) ...
Setting up sensible-utils (0.0.20) ...
Setting up ocl-icd-libopencl1:armhf (2.3.2-1) ...
Setting up libasan8:armhf (13.2.0-9+rpi1) ...
Setting up libuchardet0:armhf (0.0.8-1) ...
Setting up libnl-3-200:armhf (3.7.0-0.2) ...
Setting up openmpi-common (4.1.6-5+rpi1) ...
Setting up libsub-override-perl (0.10-1) ...
Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Setting up libfido2-1:armhf (1.14.0-1) ...
Setting up libbsd0:armhf (0.11.8-1) ...
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Setting up libevent-pthreads-2.1-7:armhf (2.1.12-stable-8) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up libevent-extra-2.1-7:armhf (2.1.12-stable-8) ...
Setting up libncurses-dev:armhf (6.4+20231209-1) ...
Setting up libxcb1:armhf (1.15-1) ...
Setting up gettext (0.21-14) ...
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Setting up libevent-openssl-2.1-7:armhf (2.1.12-stable-8) ...
Setting up libreadline-dev:armhf (8.2-3) ...
Setting up pkgconf:armhf (1.8.1-1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libnuma-dev:armhf (2.0.16-1) ...
Setting up libnl-route-3-200:armhf (3.7.0-0.2) ...
Setting up dh-autoreconf (20) ...
Setting up libltdl-dev:armhf (2.4.7-7) ...
Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
Setting up libevent-dev (2.1.12-stable-8) ...
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Setting up dwz (0.15-1) ...
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Setting up libx11-6:armhf (2:1.8.7-1) ...
Setting up libhwloc-dev:armhf (2.10.0-1) ...
Setting up libgfortran-13-dev:armhf (13.2.0-9+rpi1) ...
Setting up libstdc++-13-dev:armhf (13.2.0-9+rpi1) ...
Setting up libdrm-amdgpu1:armhf (2.4.117-1+rpi1) ...
Setting up libibverbs1:armhf (48.0-1) ...
Setting up libdrm-nouveau2:armhf (2.4.117-1+rpi1) ...
Setting up libllvmspirvlib15:armhf (15.0.0-2+rpi1) ...
Setting up libclang-common-15-dev (1:15.0.7-10+rpi1) ...
Setting up ibverbs-providers:armhf (48.0-1) ...
Setting up libdrm-radeon1:armhf (2.4.117-1+rpi1) ...
Setting up openssh-client (1:9.6p1-2) ...
Setting up po-debconf (1.0.21+nmu1) ...
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Setting up man-db (2.12.0-3) ...
Not building database; man-db/auto-update is not 'true'.
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Setting up libnl-route-3-dev:armhf (3.7.0-0.2) ...
Setting up gcc-13 (13.2.0-9+rpi1) ...
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Setting up mesa-opencl-icd:armhf (23.1.7-1+rpi1) ...
Setting up librdmacm1:armhf (48.0-1) ...
Setting up g++-13 (13.2.0-9+rpi1) ...
Setting up libhmsbeagle1v5:armhf (3.1.2+dfsg-13) ...
Setting up debhelper (13.11.9) ...
Setting up libibverbs-dev:armhf (48.0-1) ...
Setting up libhwloc-plugins:armhf (2.10.0-1) ...
Setting up gfortran-13 (13.2.0-9+rpi1) ...
Setting up libfabric1:armhf (1.17.0-3) ...
Setting up libhmsbeagle-dev (3.1.2+dfsg-13) ...
Setting up libpmix2:armhf (5.0.1-4) ...
Setting up libopenmpi3:armhf (4.1.6-5+rpi1) ...
Setting up libpmix-dev:armhf (5.0.1-4) ...
Setting up openmpi-bin (4.1.6-5+rpi1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up libopenmpi-dev:armhf (4.1.6-5+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up mpi-default-dev (1.15) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.37-12+rpi2) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.47-v8+ #1 SMP PREEMPT Fri Sep 1 07:05:33 BST 2023 arm64 (aarch64)
Toolchain package versions: binutils_2.41-6+rpi1 dpkg-dev_1.22.1+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-9+rpi1 gcc-12_12.3.0-13+rpi1 gcc-13_13.2.0-9+rpi1 libc6-dev_2.37-12+rpi2 libstdc++-12-dev_12.3.0-13+rpi1 libstdc++-13-dev_13.2.0-9+rpi1 libstdc++6_13.2.0-9+rpi1 linux-libc-dev_6.5.6-1+rpi1
Package versions: adduser_3.137 apt_2.7.6 autoconf_2.71-3 autoconf-archive_20220903-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.3 bash_5.2.21-2 binutils_2.41-6+rpi1 binutils-arm-linux-gnueabihf_2.41-6+rpi1 binutils-common_2.41-6+rpi1 bsdextrautils_2.39.3-6 bsdutils_1:2.39.3-6 build-essential_12.10 bzip2_1.0.8-5+b2 coreutils_9.1-1 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-13+rpi1 cpp-13_13.2.0-9+rpi1 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.9 debianutils_5.14 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dirmngr_2.2.40-1.1 dpkg_1.22.1+rpi1 dpkg-dev_1.22.1+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.32.2-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-1+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-9+rpi1 gcc_4:13.2.0-1+rpi1 gcc-10-base_10.4.0-7+rpi1 gcc-12_12.3.0-13+rpi1 gcc-12-base_12.3.0-13+rpi1 gcc-13_13.2.0-9+rpi1 gcc-13-base_13.2.0-9+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-14 gettext-base_0.21-14 gfortran-13_13.2.0-9+rpi1 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.11-3 groff-base_1.23.0-3 gzip_1.12-1 hostname_3.23+nmu1 ibverbs-providers_48.0-1 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libapt-pkg6.0_2.7.6 libarchive-zip-perl_1.68-1 libasan8_13.2.0-9+rpi1 libassuan0_2.5.6-1 libatomic1_13.2.0-9+rpi1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.2-1 libaudit1_1:3.1.2-1 libbinutils_2.41-6+rpi1 libblkid1_2.39.3-6 libbsd0_0.11.8-1 libbz2-1.0_1.0.8-5+b2 libc-bin_2.37-12+rpi2 libc-dev-bin_2.37-12+rpi2 libc6_2.37-12+rpi2 libc6-dev_2.37-12+rpi2 libcap-ng0_0.8.3-3 libcap2_1:2.66-4 libcbor0.10_0.10.2-1.1 libcc1-0_13.2.0-9+rpi1 libclang-common-15-dev_1:15.0.7-10+rpi1 libclang-cpp15_1:15.0.7-10+rpi1 libclc-15_1:15.0.7-10+rpi1 libclc-15-dev_1:15.0.7-10+rpi1 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libctf-nobfd0_2.41-6+rpi1 libctf0_2.41-6+rpi1 libdb5.3_5.3.28+dfsg2-4 libdebconfclient0_0.271 libdebhelper-perl_13.11.9 libdpkg-perl_1.22.1+rpi1 libdrm-amdgpu1_2.4.117-1+rpi1 libdrm-common_2.4.117-1+rpi1 libdrm-nouveau2_2.4.117-1+rpi1 libdrm-radeon1_2.4.117-1+rpi1 libdrm2_2.4.117-1+rpi1 libedit2_3.1-20230828-1 libelf1_0.188-2.1+rpi1 libevent-2.1-7_2.1.12-stable-8 libevent-core-2.1-7_2.1.12-stable-8 libevent-dev_2.1.12-stable-8 libevent-extra-2.1-7_2.1.12-stable-8 libevent-openssl-2.1-7_2.1.12-stable-8 libevent-pthreads-2.1-7_2.1.12-stable-8 libexpat1_2.5.0-2 libext2fs2_1.47.0-2 libfabric1_1.17.0-3 libfakeroot_1.32.2-1 libffi8_3.4.4-2 libfido2-1_1.14.0-1 libfile-find-rule-perl_0.34-3 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.3.0-13+rpi1 libgcc-13-dev_13.2.0-9+rpi1 libgcc-s1_13.2.0-9+rpi1 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5 libgdbm6_1.23-5 libgfortran-13-dev_13.2.0-9+rpi1 libgfortran5_13.2.0-9+rpi1 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.2-1 libgomp1_13.2.0-9+rpi1 libgpg-error0_1.47-3 libgssapi-krb5-2_1.20.1-5 libhmsbeagle-dev_3.1.2+dfsg-13 libhmsbeagle1v5_3.1.2+dfsg-13 libhogweed6_3.9.1-2 libhwloc-dev_2.10.0-1 libhwloc-plugins_2.10.0-1 libhwloc15_2.10.0-1 libibverbs-dev_48.0-1 libibverbs1_48.0-1 libicu72_72.1-4 libidn2-0_2.3.4-1 libisl23_0.26-3 libjansson4_2.14-2 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-jquery-ui_1.13.2+dfsg-1 libk5crypto3_1.20.1-5 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-5 libkrb5support0_1.20.1-5 libksba8_1.6.5-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1 libllvm15_1:15.0.7-10+rpi1 libllvmspirvlib15_15.0.0-2+rpi1 liblocale-gettext-perl_1.07-6 libltdl-dev_2.4.7-7 libltdl7_2.4.7-7 liblz4-1_1.9.4-1+rpi1+b1 liblzma5_5.4.5-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-1 libmount1_2.39.3-6 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libmunge2_0.5.15-3 libncurses-dev_6.4+20231209-1 libncurses6_6.4+20231209-1 libncursesw6_6.4+20231209-1 libnettle8_3.9.1-2 libnl-3-200_3.7.0-0.2 libnl-3-dev_3.7.0-0.2 libnl-route-3-200_3.7.0-0.2 libnl-route-3-dev_3.7.0-0.2 libnpth0_1.6-3 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnuma-dev_2.0.16-1 libnuma1_2.0.16-1 libnumber-compare-perl_0.03-3 libopenmpi-dev_4.1.6-5+rpi1 libopenmpi3_4.1.6-5+rpi1 libp11-kit0_0.25.3-2 libpam-modules_1.5.2-9.1 libpam-modules-bin_1.5.2-9.1 libpam-runtime_1.5.2-9.1 libpam0g_1.5.2-9.1 libpciaccess0_0.17-3 libpcre2-8-0_10.42-4 libperl5.36_5.36.0-10 libpipeline1_1.5.7-1 libpkgconf3_1.8.1-1 libpmix-dev_5.0.1-4 libpmix2_5.0.1-4 librdmacm1_48.0-1 libreadline-dev_8.2-3 libreadline8_8.2-3 libsasl2-2_2.1.28+dfsg1-4 libsasl2-modules-db_2.1.28+dfsg1-4 libseccomp2_2.5.4-2+rpi1 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsensors-config_1:3.6.0-8 libsensors5_1:3.6.0-8 libsepol2_3.5-2 libsframe1_2.41-6+rpi1 libsmartcols1_2.39.3-6 libsqlite3-0_3.44.2-1 libss2_1.47.0-2 libssl3_3.1.4-2 libstdc++-12-dev_12.3.0-13+rpi1 libstdc++-13-dev_13.2.0-9+rpi1 libstdc++6_13.2.0-9+rpi1 libsub-override-perl_0.10-1 libsystemd0_254.5-1+rpi1 libtasn1-6_4.19.0-3 libtext-charwidth-perl_0.04-11 libtext-glob-perl_0.11-3 libtext-iconv-perl_1.7-8 libtinfo6_6.4+20231209-1 libtirpc-common_1.3.4+ds-1 libtirpc-dev_1.3.4+ds-1 libtirpc3_1.3.4+ds-1 libtool_2.4.7-7 libubsan1_13.2.0-9+rpi1 libuchardet0_0.0.8-1 libudev1_254.5-1+rpi1 libunistring5_1.1-2 libuuid1_2.39.3-6 libx11-6_2:1.8.7-1 libx11-data_2:1.8.7-1 libxau6_1:1.0.9-1 libxcb1_1.15-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1 libxml2_2.9.14+dfsg-1.3 libxnvctrl0_525.125.06-1 libxxhash0_0.8.2-2 libz3-4_4.8.12-3.1 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.5.6-1+rpi1 login_1:4.13+dfsg1-3 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.0-3 mawk_1.3.4.20231126-1 mesa-opencl-icd_23.1.7-1+rpi1 mount_2.39.3-6 mpi-default-dev_1.15 nano_7.2-1 ncurses-base_6.4+20231209-1 ncurses-bin_6.4+20231209-1 ocl-icd-libopencl1_2.3.2-1 openmpi-bin_4.1.6-5+rpi1 openmpi-common_4.1.6-5+rpi1 openssh-client_1:9.6p1-2 passwd_1:4.13+dfsg1-3 patch_2.7.6-7 perl_5.36.0-10 perl-base_5.36.0-10 perl-modules-5.36_5.36.0-10 pinentry-curses_1.2.1-3 pkg-config_1.8.1-1 pkgconf_1.8.1-1 pkgconf-bin_1.8.1-1 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.2-3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sysvinit-utils_3.08-5 tar_1.34+dfsg-1.3 tzdata_2023c-11 usr-is-merged_38 usrmerge_38 util-linux_2.39.3-6 xz-utils_5.4.5-0.1 zlib1g_1:1.3.dfsg-3 zlib1g-dev_1:1.3.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: mrbayes
Binary: mrbayes, mrbayes-mpi, mrbayes-doc
Architecture: any all
Version: 3.2.7a-7
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>, Andreas Tille <tille@debian.org>
Homepage: http://mrbayes.csit.fsu.edu/
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/mrbayes
Vcs-Git: https://salsa.debian.org/med-team/mrbayes.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), libreadline-dev, mpi-default-dev, libhmsbeagle-dev, autoconf-archive, pkg-config
Package-List:
mrbayes deb science optional arch=any
mrbayes-doc deb doc optional arch=all
mrbayes-mpi deb science optional arch=any
Checksums-Sha1:
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99911ffc510775938111912889d2da7745b83cc9 7380 mrbayes_3.2.7a-7.debian.tar.xz
Checksums-Sha256:
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58f4e433e222389b50b62dbb92ed4667c7c5ed19c258b3802f1bbe1da988aa84 7380 mrbayes_3.2.7a-7.debian.tar.xz
Files:
504236626ce9a2de1066a8520672f0cc 9819346 mrbayes_3.2.7a.orig.tar.gz
3a68c8efba2dcdf1502e2378ed7ff21b 7380 mrbayes_3.2.7a-7.debian.tar.xz
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gpgv: Signature made Sun Jan 14 13:54:21 2024 UTC
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-7.dsc: no acceptable signature found
dpkg-source: info: extracting mrbayes in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking mrbayes_3.2.7a.orig.tar.gz
dpkg-source: info: unpacking mrbayes_3.2.7a-7.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
Check disk space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 3.2.7a-7+b1
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=124
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-9eed0b91-6fdb-412f-9e42-f13ce240b15c
SCHROOT_UID=114
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -mRaspbian pi5 test autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package mrbayes
dpkg-buildpackage: info: source version 3.2.7a-7+b1
dpkg-buildpackage: info: source distribution trixie-staging
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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... /usr/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... /usr/bin/sed
checking for C compiler version... 13.2.0
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 '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# build mb-mpi (from initial config)
LIBS="-Wl,--as-needed" dh_auto_build
make -j4
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making all in src
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
make all-am
make[4]: Entering directory '/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o mb-mbbeagle.o `test -f 'mbbeagle.c' || echo './'`mbbeagle.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o mb-model.o `test -f 'model.c' || echo './'`model.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o mb-proposal.o `test -f 'proposal.c' || echo './'`proposal.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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o mb-sumpt.o `test -f 'sumpt.c' || echo './'`sumpt.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 ());
| ~~~~~~~~~~~~~~~~~
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);
| ^
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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o mb-utils.o `test -f 'utils.c' || echo './'`utils.c
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 ());
| ~~~~~~~~~~~~~~~~~
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));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
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 ());
| ~~~~~~~~~~~~~~~~~
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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 '/<<PKGBUILDDIR>>/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
Making all in doc
make[3]: Entering directory '/<<PKGBUILDDIR>>/doc'
Making all in manual
make[4]: Entering directory '/<<PKGBUILDDIR>>/doc/manual'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc/manual'
Making all in tutorial
make[4]: Entering directory '/<<PKGBUILDDIR>>/doc/tutorial'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc/tutorial'
make[4]: Entering directory '/<<PKGBUILDDIR>>/doc'
make[4]: Nothing to be done for 'all-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc'
Making all in examples
make[3]: Entering directory '/<<PKGBUILDDIR>>/examples'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/examples'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Nothing to be done for 'all-am'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
mv src/mb ./mb-mpi
# Now - build mb
( cd src ; make clean )
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
test -z "mb" || rm -f mb
rm -f *.o
make[2]: Leaving directory '/<<PKGBUILDDIR>>/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... /usr/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... /usr/bin/sed
checking for C compiler version... 13.2.0
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 -j4
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making all in src
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
make all-am
make[4]: Entering directory '/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o mb-mbbeagle.o `test -f 'mbbeagle.c' || echo './'`mbbeagle.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o mb-model.o `test -f 'model.c' || echo './'`model.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o mb-proposal.o `test -f 'proposal.c' || echo './'`proposal.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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o mb-sumpt.o `test -f 'sumpt.c' || echo './'`sumpt.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 ());
| ~~~~~~~~~~~~~~~~~
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);
| ^
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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o mb-utils.o `test -f 'utils.c' || echo './'`utils.c
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 ());
| ~~~~~~~~~~~~~~~~~
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));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
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 ());
| ~~~~~~~~~~~~~~~~~
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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 '/<<PKGBUILDDIR>>/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
Making all in doc
make[3]: Entering directory '/<<PKGBUILDDIR>>/doc'
Making all in manual
make[4]: Entering directory '/<<PKGBUILDDIR>>/doc/manual'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc/manual'
Making all in tutorial
make[4]: Entering directory '/<<PKGBUILDDIR>>/doc/tutorial'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc/tutorial'
make[4]: Entering directory '/<<PKGBUILDDIR>>/doc'
make[4]: Nothing to be done for 'all-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc'
Making all in examples
make[3]: Entering directory '/<<PKGBUILDDIR>>/examples'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/examples'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Nothing to be done for 'all-am'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
mv src/mb .
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making check in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 '/<<PKGBUILDDIR>>/src'
Making check in doc
make[2]: Entering directory '/<<PKGBUILDDIR>>/doc'
Making check in manual
make[3]: Entering directory '/<<PKGBUILDDIR>>/doc/manual'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc/manual'
Making check in tutorial
make[3]: Entering directory '/<<PKGBUILDDIR>>/doc/tutorial'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc/tutorial'
make[3]: Entering directory '/<<PKGBUILDDIR>>/doc'
make[3]: Nothing to be done for 'check-am'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/doc'
Making check in examples
make[2]: Entering directory '/<<PKGBUILDDIR>>/examples'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/examples'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: Nothing to be done for 'check-am'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_prep -a
dh_auto_install -a
make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making install in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
make[3]: Nothing to be done for 'install-data-am'.
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c mb '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
Making install in doc
make[2]: Entering directory '/<<PKGBUILDDIR>>/doc'
Making install in manual
make[3]: Entering directory '/<<PKGBUILDDIR>>/doc/manual'
make[4]: Entering directory '/<<PKGBUILDDIR>>/doc/manual'
make[4]: Nothing to be done for 'install-exec-am'.
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/mrbayes'
/usr/bin/install -c -m 644 Manual_MrBayes_v3.2.pdf '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/mrbayes'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc/manual'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc/manual'
Making install in tutorial
make[3]: Entering directory '/<<PKGBUILDDIR>>/doc/tutorial'
make[4]: Entering directory '/<<PKGBUILDDIR>>/doc/tutorial'
make[4]: Nothing to be done for 'install-exec-am'.
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/mrbayes'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/mrbayes'
/usr/bin/install -c -m 644 hym.nex '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/mrbayes'
/usr/bin/install -c -m 644 MBDating.pdf '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/mrbayes'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc/tutorial'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc/tutorial'
make[3]: Entering directory '/<<PKGBUILDDIR>>/doc'
make[4]: Entering directory '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/doc'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/doc'
Making install in examples
make[2]: Entering directory '/<<PKGBUILDDIR>>/examples'
make[3]: Entering directory '/<<PKGBUILDDIR>>/examples'
make[3]: Nothing to be done for 'install-exec-am'.
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/debian/tmp/usr/share/examples/mrbayes'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/examples'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/examples'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Nothing to be done for 'install-exec-am'.
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/mrbayes'
/usr/bin/install -c -m 644 COPYING README NEWS '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/mrbayes'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
debian/rules override_dh_installexamples
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installexamples
find debian -name "Makefile*" -delete
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
debian/rules override_dh_compress
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_compress --exclude=.pdf
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_fixperms -a
debian/rules override_dh_missing
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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.md.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 '/<<PKGBUILDDIR>>'
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/mrbayes/usr/bin/mb was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/mrbayes-mpi/usr/lib/mrbayes-mpi/mb-mpi was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
debian/rules override_dh_installdeb
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# 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 '/<<PKGBUILDDIR>>'
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'mrbayes-dbgsym' in '../mrbayes-dbgsym_3.2.7a-7+b1_armhf.deb'.
dpkg-deb: building package 'mrbayes' in '../mrbayes_3.2.7a-7+b1_armhf.deb'.
dpkg-deb: building package 'mrbayes-mpi' in '../mrbayes-mpi_3.2.7a-7+b1_armhf.deb'.
dpkg-deb: building package 'mrbayes-mpi-dbgsym' in '../mrbayes-mpi-dbgsym_3.2.7a-7+b1_armhf.deb'.
dpkg-genbuildinfo --build=any -O../mrbayes_3.2.7a-7+b1_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi5 test autobuilder <root@raspbian.org> -O../mrbayes_3.2.7a-7+b1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2024-01-20T12:00:50Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
mrbayes_3.2.7a-7+b1_armhf.changes:
----------------------------------
Format: 1.8
Date: Sat, 20 Jan 2024 11:58:31 +0000
Source: mrbayes (3.2.7a-7)
Binary: mrbayes mrbayes-dbgsym mrbayes-mpi mrbayes-mpi-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 3.2.7a-7+b1
Distribution: trixie-staging
Urgency: low
Maintainer: Raspbian pi5 test autobuilder <root@raspbian.org>
Changed-By: Raspbian pi5 test autobuilder <root@raspbian.org>
Description:
mrbayes - Bayesian Inference of Phylogeny
mrbayes-mpi - Bayesian Inference of Phylogeny - mpi version
Changes:
mrbayes (3.2.7a-7+b1) trixie-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
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Files:
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2ac6451820b231d07c593c0f9e7b1b79 980 debug optional mrbayes-mpi-dbgsym_3.2.7a-7+b1_armhf.deb
5db9e927878e34fdebe3f9adde71506e 491612 science optional mrbayes-mpi_3.2.7a-7+b1_armhf.deb
564eb0248984afb785618c744af9307f 8714 science optional mrbayes_3.2.7a-7+b1_armhf.buildinfo
d44b7a709fc0ace0e22bd19fbe2de2f0 554544 science optional mrbayes_3.2.7a-7+b1_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: mrbayes (3.2.7a-7)
Binary: mrbayes mrbayes-dbgsym mrbayes-mpi mrbayes-mpi-dbgsym
Architecture: armhf
Version: 3.2.7a-7+b1
Binary-Only-Changes:
mrbayes (3.2.7a-7+b1) trixie-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
.
-- Raspbian pi5 test autobuilder <root@raspbian.org> Sat, 20 Jan 2024 11:58:31 +0000
Checksums-Md5:
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Sat, 20 Jan 2024 12:00:50 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
merged-usr-via-aliased-dirs
Installed-Build-Depends:
adduser (= 3.137),
autoconf (= 2.71-3),
autoconf-archive (= 20220903-3),
automake (= 1:1.16.5-1.3),
autopoint (= 0.21-14),
autotools-dev (= 20220109.1),
base-files (= 13+rpi1),
base-passwd (= 3.6.3),
bash (= 5.2.21-2),
binutils (= 2.41-6+rpi1),
binutils-arm-linux-gnueabihf (= 2.41-6+rpi1),
binutils-common (= 2.41-6+rpi1),
bsdextrautils (= 2.39.3-6),
bsdutils (= 1:2.39.3-6),
build-essential (= 12.10),
bzip2 (= 1.0.8-5+b2),
coreutils (= 9.1-1),
cpp (= 4:13.2.0-1+rpi1),
cpp-12 (= 12.3.0-13+rpi1),
cpp-13 (= 13.2.0-9+rpi1),
dash (= 0.5.12-6),
debconf (= 1.5.82),
debhelper (= 13.11.9),
debianutils (= 5.14),
dh-autoreconf (= 20),
dh-strip-nondeterminism (= 1.13.1-1),
diffutils (= 1:3.10-1),
dpkg (= 1.22.1+rpi1),
dpkg-dev (= 1.22.1+rpi1),
dwz (= 0.15-1),
file (= 1:5.45-2),
findutils (= 4.9.0-5),
g++ (= 4:13.2.0-1+rpi1),
g++-13 (= 13.2.0-9+rpi1),
gcc (= 4:13.2.0-1+rpi1),
gcc-12 (= 12.3.0-13+rpi1),
gcc-12-base (= 12.3.0-13+rpi1),
gcc-13 (= 13.2.0-9+rpi1),
gcc-13-base (= 13.2.0-9+rpi1),
gettext (= 0.21-14),
gettext-base (= 0.21-14),
gfortran-13 (= 13.2.0-9+rpi1),
grep (= 3.11-3),
groff-base (= 1.23.0-3),
gzip (= 1.12-1),
hostname (= 3.23+nmu1),
ibverbs-providers (= 48.0-1),
init-system-helpers (= 1.66),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.1-3),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 13.2.0-9+rpi1),
libatomic1 (= 13.2.0-9+rpi1),
libattr1 (= 1:2.5.1-4),
libaudit-common (= 1:3.1.2-1),
libaudit1 (= 1:3.1.2-1),
libbinutils (= 2.41-6+rpi1),
libblkid1 (= 2.39.3-6),
libbsd0 (= 0.11.8-1),
libbz2-1.0 (= 1.0.8-5+b2),
libc-bin (= 2.37-12+rpi2),
libc-dev-bin (= 2.37-12+rpi2),
libc6 (= 2.37-12+rpi2),
libc6-dev (= 2.37-12+rpi2),
libcap-ng0 (= 0.8.3-3),
libcap2 (= 1:2.66-4),
libcbor0.10 (= 0.10.2-1.1),
libcc1-0 (= 13.2.0-9+rpi1),
libclang-common-15-dev (= 1:15.0.7-10+rpi1),
libclang-cpp15 (= 1:15.0.7-10+rpi1),
libclc-15 (= 1:15.0.7-10+rpi1),
libclc-15-dev (= 1:15.0.7-10+rpi1),
libcom-err2 (= 1.47.0-2),
libcrypt-dev (= 1:4.4.36-2),
libcrypt1 (= 1:4.4.36-2),
libctf-nobfd0 (= 2.41-6+rpi1),
libctf0 (= 2.41-6+rpi1),
libdb5.3 (= 5.3.28+dfsg2-4),
libdebconfclient0 (= 0.271),
libdebhelper-perl (= 13.11.9),
libdpkg-perl (= 1.22.1+rpi1),
libdrm-amdgpu1 (= 2.4.117-1+rpi1),
libdrm-common (= 2.4.117-1+rpi1),
libdrm-nouveau2 (= 2.4.117-1+rpi1),
libdrm-radeon1 (= 2.4.117-1+rpi1),
libdrm2 (= 2.4.117-1+rpi1),
libedit2 (= 3.1-20230828-1),
libelf1 (= 0.188-2.1+rpi1),
libevent-2.1-7 (= 2.1.12-stable-8),
libevent-core-2.1-7 (= 2.1.12-stable-8),
libevent-dev (= 2.1.12-stable-8),
libevent-extra-2.1-7 (= 2.1.12-stable-8),
libevent-openssl-2.1-7 (= 2.1.12-stable-8),
libevent-pthreads-2.1-7 (= 2.1.12-stable-8),
libexpat1 (= 2.5.0-2),
libfabric1 (= 1.17.0-3),
libffi8 (= 3.4.4-2),
libfido2-1 (= 1.14.0-1),
libfile-find-rule-perl (= 0.34-3),
libfile-stripnondeterminism-perl (= 1.13.1-1),
libgcc-12-dev (= 12.3.0-13+rpi1),
libgcc-13-dev (= 13.2.0-9+rpi1),
libgcc-s1 (= 13.2.0-9+rpi1),
libgcrypt20 (= 1.10.3-2),
libgdbm-compat4 (= 1.23-5),
libgdbm6 (= 1.23-5),
libgfortran-13-dev (= 13.2.0-9+rpi1),
libgfortran5 (= 13.2.0-9+rpi1),
libgmp10 (= 2:6.3.0+dfsg-2),
libgomp1 (= 13.2.0-9+rpi1),
libgpg-error0 (= 1.47-3),
libgssapi-krb5-2 (= 1.20.1-5),
libhmsbeagle-dev (= 3.1.2+dfsg-13),
libhmsbeagle1v5 (= 3.1.2+dfsg-13),
libhwloc-dev (= 2.10.0-1),
libhwloc-plugins (= 2.10.0-1),
libhwloc15 (= 2.10.0-1),
libibverbs-dev (= 48.0-1),
libibverbs1 (= 48.0-1),
libicu72 (= 72.1-4),
libisl23 (= 0.26-3),
libjansson4 (= 2.14-2),
libjs-jquery (= 3.6.1+dfsg+~3.5.14-1),
libjs-jquery-ui (= 1.13.2+dfsg-1),
libk5crypto3 (= 1.20.1-5),
libkeyutils1 (= 1.6.3-2),
libkrb5-3 (= 1.20.1-5),
libkrb5support0 (= 1.20.1-5),
libllvm15 (= 1:15.0.7-10+rpi1),
libllvmspirvlib15 (= 15.0.0-2+rpi1),
libltdl-dev (= 2.4.7-7),
libltdl7 (= 2.4.7-7),
liblz4-1 (= 1.9.4-1+rpi1+b1),
liblzma5 (= 5.4.5-0.1),
libmagic-mgc (= 1:5.45-2),
libmagic1 (= 1:5.45-2),
libmd0 (= 1.1.0-1),
libmount1 (= 2.39.3-6),
libmpc3 (= 1.3.1-1),
libmpfr6 (= 4.2.1-1),
libmunge2 (= 0.5.15-3),
libncurses-dev (= 6.4+20231209-1),
libncurses6 (= 6.4+20231209-1),
libncursesw6 (= 6.4+20231209-1),
libnl-3-200 (= 3.7.0-0.2),
libnl-3-dev (= 3.7.0-0.2),
libnl-route-3-200 (= 3.7.0-0.2),
libnl-route-3-dev (= 3.7.0-0.2),
libnsl-dev (= 1.3.0-3),
libnsl2 (= 1.3.0-3),
libnuma-dev (= 2.0.16-1),
libnuma1 (= 2.0.16-1),
libnumber-compare-perl (= 0.03-3),
libopenmpi-dev (= 4.1.6-5+rpi1),
libopenmpi3 (= 4.1.6-5+rpi1),
libpam-modules (= 1.5.2-9.1),
libpam-modules-bin (= 1.5.2-9.1),
libpam-runtime (= 1.5.2-9.1),
libpam0g (= 1.5.2-9.1),
libpciaccess0 (= 0.17-3),
libpcre2-8-0 (= 10.42-4),
libperl5.36 (= 5.36.0-10),
libpipeline1 (= 1.5.7-1),
libpkgconf3 (= 1.8.1-1),
libpmix-dev (= 5.0.1-4),
libpmix2 (= 5.0.1-4),
librdmacm1 (= 48.0-1),
libreadline-dev (= 8.2-3),
libreadline8 (= 8.2-3),
libseccomp2 (= 2.5.4-2+rpi1),
libselinux1 (= 3.5-1),
libsemanage-common (= 3.5-1),
libsemanage2 (= 3.5-1),
libsensors-config (= 1:3.6.0-8),
libsensors5 (= 1:3.6.0-8),
libsepol2 (= 3.5-2),
libsframe1 (= 2.41-6+rpi1),
libsmartcols1 (= 2.39.3-6),
libssl3 (= 3.1.4-2),
libstdc++-13-dev (= 13.2.0-9+rpi1),
libstdc++6 (= 13.2.0-9+rpi1),
libsub-override-perl (= 0.10-1),
libsystemd0 (= 254.5-1+rpi1),
libtext-glob-perl (= 0.11-3),
libtinfo6 (= 6.4+20231209-1),
libtirpc-common (= 1.3.4+ds-1),
libtirpc-dev (= 1.3.4+ds-1),
libtirpc3 (= 1.3.4+ds-1),
libtool (= 2.4.7-7),
libubsan1 (= 13.2.0-9+rpi1),
libuchardet0 (= 0.0.8-1),
libudev1 (= 254.5-1+rpi1),
libunistring5 (= 1.1-2),
libuuid1 (= 2.39.3-6),
libx11-6 (= 2:1.8.7-1),
libx11-data (= 2:1.8.7-1),
libxau6 (= 1:1.0.9-1),
libxcb1 (= 1.15-1),
libxdmcp6 (= 1:1.1.2-3),
libxext6 (= 2:1.3.4-1),
libxml2 (= 2.9.14+dfsg-1.3),
libxnvctrl0 (= 525.125.06-1),
libz3-4 (= 4.8.12-3.1),
libzstd1 (= 1.5.5+dfsg2-2),
linux-libc-dev (= 6.5.6-1+rpi1),
login (= 1:4.13+dfsg1-3),
m4 (= 1.4.19-4),
make (= 4.3-4.1),
man-db (= 2.12.0-3),
mawk (= 1.3.4.20231126-1),
mesa-opencl-icd (= 23.1.7-1+rpi1),
mpi-default-dev (= 1.15),
ncurses-base (= 6.4+20231209-1),
ncurses-bin (= 6.4+20231209-1),
ocl-icd-libopencl1 (= 2.3.2-1),
openmpi-bin (= 4.1.6-5+rpi1),
openmpi-common (= 4.1.6-5+rpi1),
openssh-client (= 1:9.6p1-2),
passwd (= 1:4.13+dfsg1-3),
patch (= 2.7.6-7),
perl (= 5.36.0-10),
perl-base (= 5.36.0-10),
perl-modules-5.36 (= 5.36.0-10),
pkg-config (= 1.8.1-1),
pkgconf (= 1.8.1-1),
pkgconf-bin (= 1.8.1-1),
po-debconf (= 1.0.21+nmu1),
readline-common (= 8.2-3),
rpcsvc-proto (= 1.4.3-1),
sed (= 4.9-1),
sensible-utils (= 0.0.20),
sysvinit-utils (= 3.08-5),
tar (= 1.34+dfsg-1.3),
usr-is-merged (= 38),
usrmerge (= 38),
util-linux (= 2.39.3-6),
xz-utils (= 5.4.5-0.1),
zlib1g (= 1:1.3.dfsg-3),
zlib1g-dev (= 1:1.3.dfsg-3)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
LC_COLLATE="C.UTF-8"
SOURCE_DATE_EPOCH="1705751911"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
mrbayes-dbgsym_3.2.7a-7+b1_armhf.deb
------------------------------------
new Debian package, version 2.0.
size 1003248 bytes: control archive=544 bytes.
390 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: mrbayes-dbgsym
Source: mrbayes (3.2.7a-7)
Version: 3.2.7a-7+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1055
Depends: mrbayes (= 3.2.7a-7+b1)
Section: debug
Priority: optional
Description: debug symbols for mrbayes
Build-Ids: 6750e2f3451c890b9159534c3020022396b82bb0
drwxr-xr-x root/root 0 2024-01-20 11:58 ./
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/lib/
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/lib/debug/
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/lib/debug/.build-id/67/
-rw-r--r-- root/root 1069692 2024-01-20 11:58 ./usr/lib/debug/.build-id/67/50e2f3451c890b9159534c3020022396b82bb0.debug
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/share/
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/share/doc/
lrwxrwxrwx root/root 0 2024-01-20 11:58 ./usr/share/doc/mrbayes-dbgsym -> mrbayes
mrbayes-mpi-dbgsym_3.2.7a-7+b1_armhf.deb
----------------------------------------
new Debian package, version 2.0.
size 980 bytes: control archive=488 bytes.
400 bytes, 12 lines control
0 bytes, 0 lines md5sums
Package: mrbayes-mpi-dbgsym
Source: mrbayes (3.2.7a-7)
Version: 3.2.7a-7+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 10
Depends: mrbayes-mpi (= 3.2.7a-7+b1)
Section: debug
Priority: optional
Description: debug symbols for mrbayes-mpi
Build-Ids: 6750e2f3451c890b9159534c3020022396b82bb0
drwxr-xr-x root/root 0 2024-01-20 11:58 ./
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/lib/
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/lib/debug/
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/lib/debug/.build-id/67/
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/share/
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/share/doc/
lrwxrwxrwx root/root 0 2024-01-20 11:58 ./usr/share/doc/mrbayes-mpi-dbgsym -> mrbayes-mpi
mrbayes-mpi_3.2.7a-7+b1_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 491612 bytes: control archive=1072 bytes.
1017 bytes, 21 lines control
485 bytes, 7 lines md5sums
Package: mrbayes-mpi
Source: mrbayes (3.2.7a-7)
Version: 3.2.7a-7+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1401
Depends: libc6 (>= 2.34), libhmsbeagle1v5 (>= 3.1.2+dfsg), libreadline8 (>= 6.0), mpi-default-bin, ssh
Suggests: mpi-default, mrbayes-doc
Section: science
Priority: optional
Homepage: http://mrbayes.csit.fsu.edu/
Description: Bayesian Inference of Phylogeny - mpi version
Bayesian inference of phylogeny is based upon a quantity called the posterior
probability distribution of trees, which is the probability of a tree
conditioned on the observations. The conditioning is accomplished using
Bayes's theorem. The posterior probability distribution of trees is
impossible to calculate analytically; instead, MrBayes uses a simulation
technique called Markov chain Monte Carlo (or MCMC) to approximate the
posterior probabilities of trees.
.
This package offers a binary compiled for parallel computation with MPI.
drwxr-xr-x root/root 0 2024-01-20 11:58 ./
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/bin/
-rwxr-xr-x root/root 162 2024-01-14 13:35 ./usr/bin/mb-mpi
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/lib/
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/lib/mrbayes-mpi/
-rwxr-xr-x root/root 1415148 2024-01-20 11:58 ./usr/lib/mrbayes-mpi/mb-mpi
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/share/
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/share/doc/
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/share/doc/mrbayes-mpi/
-rw-r--r-- root/root 348 2024-01-14 13:35 ./usr/share/doc/mrbayes-mpi/README.Debian
-rw-r--r-- root/root 216 2024-01-20 11:58 ./usr/share/doc/mrbayes-mpi/changelog.Debian.armhf.gz
-rw-r--r-- root/root 1061 2024-01-20 11:58 ./usr/share/doc/mrbayes-mpi/changelog.Debian.gz
-rw-r--r-- root/root 1567 2024-01-14 13:35 ./usr/share/doc/mrbayes-mpi/copyright
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/share/man/
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/share/man/man1/
-rw-r--r-- root/root 226 2024-01-20 11:58 ./usr/share/man/man1/mb-mpi.1.gz
mrbayes_3.2.7a-7+b1_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 554544 bytes: control archive=1280 bytes.
887 bytes, 19 lines control
1166 bytes, 16 lines md5sums
Package: mrbayes
Source: mrbayes (3.2.7a-7)
Version: 3.2.7a-7+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2465
Depends: libc6 (>= 2.34), libhmsbeagle1v5 (>= 3.1.2+dfsg), libreadline8 (>= 6.0)
Suggests: mrbayes-doc
Section: science
Priority: optional
Homepage: http://mrbayes.csit.fsu.edu/
Description: Bayesian Inference of Phylogeny
Bayesian inference of phylogeny is based upon a quantity called the posterior
probability distribution of trees, which is the probability of a tree
conditioned on the observations. The conditioning is accomplished using
Bayes's theorem. The posterior probability distribution of trees is
impossible to calculate analytically; instead, MrBayes uses a simulation
technique called Markov chain Monte Carlo (or MCMC) to approximate the
posterior probabilities of trees.
drwxr-xr-x root/root 0 2024-01-20 11:58 ./
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/bin/
-rwxr-xr-x root/root 1415148 2024-01-20 11:58 ./usr/bin/mb
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/share/
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/share/doc/
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/share/doc/mrbayes/
-rw-r--r-- root/root 311 2024-01-14 13:35 ./usr/share/doc/mrbayes/README.Debian
-rw-r--r-- root/root 262 2024-01-14 13:35 ./usr/share/doc/mrbayes/README.test
-rw-r--r-- root/root 216 2024-01-20 11:58 ./usr/share/doc/mrbayes/changelog.Debian.armhf.gz
-rw-r--r-- root/root 1060 2024-01-20 11:58 ./usr/share/doc/mrbayes/changelog.Debian.gz
-rw-r--r-- root/root 1567 2024-01-14 13:35 ./usr/share/doc/mrbayes/copyright
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/share/doc/mrbayes/examples/
-rw-r--r-- root/root 11789 2019-03-06 16:43 ./usr/share/doc/mrbayes/examples/avian_ovomucoids.nex
-rw-r--r-- root/root 1689 2019-03-06 16:43 ./usr/share/doc/mrbayes/examples/codon.nex
-rw-r--r-- root/root 116675 2019-03-06 16:43 ./usr/share/doc/mrbayes/examples/cynmix.nex
-rw-r--r-- root/root 68673 2019-03-06 16:43 ./usr/share/doc/mrbayes/examples/finch.nex
-rw-r--r-- root/root 666195 2019-03-06 16:43 ./usr/share/doc/mrbayes/examples/hymfossil.nex
-rw-r--r-- root/root 11326 2019-03-06 16:43 ./usr/share/doc/mrbayes/examples/primates.nex
-rw-r--r-- root/root 7693 2019-03-06 16:43 ./usr/share/doc/mrbayes/examples/replicase.nex
-rw-r--r-- root/root 201334 2019-03-06 16:43 ./usr/share/doc/mrbayes/examples/sceloporus.nex
-rw-r--r-- root/root 441 2024-01-14 13:35 ./usr/share/doc/mrbayes/run-unit-test
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/share/man/
drwxr-xr-x root/root 0 2024-01-20 11:58 ./usr/share/man/man1/
-rw-r--r-- root/root 206 2024-01-20 11:58 ./usr/share/man/man1/mb.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 51740
Build-Time: 139
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 89
Job: mrbayes_3.2.7a-7
Machine Architecture: arm64
Package: mrbayes
Package-Time: 238
Source-Version: 3.2.7a-7
Space: 51740
Status: successful
Version: 3.2.7a-7+b1
--------------------------------------------------------------------------------
Finished at 2024-01-20T12:00:50Z
Build needed 00:03:58, 51740k disk space