Raspbian Package Auto-Building

Build log for mrbayes (3.2.7a-6+b1) on armhf

mrbayes → 3.2.7a-6+b1 → armhf → 2023-12-22 16:39:06 

sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01

+==============================================================================+
| mrbayes 3.2.7a-6+b1 (armhf)                  Fri, 22 Dec 2023 16:27:33 +0000 |
+==============================================================================+

Package: mrbayes
Version: 3.2.7a-6+b1
Source Version: 3.2.7a-6
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-150a7ce1-4be3-4beb-8e39-fb34c85d86b9' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| 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 [13.7 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.5 MB]
Fetched 28.2 MB in 10s (2939 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
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 (10.3 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/mrbayes-Tbb3p0/mrbayes-3.2.7a' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/mrbayes-Tbb3p0' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install build-essential                                                      |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-NIR5hk/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-NIR5hk/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-NIR5hk/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg:               imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg:              unchanged: 1
gpg:       secret keys read: 1
gpg:   secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-NIR5hk/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-NIR5hk/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-NIR5hk/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-NIR5hk/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-NIR5hk/apt_archive ./ Packages [430 B]
Fetched 2106 B in 0s (10.5 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install core 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 netbase sensible-utils sgml-base
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 25 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-NIR5hk/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (79.5 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12528 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (armhf included in any all)

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper-compat (= 13), libreadline-dev, mpi-default-dev, libhmsbeagle-dev, autoconf-archive, pkg-config
Filtered Build-Depends: debhelper-compat (= 13), libreadline-dev, mpi-default-dev, libhmsbeagle-dev, autoconf-archive, pkg-config
dpkg-deb: building package 'sbuild-build-depends-mrbayes-dummy' in '/<<BUILDDIR>>/resolver-NIR5hk/apt_archive/sbuild-build-depends-mrbayes-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy sbuild-build-depends-mrbayes-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-NIR5hk/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-NIR5hk/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-NIR5hk/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-NIR5hk/apt_archive ./ Sources [540 B]
Get:5 copy:/<<BUILDDIR>>/resolver-NIR5hk/apt_archive ./ Packages [621 B]
Fetched 2494 B in 0s (13.8 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install mrbayes 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 netbase sgml-base
Use 'apt autoremove' to remove them.
The following additional 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-15-dev libclang-cpp15
  libclc-15 libclc-15-dev libdebhelper-perl libdrm-amdgpu1 libdrm-common
  libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libevent-2.1-7
  libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7
  libevent-pthreads-2.1-7 libexpat1 libfabric1 libfido2-1
  libfile-stripnondeterminism-perl libgfortran-12-dev libgfortran5
  libhmsbeagle-dev libhmsbeagle1v5 libhwloc-dev libhwloc-plugins libhwloc15
  libibverbs-dev libibverbs1 libicu72 libjs-jquery libjs-jquery-ui libllvm15
  libllvmspirvlib15 libltdl-dev libltdl7 libmagic-mgc libmagic1 libmunge2
  libncurses-dev libncurses6 libnl-3-200 libnl-3-dev libnl-route-3-200
  libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3
  libpciaccess0 libpipeline1 libpkgconf3 libpmix-dev libpmix2 librdmacm1
  libreadline-dev libsensors-config libsensors5 libssl3 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 zlib1g-dev
Suggested packages:
  gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev
  libgettextpo-dev gfortran-12-doc libcoarrays-dev groff libjs-jquery-ui-docs
  libtool-doc ncurses-doc openmpi-doc pciutils readline-doc lm-sensors gcj-jdk
  m4-doc apparmor less www-browser gfortran | fortran-compiler keychain
  libpam-ssh monkeysphere ssh-askpass libmail-box-perl
Recommended packages:
  curl | wget | lynx libarchive-cpio-perl javascript-common libgpm2
  libcoarrays-openmpi-dev 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-15-dev libclang-cpp15
  libclc-15 libclc-15-dev libdebhelper-perl libdrm-amdgpu1 libdrm-common
  libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libevent-2.1-7
  libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7
  libevent-pthreads-2.1-7 libexpat1 libfabric1 libfido2-1
  libfile-stripnondeterminism-perl libgfortran-12-dev libgfortran5
  libhmsbeagle-dev libhmsbeagle1v5 libhwloc-dev libhwloc-plugins libhwloc15
  libibverbs-dev libibverbs1 libicu72 libjs-jquery libjs-jquery-ui libllvm15
  libllvmspirvlib15 libltdl-dev libltdl7 libmagic-mgc libmagic1 libmunge2
  libncurses-dev libncurses6 libnl-3-200 libnl-3-dev libnl-route-3-200
  libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3
  libpciaccess0 libpipeline1 libpkgconf3 libpmix-dev libpmix2 librdmacm1
  libreadline-dev libsensors-config libsensors5 libsub-override-perl libtool
  libuchardet0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2
  libxnvctrl0 libz3-4 m4 man-db mesa-opencl-icd mpi-default-dev
  ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config
  pkgconf pkgconf-bin po-debconf sbuild-build-depends-mrbayes-dummy zlib1g-dev
The following packages will be upgraded:
  libssl3
1 upgraded, 106 newly installed, 0 to remove and 24 not upgraded.
Need to get 102 MB of archives.
After this operation, 526 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-NIR5hk/apt_archive ./ sbuild-build-depends-mrbayes-dummy 0.invalid.0 [904 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf autoconf-archive all 20220903-3 [775 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-10 [774 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-5 [78.5 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.11.2-2 [1342 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.44-3 [95.3 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.44-3 [41.5 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-12 [156 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.7-2 [112 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf libedit2 armhf 3.1-20221030-2 [76.2 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf libcbor0.8 armhf 0.8.0-2 [22.8 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf libssl3 armhf 3.0.11-1~deb12u2 [1620 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf libfido2-1 armhf 1.12.0-2 [67.6 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf openssh-client armhf 1:9.2p1-2+deb12u2 [819 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-3 [256 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-12 [495 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.11.4 [81.2 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-5 [517 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libicu72 armhf 72.1-3 [9009 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3~deb12u1 [570 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-12 [1201 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.11.4 [942 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libgfortran5 armhf 12.2.0-14+rpi1 [238 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libgfortran-12-dev armhf 12.2.0-14+rpi1 [285 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf gfortran-12 armhf 12.2.0-14+rpi1 [7509 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libnl-3-200 armhf 3.7.0-0.2 [55.0 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libnl-route-3-200 armhf 3.7.0-0.2 [152 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf libibverbs1 armhf 44.0-2 [52.7 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf ibverbs-providers armhf 44.0-2 [28.1 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf libz3-4 armhf 4.8.12-3.1 [5797 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libllvm15 armhf 1:15.0.6-4+rpi1+b1 [20.7 MB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf libclang-common-15-dev armhf 1:15.0.6-4+rpi1+b1 [3474 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf libclang-cpp15 armhf 1:15.0.6-4+rpi1+b1 [9902 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf libclc-15-dev all 1:15.0.6-4+rpi1 [54.5 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libclc-15 all 1:15.0.6-4+rpi1 [10.1 MB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libdrm-common all 2.4.114-1+rpi1 [7276 B]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libdrm2 armhf 2.4.114-1+rpi1 [32.8 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libdrm-amdgpu1 armhf 2.4.114-1+rpi1 [19.3 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libdrm-nouveau2 armhf 2.4.114-1+rpi1 [17.0 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libdrm-radeon1 armhf 2.4.114-1+rpi1 [20.7 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libevent-2.1-7 armhf 2.1.12-stable-8 [160 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-8 [119 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-8 [97.3 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-8 [53.2 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-8 [58.3 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libevent-dev armhf 2.1.12-stable-8 [274 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.5.0-1 [77.2 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf librdmacm1 armhf 44.0-2 [59.4 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf libfabric1 armhf 1.17.0-3 [376 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf ocl-icd-libopencl1 armhf 2.3.1-1 [40.3 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libllvmspirvlib15 armhf 15.0.0-2+rpi1 [598 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libsensors-config all 1:3.6.0-7.1 [14.3 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libsensors5 armhf 1:3.6.0-7.1 [31.6 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf mesa-opencl-icd armhf 22.3.6-1+deb12u1+rpi1 [10.6 MB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf libhmsbeagle1v5 armhf 3.1.2+dfsg-13 [86.7 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libhmsbeagle-dev armhf 3.1.2+dfsg-13 [225 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf libhwloc15 armhf 2.9.0-1 [124 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libnuma1 armhf 2.0.16-1 [18.4 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libnuma-dev armhf 2.0.16-1 [31.5 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libltdl7 armhf 2.4.7-5 [390 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libltdl-dev armhf 2.4.7-5 [161 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libhwloc-dev armhf 2.9.0-1 [196 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libpciaccess0 armhf 0.17-2 [48.8 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf libx11-data all 2:1.8.4-2+deb12u2 [292 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.8.4-2+deb12u2 [655 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf libxnvctrl0 armhf 525.85.05-3~deb12u1 [12.3 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf libhwloc-plugins armhf 2.9.0-1 [16.0 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf libnl-3-dev armhf 3.7.0-0.2 [93.4 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf libnl-route-3-dev armhf 3.7.0-0.2 [163 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf libibverbs-dev armhf 44.0-2 [191 kB]
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Get:98 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [901 kB]
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Get:100 http://172.17.4.1/private bookworm-staging/main armhf openmpi-bin armhf 4.1.4-3+rpi1 [192 kB]
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Get:104 http://172.17.4.1/private bookworm-staging/main armhf mpi-default-dev armhf 1.14 [5548 B]
Get:105 http://172.17.4.1/private bookworm-staging/main armhf pkgconf-bin armhf 1.8.1-1 [27.8 kB]
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Get:107 http://172.17.4.1/private bookworm-staging/main armhf pkg-config armhf 1.8.1-1 [13.7 kB]
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Selecting previously unselected package mpi-default-dev.
Preparing to unpack .../102-mpi-default-dev_1.14_armhf.deb ...
Unpacking mpi-default-dev (1.14) ...
Selecting previously unselected package pkgconf-bin.
Preparing to unpack .../103-pkgconf-bin_1.8.1-1_armhf.deb ...
Unpacking pkgconf-bin (1.8.1-1) ...
Selecting previously unselected package pkgconf:armhf.
Preparing to unpack .../104-pkgconf_1.8.1-1_armhf.deb ...
Unpacking pkgconf:armhf (1.8.1-1) ...
Selecting previously unselected package pkg-config:armhf.
Preparing to unpack .../105-pkg-config_1.8.1-1_armhf.deb ...
Unpacking pkg-config:armhf (1.8.1-1) ...
Selecting previously unselected package sbuild-build-depends-mrbayes-dummy.
Preparing to unpack .../106-sbuild-build-depends-mrbayes-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-mrbayes-dummy (0.invalid.0) ...
Setting up libexpat1:armhf (2.5.0-1) ...
Setting up libpipeline1:armhf (1.5.7-1) ...
Setting up libpciaccess0:armhf (0.17-2) ...
Setting up libclc-15-dev (1:15.0.6-4+rpi1) ...
Setting up libxau6:armhf (1:1.0.9-1) ...
Setting up libicu72:armhf (72.1-3) ...
Setting up bsdextrautils (2.38.1-5) ...
Setting up libmagic-mgc (1:5.44-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libcbor0.8:armhf (0.8.0-2) ...
Setting up libdebhelper-perl (13.11.4) ...
Setting up libssl3:armhf (3.0.11-1~deb12u2) ...
Setting up libsensors-config (1:3.6.0-7.1) ...
Setting up libmagic1:armhf (1:5.44-3) ...
Setting up gettext-base (0.21-12) ...
Setting up m4 (1.4.19-3) ...
Setting up autoconf-archive (20220903-3) ...
Setting up file (1:5.44-3) ...
Setting up autotools-dev (20220109.1) ...
Setting up libz3-4:armhf (4.8.12-3.1) ...
Setting up libpkgconf3:armhf (1.8.1-1) ...
Setting up libmunge2 (0.5.15-2) ...
Setting up libx11-data (2:1.8.4-2+deb12u2) ...
Setting up libncurses6:armhf (6.4-4) ...
Setting up libhwloc15:armhf (2.9.0-1) ...
Setting up libevent-core-2.1-7:armhf (2.1.12-stable-8) ...
Setting up libevent-2.1-7:armhf (2.1.12-stable-8) ...
Setting up autopoint (0.21-12) ...
Setting up pkgconf-bin (1.8.1-1) ...
Setting up libsensors5:armhf (1:3.6.0-7.1) ...
Setting up libltdl7:armhf (2.4.7-5) ...
Setting up libgfortran5:armhf (12.2.0-14+rpi1) ...
Setting up autoconf (2.71-3) ...
Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-1) ...
Setting up libnuma1:armhf (2.0.16-1) ...
Setting up ocl-icd-libopencl1:armhf (2.3.1-1) ...
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) ...
Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Setting up libfido2-1:armhf (1.12.0-2) ...
Setting up libbsd0:armhf (0.11.7-2) ...
Setting up libdrm-common (2.4.114-1+rpi1) ...
Setting up libelf1:armhf (0.188-2.1+rpi1) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.3~deb12u1) ...
Setting up libevent-pthreads-2.1-7:armhf (2.1.12-stable-8) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up libevent-extra-2.1-7:armhf (2.1.12-stable-8) ...
Setting up libncurses-dev:armhf (6.4-4) ...
Setting up libxcb1:armhf (1.15-1) ...
Setting up gettext (0.21-12) ...
Setting up libtool (2.4.7-5) ...
Setting up libedit2:armhf (3.1-20221030-2) ...
Setting up libevent-openssl-2.1-7:armhf (2.1.12-stable-8) ...
Setting up libgfortran-12-dev:armhf (12.2.0-14+rpi1) ...
Setting up libreadline-dev:armhf (8.2-1.3) ...
Setting up pkgconf:armhf (1.8.1-1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libnuma-dev:armhf (2.0.16-1) ...
Setting up libnl-route-3-200:armhf (3.7.0-0.2) ...
Setting up dh-autoreconf (20) ...
Setting up libltdl-dev:armhf (2.4.7-5) ...
Setting up gfortran-12 (12.2.0-14+rpi1) ...
Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
Setting up libevent-dev (2.1.12-stable-8) ...
Setting up pkg-config:armhf (1.8.1-1) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up libdrm2:armhf (2.4.114-1+rpi1) ...
Setting up dwz (0.15-1) ...
Setting up libnl-3-dev:armhf (3.7.0-0.2) ...
Setting up groff-base (1.22.4-10) ...
Setting up libllvm15:armhf (1:15.0.6-4+rpi1+b1) ...
Setting up libx11-6:armhf (2:1.8.4-2+deb12u2) ...
Setting up libhwloc-dev:armhf (2.9.0-1) ...
Setting up libdrm-amdgpu1:armhf (2.4.114-1+rpi1) ...
Setting up libibverbs1:armhf (44.0-2) ...
Setting up libdrm-nouveau2:armhf (2.4.114-1+rpi1) ...
Setting up libllvmspirvlib15:armhf (15.0.0-2+rpi1) ...
Setting up libclang-common-15-dev (1:15.0.6-4+rpi1+b1) ...
Setting up ibverbs-providers:armhf (44.0-2) ...
Setting up libdrm-radeon1:armhf (2.4.114-1+rpi1) ...
Setting up openssh-client (1:9.2p1-2+deb12u2) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up man-db (2.11.2-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libxnvctrl0:armhf (525.85.05-3~deb12u1) ...
Setting up libnl-route-3-dev:armhf (3.7.0-0.2) ...
Setting up libclang-cpp15 (1:15.0.6-4+rpi1+b1) ...
Setting up libclc-15 (1:15.0.6-4+rpi1) ...
Setting up mesa-opencl-icd:armhf (22.3.6-1+deb12u1+rpi1) ...
Setting up librdmacm1:armhf (44.0-2) ...
Setting up libhmsbeagle1v5:armhf (3.1.2+dfsg-13) ...
Setting up debhelper (13.11.4) ...
Setting up libibverbs-dev:armhf (44.0-2) ...
Setting up libhwloc-plugins:armhf (2.9.0-1) ...
Setting up libfabric1:armhf (1.17.0-3) ...
Setting up libhmsbeagle-dev (3.1.2+dfsg-13) ...
Setting up libpmix2:armhf (4.2.2-1+deb12u1) ...
Setting up libopenmpi3:armhf (4.1.4-3+rpi1) ...
Setting up libpmix-dev:armhf (4.2.2-1+deb12u1) ...
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-mrbayes-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.36-9+rpi1+deb12u1) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 4.15.0-187-generic armhf (armv8l)
Toolchain package versions: binutils_2.40-2+rpi2 dpkg-dev_1.21.22+rpi1 g++-12_12.2.0-14+rpi1 gcc-12_12.2.0-14+rpi1 libc6-dev_2.36-9+rpi1+deb12u1 libstdc++-12-dev_12.2.0-14+rpi1 libstdc++6_12.2.0-14+rpi1 linux-libc-dev_6.1.38-1+rpi1
Package versions: adduser_3.134 apt_2.6.1 autoconf_2.71-3 autoconf-archive_20220903-3 automake_1:1.16.5-1.3 autopoint_0.21-12 autotools-dev_20220109.1 base-files_12.4+rpi1+deb12u1 base-passwd_3.6.1 bash_5.2.15-2 binutils_2.40-2+rpi2 binutils-arm-linux-gnueabihf_2.40-2+rpi2 binutils-common_2.40-2+rpi2 bsdextrautils_2.38.1-5 bsdutils_1:2.38.1-5 build-essential_12.9 bzip2_1.0.8-5+b2 coreutils_9.1-1 cpp_4:12.2.0-3+rpi1 cpp-12_12.2.0-14+rpi1 dash_0.5.12-2 debconf_1.5.82 debhelper_13.11.4 debianutils_5.7-0.4 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 dirmngr_2.2.40-1.1 dpkg_1.21.22+rpi1 dpkg-dev_1.21.22+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.31-1.2 file_1:5.44-3 findutils_4.9.0-4 g++_4:12.2.0-3+rpi1 g++-12_12.2.0-14+rpi1 gcc_4:12.2.0-3+rpi1 gcc-12_12.2.0-14+rpi1 gcc-12-base_12.2.0-14+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_0.21-12 gettext-base_0.21-12 gfortran-12_12.2.0-14+rpi1 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.8-5 groff-base_1.22.4-10 gzip_1.12-1 hostname_3.23+nmu1 ibverbs-providers_44.0-2 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20221126-1 krb5-locales_1.20.1-2 libacl1_2.3.1-3 libapt-pkg6.0_2.6.1 libarchive-zip-perl_1.68-1 libasan8_12.2.0-14+rpi1 libassuan0_2.5.5-5 libatomic1_12.2.0-14+rpi1 libattr1_1:2.5.1-4 libaudit-common_1:3.0.9-1 libaudit1_1:3.0.9-1 libbinutils_2.40-2+rpi2 libblkid1_2.38.1-5 libbsd0_0.11.7-2 libbz2-1.0_1.0.8-5+b2 libc-bin_2.36-9+rpi1+deb12u1 libc-dev-bin_2.36-9+rpi1+deb12u1 libc6_2.36-9+rpi1+deb12u1 libc6-dev_2.36-9+rpi1+deb12u1 libcap-ng0_0.8.3-1+b1 libcap2_1:2.66-4 libcap2-bin_1:2.66-4 libcbor0.8_0.8.0-2 libcc1-0_12.2.0-14+rpi1 libclang-common-15-dev_1:15.0.6-4+rpi1+b1 libclang-cpp15_1:15.0.6-4+rpi1+b1 libclc-15_1:15.0.6-4+rpi1 libclc-15-dev_1:15.0.6-4+rpi1 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.33-2 libcrypt1_1:4.4.33-2 libctf-nobfd0_2.40-2+rpi2 libctf0_2.40-2+rpi2 libdb5.3_5.3.28+dfsg2-1 libdebconfclient0_0.270 libdebhelper-perl_13.11.4 libdpkg-perl_1.21.22+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_3.1-20221030-2 libelf1_0.188-2.1+rpi1 libevent-2.1-7_2.1.12-stable-8 libevent-core-2.1-7_2.1.12-stable-8 libevent-dev_2.1.12-stable-8 libevent-extra-2.1-7_2.1.12-stable-8 libevent-openssl-2.1-7_2.1.12-stable-8 libevent-pthreads-2.1-7_2.1.12-stable-8 libexpat1_2.5.0-1 libext2fs2_1.47.0-2 libfabric1_1.17.0-3 libfakeroot_1.31-1.2 libffi8_3.4.4-1 libfido2-1_1.12.0-2 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.2.0-14+rpi1 libgcc-s1_12.2.0-14+rpi1 libgcrypt20_1.10.1-3 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran-12-dev_12.2.0-14+rpi1 libgfortran5_12.2.0-14+rpi1 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.9-2 libgomp1_12.2.0-14+rpi1 libgpg-error0_1.46-1 libgssapi-krb5-2_1.20.1-2 libhmsbeagle-dev_3.1.2+dfsg-13 libhmsbeagle1v5_3.1.2+dfsg-13 libhogweed6_3.8.1-2 libhwloc-dev_2.9.0-1 libhwloc-plugins_2.9.0-1 libhwloc15_2.9.0-1 libibverbs-dev_44.0-2 libibverbs1_44.0-2 libicu72_72.1-3 libidn2-0_2.3.3-1+b2 libisl23_0.25-1 libjansson4_2.14-2 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-jquery-ui_1.13.2+dfsg-1 libk5crypto3_1.20.1-2 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-2 libkrb5support0_1.20.1-2 libksba8_1.6.3-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1 libllvm15_1:15.0.6-4+rpi1+b1 libllvmspirvlib15_15.0.0-2+rpi1 libltdl-dev_2.4.7-5 libltdl7_2.4.7-5 liblz4-1_1.9.4-1+rpi1+b1 liblzma5_5.4.1-0.2 libmagic-mgc_1:5.44-3 libmagic1_1:5.44-3 libmd0_1.0.4-2 libmount1_2.38.1-5 libmpc3_1.3.1-1 libmpfr6_4.2.0-1 libmunge2_0.5.15-2 libncurses-dev_6.4-4 libncurses6_6.4-4 libncursesw6_6.4-4 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_2.0.16-1 libnuma1_2.0.16-1 libopenmpi-dev_4.1.4-3+rpi1 libopenmpi3_4.1.4-3+rpi1 libp11-kit0_0.24.1-2 libpam-cap_1:2.66-4 libpam-modules_1.5.2-6 libpam-modules-bin_1.5.2-6 libpam-runtime_1.5.2-6 libpam0g_1.5.2-6 libpciaccess0_0.17-2 libpcre2-8-0_10.42-1 libpcre3_2:8.39-15 libperl5.36_5.36.0-7 libpipeline1_1.5.7-1 libpkgconf3_1.8.1-1 libpmix-dev_4.2.2-1+deb12u1 libpmix2_4.2.2-1+deb12u1 librdmacm1_44.0-2 libreadline-dev_8.2-1.3 libreadline8_8.2-1.3 libsasl2-2_2.1.28+dfsg-10 libsasl2-modules-db_2.1.28+dfsg-10 libseccomp2_2.5.4-1+rpi1+b1 libselinux1_3.4-1+b2 libsemanage-common_3.4-1 libsemanage2_3.4-1+b2 libsensors-config_1:3.6.0-7.1 libsensors5_1:3.6.0-7.1 libsepol1_3.1-1 libsepol2_3.4-2.1 libsmartcols1_2.38.1-5 libsqlite3-0_3.40.1-2 libss2_1.47.0-2 libssl1.1_1.1.1o-1 libssl3_3.0.11-1~deb12u2 libstdc++-12-dev_12.2.0-14+rpi1 libstdc++6_12.2.0-14+rpi1 libsub-override-perl_0.09-4 libsystemd0_252.12-1~deb12u1+rpi1 libtasn1-6_4.19.0-2 libtinfo6_6.4-4 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-5 libubsan1_12.2.0-14+rpi1 libuchardet0_0.0.7-1 libudev1_252.12-1~deb12u1+rpi1 libunistring2_1.0-2 libuuid1_2.38.1-5 libx11-6_2:1.8.4-2+deb12u2 libx11-data_2:1.8.4-2+deb12u2 libxau6_1:1.0.9-1 libxcb1_1.15-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1 libxml2_2.9.14+dfsg-1.3~deb12u1 libxnvctrl0_525.85.05-3~deb12u1 libxxhash0_0.8.1-1 libz3-4_4.8.12-3.1 libzstd1_1.5.4+dfsg2-5 linux-libc-dev_6.1.38-1+rpi1 login_1:4.13+dfsg1-1 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-3 make_4.3-4.1 man-db_2.11.2-2 mawk_1.3.4.20200120-3.1 mesa-opencl-icd_22.3.6-1+deb12u1+rpi1 mount_2.38.1-5 mpi-default-dev_1.14 nano_7.2-1 ncurses-base_6.4-4 ncurses-bin_6.4-4 netbase_6.4 ocl-icd-libopencl1_2.3.1-1 openmpi-bin_4.1.4-3+rpi1 openmpi-common_4.1.4-3+rpi1 openssh-client_1:9.2p1-2+deb12u2 passwd_1:4.13+dfsg1-1 patch_2.7.6-7 perl_5.36.0-7 perl-base_5.36.0-7 perl-modules-5.36_5.36.0-7 pinentry-curses_1.2.1-1 pkg-config_1.8.1-1 pkgconf_1.8.1-1 pkgconf-bin_1.8.1-1 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.2-1.3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-mrbayes-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.17+nmu1 sgml-base_1.31 sysvinit-utils_3.06-4 tar_1.34+dfsg-1.2 tzdata_2023c-5 util-linux_2.38.1-5 util-linux-extra_2.38.1-5 xz-utils_5.4.1-0.2 zlib1g_1:1.2.13.dfsg-1 zlib1g-dev_1:1.2.13.dfsg-1

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

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 inline signature for ./mrbayes_3.2.7a-6.dsc: no acceptable signature found
dpkg-source: info: extracting mrbayes in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking mrbayes_3.2.7a.orig.tar.gz
dpkg-source: info: unpacking mrbayes_3.2.7a-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

Hack binNMU version
-------------------

Created changelog entry for binNMU version 3.2.7a-6+b1

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-150a7ce1-4be3-4beb-8e39-fb34c85d86b9
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd

dpkg-buildpackage
-----------------

dpkg-buildpackage: info: source package mrbayes
dpkg-buildpackage: info: source version 3.2.7a-6+b1
dpkg-buildpackage: info: source distribution bookworm-staging
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
 debian/rules clean
dh clean
   dh_clean
 debian/rules binary-arch
dh binary-arch
   dh_update_autotools_config -a
   dh_autoreconf -a
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- --with-beagle=/usr --enable-mpi=yes --enable-debug=yes
	./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-beagle=/usr --enable-mpi=yes --enable-debug=yes
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /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 ());
      |                                   ~~~~~~~~~~~~~~~~~
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 ());
      |                                   ~~~~~~~~~~~~~~~~~
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
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 ());
      |                                   ~~~~~~~~~~~~~~~~~
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 ());
      |                                   ~~~~~~~~~~~~~~~~~
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
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 MBDating.pdf '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/mrbayes'
 /usr/bin/install -c -m 644 hym.nex '/<<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-mpi/usr/lib/mrbayes-mpi/mb-mpi 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/usr/bin/mb 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' in '../mrbayes_3.2.7a-6+b1_armhf.deb'.
dpkg-deb: building package 'mrbayes-dbgsym' in '../mrbayes-dbgsym_3.2.7a-6+b1_armhf.deb'.
dpkg-deb: building package 'mrbayes-mpi-dbgsym' in '../mrbayes-mpi-dbgsym_3.2.7a-6+b1_armhf.deb'.
dpkg-deb: building package 'mrbayes-mpi' in '../mrbayes-mpi_3.2.7a-6+b1_armhf.deb'.
 dpkg-genbuildinfo --build=any -O../mrbayes_3.2.7a-6+b1_armhf.buildinfo
 dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> -O../mrbayes_3.2.7a-6+b1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2023-12-22T16:39:02Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Post Build Chroot                                                            |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


mrbayes_3.2.7a-6+b1_armhf.changes:
----------------------------------

Format: 1.8
Date: Thu, 24 Nov 2022 12:52:27 +0100
Source: mrbayes (3.2.7a-6)
Binary: mrbayes mrbayes-dbgsym mrbayes-mpi mrbayes-mpi-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 3.2.7a-6+b1
Distribution: bookworm-staging
Urgency: low
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Description:
 mrbayes    - Bayesian Inference of Phylogeny
 mrbayes-mpi - Bayesian Inference of Phylogeny - mpi version
Changes:
 mrbayes (3.2.7a-6+b1) bookworm-staging; urgency=low, binary-only=yes
 .
   * Binary-only non-maintainer upload for armhf; no source changes.
   * rebuild due to debcheck failure
Checksums-Sha1:
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Checksums-Sha256:
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 f9ae7c05e8aab75c3e24cb68662d0324 490152 science optional mrbayes-mpi_3.2.7a-6+b1_armhf.deb
 c524ec4e4c1150822b56d0862b90fa2a 8481 science optional mrbayes_3.2.7a-6+b1_armhf.buildinfo
 67d63f0b0f283866f58e62850f33bcc1 552880 science optional mrbayes_3.2.7a-6+b1_armhf.deb

+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


mrbayes-dbgsym_3.2.7a-6+b1_armhf.deb
------------------------------------

 new Debian package, version 2.0.
 size 999200 bytes: control archive=544 bytes.
     390 bytes,    12 lines      control              
     106 bytes,     1 lines      md5sums              
 Package: mrbayes-dbgsym
 Source: mrbayes (3.2.7a-6)
 Version: 3.2.7a-6+b1
 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+b1)
 Section: debug
 Priority: optional
 Description: debug symbols for mrbayes
 Build-Ids: 17d117d91a412c10be95b6dccff1a48d285bb5df

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/17/
-rw-r--r-- root/root   1065024 2022-11-24 11:52 ./usr/lib/debug/.build-id/17/d117d91a412c10be95b6dccff1a48d285bb5df.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+b1_armhf.deb
----------------------------------------

 new Debian package, version 2.0.
 size 976 bytes: control archive=488 bytes.
     400 bytes,    12 lines      control              
       0 bytes,     0 lines      md5sums              
 Package: mrbayes-mpi-dbgsym
 Source: mrbayes (3.2.7a-6)
 Version: 3.2.7a-6+b1
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 10
 Depends: mrbayes-mpi (= 3.2.7a-6+b1)
 Section: debug
 Priority: optional
 Description: debug symbols for mrbayes-mpi
 Build-Ids: 17d117d91a412c10be95b6dccff1a48d285bb5df

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/17/
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+b1_armhf.deb
---------------------------------

 new Debian package, version 2.0.
 size 490152 bytes: control archive=1072 bytes.
    1017 bytes,    21 lines      control              
     485 bytes,     7 lines      md5sums              
 Package: mrbayes-mpi
 Source: mrbayes (3.2.7a-6)
 Version: 3.2.7a-6+b1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 1392
 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   1406956 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       222 2022-11-24 11:52 ./usr/share/doc/mrbayes-mpi/changelog.Debian.armhf.gz
-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+b1_armhf.deb
-----------------------------

 new Debian package, version 2.0.
 size 552880 bytes: control archive=1276 bytes.
     887 bytes,    19 lines      control              
    1166 bytes,    16 lines      md5sums              
 Package: mrbayes
 Source: mrbayes (3.2.7a-6)
 Version: 3.2.7a-6+b1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 2456
 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   1406956 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       222 2022-11-24 11:52 ./usr/share/doc/mrbayes/changelog.Debian.armhf.gz
-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-Space: 51268
Build-Time: 347
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 324
Job: mrbayes_3.2.7a-6
Machine Architecture: armhf
Package: mrbayes
Package-Time: 689
Source-Version: 3.2.7a-6
Space: 51268
Status: successful
Version: 3.2.7a-6+b1
--------------------------------------------------------------------------------
Finished at 2023-12-22T16:39:02Z
Build needed 00:11:29, 51268k disk space