mrbayes →
3.2.7a-6 →
armhf → 2022-11-26 07:25:13
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| mrbayes 3.2.7a-6 (armhf) Sat, 26 Nov 2022 06:59:48 +0000 |
+==============================================================================+
Package: mrbayes
Version: 3.2.7a-6
Source Version: 3.2.7a-6
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-948c1232-edfd-4973-bfb2-c33e98e5678e' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/mrbayes-eHRPHu/resolver-oePBCS' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.4 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.3 MB]
Fetched 27.7 MB in 14s (1981 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/bookworm-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 bookworm-staging/main mrbayes 3.2.7a-6 (dsc) [2184 B]
Get:2 http://172.17.4.1/private bookworm-staging/main mrbayes 3.2.7a-6 (tar) [9819 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main mrbayes 3.2.7a-6 (diff) [7304 B]
Fetched 9829 kB in 1s (8048 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/mrbayes-eHRPHu/mrbayes-3.2.7a' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/mrbayes-eHRPHu' 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 [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [415 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [499 B]
Fetched 1871 B in 0s (49.2 kB/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 packages were automatically installed and are no longer required:
krb5-locales libpam-cap libperl5.34 perl-modules-5.34
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf autoconf-archive automake autopoint autotools-dev bsdextrautils
bsdutils cpp-12 debhelper dh-autoreconf dh-strip-nondeterminism dwz file
g++-12 gcc-12 gcc-12-base gettext gettext-base gfortran-12 groff-base
ibverbs-providers intltool-debian libarchive-zip-perl libasan8 libatomic1
libblkid1 libbsd0 libcbor0.8 libcc1-0 libclang-common-14-dev libclang-cpp14
libclc-14 libclc-14-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-12-dev libgcc-s1 libgfortran-12-dev
libgfortran5 libgomp1 libhmsbeagle-dev libhmsbeagle1v5 libhwloc-dev
libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu72 libjs-jquery
libjs-jquery-ui libllvm14 libltdl-dev libltdl7 libmagic-mgc libmagic1 libmd0
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 libreadline8 libsmartcols1 libssl3
libstdc++-12-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 util-linux util-linux-extra
zlib1g-dev
Suggested packages:
gnu-standards autoconf-doc gcc-12-locales cpp-12-doc dh-make gcc-12-doc
gettext-doc libasprintf-dev libgettextpo-dev gfortran-12-doc libcoarrays-dev
groff libjs-jquery-ui-docs libtool-doc cryptsetup-bin ncurses-doc
openmpi-doc pciutils readline-doc libstdc++-12-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-locales
Recommended packages:
curl | wget | lynx 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-12 groff-base ibverbs-providers intltool-debian
libarchive-zip-perl libbsd0 libcbor0.8 libclang-common-14-dev libclang-cpp14
libclc-14 libclc-14-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-12-dev libgfortran5
libhmsbeagle-dev libhmsbeagle1v5 libhwloc-dev libhwloc-plugins libhwloc15
libibverbs-dev libibverbs1 libicu72 libjs-jquery libjs-jquery-ui libllvm14
libltdl-dev libltdl7 libmagic-mgc libmagic1 libmd0 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
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 zlib1g-dev
The following packages will be upgraded:
bsdutils cpp-12 g++-12 gcc-12 gcc-12-base libasan8 libatomic1 libblkid1
libcc1-0 libgcc-12-dev libgcc-s1 libgomp1 libmount1 libreadline8
libsmartcols1 libssl3 libstdc++-12-dev libstdc++6 libubsan1 libuuid1 mount
util-linux util-linux-extra
23 upgraded, 104 newly installed, 0 to remove and 53 not upgraded.
Need to get 131 MB of archives.
After this operation, 499 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [920 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf bsdutils armhf 1:2.38.1-3 [83.8 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libsmartcols1 armhf 2.38.1-3 [91.0 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf util-linux-extra armhf 2.38.1-3 [97.9 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf util-linux armhf 2.38.1-3 [1062 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf mount armhf 2.38.1-3 [125 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf autoconf-archive all 20220903-3 [775 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libcc1-0 armhf 12.2.0-9+rpi1 [32.2 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf libgomp1 armhf 12.2.0-9+rpi1 [95.4 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libatomic1 armhf 12.2.0-9+rpi1 [8224 B]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libasan8 armhf 12.2.0-9+rpi1 [2089 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf libubsan1 armhf 12.2.0-9+rpi1 [861 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf gcc-12-base armhf 12.2.0-9+rpi1 [37.2 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf libstdc++6 armhf 12.2.0-9+rpi1 [504 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf g++-12 armhf 12.2.0-9+rpi1 [7913 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf libstdc++-12-dev armhf 12.2.0-9+rpi1 [2025 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf libgcc-12-dev armhf 12.2.0-9+rpi1 [725 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf gcc-12 armhf 12.2.0-9+rpi1 [14.2 MB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf cpp-12 armhf 12.2.0-9+rpi1 [7156 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf libgcc-s1 armhf 12.2.0-9+rpi1 [36.1 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libblkid1 armhf 2.38.1-3 [130 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf libmount1 armhf 2.38.1-3 [143 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libreadline8 armhf 8.2-1.1 [141 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libuuid1 armhf 2.38.1-3 [27.1 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-3 [78.7 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.11.1-1 [1341 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-10 [156 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-2 [28.6 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.7-1 [112 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libedit2 armhf 3.1-20221030-1 [76.1 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libcbor0.8 armhf 0.8.0-2 [22.8 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libssl3 armhf 3.0.7-1 [1614 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libfido2-1 armhf 1.12.0-2 [67.6 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf openssh-client armhf 1:9.1p1-1 [813 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-10 [495 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.11.1 [80.8 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-4 [526 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14+20220924-2 [93.1 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libicu72 armhf 72.1-2 [9008 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.1 [570 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-10 [1203 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.11.1 [941 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libgfortran5 armhf 12.2.0-9+rpi1 [238 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf libgfortran-12-dev armhf 12.2.0-9+rpi1 [285 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf gfortran-12 armhf 12.2.0-9+rpi1 [7509 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf libnl-3-200 armhf 3.7.0-0.2 [55.0 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libnl-route-3-200 armhf 3.7.0-0.2 [152 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libibverbs1 armhf 42.0-1 [53.7 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf ibverbs-providers armhf 42.0-1 [28.8 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libz3-4 armhf 4.8.12-3 [5798 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libllvm14 armhf 1:14.0.6-2+rpi1 [19.5 MB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf libclang-common-14-dev armhf 1:14.0.6-2+rpi1 [3698 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libclang-cpp14 armhf 1:14.0.6-2+rpi1 [9481 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf libclc-14-dev all 1:14.0.6-2+rpi1 [79.1 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libclc-14 all 1:14.0.6-2+rpi1 [8688 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libdrm-common all 2.4.114-1+rpi1 [7276 B]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libdrm2 armhf 2.4.114-1+rpi1 [32.8 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libdrm-amdgpu1 armhf 2.4.114-1+rpi1 [19.3 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libdrm-nouveau2 armhf 2.4.114-1+rpi1 [17.0 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libdrm-radeon1 armhf 2.4.114-1+rpi1 [20.7 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf libevent-2.1-7 armhf 2.1.12-stable-5+b1 [166 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-5+b1 [125 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-5+b1 [102 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-5+b1 [57.6 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-5+b1 [62.5 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf libevent-dev armhf 2.1.12-stable-5+b1 [280 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.5.0-1 [77.2 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf librdmacm1 armhf 42.0-1 [60.3 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf libfabric1 armhf 1.11.0-3 [310 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf ocl-icd-libopencl1 armhf 2.3.1-1 [40.3 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf mesa-opencl-icd armhf 22.2.0-1+rpi1 [5678 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf libhmsbeagle1v5 armhf 3.1.2+dfsg-12 [139 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf libhmsbeagle-dev armhf 3.1.2+dfsg-12 [280 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf libhwloc15 armhf 2.8.0-1 [130 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf libnuma1 armhf 2.0.15-1 [22.3 kB]
Get:94 http://172.17.4.1/private bookworm-staging/main armhf libnuma-dev armhf 2.0.15-1 [35.5 kB]
Get:95 http://172.17.4.1/private bookworm-staging/main armhf libltdl7 armhf 2.4.7-4 [399 kB]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf libltdl-dev armhf 2.4.7-4 [161 kB]
Get:97 http://172.17.4.1/private bookworm-staging/main armhf libhwloc-dev armhf 2.8.0-1 [202 kB]
Get:98 http://172.17.4.1/private bookworm-staging/main armhf libpciaccess0 armhf 0.17-2 [48.8 kB]
Get:99 http://172.17.4.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:100 http://172.17.4.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:101 http://172.17.4.1/private bookworm-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
Get:102 http://172.17.4.1/private bookworm-staging/main armhf libx11-data all 2:1.8.1-2 [308 kB]
Get:103 http://172.17.4.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.8.1-2 [704 kB]
Get:104 http://172.17.4.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:105 http://172.17.4.1/private bookworm-staging/main armhf libxnvctrl0 armhf 510.85.02-2 [26.6 kB]
Get:106 http://172.17.4.1/private bookworm-staging/main armhf libhwloc-plugins armhf 2.8.0-1 [20.4 kB]
Get:107 http://172.17.4.1/private bookworm-staging/main armhf libnl-3-dev armhf 3.7.0-0.2 [93.4 kB]
Get:108 http://172.17.4.1/private bookworm-staging/main armhf libnl-route-3-dev armhf 3.7.0-0.2 [163 kB]
Get:109 http://172.17.4.1/private bookworm-staging/main armhf libibverbs-dev armhf 42.0-1 [188 kB]
Get:110 http://172.17.4.1/private bookworm-staging/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:111 http://172.17.4.1/private bookworm-staging/main armhf libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get:112 http://172.17.4.1/private bookworm-staging/main armhf libmunge2 armhf 0.5.14-6 [18.6 kB]
Get:113 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3+20220423-2 [79.6 kB]
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Get:115 http://172.17.4.1/private bookworm-staging/main armhf libpmix2 armhf 4.2.1-3+b1 [530 kB]
Get:116 http://172.17.4.1/private bookworm-staging/main armhf libopenmpi3 armhf 4.1.4-3+rpi1 [1795 kB]
Get:117 http://172.17.4.1/private bookworm-staging/main armhf openmpi-common all 4.1.4-3+rpi1 [165 kB]
Get:118 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4.1 [183 kB]
Get:119 http://172.17.4.1/private bookworm-staging/main armhf libpmix-dev armhf 4.2.1-3+b1 [844 kB]
Get:120 http://172.17.4.1/private bookworm-staging/main armhf openmpi-bin armhf 4.1.4-3+rpi1 [192 kB]
Get:121 http://172.17.4.1/private bookworm-staging/main armhf libopenmpi-dev armhf 4.1.4-3+rpi1 [920 kB]
Get:122 http://172.17.4.1/private bookworm-staging/main armhf libpkgconf3 armhf 1.8.0-11 [30.8 kB]
Get:123 http://172.17.4.1/private bookworm-staging/main armhf libreadline-dev armhf 8.2-1.1 [123 kB]
Get:124 http://172.17.4.1/private bookworm-staging/main armhf mpi-default-dev armhf 1.14 [5548 B]
Get:125 http://172.17.4.1/private bookworm-staging/main armhf pkgconf-bin armhf 1.8.0-11 [27.6 kB]
Get:126 http://172.17.4.1/private bookworm-staging/main armhf pkgconf armhf 1.8.0-11 [25.6 kB]
Get:127 http://172.17.4.1/private bookworm-staging/main armhf pkg-config armhf 1.8.0-11 [13.4 kB]
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Setting up mount (2.38.1-3) ...
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Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libnl-3-200:armhf (3.7.0-0.2) ...
Setting up openmpi-common (4.1.4-3+rpi1) ...
Setting up libsub-override-perl (0.09-4) ...
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Setting up libevent-pthreads-2.1-7:armhf (2.1.12-stable-5+b1) ...
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 (1.13.0-1) ...
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Setting up libreadline-dev:armhf (8.2-1.1) ...
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Setting up libnuma-dev:armhf (2.0.15-1) ...
Setting up libnl-route-3-200:armhf (3.7.0-0.2) ...
Setting up dh-autoreconf (20) ...
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Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
Setting up libgcc-12-dev:armhf (12.2.0-9+rpi1) ...
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Setting up libllvm14:armhf (1:14.0.6-2+rpi1) ...
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Setting up dwz (0.14+20220924-2) ...
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Setting up groff-base (1.22.4-8) ...
Setting up libx11-6:armhf (2:1.8.1-2) ...
Setting up libhwloc-dev:armhf (2.8.0-1) ...
Setting up libfido2-1:armhf (1.12.0-2) ...
Setting up libdrm-amdgpu1:armhf (2.4.114-1+rpi1) ...
Setting up libibverbs1:armhf (42.0-1) ...
Setting up libdrm-nouveau2:armhf (2.4.114-1+rpi1) ...
Setting up libstdc++-12-dev:armhf (12.2.0-9+rpi1) ...
Setting up ibverbs-providers:armhf (42.0-1) ...
Setting up libdrm-radeon1:armhf (2.4.114-1+rpi1) ...
Setting up openssh-client (1:9.1p1-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
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Setting up libgfortran-12-dev:armhf (12.2.0-9+rpi1) ...
Setting up man-db (2.11.1-1) ...
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-12 (12.2.0-9+rpi1) ...
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Setting up libclang-cpp14 (1:14.0.6-2+rpi1) ...
Setting up libclc-14 (1:14.0.6-2+rpi1) ...
Setting up g++-12 (12.2.0-9+rpi1) ...
Setting up mesa-opencl-icd:armhf (22.2.0-1+rpi1) ...
Setting up librdmacm1:armhf (42.0-1) ...
Setting up libhmsbeagle1v5:armhf (3.1.2+dfsg-12) ...
Setting up debhelper (13.11.1) ...
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Setting up gfortran-12 (12.2.0-9+rpi1) ...
Setting up libfabric1:armhf (1.11.0-3) ...
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Setting up libpmix2:armhf (4.2.1-3+b1) ...
Setting up libopenmpi3:armhf (4.1.4-3+rpi1) ...
Setting up libpmix-dev:armhf (4.2.1-3+b1) ...
Setting up openmpi-bin (4.1.4-3+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 (4.1.4-3+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 (1.14) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.35-2+rpi1) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.39-6+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.2.0-9+rpi1 gcc-12_12.2.0-9+rpi1 libc6-dev_2.35-2+rpi1 libstdc++-12-dev_12.2.0-9+rpi1 libstdc++6_12.2.0-9+rpi1 linux-libc-dev_5.19.6-1+rpi1
Package versions: adduser_3.129 apt_2.5.3 autoconf_2.71-2 autoconf-archive_20220903-3 automake_1:1.16.5-1.3 autopoint_0.21-10 autotools-dev_20220109.1 base-files_12.3+rpi1 base-passwd_3.6.1 bash_5.2~rc2-2 binutils_2.39-6+rpi1 binutils-arm-linux-gnueabihf_2.39-6+rpi1 binutils-common_2.39-6+rpi1 bsdextrautils_2.38.1-3 bsdutils_1:2.38.1-3 build-essential_12.9 bzip2_1.0.8-5+b2 coreutils_9.1-1 cpp_4:12.2.0-1+rpi1 cpp-12_12.2.0-9+rpi1 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.79 debhelper_13.11.1 debianutils_5.7-0.3 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-1 dirmngr_2.2.39-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.14+20220924-2 e2fsprogs_1.46.6~rc1-1 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 g++_4:12.2.0-1+rpi1 g++-12_12.2.0-9+rpi1 gcc_4:12.2.0-1+rpi1 gcc-12_12.2.0-9+rpi1 gcc-12-base_12.2.0-9+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_0.21-10 gettext-base_0.21-10 gfortran-12_12.2.0-9+rpi1 gnupg_2.2.39-1 gnupg-l10n_2.2.39-1 gnupg-utils_2.2.39-1 gpg_2.2.39-1 gpg-agent_2.2.39-1 gpg-wks-client_2.2.39-1 gpg-wks-server_2.2.39-1 gpgconf_2.2.39-1 gpgsm_2.2.39-1 gpgv_2.2.39-1 grep_3.7-1 groff-base_1.22.4-8 gzip_1.12-1 hostname_3.23 ibverbs-providers_42.0-1 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20211215-1 krb5-locales_1.20-1 libacl1_2.3.1-1 libapt-pkg6.0_2.5.3 libarchive-zip-perl_1.68-1 libasan8_12.2.0-9+rpi1 libassuan0_2.5.5-4 libatomic1_12.2.0-9+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libbinutils_2.39-6+rpi1 libblkid1_2.38.1-3 libbsd0_0.11.7-1 libbz2-1.0_1.0.8-5+b2 libc-bin_2.35-2+rpi1 libc-dev-bin_2.35-2+rpi1 libc6_2.35-2+rpi1 libc6-dev_2.35-2+rpi1 libcap-ng0_0.8.3-1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcbor0.8_0.8.0-2 libcc1-0_12.2.0-9+rpi1 libclang-common-14-dev_1:14.0.6-2+rpi1 libclang-cpp14_1:14.0.6-2+rpi1 libclc-14_1:14.0.6-2+rpi1 libclc-14-dev_1:14.0.6-2+rpi1 libcom-err2_1.46.6~rc1-1 libcrypt-dev_1:4.4.28-2 libcrypt1_1:4.4.28-2 libctf-nobfd0_2.39-6+rpi1 libctf0_2.39-6+rpi1 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.264 libdebhelper-perl_13.11.1 libdpkg-perl_1.21.9+rpi1 libdrm-amdgpu1_2.4.114-1+rpi1 libdrm-common_2.4.114-1+rpi1 libdrm-nouveau2_2.4.114-1+rpi1 libdrm-radeon1_2.4.114-1+rpi1 libdrm2_2.4.114-1+rpi1 libedit2_3.1-20221030-1 libelf1_0.187-2+rpi2 libevent-2.1-7_2.1.12-stable-5+b1 libevent-core-2.1-7_2.1.12-stable-5+b1 libevent-dev_2.1.12-stable-5+b1 libevent-extra-2.1-7_2.1.12-stable-5+b1 libevent-openssl-2.1-7_2.1.12-stable-5+b1 libevent-pthreads-2.1-7_2.1.12-stable-5+b1 libexpat1_2.5.0-1 libext2fs2_1.46.6~rc1-1 libfabric1_1.11.0-3 libfakeroot_1.29-1 libffi8_3.4.2-4 libfido2-1_1.12.0-2 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-12-dev_12.2.0-9+rpi1 libgcc-s1_12.2.0-9+rpi1 libgcrypt20_1.10.1-2+b2 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran-12-dev_12.2.0-9+rpi1 libgfortran5_12.2.0-9+rpi1 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.8-2 libgomp1_12.2.0-9+rpi1 libgpg-error0_1.45-2 libgssapi-krb5-2_1.20-1 libhmsbeagle-dev_3.1.2+dfsg-12 libhmsbeagle1v5_3.1.2+dfsg-12 libhogweed6_3.8.1-2 libhwloc-dev_2.8.0-1 libhwloc-plugins_2.8.0-1 libhwloc15_2.8.0-1 libibverbs-dev_42.0-1 libibverbs1_42.0-1 libicu72_72.1-2 libidn2-0_2.3.3-1 libisl23_0.25-1 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-jquery-ui_1.13.2+dfsg-1 libk5crypto3_1.20-1 libkeyutils1_1.6.3-1 libkrb5-3_1.20-1 libkrb5support0_1.20-1 libksba8_1.6.0-3 libldap-2.5-0_2.5.13+dfsg-2+rpi1 libllvm14_1:14.0.6-2+rpi1 libltdl-dev_2.4.7-4 libltdl7_2.4.7-4 liblz4-1_1.9.4-1+rpi1 liblzma5_5.2.5-2.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmd0_1.0.4-2 libmount1_2.38.1-3 libmpc3_1.2.1-2 libmpfr6_4.1.0-3 libmunge2_0.5.14-6 libncurses-dev_6.3+20220423-2 libncurses6_6.3+20220423-2 libncursesw6_6.3+20220423-2 libnettle8_3.8.1-2 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_1.3.0-2 libnsl2_1.3.0-2 libnuma-dev_2.0.15-1 libnuma1_2.0.15-1 libopenmpi-dev_4.1.4-3+rpi1 libopenmpi3_4.1.4-3+rpi1 libp11-kit0_0.24.1-1 libpam-cap_1:2.44-1 libpam-modules_1.5.2-5 libpam-modules-bin_1.5.2-5 libpam-runtime_1.5.2-5 libpam0g_1.5.2-5 libpciaccess0_0.17-2 libpcre2-8-0_10.40-1+b2 libpcre3_2:8.39-14 libperl5.32_5.32.1-6 libperl5.34_5.34.0-5 libperl5.36_5.36.0-4 libpipeline1_1.5.7-1 libpkgconf3_1.8.0-11 libpmix-dev_4.2.1-3+b1 libpmix2_4.2.1-3+b1 librdmacm1_42.0-1 libreadline-dev_8.2-1.1 libreadline8_8.2-1.1 libsasl2-2_2.1.28+dfsg-8 libsasl2-modules-db_2.1.28+dfsg-8 libseccomp2_2.5.4-1+rpi1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsepol1_3.1-1 libsepol2_3.4-2 libsmartcols1_2.38.1-3 libsqlite3-0_3.39.4-1 libss2_1.46.6~rc1-1 libssl1.1_1.1.1o-1 libssl3_3.0.7-1 libstdc++-12-dev_12.2.0-9+rpi1 libstdc++6_12.2.0-9+rpi1 libsub-override-perl_0.09-4 libsystemd0_251.5-1+rpi1 libtasn1-6_4.19.0-2 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-4 libubsan1_12.2.0-9+rpi1 libuchardet0_0.0.7-1 libudev1_251.5-1+rpi1 libunistring2_1.0-2 libuuid1_2.38.1-3 libx11-6_2:1.8.1-2 libx11-data_2:1.8.1-2 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-1.1 libxnvctrl0_510.85.02-2 libxxhash0_0.8.1-1 libz3-4_4.8.12-3 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.19.6-1+rpi1 login_1:4.12.3+dfsg1-1 logsave_1.46.6~rc1-1 lsb-base_11.4+rpi1 m4_1.4.19-1 make_4.3-4.1 man-db_2.11.1-1 mawk_1.3.4.20200120-3.1 mesa-opencl-icd_22.2.0-1+rpi1 mount_2.38.1-3 mpi-default-dev_1.14 nano_6.4-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 ocl-icd-libopencl1_2.3.1-1 openmpi-bin_4.1.4-3+rpi1 openmpi-common_4.1.4-3+rpi1 openssh-client_1:9.1p1-1 passwd_1:4.12.3+dfsg1-1 patch_2.7.6-7 perl_5.36.0-4 perl-base_5.36.0-4 perl-modules-5.32_5.32.1-6 perl-modules-5.34_5.34.0-5 perl-modules-5.36_5.36.0-4 pinentry-curses_1.2.0-2 pkg-config_1.8.0-11 pkgconf_1.8.0-11 pkgconf-bin_1.8.0-11 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.2-1 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.31 sysvinit-utils_3.05-6 tar_1.34+dfsg-1 tzdata_2022d-1 util-linux_2.38.1-3 util-linux-extra_2.38.1-3 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4.1 zlib1g-dev_1:1.2.11.dfsg-4.1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: mrbayes
Binary: mrbayes, mrbayes-mpi, mrbayes-doc
Architecture: any all
Version: 3.2.7a-6
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: 4.6.1
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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8b9526bc52c293a5a630d8fd0f8baeddc93566ab 7304 mrbayes_3.2.7a-6.debian.tar.xz
Checksums-Sha256:
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e27a201610c459f77ab22877ee7fd00def16562d41970e75eed28600a5497d9a 7304 mrbayes_3.2.7a-6.debian.tar.xz
Files:
504236626ce9a2de1066a8520672f0cc 9819346 mrbayes_3.2.7a.orig.tar.gz
30acb34b134a17b7764ece286f625c35 7304 mrbayes_3.2.7a-6.debian.tar.xz
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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.iuLuDGv5/trustedkeys.kbx': General error
gpgv: Signature made Thu Nov 24 12:00:25 2022 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./mrbayes_3.2.7a-6.dsc
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-6.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying no_rpath.patch
dpkg-source: info: applying autoreconf.patch
dpkg-source: info: applying no_baseline_violation.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=f89ee6850c51463faed427366eb0b008
JOURNAL_STREAM=8:31299
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
PWD=/
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-948c1232-edfd-4973-bfb2-c33e98e5678e
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c19041
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package mrbayes
dpkg-buildpackage: info: source version 3.2.7a-6
dpkg-buildpackage: info: source distribution unstable
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... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for pdflatex... no
checking for bibtex... no
configure: WARNING: pdflatex or bibtex is missing, documentation will not be rebuilt
checking whether make supports the include directive... yes (GNU style)
checking whether to compile using MPI... no
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... unsupported
checking for gcc option to enable C99 features... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for sqrt in -lm... yes
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
configure: Trying to locate Beagle (hmsbeagle-1) in '/usr'
checking for libhmsbeagle/beagle.h... yes
checking for beagleCreateInstance in -lhmsbeagle... yes
configure: Found Beagle in '/usr'
checking for beagleSetCPUThreadCount in -lhmsbeagle... yes
configure: Using BEAGLE_CFLAGS="-I/usr/include/libhmsbeagle-1 -pthread"
configure: Using BEAGLE_LIBS="-L/usr/lib -lhmsbeagle"
checking for a readline compatible library... -lreadline
checking for readline.h... no
checking for readline/readline.h... yes
checking whether readline supports history... yes
checking for history.h... no
checking for readline/history.h... yes
checking for float.h... yes
checking for limits.h... yes
checking for memory.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for size_t... yes
checking for _Bool... yes
checking for stdbool.h that conforms to C99... yes
checking for C compiler vendor... gnu
checking for a sed that does not truncate output... /bin/sed
checking for C compiler version... 12.2.0
checking CFLAGS for most reasonable warnings... -Wall
checking for floor... yes
checking for memset... yes
checking for pow... yes
checking for sqrt... yes
checking for strchr... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating doc/Makefile
config.status: creating doc/manual/Makefile
config.status: creating doc/tutorial/Makefile
config.status: creating examples/Makefile
config.status: creating src/Makefile
config.status: creating src/config.h
config.status: executing depfiles commands
make[1]: Leaving directory '/<<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 -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 -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 -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 -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 -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 -Wformat -Werror=format-security -c -o mb-mcmc.o `test -f 'mcmc.c' || echo './'`mcmc.c
mbbeagle.c: In function ‘TreeLikelihood_BeagleMultiPartition’:
mbbeagle.c:2618:33: warning: ‘nStates’ may be used uninitialized [-Wmaybe-uninitialized]
2618 | int i, j, d, c = 0, nStates, beagleReturn, site, dIndex, divisionOffset;
| ^~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-model.o `test -f 'model.c' || echo './'`model.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -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 -Wformat -Werror=format-security -c -o mb-sumpt.o `test -f 'sumpt.c' || echo './'`sumpt.c
sumpt.c: In function ‘DoSump’:
sumpt.c:335:5: warning: ‘__builtin_strncpy’ output may be truncated copying 90 bytes from a string of length 119 [-Wstringop-truncation]
335 | strncpy (temp, sumpParams.sumpOutfile, 90);
| ^
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 ‘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 ());
| ~~~~~~~~~~~~~~~~~
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 -Wformat -Werror=format-security -c -o mb-utils.o `test -f 'utils.c' || echo './'`utils.c
In function ‘sprintf’,
inlined from ‘ShowConTree’ at sumpt.c:8173:21:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: warning: ‘__builtin_sprintf’ argument 3 may overlap destination object ‘printLine’ [-Wrestrict]
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
sumpt.c: In function ‘DoSumt’:
sumpt.c:4958:39: warning: ‘.run’ directive writing 4 bytes into a region of size between 1 and 120 [-Wformat-overflow=]
4958 | sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1);
| ^~~~
sumpt.c:4958:36: note: directive argument in the range [-2147483647, 2147483647]
4958 | sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1);
| ^~~~~~~~~~~~
In function ‘sprintf’,
inlined from ‘DoSumt’ at sumpt.c:4958:17:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 8 and 137 bytes into a destination of size 120
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
sumpt.c: In function ‘DoSumt’:
sumpt.c:4956:39: warning: ‘.t’ directive writing 2 bytes into a region of size between 1 and 120 [-Wformat-overflow=]
4956 | sprintf (tempName, "%s.t", fileName);
| ^~
In function ‘sprintf’,
inlined from ‘DoSumt’ at sumpt.c:4956:17:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 3 and 122 bytes into a destination of size 120
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:535,
from /usr/include/memory.h:29,
from bayes.h:31,
from utils.c:38:
In function ‘strncpy’,
inlined from ‘CopyResults’ at utils.c:311:9:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ accessing 0 or more bytes at offsets [-1073741824, 1073741823] and 0 may overlap up to 1073741824 bytes at offset [0, 1073741823] [-Wrestrict]
95 | return __builtin___strncpy_chk (__dest, __src, __len,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
96 | __glibc_objsize (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncpy’,
inlined from ‘CopyProcessSsFile’ at utils.c:350:9:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ accessing 0 or more bytes at offsets [-1073741824, 1073741823] and 0 may overlap up to 1073741824 bytes at offset [0, 1073741823] [-Wrestrict]
95 | return __builtin___strncpy_chk (__dest, __src, __len,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
96 | __glibc_objsize (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncpy’,
inlined from ‘CopyTreeResults’ at utils.c:422:9:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ accessing 0 or more bytes at offsets [-1073741824, 1073741823] and 0 may overlap up to 1073741824 bytes at offset [0, 1073741823] [-Wrestrict]
95 | return __builtin___strncpy_chk (__dest, __src, __len,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
96 | __glibc_objsize (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
model.c: In function ‘SetModelParams’:
model.c:19111:48: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
19111 | sprintf (tempMult, "g_m{%d}", i+1);
| ^
In file included from /usr/include/stdio.h:906,
from bayes.h:32,
from model.c:38:
In function ‘sprintf’,
inlined from ‘SetModelParams’ at model.c:19111:21:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 7 and 16 bytes into a destination of size 15
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
gcc -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o mb mb-bayes.o mb-best.o mb-command.o mb-likelihood.o mb-mbbeagle.o mb-mcmc.o mb-model.o mb-proposal.o mb-sumpt.o mb-utils.o -L/usr/lib -lhmsbeagle -lm -lreadline
make[4]: Leaving directory '/<<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... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for pdflatex... no
checking for bibtex... no
configure: WARNING: pdflatex or bibtex is missing, documentation will not be rebuilt
checking whether make supports the include directive... yes (GNU style)
checking whether to compile using MPI... no
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... unsupported
checking for gcc option to enable C99 features... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for sqrt in -lm... yes
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
configure: Trying to locate Beagle (hmsbeagle-1) in '/usr'
checking for libhmsbeagle/beagle.h... yes
checking for beagleCreateInstance in -lhmsbeagle... yes
configure: Found Beagle in '/usr'
checking for beagleSetCPUThreadCount in -lhmsbeagle... yes
configure: Using BEAGLE_CFLAGS="-I/usr/include/libhmsbeagle-1 -pthread"
configure: Using BEAGLE_LIBS="-L/usr/lib -lhmsbeagle"
checking for a readline compatible library... -lreadline
checking for readline.h... no
checking for readline/readline.h... yes
checking whether readline supports history... yes
checking for history.h... no
checking for readline/history.h... yes
checking for float.h... yes
checking for limits.h... yes
checking for memory.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for size_t... yes
checking for _Bool... yes
checking for stdbool.h that conforms to C99... yes
checking for C compiler vendor... gnu
checking for a sed that does not truncate output... /bin/sed
checking for C compiler version... 12.2.0
checking CFLAGS for most reasonable warnings... -Wall
checking for floor... yes
checking for memset... yes
checking for pow... yes
checking for sqrt... yes
checking for strchr... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating doc/Makefile
config.status: creating doc/manual/Makefile
config.status: creating doc/tutorial/Makefile
config.status: creating examples/Makefile
config.status: creating src/Makefile
config.status: creating src/config.h
config.status: src/config.h is unchanged
config.status: executing depfiles commands
LIBS="-Wl,--as-needed" dh_auto_build
make -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 -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 -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 -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 -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 -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 -Wformat -Werror=format-security -c -o mb-mcmc.o `test -f 'mcmc.c' || echo './'`mcmc.c
mbbeagle.c: In function ‘TreeLikelihood_BeagleMultiPartition’:
mbbeagle.c:2618:33: warning: ‘nStates’ may be used uninitialized [-Wmaybe-uninitialized]
2618 | int i, j, d, c = 0, nStates, beagleReturn, site, dIndex, divisionOffset;
| ^~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-model.o `test -f 'model.c' || echo './'`model.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -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 -Wformat -Werror=format-security -c -o mb-sumpt.o `test -f 'sumpt.c' || echo './'`sumpt.c
sumpt.c: In function ‘DoSump’:
sumpt.c:335:5: warning: ‘__builtin_strncpy’ output may be truncated copying 90 bytes from a string of length 119 [-Wstringop-truncation]
335 | strncpy (temp, sumpParams.sumpOutfile, 90);
| ^
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 ‘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 ());
| ~~~~~~~~~~~~~~~~~
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 -Wformat -Werror=format-security -c -o mb-utils.o `test -f 'utils.c' || echo './'`utils.c
In function ‘sprintf’,
inlined from ‘ShowConTree’ at sumpt.c:8173:21:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: warning: ‘__builtin_sprintf’ argument 3 may overlap destination object ‘printLine’ [-Wrestrict]
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
sumpt.c: In function ‘DoSumt’:
sumpt.c:4958:39: warning: ‘.run’ directive writing 4 bytes into a region of size between 1 and 120 [-Wformat-overflow=]
4958 | sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1);
| ^~~~
sumpt.c:4958:36: note: directive argument in the range [-2147483647, 2147483647]
4958 | sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1);
| ^~~~~~~~~~~~
In function ‘sprintf’,
inlined from ‘DoSumt’ at sumpt.c:4958:17:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 8 and 137 bytes into a destination of size 120
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
sumpt.c: In function ‘DoSumt’:
sumpt.c:4956:39: warning: ‘.t’ directive writing 2 bytes into a region of size between 1 and 120 [-Wformat-overflow=]
4956 | sprintf (tempName, "%s.t", fileName);
| ^~
In function ‘sprintf’,
inlined from ‘DoSumt’ at sumpt.c:4956:17:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 3 and 122 bytes into a destination of size 120
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:535,
from /usr/include/memory.h:29,
from bayes.h:31,
from utils.c:38:
In function ‘strncpy’,
inlined from ‘CopyResults’ at utils.c:311:9:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ accessing 0 or more bytes at offsets [-1073741824, 1073741823] and 0 may overlap up to 1073741824 bytes at offset [0, 1073741823] [-Wrestrict]
95 | return __builtin___strncpy_chk (__dest, __src, __len,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
96 | __glibc_objsize (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncpy’,
inlined from ‘CopyProcessSsFile’ at utils.c:350:9:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ accessing 0 or more bytes at offsets [-1073741824, 1073741823] and 0 may overlap up to 1073741824 bytes at offset [0, 1073741823] [-Wrestrict]
95 | return __builtin___strncpy_chk (__dest, __src, __len,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
96 | __glibc_objsize (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncpy’,
inlined from ‘CopyTreeResults’ at utils.c:422:9:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ accessing 0 or more bytes at offsets [-1073741824, 1073741823] and 0 may overlap up to 1073741824 bytes at offset [0, 1073741823] [-Wrestrict]
95 | return __builtin___strncpy_chk (__dest, __src, __len,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
96 | __glibc_objsize (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
model.c: In function ‘SetModelParams’:
model.c:19111:48: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
19111 | sprintf (tempMult, "g_m{%d}", i+1);
| ^
In file included from /usr/include/stdio.h:906,
from bayes.h:32,
from model.c:38:
In function ‘sprintf’,
inlined from ‘SetModelParams’ at model.c:19111:21:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 7 and 16 bytes into a destination of size 15
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
gcc -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o mb mb-bayes.o mb-best.o mb-command.o mb-likelihood.o mb-mbbeagle.o mb-mcmc.o mb-model.o mb-proposal.o mb-sumpt.o mb-utils.o -L/usr/lib -lhmsbeagle -lm -lreadline
make[4]: Leaving directory '/<<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 -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'.
/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'.
/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'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/mrbayes'
/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'.
/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'.
/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.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-6_armhf.deb'.
dpkg-deb: building package 'mrbayes' in '../mrbayes_3.2.7a-6_armhf.deb'.
dpkg-deb: building package 'mrbayes-mpi' in '../mrbayes-mpi_3.2.7a-6_armhf.deb'.
dpkg-deb: building package 'mrbayes-mpi-dbgsym' in '../mrbayes-mpi-dbgsym_3.2.7a-6_armhf.deb'.
dpkg-genbuildinfo --build=any -O../mrbayes_3.2.7a-6_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> -O../mrbayes_3.2.7a-6_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 2022-11-26T07:25:02Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
mrbayes_3.2.7a-6_armhf.changes:
-------------------------------
Format: 1.8
Date: Thu, 24 Nov 2022 12:52:27 +0100
Source: mrbayes
Binary: mrbayes mrbayes-dbgsym mrbayes-mpi mrbayes-mpi-dbgsym
Architecture: armhf
Version: 3.2.7a-6
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
mrbayes - Bayesian Inference of Phylogeny
mrbayes-mpi - Bayesian Inference of Phylogeny - mpi version
Changes:
mrbayes (3.2.7a-6) unstable; urgency=medium
.
* Fix watch file
* Standards-Version: 4.6.1 (routine-update)
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Files:
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6930d84bb253e5c8e990ea84a594b5ca 968 debug optional mrbayes-mpi-dbgsym_3.2.7a-6_armhf.deb
7e73ab78b09fb832d9eebbf2c7b619da 490164 science optional mrbayes-mpi_3.2.7a-6_armhf.deb
df3a2fc187958097ad5364d00a34cbb7 7992 science optional mrbayes_3.2.7a-6_armhf.buildinfo
a2b5982aade084862af3d3ac4bf6e5b6 552832 science optional mrbayes_3.2.7a-6_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: mrbayes
Binary: mrbayes mrbayes-dbgsym mrbayes-mpi mrbayes-mpi-dbgsym
Architecture: armhf
Version: 3.2.7a-6
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Sat, 26 Nov 2022 07:25:00 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
adduser (= 3.129),
autoconf (= 2.71-2),
autoconf-archive (= 20220903-3),
automake (= 1:1.16.5-1.3),
autopoint (= 0.21-10),
autotools-dev (= 20220109.1),
base-files (= 12.3+rpi1),
base-passwd (= 3.6.1),
bash (= 5.2~rc2-2),
binutils (= 2.39-6+rpi1),
binutils-arm-linux-gnueabihf (= 2.39-6+rpi1),
binutils-common (= 2.39-6+rpi1),
bsdextrautils (= 2.38.1-3),
bsdutils (= 1:2.38.1-3),
build-essential (= 12.9),
bzip2 (= 1.0.8-5+b2),
coreutils (= 9.1-1),
cpp (= 4:12.2.0-1+rpi1),
cpp-12 (= 12.2.0-9+rpi1),
dash (= 0.5.11+git20210903+057cd650a4ed-9),
debconf (= 1.5.79),
debhelper (= 13.11.1),
debianutils (= 5.7-0.3),
dh-autoreconf (= 20),
dh-strip-nondeterminism (= 1.13.0-1),
diffutils (= 1:3.8-1),
dpkg (= 1.21.9+rpi1),
dpkg-dev (= 1.21.9+rpi1),
dwz (= 0.14+20220924-2),
file (= 1:5.41-4),
findutils (= 4.9.0-3),
g++ (= 4:12.2.0-1+rpi1),
g++-12 (= 12.2.0-9+rpi1),
gcc (= 4:12.2.0-1+rpi1),
gcc-12 (= 12.2.0-9+rpi1),
gcc-12-base (= 12.2.0-9+rpi1),
gettext (= 0.21-10),
gettext-base (= 0.21-10),
gfortran-12 (= 12.2.0-9+rpi1),
grep (= 3.7-1),
groff-base (= 1.22.4-8),
gzip (= 1.12-1),
hostname (= 3.23),
ibverbs-providers (= 42.0-1),
init-system-helpers (= 1.64),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.1-1),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 12.2.0-9+rpi1),
libatomic1 (= 12.2.0-9+rpi1),
libattr1 (= 1:2.5.1-1),
libaudit-common (= 1:3.0.7-1.1),
libaudit1 (= 1:3.0.7-1.1),
libbinutils (= 2.39-6+rpi1),
libblkid1 (= 2.38.1-3),
libbsd0 (= 0.11.7-1),
libbz2-1.0 (= 1.0.8-5+b2),
libc-bin (= 2.35-2+rpi1),
libc-dev-bin (= 2.35-2+rpi1),
libc6 (= 2.35-2+rpi1),
libc6-dev (= 2.35-2+rpi1),
libcap-ng0 (= 0.8.3-1),
libcap2 (= 1:2.44-1),
libcbor0.8 (= 0.8.0-2),
libcc1-0 (= 12.2.0-9+rpi1),
libclang-common-14-dev (= 1:14.0.6-2+rpi1),
libclang-cpp14 (= 1:14.0.6-2+rpi1),
libclc-14 (= 1:14.0.6-2+rpi1),
libclc-14-dev (= 1:14.0.6-2+rpi1),
libcom-err2 (= 1.46.6~rc1-1),
libcrypt-dev (= 1:4.4.28-2),
libcrypt1 (= 1:4.4.28-2),
libctf-nobfd0 (= 2.39-6+rpi1),
libctf0 (= 2.39-6+rpi1),
libdb5.3 (= 5.3.28+dfsg1-0.10),
libdebconfclient0 (= 0.264),
libdebhelper-perl (= 13.11.1),
libdpkg-perl (= 1.21.9+rpi1),
libdrm-amdgpu1 (= 2.4.114-1+rpi1),
libdrm-common (= 2.4.114-1+rpi1),
libdrm-nouveau2 (= 2.4.114-1+rpi1),
libdrm-radeon1 (= 2.4.114-1+rpi1),
libdrm2 (= 2.4.114-1+rpi1),
libedit2 (= 3.1-20221030-1),
libelf1 (= 0.187-2+rpi2),
libevent-2.1-7 (= 2.1.12-stable-5+b1),
libevent-core-2.1-7 (= 2.1.12-stable-5+b1),
libevent-dev (= 2.1.12-stable-5+b1),
libevent-extra-2.1-7 (= 2.1.12-stable-5+b1),
libevent-openssl-2.1-7 (= 2.1.12-stable-5+b1),
libevent-pthreads-2.1-7 (= 2.1.12-stable-5+b1),
libexpat1 (= 2.5.0-1),
libfabric1 (= 1.11.0-3),
libffi8 (= 3.4.2-4),
libfido2-1 (= 1.12.0-2),
libfile-stripnondeterminism-perl (= 1.13.0-1),
libgcc-12-dev (= 12.2.0-9+rpi1),
libgcc-s1 (= 12.2.0-9+rpi1),
libgcrypt20 (= 1.10.1-2+b2),
libgdbm-compat4 (= 1.23-3),
libgdbm6 (= 1.23-3),
libgfortran-12-dev (= 12.2.0-9+rpi1),
libgfortran5 (= 12.2.0-9+rpi1),
libgmp10 (= 2:6.2.1+dfsg1-1.1),
libgomp1 (= 12.2.0-9+rpi1),
libgpg-error0 (= 1.45-2),
libgssapi-krb5-2 (= 1.20-1),
libhmsbeagle-dev (= 3.1.2+dfsg-12),
libhmsbeagle1v5 (= 3.1.2+dfsg-12),
libhwloc-dev (= 2.8.0-1),
libhwloc-plugins (= 2.8.0-1),
libhwloc15 (= 2.8.0-1),
libibverbs-dev (= 42.0-1),
libibverbs1 (= 42.0-1),
libicu72 (= 72.1-2),
libisl23 (= 0.25-1),
libjs-jquery (= 3.6.1+dfsg+~3.5.14-1),
libjs-jquery-ui (= 1.13.2+dfsg-1),
libk5crypto3 (= 1.20-1),
libkeyutils1 (= 1.6.3-1),
libkrb5-3 (= 1.20-1),
libkrb5support0 (= 1.20-1),
libllvm14 (= 1:14.0.6-2+rpi1),
libltdl-dev (= 2.4.7-4),
libltdl7 (= 2.4.7-4),
liblz4-1 (= 1.9.4-1+rpi1),
liblzma5 (= 5.2.5-2.1),
libmagic-mgc (= 1:5.41-4),
libmagic1 (= 1:5.41-4),
libmd0 (= 1.0.4-2),
libmount1 (= 2.38.1-3),
libmpc3 (= 1.2.1-2),
libmpfr6 (= 4.1.0-3),
libmunge2 (= 0.5.14-6),
libncurses-dev (= 6.3+20220423-2),
libncurses6 (= 6.3+20220423-2),
libncursesw6 (= 6.3+20220423-2),
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),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libnuma-dev (= 2.0.15-1),
libnuma1 (= 2.0.15-1),
libopenmpi-dev (= 4.1.4-3+rpi1),
libopenmpi3 (= 4.1.4-3+rpi1),
libpam-modules (= 1.5.2-5),
libpam-modules-bin (= 1.5.2-5),
libpam-runtime (= 1.5.2-5),
libpam0g (= 1.5.2-5),
libpciaccess0 (= 0.17-2),
libpcre2-8-0 (= 10.40-1+b2),
libpcre3 (= 2:8.39-14),
libperl5.36 (= 5.36.0-4),
libpipeline1 (= 1.5.7-1),
libpkgconf3 (= 1.8.0-11),
libpmix-dev (= 4.2.1-3+b1),
libpmix2 (= 4.2.1-3+b1),
librdmacm1 (= 42.0-1),
libreadline-dev (= 8.2-1.1),
libreadline8 (= 8.2-1.1),
libseccomp2 (= 2.5.4-1+rpi1),
libselinux1 (= 3.4-1),
libsemanage-common (= 3.4-1),
libsemanage2 (= 3.4-1),
libsepol2 (= 3.4-2),
libsmartcols1 (= 2.38.1-3),
libssl3 (= 3.0.7-1),
libstdc++-12-dev (= 12.2.0-9+rpi1),
libstdc++6 (= 12.2.0-9+rpi1),
libsub-override-perl (= 0.09-4),
libsystemd0 (= 251.5-1+rpi1),
libtinfo6 (= 6.3+20220423-2),
libtirpc-common (= 1.3.3+ds-1),
libtirpc-dev (= 1.3.3+ds-1),
libtirpc3 (= 1.3.3+ds-1),
libtool (= 2.4.7-4),
libubsan1 (= 12.2.0-9+rpi1),
libuchardet0 (= 0.0.7-1),
libudev1 (= 251.5-1+rpi1),
libunistring2 (= 1.0-2),
libuuid1 (= 2.38.1-3),
libx11-6 (= 2:1.8.1-2),
libx11-data (= 2:1.8.1-2),
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-1.1),
libxnvctrl0 (= 510.85.02-2),
libz3-4 (= 4.8.12-3),
libzstd1 (= 1.5.2+dfsg-1),
linux-libc-dev (= 5.19.6-1+rpi1),
login (= 1:4.12.3+dfsg1-1),
m4 (= 1.4.19-1),
make (= 4.3-4.1),
man-db (= 2.11.1-1),
mawk (= 1.3.4.20200120-3.1),
mesa-opencl-icd (= 22.2.0-1+rpi1),
mpi-default-dev (= 1.14),
ncurses-base (= 6.3+20220423-2),
ncurses-bin (= 6.3+20220423-2),
ocl-icd-libopencl1 (= 2.3.1-1),
openmpi-bin (= 4.1.4-3+rpi1),
openmpi-common (= 4.1.4-3+rpi1),
openssh-client (= 1:9.1p1-1),
passwd (= 1:4.12.3+dfsg1-1),
patch (= 2.7.6-7),
perl (= 5.36.0-4),
perl-base (= 5.36.0-4),
perl-modules-5.36 (= 5.36.0-4),
pkg-config (= 1.8.0-11),
pkgconf (= 1.8.0-11),
pkgconf-bin (= 1.8.0-11),
po-debconf (= 1.0.21+nmu1),
readline-common (= 8.2-1),
rpcsvc-proto (= 1.4.2-4),
sed (= 4.8-1),
sensible-utils (= 0.0.17),
sysvinit-utils (= 3.05-6),
tar (= 1.34+dfsg-1),
util-linux (= 2.38.1-3),
util-linux-extra (= 2.38.1-3),
xz-utils (= 5.2.5-2.1),
zlib1g (= 1:1.2.11.dfsg-4.1),
zlib1g-dev (= 1:1.2.11.dfsg-4.1)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
SOURCE_DATE_EPOCH="1669290747"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
mrbayes-dbgsym_3.2.7a-6_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 999160 bytes: control archive=536 bytes.
373 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: mrbayes-dbgsym
Source: mrbayes
Version: 3.2.7a-6
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1051
Depends: mrbayes (= 3.2.7a-6)
Section: debug
Priority: optional
Description: debug symbols for mrbayes
Build-Ids: e643003b1d2175f6634bfb925355196f1a70de1a
drwxr-xr-x root/root 0 2022-11-24 11:52 ./
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/lib/
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/lib/debug/
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/lib/debug/.build-id/e6/
-rw-r--r-- root/root 1065032 2022-11-24 11:52 ./usr/lib/debug/.build-id/e6/43003b1d2175f6634bfb925355196f1a70de1a.debug
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/share/
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/share/doc/
lrwxrwxrwx root/root 0 2022-11-24 11:52 ./usr/share/doc/mrbayes-dbgsym -> mrbayes
mrbayes-mpi-dbgsym_3.2.7a-6_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 968 bytes: control archive=480 bytes.
383 bytes, 12 lines control
0 bytes, 0 lines md5sums
Package: mrbayes-mpi-dbgsym
Source: mrbayes
Version: 3.2.7a-6
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-6)
Section: debug
Priority: optional
Description: debug symbols for mrbayes-mpi
Build-Ids: e643003b1d2175f6634bfb925355196f1a70de1a
drwxr-xr-x root/root 0 2022-11-24 11:52 ./
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/lib/
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/lib/debug/
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/lib/debug/.build-id/e6/
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/share/
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/share/doc/
lrwxrwxrwx root/root 0 2022-11-24 11:52 ./usr/share/doc/mrbayes-mpi-dbgsym -> mrbayes-mpi
mrbayes-mpi_3.2.7a-6_armhf.deb
------------------------------
new Debian package, version 2.0.
size 490164 bytes: control archive=1040 bytes.
1003 bytes, 21 lines control
399 bytes, 6 lines md5sums
Package: mrbayes-mpi
Source: mrbayes
Version: 3.2.7a-6
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1435
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 2022-11-24 11:52 ./
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/bin/
-rwxr-xr-x root/root 162 2022-11-24 11:52 ./usr/bin/mb-mpi
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/lib/
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/lib/mrbayes-mpi/
-rwxr-xr-x root/root 1452012 2022-11-24 11:52 ./usr/lib/mrbayes-mpi/mb-mpi
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/share/
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/share/doc/mrbayes-mpi/
-rw-r--r-- root/root 348 2022-11-24 11:52 ./usr/share/doc/mrbayes-mpi/README.Debian
-rw-r--r-- root/root 1005 2022-11-24 11:52 ./usr/share/doc/mrbayes-mpi/changelog.Debian.gz
-rw-r--r-- root/root 1567 2022-11-24 11:52 ./usr/share/doc/mrbayes-mpi/copyright
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/share/man/
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/share/man/man1/
-rw-r--r-- root/root 226 2022-11-24 11:52 ./usr/share/man/man1/mb-mpi.1.gz
mrbayes_3.2.7a-6_armhf.deb
--------------------------
new Debian package, version 2.0.
size 552832 bytes: control archive=1236 bytes.
857 bytes, 18 lines control
1084 bytes, 15 lines md5sums
Package: mrbayes
Version: 3.2.7a-6
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2499
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 2022-11-24 11:52 ./
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/bin/
-rwxr-xr-x root/root 1452012 2022-11-24 11:52 ./usr/bin/mb
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/share/
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/share/doc/mrbayes/
-rw-r--r-- root/root 311 2022-11-24 11:52 ./usr/share/doc/mrbayes/README.Debian
-rw-r--r-- root/root 262 2022-11-24 11:52 ./usr/share/doc/mrbayes/README.test
-rw-r--r-- root/root 1005 2022-11-24 11:52 ./usr/share/doc/mrbayes/changelog.Debian.gz
-rw-r--r-- root/root 1567 2022-11-24 11:52 ./usr/share/doc/mrbayes/copyright
drwxr-xr-x root/root 0 2022-11-24 11:52 ./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 2022-11-24 11:52 ./usr/share/doc/mrbayes/run-unit-test
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/share/man/
drwxr-xr-x root/root 0 2022-11-24 11:52 ./usr/share/man/man1/
-rw-r--r-- root/root 206 2022-11-24 11:52 ./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: 51340
Build-Time: 551
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 924
Job: mrbayes_3.2.7a-6
Machine Architecture: armhf
Package: mrbayes
Package-Time: 1514
Source-Version: 3.2.7a-6
Space: 51340
Status: successful
Version: 3.2.7a-6
--------------------------------------------------------------------------------
Finished at 2022-11-26T07:25:02Z
Build needed 00:25:14, 51340k disk space