mrbayes →
3.2.7a-4 →
armhf → 2020-07-25 13:08:15
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04
+==============================================================================+
| mrbayes 3.2.7a-4 (armhf) Sat, 25 Jul 2020 12:38:25 +0000 |
+==============================================================================+
Package: mrbayes
Version: 3.2.7a-4
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-926a53f4-8c91-49d8-bb69-ac5f0fa4efef' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.8 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
Fetched 24.7 MB in 29s (865 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://172.17.0.1/private bullseye-staging/main mrbayes 3.2.7a-4 (dsc) [2184 B]
Get:2 http://172.17.0.1/private bullseye-staging/main mrbayes 3.2.7a-4 (tar) [9819 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main mrbayes 3.2.7a-4 (diff) [7136 B]
Fetched 9829 kB in 1s (10.2 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/mrbayes-I6XPac/mrbayes-3.2.7a' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/mrbayes-I6XPac' 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-qh5f91/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-qh5f91/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-qh5f91/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-qh5f91/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-qh5f91/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-qh5f91/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-qh5f91/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-qh5f91/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2720 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 libpam-cap netbase
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 28 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-qh5f91/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (22.5 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12307 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-qh5f91/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-qh5f91/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-qh5f91/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-qh5f91/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-qh5f91/apt_archive ./ Sources [540 B]
Get:5 copy:/<<BUILDDIR>>/resolver-qh5f91/apt_archive ./ Packages [621 B]
Fetched 2494 B in 1s (3043 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:
dmsetup libargon2-1 libcryptsetup12 libdevmapper1.02.1 libjson-c4 libpam-cap
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-9 groff-base ibverbs-providers intltool-debian libarchive-zip-perl
libbsd0 libcbor0 libclang-common-10-dev libclc-amdgcn libclc-dev libclc-r600
libcroco3 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 libfido2-1
libfile-stripnondeterminism-perl libgfortran-9-dev libgfortran5 libglib2.0-0
libgssapi-krb5-2 libhmsbeagle-dev libhmsbeagle1v5 libhwloc-dev
libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu67 libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 libllvm10 libltdl-dev libltdl7
libmagic-mgc libmagic1 libmount1 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 libpmix2
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
sensible-utils zlib1g-dev
Suggested packages:
gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev
libgettextpo-dev gfortran-9-doc libcoarrays-dev groff krb5-doc krb5-user
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 krb5-locales 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-9 groff-base ibverbs-providers intltool-debian libarchive-zip-perl
libbsd0 libcbor0 libclang-common-10-dev libclc-amdgcn libclc-dev libclc-r600
libcroco3 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 libfido2-1
libfile-stripnondeterminism-perl libgfortran-9-dev libgfortran5 libglib2.0-0
libgssapi-krb5-2 libhmsbeagle-dev libhmsbeagle1v5 libhwloc-dev
libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu67 libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 libllvm10 libltdl-dev libltdl7
libmagic-mgc libmagic1 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 libpmix2 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 sensible-utils zlib1g-dev
The following packages will be upgraded:
libmount1
1 upgraded, 102 newly installed, 0 to remove and 27 not upgraded.
Need to get 74.8 MB of archives.
After this operation, 358 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-qh5f91/apt_archive ./ sbuild-build-depends-mrbayes-dummy 0.invalid.0 [908 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf autoconf-archive all 20190106-2.1 [746 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libmount1 armhf 2.35.2-7 [190 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libedit2 armhf 3.1-20191231-1 [79.2 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libcbor0 armhf 0.5.0+dfsg-2 [19.5 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libfido2-1 armhf 1.4.0-2 [43.9 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-10 [61.7 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-10 [112 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-10 [320 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-10 [135 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf openssh-client armhf 1:8.3p1-1 [783 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-3 [801 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2 [187 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.4-1 [1159 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-3 [8287 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-5+b1 [593 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2 [1007 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.1.0-4+rpi1 [231 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libgfortran-9-dev armhf 9.3.0-14+rpi1 [278 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf gfortran-9 armhf 9.3.0-14+rpi1 [8112 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libnl-3-200 armhf 3.4.0-1 [55.0 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libnl-route-3-200 armhf 3.4.0-1 [132 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libibverbs1 armhf 29.0-1 [47.5 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf ibverbs-providers armhf 29.0-1 [24.2 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libz3-4 armhf 4.8.8-1 [5913 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libllvm10 armhf 1:10.0.1~+rc4-1+rpi1 [14.6 MB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libclang-common-10-dev armhf 1:10.0.1~+rc4-1+rpi1 [2638 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libclc-dev all 0.2.0+git20190827-6 [26.3 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libclc-amdgcn all 0.2.0+git20190827-6 [2129 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libclc-r600 all 0.2.0+git20190827-6 [1387 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libdrm-common all 2.4.102-1+rpi1 [14.6 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libdrm2 armhf 2.4.102-1+rpi1 [37.7 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libdrm-amdgpu1 armhf 2.4.102-1+rpi1 [27.2 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libdrm-nouveau2 armhf 2.4.102-1+rpi1 [24.9 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libdrm-radeon1 armhf 2.4.102-1+rpi1 [29.2 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libevent-2.1-7 armhf 2.1.12-stable-1 [167 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-1 [126 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-1 [100 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-1 [56.8 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-1 [61.7 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libevent-dev armhf 2.1.12-stable-1 [281 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf ocl-icd-libopencl1 armhf 2.2.12-4 [36.0 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf mesa-opencl-icd armhf 20.1.2-1+rpi1 [10.1 MB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libhmsbeagle1v5 armhf 3.1.2+dfsg-8 [144 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libhmsbeagle-dev armhf 3.1.2+dfsg-8 [223 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libhwloc15 armhf 2.2.0+dfsg-3 [113 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libnuma1 armhf 2.0.12-1 [22.5 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libnuma-dev armhf 2.0.12-1 [35.6 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libltdl7 armhf 2.4.6-14 [388 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libltdl-dev armhf 2.4.6-14 [159 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libhwloc-dev armhf 2.2.0+dfsg-3 [174 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libpciaccess0 armhf 0.14-1 [51.0 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.14-2 [135 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.6.9-2 [298 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.6.9-2 [692 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libxnvctrl0 armhf 440.100-1 [25.3 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libhwloc-plugins armhf 2.2.0+dfsg-3 [19.0 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libnl-3-dev armhf 3.4.0-1 [92.4 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libnl-route-3-dev armhf 3.4.0-1 [145 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libibverbs-dev armhf 29.0-1 [199 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2-1 [79.5 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libncurses-dev armhf 6.2-1 [284 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libpmix2 armhf 3.1.5-1+b1 [378 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libopenmpi3 armhf 4.0.4-1+rpi1 [1689 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf openmpi-common all 4.0.4-1+rpi1 [173 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf openmpi-bin armhf 4.0.4-1+rpi1 [189 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf libopenmpi-dev armhf 4.0.4-1+rpi1 [927 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf libreadline-dev armhf 8.0-4 [116 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf mpi-default-dev armhf 1.13 [5476 B]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
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Setting up libmagic1:armhf (1:5.38-5) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up autoconf-archive (20190106-2.1) ...
Setting up file (1:5.38-5) ...
Setting up libkrb5support0:armhf (1.17-10) ...
Setting up autotools-dev (20180224.1) ...
Setting up libz3-4:armhf (4.8.8-1) ...
Setting up libx11-data (2:1.6.9-2) ...
Setting up libncurses6:armhf (6.2-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libhwloc15:armhf (2.2.0+dfsg-3) ...
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 (0.19.8.1-10) ...
Setting up pkg-config (0.29.2-1) ...
Setting up libk5crypto3:armhf (1.17-10) ...
Setting up libltdl7:armhf (2.4.6-14) ...
Setting up libgfortran5:armhf (10.1.0-4+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libnuma1:armhf (2.0.12-1) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up ocl-icd-libopencl1:armhf (2.2.12-4) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libnl-3-200:armhf (3.4.0-1) ...
Setting up openmpi-common (4.0.4-1+rpi1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libkrb5-3:armhf (1.17-10) ...
Setting up libfido2-1:armhf (1.4.0-2) ...
Setting up libclc-dev (0.2.0+git20190827-6) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libdrm-common (2.4.102-1+rpi1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.10+dfsg-5+b1) ...
Setting up libevent-pthreads-2.1-7:armhf (2.1.12-stable-1) ...
Setting up libfile-stripnondeterminism-perl (1.9.0-1) ...
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 (6.2-1) ...
Setting up libxcb1:armhf (1.14-2) ...
Setting up libtool (2.4.6-14) ...
Setting up libedit2:armhf (3.1-20191231-1) ...
Setting up libgfortran-9-dev:armhf (9.3.0-14+rpi1) ...
Setting up libevent-openssl-2.1-7:armhf (2.1.12-stable-1) ...
Setting up m4 (1.4.18-4) ...
Setting up libreadline-dev:armhf (8.0-4) ...
Setting up libnuma-dev:armhf (2.0.12-1) ...
Setting up libnl-route-3-200:armhf (3.4.0-1) ...
Setting up libllvm10:armhf (1:10.0.1~+rc4-1+rpi1) ...
Setting up libevent-dev (2.1.12-stable-1) ...
Setting up libgssapi-krb5-2:armhf (1.17-10) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.9.0-1) ...
Setting up libdrm2:armhf (2.4.102-1+rpi1) ...
Setting up dwz (0.13-5) ...
Setting up libnl-3-dev:armhf (3.4.0-1) ...
Setting up groff-base (1.22.4-5) ...
Setting up libx11-6:armhf (2:1.6.9-2) ...
Setting up libdrm-amdgpu1:armhf (2.4.102-1+rpi1) ...
Setting up automake (1:1.16.2-3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libibverbs1:armhf (29.0-1) ...
Setting up libdrm-nouveau2:armhf (2.4.102-1+rpi1) ...
Setting up gettext (0.19.8.1-10) ...
Setting up gfortran-9 (9.3.0-14+rpi1) ...
Setting up ibverbs-providers:armhf (29.0-1) ...
Setting up libclang-common-10-dev (1:10.0.1~+rc4-1+rpi1) ...
Setting up libdrm-radeon1:armhf (2.4.102-1+rpi1) ...
Setting up openssh-client (1:8.3p1-1) ...
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libxnvctrl0:armhf (440.100-1) ...
Setting up libnl-route-3-dev:armhf (3.4.0-1) ...
Setting up libltdl-dev:armhf (2.4.6-14) ...
Setting up libclc-r600 (0.2.0+git20190827-6) ...
Setting up libhwloc-dev:armhf (2.2.0+dfsg-3) ...
Setting up libclc-amdgcn (0.2.0+git20190827-6) ...
Setting up mesa-opencl-icd:armhf (20.1.2-1+rpi1) ...
Setting up po-debconf (1.0.21) ...
Setting up libhmsbeagle1v5 (3.1.2+dfsg-8) ...
Setting up libibverbs-dev:armhf (29.0-1) ...
Setting up libhwloc-plugins:armhf (2.2.0+dfsg-3) ...
Setting up libhmsbeagle-dev (3.1.2+dfsg-8) ...
Setting up libpmix2:armhf (3.1.5-1+b1) ...
Setting up libopenmpi3:armhf (4.0.4-1+rpi1) ...
Setting up openmpi-bin (4.0.4-1+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 (4.0.4-1+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 debhelper (13.2) ...
Setting up dh-autoreconf (19) ...
Setting up sbuild-build-depends-mrbayes-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.30-8+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.4-armmp armhf (armv7l)
Toolchain package versions: binutils_2.34-8+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-14+rpi1 gcc-9_9.3.0-14+rpi1 libc6-dev_2.30-8+rpi1 libstdc++-9-dev_9.3.0-14+rpi1 libstdc++6_10.1.0-4+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_2.1.6 autoconf_2.69-11.1 autoconf-archive_20190106-2.1 automake_1:1.16.2-3 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-8+rpi1 binutils-arm-linux-gnueabihf_2.34-8+rpi1 binutils-common_2.34-8+rpi1 bsdextrautils_2.35.2-6 bsdutils_1:2.35.2-6 build-essential_12.8 bzip2_1.0.8-3 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-14+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dmsetup_2:1.02.167-1+b2 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.35.2-6 file_1:5.38-5 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-14+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10.1.0-4+rpi1 gcc-9_9.3.0-14+rpi1 gcc-9-base_9.3.0-14+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gfortran-9_9.3.0-14+rpi1 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 ibverbs-providers_29.0-1 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 libacl1_2.2.53-8 libapt-pkg6.0_2.1.6 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2 libasan5_9.3.0-14+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.1.0-4+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34-8+rpi1 libblkid1_2.35.2-6 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-3 libc-bin_2.30-8+rpi1 libc-dev-bin_2.30-8+rpi1 libc6_2.30-8+rpi1 libc6-dev_2.30-8+rpi1 libcap-ng0_0.7.9-2.2 libcap2_1:2.36-1 libcap2-bin_1:2.36-1 libcbor0_0.5.0+dfsg-2 libcc1-0_10.1.0-4+rpi1 libclang-common-10-dev_1:10.0.1~+rc4-1+rpi1 libclc-amdgcn_0.2.0+git20190827-6 libclc-dev_0.2.0+git20190827-6 libclc-r600_0.2.0+git20190827-6 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libcryptsetup12_2:2.3.3-1 libctf-nobfd0_2.34-8+rpi1 libctf0_2.34-8+rpi1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.252 libdebhelper-perl_13.2 libdevmapper1.02.1_2:1.02.167-1+b2 libdpkg-perl_1.19.7 libdrm-amdgpu1_2.4.102-1+rpi1 libdrm-common_2.4.102-1+rpi1 libdrm-nouveau2_2.4.102-1+rpi1 libdrm-radeon1_2.4.102-1+rpi1 libdrm2_2.4.102-1+rpi1 libedit2_3.1-20191231-1 libelf1_0.176-1.1 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_2.2.9-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.35.2-6 libffi7_3.3-4 libfido2-1_1.4.0-2 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-9-dev_9.3.0-14+rpi1 libgcc-s1_10.1.0-4+rpi1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran-9-dev_9.3.0-14+rpi1 libgfortran5_10.1.0-4+rpi1 libglib2.0-0_2.64.4-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.14-2 libgomp1_10.1.0-4+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10 libhmsbeagle-dev_3.1.2+dfsg-8 libhmsbeagle1v5_3.1.2+dfsg-8 libhogweed5_3.5.1+really3.5.1-2 libhwloc-dev_2.2.0+dfsg-3 libhwloc-plugins_2.2.0+dfsg-3 libhwloc15_2.2.0+dfsg-3 libibverbs-dev_29.0-1 libibverbs1_29.0-1 libicu67_67.1-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libjson-c4_0.13.1+dfsg-9 libk5crypto3_1.17-10 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10 libkrb5support0_1.17-10 libksba8_1.4.0-2 libldap-2.4-2_2.4.50+dfsg-1 libldap-common_2.4.50+dfsg-1 libllvm10_1:10.0.1~+rc4-1+rpi1 libltdl-dev_2.4.6-14 libltdl7_2.4.6-14 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.2-7 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses-dev_6.2-1 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 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_1.6-2 libnuma-dev_2.0.12-1 libnuma1_2.0.12-1 libopenmpi-dev_4.0.4-1+rpi1 libopenmpi3_4.0.4-1+rpi1 libp11-kit0_0.23.20-1 libpam-cap_1:2.36-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpciaccess0_0.14-1 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.2-2 libpmix2_3.1.5-1+b1 libreadline-dev_8.0-4 libreadline7_7.0-5 libreadline8_8.0-4 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.35.2-6 libsqlite3-0_3.32.3-1 libss2_1.45.6-1 libssl1.1_1.1.1g-1 libstdc++-9-dev_9.3.0-14+rpi1 libstdc++6_10.1.0-4+rpi1 libsub-override-perl_0.09-2 libsystemd0_245.6-2+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.1.0-4+rpi1 libuchardet0_0.0.7-1 libudev1_245.6-2+rpi1 libunistring2_0.9.10-4 libuuid1_2.35.2-6 libx11-6_2:1.6.9-2 libx11-data_2:1.6.9-2 libxau6_1:1.0.8-1+b2 libxcb1_1.14-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxml2_2.9.10+dfsg-5+b1 libxnvctrl0_440.100-1 libz3-4_4.8.8-1 libzstd1_1.4.5+dfsg-3+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-2 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mesa-opencl-icd_20.1.2-1+rpi1 mount_2.35.2-6 mpi-default-dev_1.13 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 ocl-icd-libopencl1_2.2.12-4 openmpi-bin_4.0.4-1+rpi1 openmpi-common_4.0.4-1+rpi1 openssh-client_1:8.3p1-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-mrbayes-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.35.2-6 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/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
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-926a53f4-8c91-49d8-bb69-ac5f0fa4efef
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
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- --with-beagle=/usr --enable-mpi=yes --enable-debug=yes
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-beagle=/usr --enable-mpi=yes --enable-debug=yes
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a 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... 9.3.0
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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 'ReusePreviousResults.part.0':
mcmc.c:15950:52: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 3 and 210 [-Wformat-overflow=]
15950 | sprintf (fileName, "%s%s.tree%d.run%d.t", workingDir, localFileName, i+1, n+1);
| ^~
mcmc.c:15950:36: note: directive argument in the range [1, 2147483647]
15950 | sprintf (fileName, "%s%s.tree%d.run%d.t", workingDir, 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 230 bytes into a destination of size 220
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -fdebug-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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -g -std=c99 -pedantic -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o mb-utils.o `test -f 'utils.c' || echo './'`utils.c
In function 'sprintf',
inlined from 'ShowConTree' at sumpt.c:8173:21:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: warning: '__builtin_strcpy' accessing 1 byte may overlap 1 byte [-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 [2147483646, 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 [2147483646, 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 [2147483646, 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 -fdebug-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... 9.3.0
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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 'ReusePreviousResults.part.0':
mcmc.c:15950:52: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 3 and 210 [-Wformat-overflow=]
15950 | sprintf (fileName, "%s%s.tree%d.run%d.t", workingDir, localFileName, i+1, n+1);
| ^~
mcmc.c:15950:36: note: directive argument in the range [1, 2147483647]
15950 | sprintf (fileName, "%s%s.tree%d.run%d.t", workingDir, 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 230 bytes into a destination of size 220
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o mb-sumpt.o `test -f 'sumpt.c' || echo './'`sumpt.c
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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 may overlap 1 byte [-Wrestrict]
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -g -std=c99 -pedantic -g -O2 -fdebug-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 '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 ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 [2147483646, 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 [2147483646, 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 [2147483646, 1073741823] [-Wrestrict]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__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: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 -fdebug-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 -fdebug-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_testroot -a
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/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/hym.nex 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/COPYING 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/NEWS 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
Some of the files had a file that looked similar to a missing counter part. Perhaps
one of the debhelper tools should installed the missing file instead of its related
file assuming the content is identical.
As an example, perhaps you 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-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-dbgsym' in '../mrbayes-dbgsym_3.2.7a-4_armhf.deb'.
dpkg-deb: building package 'mrbayes' in '../mrbayes_3.2.7a-4_armhf.deb'.
dpkg-deb: building package 'mrbayes-mpi' in '../mrbayes-mpi_3.2.7a-4_armhf.deb'.
dpkg-deb: building package 'mrbayes-mpi-dbgsym' in '../mrbayes-mpi-dbgsym_3.2.7a-4_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../mrbayes_3.2.7a-4_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 2020-07-25T13:08:05Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
mrbayes_3.2.7a-4_armhf.changes:
-------------------------------
Format: 1.8
Date: Mon, 20 Jul 2020 09:50:56 +0200
Source: mrbayes
Binary: mrbayes mrbayes-dbgsym mrbayes-mpi mrbayes-mpi-dbgsym
Architecture: armhf
Version: 3.2.7a-4
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
mrbayes - Bayesian Inference of Phylogeny
mrbayes-mpi - Bayesian Inference of Phylogeny - mpi version
Closes: 965319
Changes:
mrbayes (3.2.7a-4) unstable; urgency=medium
.
[ Chris Lamb ]
* Build reproducibly
Closes: #965319
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c4739ba13b64e9623a2556e7c4d9ea26 972 debug optional mrbayes-mpi-dbgsym_3.2.7a-4_armhf.deb
96fb5be78edf0c26de991b798c4dba0e 495268 science optional mrbayes-mpi_3.2.7a-4_armhf.deb
5a4e038d24604686b82055f5d5397973 7470 science optional mrbayes_3.2.7a-4_armhf.buildinfo
957108e93a72d9fe266206c2aa05d9d6 558040 science optional mrbayes_3.2.7a-4_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
mrbayes-dbgsym_3.2.7a-4_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 985000 bytes: control archive=536 bytes.
373 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: mrbayes-dbgsym
Source: mrbayes
Version: 3.2.7a-4
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1036
Depends: mrbayes (= 3.2.7a-4)
Section: debug
Priority: optional
Description: debug symbols for mrbayes
Build-Ids: b300ec623ee581a9b25f6781bcff9e07390d6be6
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/b3/
-rw-r--r-- root/root 1049724 2020-07-20 07:50 ./usr/lib/debug/.build-id/b3/00ec623ee581a9b25f6781bcff9e07390d6be6.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_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 972 bytes: control archive=484 bytes.
383 bytes, 12 lines control
0 bytes, 0 lines md5sums
Package: mrbayes-mpi-dbgsym
Source: mrbayes
Version: 3.2.7a-4
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)
Section: debug
Priority: optional
Description: debug symbols for mrbayes-mpi
Build-Ids: b300ec623ee581a9b25f6781bcff9e07390d6be6
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/b3/
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_armhf.deb
------------------------------
new Debian package, version 2.0.
size 495268 bytes: control archive=1036 bytes.
1003 bytes, 21 lines control
399 bytes, 6 lines md5sums
Package: mrbayes-mpi
Source: mrbayes
Version: 3.2.7a-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1401
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 1415148 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 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_armhf.deb
--------------------------
new Debian package, version 2.0.
size 558040 bytes: control archive=1236 bytes.
857 bytes, 18 lines control
1084 bytes, 15 lines md5sums
Package: mrbayes
Version: 3.2.7a-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2465
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 1415148 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 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: 52160
Build-Time: 973
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 752
Job: mrbayes_3.2.7a-4
Machine Architecture: armhf
Package: mrbayes
Package-Time: 1780
Source-Version: 3.2.7a-4
Space: 52160
Status: successful
Version: 3.2.7a-4
--------------------------------------------------------------------------------
Finished at 2020-07-25T13:08:05Z
Build needed 00:29:40, 52160k disc space