mrbayes →
3.2.7a-4+b1 →
armhf → 2023-12-22 22:53:16
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd
+==============================================================================+
| mrbayes 3.2.7a-4+b1 (armhf) Fri, 22 Dec 2023 22:18:09 +0000 |
+==============================================================================+
Package: mrbayes
Version: 3.2.7a-4+b1
Source Version: 3.2.7a-4
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-438c3452-1985-40ac-95c1-d03d657755b8' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bullseye-staging/main Sources [12.2 MB]
Get:3 http://172.17.4.1/private bullseye-staging/main armhf Packages [13.2 MB]
Fetched 25.5 MB in 26s (971 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| 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 bullseye-staging/main mrbayes 3.2.7a-4 (dsc) [2184 B]
Get:2 http://172.17.4.1/private bullseye-staging/main mrbayes 3.2.7a-4 (tar) [9819 kB]
Get:3 http://172.17.4.1/private bullseye-staging/main mrbayes 3.2.7a-4 (diff) [7136 B]
Fetched 9829 kB in 2s (5025 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/mrbayes-U8JaKU/mrbayes-3.2.7a' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/mrbayes-U8JaKU' 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-nRAHOA/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-nRAHOA/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-nRAHOA/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: 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 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: 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-nRAHOA/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-nRAHOA/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-nRAHOA/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-nRAHOA/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-nRAHOA/apt_archive ./ Packages [429 B]
Fetched 2105 B in 1s (2919 B/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:
bsdextrautils libnss-nis libnss-nisplus netbase sensible-utils
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 69 not upgraded.
Need to get 856 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-nRAHOA/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 856 B in 0s (22.9 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12527 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-nRAHOA/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-nRAHOA/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-nRAHOA/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-nRAHOA/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-nRAHOA/apt_archive ./ Sources [540 B]
Get:5 copy:/<<BUILDDIR>>/resolver-nRAHOA/apt_archive ./ Packages [620 B]
Fetched 2493 B in 1s (3428 B/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:
libnss-nis libnss-nisplus netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf autoconf-archive automake autopoint autotools-dev debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
gfortran-10 groff-base ibverbs-providers intltool-debian libarchive-zip-perl
libbsd0 libcbor0 libclang-common-11-dev libclang-cpp11 libclc-amdgcn
libclc-dev libclc-r600 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-10-dev libgfortran5
libglib2.0-0 libhmsbeagle-dev libhmsbeagle1v5 libhwloc-dev libhwloc-plugins
libhwloc15 libibverbs-dev libibverbs1 libicu67 libjs-jquery libjs-jquery-ui
libllvm11 libltdl-dev libltdl7 libmagic-mgc libmagic1 libmd0 libncurses-dev
libncurses6 libncursesw6 libnl-3-200 libnl-3-dev libnl-route-3-200
libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3
libpciaccess0 libpipeline1 libpmix-dev libpmix2 librdmacm1 libreadline-dev
libsigsegv2 libsub-override-perl libtinfo6 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 po-debconf zlib1g zlib1g-dev
Suggested packages:
gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev
libgettextpo-dev gfortran-10-doc libcoarrays-dev groff libjs-jquery-ui-docs
libtool-doc ncurses-doc openmpi-doc pciutils readline-doc 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 libglib2.0-data shared-mime-info
xdg-user-dirs javascript-common libgpm2 libcoarrays-openmpi-dev xauth
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf autoconf-archive automake autopoint autotools-dev debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
gfortran-10 groff-base ibverbs-providers intltool-debian libarchive-zip-perl
libbsd0 libcbor0 libclang-common-11-dev libclang-cpp11 libclc-amdgcn
libclc-dev libclc-r600 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-10-dev libgfortran5
libglib2.0-0 libhmsbeagle-dev libhmsbeagle1v5 libhwloc-dev libhwloc-plugins
libhwloc15 libibverbs-dev libibverbs1 libicu67 libjs-jquery libjs-jquery-ui
libllvm11 libltdl-dev libltdl7 libmagic-mgc libmagic1 libmd0 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
libpmix-dev libpmix2 librdmacm1 libreadline-dev libsigsegv2
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 po-debconf
sbuild-build-depends-mrbayes-dummy zlib1g-dev
The following packages will be upgraded:
libncursesw6 libtinfo6 zlib1g
3 upgraded, 102 newly installed, 0 to remove and 66 not upgraded.
Need to get 79.0 MB of archives.
After this operation, 384 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-nRAHOA/apt_archive ./ sbuild-build-depends-mrbayes-dummy 0.invalid.0 [912 B]
Get:2 http://172.17.4.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.4.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-6 [793 kB]
Get:4 http://172.17.4.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:5 http://172.17.4.1/private bullseye-staging/main armhf zlib1g armhf 1:1.2.11.dfsg-2+deb11u2 [84.8 kB]
Get:6 http://172.17.4.1/private bullseye-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.4.1/private bullseye-staging/main armhf autoconf-archive all 20190106-2.1 [746 kB]
Get:8 http://172.17.4.1/private bullseye-staging/main armhf libtinfo6 armhf 6.2+20201114-2+deb11u2 [329 kB]
Get:9 http://172.17.4.1/private bullseye-staging/main armhf libncursesw6 armhf 6.2+20201114-2+deb11u2 [105 kB]
Get:10 http://172.17.4.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.39-3+deb11u1 [273 kB]
Get:11 http://172.17.4.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.39-3+deb11u1 [119 kB]
Get:12 http://172.17.4.1/private bullseye-staging/main armhf file armhf 1:5.39-3+deb11u1 [68.1 kB]
Get:13 http://172.17.4.1/private bullseye-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:14 http://172.17.4.1/private bullseye-staging/main armhf libmd0 armhf 1.0.3-3 [27.2 kB]
Get:15 http://172.17.4.1/private bullseye-staging/main armhf libbsd0 armhf 0.11.3-1+deb11u1 [103 kB]
Get:16 http://172.17.4.1/private bullseye-staging/main armhf libedit2 armhf 3.1-20191231-2 [80.2 kB]
Get:17 http://172.17.4.1/private bullseye-staging/main armhf libcbor0 armhf 0.5.0+dfsg-2 [19.5 kB]
Get:18 http://172.17.4.1/private bullseye-staging/main armhf libfido2-1 armhf 1.6.0-2 [47.2 kB]
Get:19 http://172.17.4.1/private bullseye-staging/main armhf openssh-client armhf 1:8.4p1-5+deb11u3 [796 kB]
Get:20 http://172.17.4.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:21 http://172.17.4.1/private bullseye-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:22 http://172.17.4.1/private bullseye-staging/main armhf autoconf all 2.69-14 [313 kB]
Get:23 http://172.17.4.1/private bullseye-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:24 http://172.17.4.1/private bullseye-staging/main armhf automake all 1:1.16.3-2 [814 kB]
Get:25 http://172.17.4.1/private bullseye-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:26 http://172.17.4.1/private bullseye-staging/main armhf libdebhelper-perl all 13.3.4 [189 kB]
Get:27 http://172.17.4.1/private bullseye-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:28 http://172.17.4.1/private bullseye-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:29 http://172.17.4.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:30 http://172.17.4.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:31 http://172.17.4.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:32 http://172.17.4.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:33 http://172.17.4.1/private bullseye-staging/main armhf libelf1 armhf 0.183-1 [161 kB]
Get:34 http://172.17.4.1/private bullseye-staging/main armhf dwz armhf 0.13+20210201-1 [164 kB]
Get:35 http://172.17.4.1/private bullseye-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:36 http://172.17.4.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.7+deb11u4 [581 kB]
Get:37 http://172.17.4.1/private bullseye-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:38 http://172.17.4.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:39 http://172.17.4.1/private bullseye-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:40 http://172.17.4.1/private bullseye-staging/main armhf debhelper all 13.3.4 [1049 kB]
Get:41 http://172.17.4.1/private bullseye-staging/main armhf libgfortran5 armhf 10.2.1-6+rpi1 [232 kB]
Get:42 http://172.17.4.1/private bullseye-staging/main armhf libgfortran-10-dev armhf 10.2.1-6+rpi1 [278 kB]
Get:43 http://172.17.4.1/private bullseye-staging/main armhf gfortran-10 armhf 10.2.1-6+rpi1 [7195 kB]
Get:44 http://172.17.4.1/private bullseye-staging/main armhf libnl-3-200 armhf 3.4.0-1 [55.0 kB]
Get:45 http://172.17.4.1/private bullseye-staging/main armhf libnl-route-3-200 armhf 3.4.0-1 [132 kB]
Get:46 http://172.17.4.1/private bullseye-staging/main armhf libibverbs1 armhf 33.2-1 [52.4 kB]
Get:47 http://172.17.4.1/private bullseye-staging/main armhf ibverbs-providers armhf 33.2-1 [25.0 kB]
Get:48 http://172.17.4.1/private bullseye-staging/main armhf libz3-4 armhf 4.8.10-1 [5689 kB]
Get:49 http://172.17.4.1/private bullseye-staging/main armhf libllvm11 armhf 1:11.0.1-2+rpi1 [15.6 MB]
Get:50 http://172.17.4.1/private bullseye-staging/main armhf libclang-common-11-dev armhf 1:11.0.1-2+rpi1 [2832 kB]
Get:51 http://172.17.4.1/private bullseye-staging/main armhf libclang-cpp11 armhf 1:11.0.1-2+rpi1 [8275 kB]
Get:52 http://172.17.4.1/private bullseye-staging/main armhf libclc-dev all 0.2.0+git20190827-8 [26.4 kB]
Get:53 http://172.17.4.1/private bullseye-staging/main armhf libclc-amdgcn all 0.2.0+git20190827-8 [2268 kB]
Get:54 http://172.17.4.1/private bullseye-staging/main armhf libclc-r600 all 0.2.0+git20190827-8 [1668 kB]
Get:55 http://172.17.4.1/private bullseye-staging/main armhf libdrm-common all 2.4.104-1+rpi1 [15.0 kB]
Get:56 http://172.17.4.1/private bullseye-staging/main armhf libdrm2 armhf 2.4.104-1+rpi1 [37.8 kB]
Get:57 http://172.17.4.1/private bullseye-staging/main armhf libdrm-amdgpu1 armhf 2.4.104-1+rpi1 [27.4 kB]
Get:58 http://172.17.4.1/private bullseye-staging/main armhf libdrm-nouveau2 armhf 2.4.104-1+rpi1 [25.0 kB]
Get:59 http://172.17.4.1/private bullseye-staging/main armhf libdrm-radeon1 armhf 2.4.104-1+rpi1 [29.2 kB]
Get:60 http://172.17.4.1/private bullseye-staging/main armhf libevent-2.1-7 armhf 2.1.12-stable-1 [167 kB]
Get:61 http://172.17.4.1/private bullseye-staging/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-1 [126 kB]
Get:62 http://172.17.4.1/private bullseye-staging/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-1 [100 kB]
Get:63 http://172.17.4.1/private bullseye-staging/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-1 [56.8 kB]
Get:64 http://172.17.4.1/private bullseye-staging/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-1 [61.7 kB]
Get:65 http://172.17.4.1/private bullseye-staging/main armhf libevent-dev armhf 2.1.12-stable-1 [281 kB]
Get:66 http://172.17.4.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.10-2+deb11u5 [75.0 kB]
Get:67 http://172.17.4.1/private bullseye-staging/main armhf librdmacm1 armhf 33.2-1 [60.0 kB]
Get:68 http://172.17.4.1/private bullseye-staging/main armhf libfabric1 armhf 1.11.0-2 [311 kB]
Get:69 http://172.17.4.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.8-1 [1183 kB]
Get:70 http://172.17.4.1/private bullseye-staging/main armhf ocl-icd-libopencl1 armhf 2.2.14-2 [39.9 kB]
Get:71 http://172.17.4.1/private bullseye-staging/main armhf mesa-opencl-icd armhf 20.3.5-1+rpi1 [3574 kB]
Get:72 http://172.17.4.1/private bullseye-staging/main armhf libhmsbeagle1v5 armhf 3.1.2+dfsg-10 [139 kB]
Get:73 http://172.17.4.1/private bullseye-staging/main armhf libhmsbeagle-dev armhf 3.1.2+dfsg-10 [280 kB]
Get:74 http://172.17.4.1/private bullseye-staging/main armhf libhwloc15 armhf 2.4.1+dfsg-1 [122 kB]
Get:75 http://172.17.4.1/private bullseye-staging/main armhf libnuma1 armhf 2.0.12-1 [22.5 kB]
Get:76 http://172.17.4.1/private bullseye-staging/main armhf libnuma-dev armhf 2.0.12-1 [35.6 kB]
Get:77 http://172.17.4.1/private bullseye-staging/main armhf libltdl7 armhf 2.4.6-15 [388 kB]
Get:78 http://172.17.4.1/private bullseye-staging/main armhf libltdl-dev armhf 2.4.6-15 [159 kB]
Get:79 http://172.17.4.1/private bullseye-staging/main armhf libhwloc-dev armhf 2.4.1+dfsg-1 [190 kB]
Get:80 http://172.17.4.1/private bullseye-staging/main armhf libpciaccess0 armhf 0.16-1 [51.0 kB]
Get:81 http://172.17.4.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:82 http://172.17.4.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:83 http://172.17.4.1/private bullseye-staging/main armhf libxcb1 armhf 1.14-3 [136 kB]
Get:84 http://172.17.4.1/private bullseye-staging/main armhf libx11-data all 2:1.7.2-1+deb11u2 [311 kB]
Get:85 http://172.17.4.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.7.2-1+deb11u2 [706 kB]
Get:86 http://172.17.4.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1.1 [47.8 kB]
Get:87 http://172.17.4.1/private bullseye-staging/main armhf libxnvctrl0 armhf 470.141.03-1~deb11u1 [26.4 kB]
Get:88 http://172.17.4.1/private bullseye-staging/main armhf libhwloc-plugins armhf 2.4.1+dfsg-1 [19.9 kB]
Get:89 http://172.17.4.1/private bullseye-staging/main armhf libnl-3-dev armhf 3.4.0-1 [92.4 kB]
Get:90 http://172.17.4.1/private bullseye-staging/main armhf libnl-route-3-dev armhf 3.4.0-1 [145 kB]
Get:91 http://172.17.4.1/private bullseye-staging/main armhf libibverbs-dev armhf 33.2-1 [179 kB]
Get:92 http://172.17.4.1/private bullseye-staging/main armhf libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB]
Get:93 http://172.17.4.1/private bullseye-staging/main armhf libjs-jquery-ui all 1.12.1+dfsg-8+deb11u1 [232 kB]
Get:94 http://172.17.4.1/private bullseye-staging/main armhf libncurses6 armhf 6.2+20201114-2+deb11u2 [79.5 kB]
Get:95 http://172.17.4.1/private bullseye-staging/main armhf libncurses-dev armhf 6.2+20201114-2+deb11u2 [288 kB]
Get:96 http://172.17.4.1/private bullseye-staging/main armhf libpmix2 armhf 4.0.0-4.1+deb11u1 [468 kB]
Get:97 http://172.17.4.1/private bullseye-staging/main armhf libopenmpi3 armhf 4.1.0-10+rpi1 [1768 kB]
Get:98 http://172.17.4.1/private bullseye-staging/main armhf openmpi-common all 4.1.0-10+rpi1 [177 kB]
Get:99 http://172.17.4.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2+deb11u2 [184 kB]
Get:100 http://172.17.4.1/private bullseye-staging/main armhf libpmix-dev armhf 4.0.0-4.1+deb11u1 [602 kB]
Get:101 http://172.17.4.1/private bullseye-staging/main armhf openmpi-bin armhf 4.1.0-10+rpi1 [205 kB]
Get:102 http://172.17.4.1/private bullseye-staging/main armhf libopenmpi-dev armhf 4.1.0-10+rpi1 [1143 kB]
Get:103 http://172.17.4.1/private bullseye-staging/main armhf libreadline-dev armhf 8.1-1 [121 kB]
Get:104 http://172.17.4.1/private bullseye-staging/main armhf mpi-default-dev armhf 1.13 [5476 B]
Get:105 http://172.17.4.1/private bullseye-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
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Unpacking openmpi-bin (4.1.0-10+rpi1) ...
Selecting previously unselected package libopenmpi-dev:armhf.
Preparing to unpack .../92-libopenmpi-dev_4.1.0-10+rpi1_armhf.deb ...
Unpacking libopenmpi-dev:armhf (4.1.0-10+rpi1) ...
Selecting previously unselected package libreadline-dev:armhf.
Preparing to unpack .../93-libreadline-dev_8.1-1_armhf.deb ...
Unpacking libreadline-dev:armhf (8.1-1) ...
Selecting previously unselected package mpi-default-dev.
Preparing to unpack .../94-mpi-default-dev_1.13_armhf.deb ...
Unpacking mpi-default-dev (1.13) ...
Selecting previously unselected package pkg-config.
Preparing to unpack .../95-pkg-config_0.29.2-1_armhf.deb ...
Unpacking pkg-config (0.29.2-1) ...
Selecting previously unselected package sbuild-build-depends-mrbayes-dummy.
Preparing to unpack .../96-sbuild-build-depends-mrbayes-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-mrbayes-dummy (0.invalid.0) ...
Setting up libexpat1:armhf (2.2.10-2+deb11u5) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libpciaccess0:armhf (0.16-1) ...
Setting up libxau6:armhf (1:1.0.9-1) ...
Setting up libicu67:armhf (67.1-7) ...
Setting up libmagic-mgc (1:5.39-3+deb11u1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.66.8-1) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (13.3.4) ...
Setting up libcbor0:armhf (0.5.0+dfsg-2) ...
Setting up libmagic1:armhf (1:5.39-3+deb11u1) ...
Setting up gettext-base (0.21-4) ...
Setting up autoconf-archive (20190106-2.1) ...
Setting up file (1:5.39-3+deb11u1) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up libz3-4:armhf (4.8.10-1) ...
Setting up libx11-data (2:1.7.2-1+deb11u2) ...
Setting up libncurses6:armhf (6.2+20201114-2+deb11u2) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up libhwloc15:armhf (2.4.1+dfsg-1) ...
Setting up libevent-core-2.1-7:armhf (2.1.12-stable-1) ...
Setting up libevent-2.1-7:armhf (2.1.12-stable-1) ...
Setting up autopoint (0.21-4) ...
Setting up pkg-config (0.29.2-1) ...
Setting up libltdl7:armhf (2.4.6-15) ...
Setting up libgfortran5:armhf (10.2.1-6+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2+deb11u2) ...
Setting up libnuma1:armhf (2.0.12-1) ...
Setting up libmd0:armhf (1.0.3-3) ...
Setting up ocl-icd-libopencl1:armhf (2.2.14-2) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libnl-3-200:armhf (3.4.0-1) ...
Setting up openmpi-common (4.1.0-10+rpi1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libgfortran-10-dev:armhf (10.2.1-6+rpi1) ...
Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ...
Setting up libfido2-1:armhf (1.6.0-2) ...
Setting up libclc-dev (0.2.0+git20190827-8) ...
Setting up libbsd0:armhf (0.11.3-1+deb11u1) ...
Setting up libdrm-common (2.4.104-1+rpi1) ...
Setting up libelf1:armhf (0.183-1) ...
Setting up libxml2:armhf (2.9.10+dfsg-6.7+deb11u4) ...
Setting up libevent-pthreads-2.1-7:armhf (2.1.12-stable-1) ...
Setting up libfile-stripnondeterminism-perl (1.12.0-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up libevent-extra-2.1-7:armhf (2.1.12-stable-1) ...
Setting up libncurses-dev:armhf (6.2+20201114-2+deb11u2) ...
Setting up libxcb1:armhf (1.14-3) ...
Setting up gettext (0.21-4) ...
Setting up libtool (2.4.6-15) ...
Setting up libedit2:armhf (3.1-20191231-2) ...
Setting up libevent-openssl-2.1-7:armhf (2.1.12-stable-1) ...
Setting up m4 (1.4.18-5) ...
Setting up libreadline-dev:armhf (8.1-1) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libnuma-dev:armhf (2.0.12-1) ...
Setting up libnl-route-3-200:armhf (3.4.0-1) ...
Setting up libllvm11:armhf (1:11.0.1-2+rpi1) ...
Setting up libjs-jquery-ui (1.12.1+dfsg-8+deb11u1) ...
Setting up libevent-dev (2.1.12-stable-1) ...
Setting up gfortran-10 (10.2.1-6+rpi1) ...
Setting up autoconf (2.69-14) ...
Setting up dh-strip-nondeterminism (1.12.0-1) ...
Setting up libdrm2:armhf (2.4.104-1+rpi1) ...
Setting up dwz (0.13+20210201-1) ...
Setting up libnl-3-dev:armhf (3.4.0-1) ...
Setting up groff-base (1.22.4-6) ...
Setting up libclang-common-11-dev (1:11.0.1-2+rpi1) ...
Setting up libx11-6:armhf (2:1.7.2-1+deb11u2) ...
Setting up libdrm-amdgpu1:armhf (2.4.104-1+rpi1) ...
Setting up automake (1:1.16.3-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libclc-amdgcn (0.2.0+git20190827-8) ...
Setting up libibverbs1:armhf (33.2-1) ...
Setting up libdrm-nouveau2:armhf (2.4.104-1+rpi1) ...
Setting up ibverbs-providers:armhf (33.2-1) ...
Setting up libdrm-radeon1:armhf (2.4.104-1+rpi1) ...
Setting up openssh-client (1:8.4p1-5+deb11u3) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libxext6:armhf (2:1.3.3-1.1) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libxnvctrl0:armhf (470.141.03-1~deb11u1) ...
Setting up libclang-cpp11 (1:11.0.1-2+rpi1) ...
Setting up dh-autoreconf (20) ...
Setting up libnl-route-3-dev:armhf (3.4.0-1) ...
Setting up libltdl-dev:armhf (2.4.6-15) ...
Setting up libclc-r600 (0.2.0+git20190827-8) ...
Setting up libhwloc-dev:armhf (2.4.1+dfsg-1) ...
Setting up mesa-opencl-icd:armhf (20.3.5-1+rpi1) ...
Setting up librdmacm1:armhf (33.2-1) ...
Setting up libhmsbeagle1v5 (3.1.2+dfsg-10) ...
Setting up debhelper (13.3.4) ...
Setting up libibverbs-dev:armhf (33.2-1) ...
Setting up libhwloc-plugins:armhf (2.4.1+dfsg-1) ...
Setting up libfabric1 (1.11.0-2) ...
Setting up libhmsbeagle-dev (3.1.2+dfsg-10) ...
Setting up libpmix2:armhf (4.0.0-4.1+deb11u1) ...
Setting up libopenmpi3:armhf (4.1.0-10+rpi1) ...
Setting up libpmix-dev:armhf (4.0.0-4.1+deb11u1) ...
Setting up openmpi-bin (4.1.0-10+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 (4.1.0-10+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 (1.13) ...
Setting up sbuild-build-depends-mrbayes-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-13+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.35.2-2+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.2.1-6+rpi1 gcc-10_10.2.1-6+rpi1 libc6-dev_2.31-13+rpi1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.2.4 autoconf_2.69-14 autoconf-archive_20190106-2.1 automake_1:1.16.3-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_11.1+rpi1 base-passwd_3.5.51 bash_5.1-2 binutils_2.35.2-2+rpi1 binutils-arm-linux-gnueabihf_2.35.2-2+rpi1 binutils-common_2.35.2-2+rpi1 bsdextrautils_2.36.1-8 bsdutils_1:2.36.1-8 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.2.1-6+rpi1 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.77 debhelper_13.3.4 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.13+20210201-1 e2fsprogs_1.46.2-2 fakeroot_1.25.3-1.1 file_1:5.39-3+deb11u1 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.2.1-6+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.2.1-6+rpi1 gcc-10-base_10.2.1-6+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gettext_0.21-4 gettext-base_0.21-4 gfortran-10_10.2.1-6+rpi1 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.6-1 groff-base_1.22.4-6 gzip_1.10-4 hostname_3.23 ibverbs-providers_33.2-1 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-10 libapt-pkg6.0_2.2.4 libarchive-zip-perl_1.68-1 libasan6_10.2.1-6+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.1-6+rpi1 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libbinutils_2.35.2-2+rpi1 libblkid1_2.36.1-8 libbsd0_0.11.3-1+deb11u1 libbz2-1.0_1.0.8-4 libc-bin_2.31-13+rpi1 libc-dev-bin_2.31-13+rpi1 libc6_2.31-13+rpi1 libc6-dev_2.31-13+rpi1 libcap-ng0_0.7.9-2.2+b1 libcbor0_0.5.0+dfsg-2 libcc1-0_10.2.1-6+rpi1 libclang-common-11-dev_1:11.0.1-2+rpi1 libclang-cpp11_1:11.0.1-2+rpi1 libclc-amdgcn_0.2.0+git20190827-8 libclc-dev_0.2.0+git20190827-8 libclc-r600_0.2.0+git20190827-8 libcom-err2_1.46.2-2 libcrypt-dev_1:4.4.18-4 libcrypt1_1:4.4.18-4 libctf-nobfd0_2.35.2-2+rpi1 libctf0_2.35.2-2+rpi1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.3.4 libdpkg-perl_1.20.9+rpi1 libdrm-amdgpu1_2.4.104-1+rpi1 libdrm-common_2.4.104-1+rpi1 libdrm-nouveau2_2.4.104-1+rpi1 libdrm-radeon1_2.4.104-1+rpi1 libdrm2_2.4.104-1+rpi1 libedit2_3.1-20191231-2 libelf1_0.183-1 libevent-2.1-7_2.1.12-stable-1 libevent-core-2.1-7_2.1.12-stable-1 libevent-dev_2.1.12-stable-1 libevent-extra-2.1-7_2.1.12-stable-1 libevent-openssl-2.1-7_2.1.12-stable-1 libevent-pthreads-2.1-7_2.1.12-stable-1 libexpat1_2.2.10-2+deb11u5 libext2fs2_1.46.2-2 libfabric1_1.11.0-2 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libfido2-1_1.6.0-2 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.2.1-6+rpi1 libgcc-s1_10.2.1-6+rpi1 libgcrypt20_1.8.7-6 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgfortran-10-dev_10.2.1-6+rpi1 libgfortran5_10.2.1-6+rpi1 libglib2.0-0_2.66.8-1 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.1-5 libgomp1_10.2.1-6+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-6 libhmsbeagle-dev_3.1.2+dfsg-10 libhmsbeagle1v5_3.1.2+dfsg-10 libhogweed6_3.7.3-1 libhwloc-dev_2.4.1+dfsg-1 libhwloc-plugins_2.4.1+dfsg-1 libhwloc15_2.4.1+dfsg-1 libibverbs-dev_33.2-1 libibverbs1_33.2-1 libicu67_67.1-7 libidn2-0_2.3.0-5 libisl23_0.23-1 libjs-jquery_3.5.1+dfsg+~3.5.5-7 libjs-jquery-ui_1.12.1+dfsg-8+deb11u1 libk5crypto3_1.18.3-6 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-6 libkrb5support0_1.18.3-6 libksba8_1.5.0-3 libldap-2.4-2_2.4.57+dfsg-3 libldap-common_2.4.57+dfsg-3 libllvm11_1:11.0.1-2+rpi1 libltdl-dev_2.4.6-15 libltdl7_2.4.6-15 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3+deb11u1 libmagic1_1:5.39-3+deb11u1 libmd0_1.0.3-3 libmount1_2.36.1-8 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses-dev_6.2+20201114-2+deb11u2 libncurses6_6.2+20201114-2+deb11u2 libncursesw6_6.2+20201114-2+deb11u2 libnettle8_3.7.3-1 libnl-3-200_3.4.0-1 libnl-3-dev_3.4.0-1 libnl-route-3-200_3.4.0-1 libnl-route-3-dev_3.4.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libnuma-dev_2.0.12-1 libnuma1_2.0.12-1 libopenmpi-dev_4.1.0-10+rpi1 libopenmpi3_4.1.0-10+rpi1 libp11-kit0_0.23.22-1 libpam-modules_1.4.0-9 libpam-modules-bin_1.4.0-9 libpam-runtime_1.4.0-9 libpam0g_1.4.0-9 libpciaccess0_0.16-1 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-4+deb11u1 libpipeline1_1.5.3-1 libpmix-dev_4.0.0-4.1+deb11u1 libpmix2_4.0.0-4.1+deb11u1 librdmacm1_33.2-1 libreadline-dev_8.1-1 libreadline8_8.1-1 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.36.1-8 libsqlite3-0_3.34.1-3 libss2_1.46.2-2 libssl1.1_1.1.1k-1+deb11u1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.3-6+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20201114-2+deb11u2 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtool_2.4.6-15 libubsan1_10.2.1-6+rpi1 libuchardet0_0.0.7-1 libudev1_247.3-6+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-8 libx11-6_2:1.7.2-1+deb11u2 libx11-data_2:1.7.2-1+deb11u2 libxau6_1:1.0.9-1 libxcb1_1.14-3 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1.1 libxml2_2.9.10+dfsg-6.7+deb11u4 libxnvctrl0_470.141.03-1~deb11u1 libxxhash0_0.8.0-2+rpi1 libz3-4_4.8.10-1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.2-2 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mesa-opencl-icd_20.3.5-1+rpi1 mount_2.36.1-8 mpi-default-dev_1.13 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 netbase_6.3 ocl-icd-libopencl1_2.2.14-2 openmpi-bin_4.1.0-10+rpi1 openmpi-common_4.1.0-10+rpi1 openssh-client_1:8.4p1-5+deb11u3 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-4+deb11u1 perl-base_5.32.1-4+deb11u1 perl-modules-5.32_5.32.1-4+deb11u1 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-mrbayes-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.14 sysvinit-utils_2.96-7 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.36.1-8 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2+deb11u2 zlib1g-dev_1:1.2.11.dfsg-2+deb11u2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.92dKwnzL/trustedkeys.kbx': General error
gpgv: Signature made Mon Jul 20 07:57:10 2020 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./mrbayes_3.2.7a-4.dsc
dpkg-source: info: extracting mrbayes in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking mrbayes_3.2.7a.orig.tar.gz
dpkg-source: info: unpacking mrbayes_3.2.7a-4.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 disc space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 3.2.7a-4+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=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-438c3452-1985-40ac-95c1-d03d657755b8
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package mrbayes
dpkg-buildpackage: info: source version 3.2.7a-4+b1
dpkg-buildpackage: info: source distribution bullseye-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 thread-safe 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 we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for sqrt in -lm... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
configure: Trying to locate Beagle (hmsbeagle-1) in '/usr'
checking libhmsbeagle/beagle.h usability... yes
checking libhmsbeagle/beagle.h presence... yes
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 readline.h usability... no
checking readline.h presence... no
checking for readline.h... no
checking readline/readline.h usability... yes
checking readline/readline.h presence... yes
checking for readline/readline.h... yes
checking whether readline supports history... yes
checking history.h usability... no
checking history.h presence... no
checking for history.h... no
checking readline/history.h usability... yes
checking readline/history.h presence... yes
checking for readline/history.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for memory.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for size_t... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for C compiler vendor... gnu
checking for a sed that does not truncate output... /bin/sed
checking for C compiler version... 10.2.1
checking CFLAGS for maximum 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 -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -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 -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -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 -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -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 -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -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 -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -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 -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o mb-mcmc.o `test -f 'mcmc.c' || echo './'`mcmc.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -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 -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -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:867,
from bayes.h:32,
from mcmc.c:45:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 14 and 131 bytes into a destination of size 120
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/memory.h:29,
from bayes.h:31,
from command.c:38:
In function 'strncpy',
inlined from 'DoExecute' at command.c:3560:5:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 98 bytes from a string of length 99 [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o mb-sumpt.o `test -f 'sumpt.c' || echo './'`sumpt.c
mcmc.c: In function 'RunChain':
mcmc.c:17362:46: warning: '.ss' directive writing 3 bytes into a region of size between 1 and 220 [-Wformat-overflow=]
17362 | sprintf (bkupFileName,"%s.ss%d", ckpFileName,chainParams.numStepsSS-stepIndexSS);
| ^~~
In file included from /usr/include/stdio.h:867,
from bayes.h:32,
from mcmc.c:45:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 5 and 234 bytes into a destination of size 220
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/memory.h:29,
from bayes.h:31,
from sumpt.c:38:
In function 'strncpy',
inlined from 'DoSump' at sumpt.c:335:5:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 90 bytes from a string of length 119 [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o mb-utils.o `test -f 'utils.c' || echo './'`utils.c
sumpt.c: In function 'DoCompRefTree':
sumpt.c:4612:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 7 and 126 [-Wformat-overflow=]
4612 | sprintf (inRefName, "%s.run%d.t", comptreeParams.comptFileName2, n+1);
| ^~
sumpt.c:4612:33: note: directive argument in the range [1, 2147483647]
4612 | sprintf (inRefName, "%s.run%d.t", comptreeParams.comptFileName2, n+1);
| ^~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from bayes.h:32,
from sumpt.c:38:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 8 and 136 bytes into a destination of size 130
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'sprintf',
inlined from 'ShowConTree' at sumpt.c:8173:21:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: warning: '__builtin_strcpy' accessing 1 byte at offsets [-2147483648, 2147483647] and [-2147483648, 2147483646] overlaps 1 byte at offset [-2147483648, 2147483646] [-Wrestrict]
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
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:106:10: 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]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'strncpy',
inlined from 'CopyProcessSsFile' at utils.c:350:9:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: 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]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'strncpy',
inlined from 'CopyTreeResults' at utils.c:422:9:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: 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]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sumpt.c: In function 'DoSumt':
sumpt.c:4958:39: warning: '.run' directive writing 4 bytes into a region of size between 1 and 120 [-Wformat-overflow=]
4958 | sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1);
| ^~~~
sumpt.c:4958:36: note: directive argument in the range [-2147483647, 2147483647]
4958 | sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1);
| ^~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from bayes.h:32,
from sumpt.c:38:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 8 and 137 bytes into a destination of size 120
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 file included from /usr/include/stdio.h:867,
from bayes.h:32,
from sumpt.c:38:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 3 and 122 bytes into a destination of size 120
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.c: In function 'SetModelParams':
model.c:19111:48: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
19111 | sprintf (tempMult, "g_m{%d}", i+1);
| ^
In file included from /usr/include/stdio.h:867,
from bayes.h:32,
from model.c:38:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 15
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I/usr/include/libhmsbeagle-1 -pthread -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -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 thread-safe 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 we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for sqrt in -lm... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
configure: Trying to locate Beagle (hmsbeagle-1) in '/usr'
checking libhmsbeagle/beagle.h usability... yes
checking libhmsbeagle/beagle.h presence... yes
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 readline.h usability... no
checking readline.h presence... no
checking for readline.h... no
checking readline/readline.h usability... yes
checking readline/readline.h presence... yes
checking for readline/readline.h... yes
checking whether readline supports history... yes
checking history.h usability... no
checking history.h presence... no
checking for history.h... no
checking readline/history.h usability... yes
checking readline/history.h presence... yes
checking for readline/history.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for memory.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for size_t... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for C compiler vendor... gnu
checking for a sed that does not truncate output... /bin/sed
checking for C compiler version... 10.2.1
checking CFLAGS for maximum 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 -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -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 -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -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 -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -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 -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -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 -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -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 -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o mb-mcmc.o `test -f 'mcmc.c' || echo './'`mcmc.c
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -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 -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -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:867,
from bayes.h:32,
from mcmc.c:45:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 14 and 131 bytes into a destination of size 120
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/memory.h:29,
from bayes.h:31,
from command.c:38:
In function 'strncpy',
inlined from 'DoExecute' at command.c:3560:5:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 98 bytes from a string of length 99 [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o mb-sumpt.o `test -f 'sumpt.c' || echo './'`sumpt.c
mcmc.c: In function 'RunChain':
mcmc.c:17362:46: warning: '.ss' directive writing 3 bytes into a region of size between 1 and 220 [-Wformat-overflow=]
17362 | sprintf (bkupFileName,"%s.ss%d", ckpFileName,chainParams.numStepsSS-stepIndexSS);
| ^~~
In file included from /usr/include/stdio.h:867,
from bayes.h:32,
from mcmc.c:45:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 5 and 234 bytes into a destination of size 220
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/memory.h:29,
from bayes.h:31,
from sumpt.c:38:
In function 'strncpy',
inlined from 'DoSump' at sumpt.c:335:5:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 90 bytes from a string of length 119 [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o mb-utils.o `test -f 'utils.c' || echo './'`utils.c
sumpt.c: In function 'DoCompRefTree':
sumpt.c:4612:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 7 and 126 [-Wformat-overflow=]
4612 | sprintf (inRefName, "%s.run%d.t", comptreeParams.comptFileName2, n+1);
| ^~
sumpt.c:4612:33: note: directive argument in the range [1, 2147483647]
4612 | sprintf (inRefName, "%s.run%d.t", comptreeParams.comptFileName2, n+1);
| ^~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from bayes.h:32,
from sumpt.c:38:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 8 and 136 bytes into a destination of size 130
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'sprintf',
inlined from 'ShowConTree' at sumpt.c:8173:21:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: warning: '__builtin_strcpy' accessing 1 byte at offsets [-2147483648, 2147483647] and [-2147483648, 2147483646] overlaps 1 byte at offset [-2147483648, 2147483646] [-Wrestrict]
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
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:106:10: 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]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'strncpy',
inlined from 'CopyProcessSsFile' at utils.c:350:9:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: 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]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'strncpy',
inlined from 'CopyTreeResults' at utils.c:422:9:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: 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]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sumpt.c: In function 'DoSumt':
sumpt.c:4958:39: warning: '.run' directive writing 4 bytes into a region of size between 1 and 120 [-Wformat-overflow=]
4958 | sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1);
| ^~~~
sumpt.c:4958:36: note: directive argument in the range [-2147483647, 2147483647]
4958 | sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1);
| ^~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from bayes.h:32,
from sumpt.c:38:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 8 and 137 bytes into a destination of size 120
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 file included from /usr/include/stdio.h:867,
from bayes.h:32,
from sumpt.c:38:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 3 and 122 bytes into a destination of size 120
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.c: In function 'SetModelParams':
model.c:19111:48: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
19111 | sprintf (tempMult, "g_m{%d}", i+1);
| ^
In file included from /usr/include/stdio.h:867,
from bayes.h:32,
from model.c:38:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 15
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I/usr/include/libhmsbeagle-1 -pthread -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -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 VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making check in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -I/usr/include/libhmsbeagle-1 -pthread -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wl,-z,relro -Wl,-z,now -o mb mb-bayes.o mb-best.o mb-command.o mb-likelihood.o mb-mbbeagle.o mb-mcmc.o mb-model.o mb-proposal.o mb-sumpt.o mb-utils.o -L/usr/lib -lhmsbeagle -lm -lreadline
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
Making check in doc
make[2]: Entering directory '/<<PKGBUILDDIR>>/doc'
Making check in manual
make[3]: Entering directory '/<<PKGBUILDDIR>>/doc/manual'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc/manual'
Making check in tutorial
make[3]: Entering directory '/<<PKGBUILDDIR>>/doc/tutorial'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc/tutorial'
make[3]: Entering directory '/<<PKGBUILDDIR>>/doc'
make[3]: Nothing to be done for 'check-am'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/doc'
Making check in examples
make[2]: Entering directory '/<<PKGBUILDDIR>>/examples'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/examples'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: Nothing to be done for 'check-am'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_prep -a
dh_auto_install -a
make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making install in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
make[3]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c mb '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
Making install in doc
make[2]: Entering directory '/<<PKGBUILDDIR>>/doc'
Making install in manual
make[3]: Entering directory '/<<PKGBUILDDIR>>/doc/manual'
make[4]: Entering directory '/<<PKGBUILDDIR>>/doc/manual'
make[4]: Nothing to be done for 'install-exec-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/mrbayes'
/usr/bin/install -c -m 644 Manual_MrBayes_v3.2.pdf '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/mrbayes'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc/manual'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc/manual'
Making install in tutorial
make[3]: Entering directory '/<<PKGBUILDDIR>>/doc/tutorial'
make[4]: Entering directory '/<<PKGBUILDDIR>>/doc/tutorial'
make[4]: Nothing to be done for 'install-exec-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/mrbayes'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/mrbayes'
/usr/bin/install -c -m 644 hym.nex '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/mrbayes'
/usr/bin/install -c -m 644 MBDating.pdf '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/mrbayes'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc/tutorial'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc/tutorial'
make[3]: Entering directory '/<<PKGBUILDDIR>>/doc'
make[4]: Entering directory '/<<PKGBUILDDIR>>/doc'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/doc'
Making install in examples
make[2]: Entering directory '/<<PKGBUILDDIR>>/examples'
make[3]: Entering directory '/<<PKGBUILDDIR>>/examples'
make[3]: Nothing to be done for 'install-exec-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/examples/mrbayes'
/usr/bin/install -c -m 644 avian_ovomucoids.nex codon.nex cynmix.nex finch.nex hymfossil.nex primates.nex replicase.nex sceloporus.nex '/<<PKGBUILDDIR>>/debian/tmp/usr/share/examples/mrbayes'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/examples'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/examples'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Nothing to be done for 'install-exec-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/mrbayes'
/usr/bin/install -c -m 644 COPYING README NEWS '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/mrbayes'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
debian/rules override_dh_installexamples
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installexamples
find debian -name "Makefile*" -delete
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
debian/rules override_dh_compress
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_compress --exclude=.pdf
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_fixperms -a
debian/rules override_dh_missing
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_missing --list-missing
dh_missing: warning: usr/bin/mb exists in debian/tmp but is not installed to anywhere (related file: "mb")
dh_missing: warning: usr/share/doc/mrbayes/COPYING exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/doc/mrbayes/MBDating.pdf exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/doc/mrbayes/Manual_MrBayes_v3.2.pdf exists in debian/tmp but is not installed to anywhere (related file: "doc/manual/Manual_MrBayes_v3.2.pdf")
dh_missing: warning: usr/share/doc/mrbayes/NEWS exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/doc/mrbayes/README exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/doc/mrbayes/hym.nex exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/examples/mrbayes/avian_ovomucoids.nex exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/examples/mrbayes/codon.nex exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/examples/mrbayes/cynmix.nex exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/examples/mrbayes/finch.nex exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/examples/mrbayes/hymfossil.nex exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/examples/mrbayes/primates.nex exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/examples/mrbayes/replicase.nex exists in debian/tmp but is not installed to anywhere
dh_missing: warning: usr/share/examples/mrbayes/sceloporus.nex exists in debian/tmp but is not installed to anywhere
While detecting missing files, dh_missing noted some files with a similar name to those
that were missing. This warning /might/ be resolved by replacing references to the
missing files with the similarly named ones that dh_missing found - assuming the content
is identical.
As an example, you might want to replace:
* mb
with:
* usr/bin/mb
in a file in debian/ or as argument to one of the dh_* tools called from debian/rules.
(Note it is possible the paths are not used verbatim but instead directories
containing or globs matching them are used instead)
Alternatively, add the missing file to debian/not-installed if it cannot and should not
be used.
The following debhelper tools have reported what they installed (with files per package)
* dh_install: mrbayes (1), mrbayes-doc (1), mrbayes-mpi (2)
* dh_installdocs: mrbayes (3), mrbayes-doc (0), mrbayes-mpi (0)
* dh_installexamples: mrbayes (0), mrbayes-doc (0), mrbayes-mpi (0)
* dh_installman: mrbayes (1), mrbayes-doc (0), mrbayes-mpi (1)
If the missing files are installed by another tool, please file a bug against it.
When filing the report, if the tool is not part of debhelper itself, please reference the
"Logging helpers and dh_missing" section from the "PROGRAMMING" guide for debhelper (10.6.3+).
(in the debhelper package: /usr/share/doc/debhelper/PROGRAMMING.gz)
Be sure to test with dpkg-buildpackage -A/-B as the results may vary when only a subset is built
If the omission is intentional or no other helper can take care of this consider adding the
paths to debian/not-installed.
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_dwz -a -a
dh_strip -a -a
dh_makeshlibs -a -a
dh_shlibdeps -a -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/mrbayes/usr/bin/mb was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/mrbayes-mpi/usr/lib/mrbayes-mpi/mb-mpi was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
debian/rules override_dh_installdeb
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# FIXME: That's a dirty hack by simply removing debug information in mrbayes-mpi-dbgsym
# Due to the duplicated build above this is just a duplicate of mrbayes-dbgsym and creates a file conflict
if [ -d debian/.debhelper/mrbayes-mpi/dbgsym-root/usr/lib/debug ] ; then \
find debian/.debhelper/mrbayes-mpi/dbgsym-root/usr/lib/debug -name "*.debug" -delete ; \
fi
dh_installdeb
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'mrbayes-dbgsym' in '../mrbayes-dbgsym_3.2.7a-4+b1_armhf.deb'.
dpkg-deb: building package 'mrbayes' in '../mrbayes_3.2.7a-4+b1_armhf.deb'.
dpkg-deb: building package 'mrbayes-mpi' in '../mrbayes-mpi_3.2.7a-4+b1_armhf.deb'.
dpkg-deb: building package 'mrbayes-mpi-dbgsym' in '../mrbayes-mpi-dbgsym_3.2.7a-4+b1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../mrbayes_3.2.7a-4+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 2023-12-22T22:53:06Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
mrbayes_3.2.7a-4+b1_armhf.changes:
----------------------------------
Format: 1.8
Date: Mon, 20 Jul 2020 09:50:56 +0200
Source: mrbayes (3.2.7a-4)
Binary: mrbayes mrbayes-dbgsym mrbayes-mpi mrbayes-mpi-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 3.2.7a-4+b1
Distribution: bullseye-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Raspbian wandboard test autobuilder <root@raspbian.org>
Description:
mrbayes - Bayesian Inference of Phylogeny
mrbayes-mpi - Bayesian Inference of Phylogeny - mpi version
Changes:
mrbayes (3.2.7a-4+b1) bullseye-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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Files:
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74985cc91947a65c47b22c7dd75c7634 553328 science optional mrbayes_3.2.7a-4+b1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
mrbayes-dbgsym_3.2.7a-4+b1_armhf.deb
------------------------------------
new Debian package, version 2.0.
size 1002996 bytes: control archive=544 bytes.
390 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: mrbayes-dbgsym
Source: mrbayes (3.2.7a-4)
Version: 3.2.7a-4+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1052
Depends: mrbayes (= 3.2.7a-4+b1)
Section: debug
Priority: optional
Description: debug symbols for mrbayes
Build-Ids: 4e6d877342f1b36a709ae6b9f04dd5abf6227fc4
drwxr-xr-x root/root 0 2020-07-20 07:50 ./
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/lib/
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/lib/debug/.build-id/4e/
-rw-r--r-- root/root 1066604 2020-07-20 07:50 ./usr/lib/debug/.build-id/4e/6d877342f1b36a709ae6b9f04dd5abf6227fc4.debug
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/share/
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-07-20 07:50 ./usr/share/doc/mrbayes-dbgsym -> mrbayes
mrbayes-mpi-dbgsym_3.2.7a-4+b1_armhf.deb
----------------------------------------
new Debian package, version 2.0.
size 972 bytes: control archive=488 bytes.
400 bytes, 12 lines control
0 bytes, 0 lines md5sums
Package: mrbayes-mpi-dbgsym
Source: mrbayes (3.2.7a-4)
Version: 3.2.7a-4+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-4+b1)
Section: debug
Priority: optional
Description: debug symbols for mrbayes-mpi
Build-Ids: 4e6d877342f1b36a709ae6b9f04dd5abf6227fc4
drwxr-xr-x root/root 0 2020-07-20 07:50 ./
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/lib/
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/lib/debug/.build-id/4e/
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/share/
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-07-20 07:50 ./usr/share/doc/mrbayes-mpi-dbgsym -> mrbayes-mpi
mrbayes-mpi_3.2.7a-4+b1_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 488484 bytes: control archive=1068 bytes.
1017 bytes, 21 lines control
485 bytes, 7 lines md5sums
Package: mrbayes-mpi
Source: mrbayes (3.2.7a-4)
Version: 3.2.7a-4+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1398
Depends: libc6 (>= 2.29), 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 2020-07-20 07:50 ./
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/bin/
-rwxr-xr-x root/root 162 2020-07-20 07:50 ./usr/bin/mb-mpi
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/lib/
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/lib/mrbayes-mpi/
-rwxr-xr-x root/root 1411052 2020-07-20 07:50 ./usr/lib/mrbayes-mpi/mb-mpi
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/share/
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/share/doc/mrbayes-mpi/
-rw-r--r-- root/root 348 2020-07-20 07:50 ./usr/share/doc/mrbayes-mpi/README.Debian
-rw-r--r-- root/root 222 2020-07-20 07:50 ./usr/share/doc/mrbayes-mpi/changelog.Debian.armhf.gz
-rw-r--r-- root/root 2590 2020-07-20 07:50 ./usr/share/doc/mrbayes-mpi/changelog.Debian.gz
-rw-r--r-- root/root 1567 2020-07-20 07:50 ./usr/share/doc/mrbayes-mpi/copyright
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/share/man/
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/share/man/man1/
-rw-r--r-- root/root 226 2020-07-20 07:50 ./usr/share/man/man1/mb-mpi.1.gz
mrbayes_3.2.7a-4+b1_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 553328 bytes: control archive=1276 bytes.
887 bytes, 19 lines control
1166 bytes, 16 lines md5sums
Package: mrbayes
Source: mrbayes (3.2.7a-4)
Version: 3.2.7a-4+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2462
Depends: libc6 (>= 2.29), 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 2020-07-20 07:50 ./
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/bin/
-rwxr-xr-x root/root 1411052 2020-07-20 07:50 ./usr/bin/mb
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/share/
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/share/doc/mrbayes/
-rw-r--r-- root/root 311 2020-07-20 07:50 ./usr/share/doc/mrbayes/README.Debian
-rw-r--r-- root/root 262 2020-07-20 07:50 ./usr/share/doc/mrbayes/README.test
-rw-r--r-- root/root 222 2020-07-20 07:50 ./usr/share/doc/mrbayes/changelog.Debian.armhf.gz
-rw-r--r-- root/root 2590 2020-07-20 07:50 ./usr/share/doc/mrbayes/changelog.Debian.gz
-rw-r--r-- root/root 1567 2020-07-20 07:50 ./usr/share/doc/mrbayes/copyright
drwxr-xr-x root/root 0 2020-07-20 07:50 ./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 2020-07-20 07:50 ./usr/share/doc/mrbayes/run-unit-test
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/share/man/
drwxr-xr-x root/root 0 2020-07-20 07:50 ./usr/share/man/man1/
-rw-r--r-- root/root 206 2020-07-20 07:50 ./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: 52040
Build-Time: 1171
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 872
Job: mrbayes_3.2.7a-4
Machine Architecture: armhf
Package: mrbayes
Package-Time: 2097
Source-Version: 3.2.7a-4
Space: 52040
Status: successful
Version: 3.2.7a-4+b1
--------------------------------------------------------------------------------
Finished at 2023-12-22T22:53:06Z
Build needed 00:34:57, 52040k disc space