phyml →
3:3.3.20180214+dfsg-1 →
armhf → 2018-05-02 16:46:50
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| phyml 3:3.3.20180214+dfsg-1 (armhf) Wed, 02 May 2018 16:41:08 +0000 |
+==============================================================================+
Package: phyml
Version: 3:3.3.20180214+dfsg-1
Source Version: 3:3.3.20180214+dfsg-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-70b97ef8-5bba-43cc-8294-1d86076d8e15' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.7 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.5 MB]
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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: 'phyml' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/phyml.git
Please use:
git clone https://salsa.debian.org/med-team/phyml.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1558 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main phyml 3:3.3.20180214+dfsg-1 (dsc) [2124 B]
Get:2 http://172.17.0.1/private buster-staging/main phyml 3:3.3.20180214+dfsg-1 (tar) [1540 kB]
Get:3 http://172.17.0.1/private buster-staging/main phyml 3:3.3.20180214+dfsg-1 (diff) [16.6 kB]
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Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/phyml-dCoZQF/phyml-3.3.20180214+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/phyml-dCoZQF' 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-mNCqku/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-mNCqku/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-mNCqku/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-mNCqku/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-mNCqku/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-mNCqku/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-mNCqku/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-mNCqku/apt_archive ./ Packages [433 B]
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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:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
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 0 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-mNCqku/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 15689 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)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), pkg-config, libopenmpi-dev, chrpath
Filtered Build-Depends: debhelper (>= 11~), pkg-config, libopenmpi-dev, chrpath
dpkg-deb: building package 'sbuild-build-depends-phyml-dummy' in '/<<BUILDDIR>>/resolver-mNCqku/apt_archive/sbuild-build-depends-phyml-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-phyml-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-mNCqku/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-mNCqku/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-mNCqku/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-mNCqku/apt_archive ./ Sources [512 B]
Get:5 copy:/<<BUILDDIR>>/resolver-mNCqku/apt_archive ./ Packages [593 B]
Fetched 2438 B in 0s (13.6 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install phyml 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:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils chrpath debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
ibverbs-providers intltool-debian libarchive-zip-perl libbsd0 libcroco3
libedit2 libevent-2.1-6 libevent-core-2.1-6 libevent-pthreads-2.1-6
libfile-stripnondeterminism-perl libgfortran4 libglib2.0-0 libgssapi-krb5-2
libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu57
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libltdl-dev libltdl7
libmagic-mgc libmagic1 libnl-3-200 libnl-route-3-200 libopenmpi-dev
libopenmpi3 libpciaccess0 libpipeline1 libpmix2 libsigsegv2 libssl1.0.2
libtimedate-perl libtool libxml2 m4 man-db ocl-icd-libopencl1 openmpi-bin
openmpi-common openssh-client pkg-config po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff
krb5-doc krb5-user libhwloc-contrib-plugins libtool-doc openmpi-doc pciutils
gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
opencl-icd gfortran 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 xauth libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils chrpath debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
ibverbs-providers intltool-debian libarchive-zip-perl libbsd0 libcroco3
libedit2 libevent-2.1-6 libevent-core-2.1-6 libevent-pthreads-2.1-6
libfile-stripnondeterminism-perl libgfortran4 libglib2.0-0 libgssapi-krb5-2
libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu57
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libltdl-dev libltdl7
libmagic-mgc libmagic1 libnl-3-200 libnl-route-3-200 libopenmpi-dev
libopenmpi3 libpciaccess0 libpipeline1 libpmix2 libsigsegv2 libssl1.0.2
libtimedate-perl libtool libxml2 m4 man-db ocl-icd-libopencl1 openmpi-bin
openmpi-common openssh-client pkg-config po-debconf
sbuild-build-depends-phyml-dummy
0 upgraded, 61 newly installed, 0 to remove and 0 not upgraded.
Need to get 16.6 MB/26.2 MB of archives.
After this operation, 89.7 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-mNCqku/apt_archive ./ sbuild-build-depends-phyml-dummy 0.invalid.0 [880 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.3-2 [1146 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libssl1.0.2 armhf 1.0.2o-1 [888 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-6 [117 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libevent-2.1-6 armhf 2.1.8-stable-4 [156 kB]
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Get:10 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3.1 [736 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-6 [434 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf chrpath armhf 0.16-2 [15.4 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2.1 [547 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 17 [16.5 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.041-1 [19.9 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.041-1 [12.0 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.1-2 [2754 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-6 [1218 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.2.1 [1013 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libibverbs1 armhf 17.1-1 [38.9 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf ibverbs-providers armhf 17.1-1 [19.3 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libevent-core-2.1-6 armhf 2.1.8-stable-4 [117 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libevent-pthreads-2.1-6 armhf 2.1.8-stable-4 [47.6 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.3.0-12 [191 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libltdl7 armhf 2.4.6-2.1 [386 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libhwloc5 armhf 1.11.10-1+rpi1 [85.7 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libltdl-dev armhf 2.4.6-2.1 [158 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libhwloc-dev armhf 1.11.10-1+rpi1 [141 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libpciaccess0 armhf 0.14-1 [51.0 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libhwloc-plugins armhf 1.11.10-1+rpi1 [15.4 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libibverbs-dev armhf 17.1-1 [89.8 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libpmix2 armhf 2.1.1~rc1-2 [284 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libopenmpi3 armhf 3.0.1-9+rpi1 [1725 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf openmpi-common all 3.0.1-9+rpi1 [158 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf openmpi-bin armhf 3.0.1-9+rpi1 [198 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libopenmpi-dev armhf 3.0.1-9+rpi1 [928 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking ibverbs-providers:armhf (17.1-1) ...
Selecting previously unselected package libevent-core-2.1-6:armhf.
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Unpacking libevent-core-2.1-6:armhf (2.1.8-stable-4) ...
Selecting previously unselected package libevent-pthreads-2.1-6:armhf.
Preparing to unpack .../44-libevent-pthreads-2.1-6_2.1.8-stable-4_armhf.deb ...
Unpacking libevent-pthreads-2.1-6:armhf (2.1.8-stable-4) ...
Selecting previously unselected package libgfortran4:armhf.
Preparing to unpack .../45-libgfortran4_7.3.0-12_armhf.deb ...
Unpacking libgfortran4:armhf (7.3.0-12) ...
Selecting previously unselected package libltdl7:armhf.
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Unpacking libltdl7:armhf (2.4.6-2.1) ...
Selecting previously unselected package libhwloc5:armhf.
Preparing to unpack .../47-libhwloc5_1.11.10-1+rpi1_armhf.deb ...
Unpacking libhwloc5:armhf (1.11.10-1+rpi1) ...
Selecting previously unselected package libltdl-dev:armhf.
Preparing to unpack .../48-libltdl-dev_2.4.6-2.1_armhf.deb ...
Unpacking libltdl-dev:armhf (2.4.6-2.1) ...
Selecting previously unselected package libhwloc-dev:armhf.
Preparing to unpack .../49-libhwloc-dev_1.11.10-1+rpi1_armhf.deb ...
Unpacking libhwloc-dev:armhf (1.11.10-1+rpi1) ...
Selecting previously unselected package libpciaccess0:armhf.
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Unpacking libpciaccess0:armhf (0.14-1) ...
Selecting previously unselected package ocl-icd-libopencl1:armhf.
Preparing to unpack .../51-ocl-icd-libopencl1_2.2.12-1_armhf.deb ...
Unpacking ocl-icd-libopencl1:armhf (2.2.12-1) ...
Selecting previously unselected package libhwloc-plugins.
Preparing to unpack .../52-libhwloc-plugins_1.11.10-1+rpi1_armhf.deb ...
Unpacking libhwloc-plugins (1.11.10-1+rpi1) ...
Selecting previously unselected package libibverbs-dev:armhf.
Preparing to unpack .../53-libibverbs-dev_17.1-1_armhf.deb ...
Unpacking libibverbs-dev:armhf (17.1-1) ...
Selecting previously unselected package libpmix2:armhf.
Preparing to unpack .../54-libpmix2_2.1.1~rc1-2_armhf.deb ...
Unpacking libpmix2:armhf (2.1.1~rc1-2) ...
Selecting previously unselected package libopenmpi3:armhf.
Preparing to unpack .../55-libopenmpi3_3.0.1-9+rpi1_armhf.deb ...
Unpacking libopenmpi3:armhf (3.0.1-9+rpi1) ...
Selecting previously unselected package openmpi-common.
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Unpacking openmpi-common (3.0.1-9+rpi1) ...
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Unpacking openmpi-bin (3.0.1-9+rpi1) ...
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Unpacking libopenmpi-dev:armhf (3.0.1-9+rpi1) ...
Selecting previously unselected package pkg-config.
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Unpacking pkg-config (0.29-4) ...
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Preparing to unpack .../60-sbuild-build-depends-phyml-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-phyml-dummy (0.invalid.0) ...
Setting up chrpath (0.16-2) ...
Setting up libevent-2.1-6:armhf (2.1.8-stable-4) ...
Setting up libevent-core-2.1-6:armhf (2.1.8-stable-4) ...
Setting up libarchive-zip-perl (1.60-1) ...
Setting up libgfortran4:armhf (7.3.0-12) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up groff-base (1.22.3-10) ...
Setting up libglib2.0-0:armhf (2.56.1-2) ...
No schema files found: removed existing output file.
Setting up gettext-base (0.19.8.1-6) ...
Setting up libpipeline1:armhf (1.5.0-1) ...
Setting up m4 (1.4.18-1) ...
Setting up libicu57:armhf (57.1-9) ...
Setting up libbsd0:armhf (0.8.7-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-6.1) ...
Setting up libmagic-mgc (1:5.32-2) ...
Setting up libmagic1:armhf (1:5.32-2) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up libssl1.0.2:armhf (1.0.2o-1) ...
Setting up pkg-config (0.29-4) ...
Setting up libevent-pthreads-2.1-6:armhf (2.1.8-stable-4) ...
Setting up openmpi-common (3.0.1-9+rpi1) ...
Processing triggers for libc-bin (2.27-3+rpi1) ...
Setting up autotools-dev (20180224.1) ...
Setting up libltdl7:armhf (2.4.6-2.1) ...
Setting up libpciaccess0:armhf (0.14-1) ...
Setting up ocl-icd-libopencl1:armhf (2.2.12-1) ...
Setting up libkeyutils1:armhf (1.5.9-9.2) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libnl-3-200:armhf (3.2.27-2) ...
Setting up autopoint (0.19.8.1-6) ...
Setting up libfile-stripnondeterminism-perl (0.041-1) ...
Setting up libedit2:armhf (3.1-20170329-1) ...
Setting up libltdl-dev:armhf (2.4.6-2.1) ...
Setting up gettext (0.19.8.1-6) ...
Setting up libnl-route-3-200:armhf (3.2.27-2) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.32-2) ...
Setting up libhwloc5:armhf (1.11.10-1+rpi1) ...
Setting up libkrb5support0:armhf (1.16-2) ...
Setting up libhwloc-plugins (1.11.10-1+rpi1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up automake (1:1.15.1-3.1) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-2.1) ...
Setting up libibverbs1:armhf (17.1-1) ...
Setting up libk5crypto3:armhf (1.16-2) ...
Setting up po-debconf (1.0.20) ...
Setting up libhwloc-dev:armhf (1.11.10-1+rpi1) ...
Setting up libpmix2:armhf (2.1.1~rc1-2) ...
Setting up ibverbs-providers:armhf (17.1-1) ...
Setting up libkrb5-3:armhf (1.16-2) ...
Setting up libibverbs-dev:armhf (17.1-1) ...
Setting up libopenmpi3:armhf (3.0.1-9+rpi1) ...
Setting up libgssapi-krb5-2:armhf (1.16-2) ...
Setting up openssh-client (1:7.7p1-2) ...
Setting up openmpi-bin (3.0.1-9+rpi1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: error: no alternatives for mpi
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up libopenmpi-dev:armhf (3.0.1-9+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 dh-autoreconf (17) ...
Setting up dh-strip-nondeterminism (0.041-1) ...
Setting up debhelper (11.2.1) ...
Setting up sbuild-build-depends-phyml-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-3+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-119-generic armhf (armv8l)
Toolchain package versions: binutils_2.30-15+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-12 gcc-7_7.3.0-12 libc6-dev_2.27-3+rpi1 libstdc++-7-dev_7.3.0-12 libstdc++6_8-20180414-1+rpi1 linux-libc-dev_4.15.17-1+rpi1
Package versions: adduser_3.117 apt_1.6.1 autoconf_2.69-11 automake_1:1.15.1-3.1 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-2+b1 binutils_2.30-15+rpi1 binutils-arm-linux-gnueabihf_2.30-15+rpi1 binutils-common_2.30-15+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.31.1-0.5 build-essential_12.4+b1 bzip2_1.0.6-8.1 ca-certificates_20170717 chrpath_0.16-2 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.3.0-12 dash_0.5.8-2.10 dbus_1.12.6-2 dbus-user-session_1.12.6-2 debconf_1.5.66 debhelper_11.2.1 debianutils_4.8.4 dh-autoreconf_17 dh-strip-nondeterminism_0.041-1 diffutils_1:3.6-1 dirmngr_2.2.5-1 dmsetup_2:1.02.145-4.1 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 e2fslibs_1.44.1-2 e2fsprogs_1.44.1-2 e2fsprogs-l10n_1.44.1-2 fakeroot_1.22-2 fdisk_2.31.1-0.5 file_1:5.32-2 findutils_4.6.0+git+20171230-2 g++_4:7.2.0-1d1 g++-7_7.3.0-12 gcc_4:7.2.0-1d1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1 gcc-5-base_5.5.0-8 gcc-7_7.3.0-12 gcc-7-base_7.3.0-12 gcc-8-base_8-20180414-1+rpi1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gnupg_2.2.5-1 gnupg-agent_2.2.5-1 gnupg-l10n_2.2.5-1 gnupg-utils_2.2.5-1 gpg_2.2.5-1 gpg-agent_2.2.5-1 gpg-wks-client_2.2.5-1 gpg-wks-server_2.2.5-1 gpgconf_2.2.5-1 gpgsm_2.2.5-1 gpgv_2.2.5-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5 hostname_3.20 ibverbs-providers_17.1-1 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-11+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.12-4 libapt-pkg5.0_1.6.1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-2 libasan4_7.3.0-12 libassuan0_2.5.1-2 libatomic1_8-20180414-1+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.2-1 libaudit1_1:2.8.2-1 libbinutils_2.30-15+rpi1 libblkid1_2.31.1-0.5 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3+rpi1 libc-dev-bin_2.27-3+rpi1 libc6_2.27-3+rpi1 libc6-dev_2.27-3+rpi1 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.2 libcc1-0_8-20180414-1+rpi1 libcilkrts5_7.3.0-12 libcom-err2_1.44.1-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.6-2 libdebconfclient0_0.243 libdevmapper1.02.1_2:1.02.145-4.1 libdpkg-perl_1.19.0.5 libdrm-common_2.4.91-2+rpi1 libdrm2_2.4.91-2+rpi1 libedit2_3.1-20170329-1 libevent-2.1-6_2.1.8-stable-4 libevent-core-2.1-6_2.1.8-stable-4 libevent-pthreads-2.1-6_2.1.8-stable-4 libexpat1_2.2.5-3 libext2fs2_1.44.1-2 libfakeroot_1.22-2 libfdisk1_2.31.1-0.5 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.041-1 libgcc-7-dev_7.3.0-12 libgcc1_1:8-20180414-1+rpi1 libgcrypt20_1.8.2-2 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libgfortran4_7.3.0-12 libglib2.0-0_2.56.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8-20180414-1+rpi1 libgpg-error0_1.29-4 libgssapi-krb5-2_1.16-2 libhogweed4_3.4-1 libhwloc-dev_1.11.10-1+rpi1 libhwloc-plugins_1.11.10-1+rpi1 libhwloc5_1.11.10-1+rpi1 libibverbs-dev_17.1-1 libibverbs1_17.1-1 libicu57_57.1-9 libidn11_1.33-2.2 libidn2-0_2.0.4-1.1 libip4tc0_1.6.2-1 libisl15_0.18-4 libjson-c3_0.12.1-1.3 libk5crypto3_1.16-2 libkeyutils1_1.5.9-9.2 libklibc_2.0.4-11+rpi1 libkmod2_25-1 libkrb5-3_1.16-2 libkrb5support0_1.16-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 libltdl-dev_2.4.6-2.1 libltdl7_2.4.6-2.1 liblz4-1_1.8.1.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-2 libmagic1_1:5.32-2 libmount1_2.31.1-0.5 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1-1 libncursesw5_6.1-1 libnettle6_3.4-1 libnl-3-200_3.2.27-2 libnl-route-3-200_3.2.27-2 libnpth0_1.5-3 libnss-systemd_238-4 libopenmpi-dev_3.0.1-9+rpi1 libopenmpi3_3.0.1-9+rpi1 libp11-kit0_0.23.10-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_238-4 libpam0g_1.1.8-3.7 libpciaccess0_0.14-1 libpcre3_2:8.39-9 libperl5.24_5.24.1-7 libperl5.26_5.26.2-2 libpipeline1_1.5.0-1 libplymouth4_0.9.3-2 libpmix2_2.1.1~rc1-2 libpng16-16_1.6.34-1 libprocps6_2:3.3.14-1 libreadline7_7.0-3 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.12-2 libsmartcols1_2.31.1-0.5 libsqlite3-0_3.23.1-1 libss2_1.44.1-2 libssl1.0.2_1.0.2o-1 libssl1.1_1.1.0h-2 libstdc++-7-dev_7.3.0-12 libstdc++6_8-20180414-1+rpi1 libsystemd0_238-4 libtasn1-6_4.13-2 libtimedate-perl_2.3000-2 libtinfo5_6.1-1 libtool_2.4.6-2.1 libubsan0_7.3.0-12 libudev1_238-4 libunistring2_0.9.8-1 libustr-1.0-1_1.0.4-6 libuuid1_2.31.1-0.5 libxml2_2.9.4+dfsg1-6.1 libzstd1_1.3.3+dfsg-1+rpi1 linux-base_4.5 linux-libc-dev_4.15.17-1+rpi1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.3-2 mawk_1.3.3-17 mount_2.31.1-0.5 multiarch-support_2.27-3+rpi1 nano_2.9.5-1 ncurses-base_6.1-1 ncurses-bin_6.1-1 netbase_5.4 ocl-icd-libopencl1_2.2.12-1 openmpi-bin_3.0.1-9+rpi1 openmpi-common_3.0.1-9+rpi1 openssh-client_1:7.7p1-2 openssl_1.1.0h-2 passwd_1:4.5-1 patch_2.7.6-2 perl_5.26.2-2 perl-base_5.26.2-2 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-2 pinentry-curses_1.1.0-1 pkg-config_0.29-4 plymouth_0.9.3-2 po-debconf_1.0.20 procps_2:3.3.14-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-phyml-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_238-4 systemd-sysv_238-4 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2018d-1 udev_238-4 util-linux_2.31.1-0.5 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Fri Apr 27 06:32:06 2018 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 ./phyml_3.3.20180214+dfsg-1.dsc
dpkg-source: info: extracting phyml in /<<BUILDDIR>>/phyml-3.3.20180214+dfsg
dpkg-source: info: unpacking phyml_3.3.20180214+dfsg.orig.tar.xz
dpkg-source: info: unpacking phyml_3.3.20180214+dfsg-1.debian.tar.xz
dpkg-source: info: applying sse_only_if_supported.patch
dpkg-source: info: applying no-stdc++.patch
dpkg-source: info: applying no-configure-ac-date.patch
dpkg-source: info: applying fix_declaration_of_temp.patch
dpkg-source: info: applying fix_wrong_initialisation_of_array.patch
dpkg-source: info: applying no-march-native.patch
Check disk 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=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-70b97ef8-5bba-43cc-8294-1d86076d8e15
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package phyml
dpkg-buildpackage: info: source version 3:3.3.20180214+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build phyml-3.3.20180214+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg'
# save pdf from cleaning
mv doc/phyml-manual.pdf .
dh_auto_clean
mv phyml-manual.pdf doc
# remove temporary bin dir for phyml (see above hack)
rm -rf debian/bin
make[1]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg'
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
debian/rules override_dh_autoreconf
make[1]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg'
dh_autoreconf --as-needed
configure.ac:16: installing './compile'
configure.ac:14: installing './config.guess'
configure.ac:14: installing './config.sub'
configure.ac:5: installing './install-sh'
configure.ac:5: installing './missing'
src/Makefile.am: installing './depcomp'
make[1]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg'
# According to README you need different configure options to get different executables
# Here we hack in a full build process for phyml executable
# The hack includes saving the documentation from beeing cleaned up
mv doc/phyml-manual.pdf .
dh_auto_configure
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
configure: WARNING: unrecognized options: --disable-maintainer-mode
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 build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
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 for style of include used by make... GNU
checking dependency style of gcc... none
checking dependency style of gcc... (cached) none
configure: "Do not use MSSE = because not available on arch arm-unknown-linux-gnueabihf"
checking for log 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
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
checking for pdflatex... no
checking for latex... no
configure: WARNING: Documentation will not be built!
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for vprintf... yes
checking for _doprnt... no
checking for floor... yes
checking for pow... yes
checking for rint... yes
checking for sqrt... yes
checking for strchr... yes
checking for strstr... yes
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating doc/Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
dh_auto_build -- LDFLAGS="-Wl,-z,relro -Wl,-z,now"
make -j4 -Oline "LDFLAGS=-Wl,-z,relro -Wl,-z,now"
make all-recursive
Making all in src
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
.: Building [phyml]. Version 3.3.3:3.3.20180214+dfsg-1 :.
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o main.o main.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o bionj.o bionj.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o models.o models.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o optimiz.o optimiz.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o free.o free.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o help.o help.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o lk.o lk.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o simu.o simu.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o pars.o pars.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o alrt.o alrt.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o interface.o interface.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o eigen.o eigen.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o cl.o cl.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o draw.o draw.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o spr.o spr.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o utilities.o utilities.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o rates.o rates.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o times.o times.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o mcmc.o mcmc.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o tiporder.o tiporder.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o stats.o stats.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o make.o make.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o nexus.o nexus.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o m4.o m4.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o xml.o xml.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o sse.o sse.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o avx.o avx.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o date.o date.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o tbe.o tbe.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o io.o io.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o mixt.o mixt.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o init.o init.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
gcc -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -Wl,-z,relro -Wl,-z,now -o phyml main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o rates.o mcmc.o times.o tiporder.o m4.o io.o make.o nexus.o init.o xml.o date.o sse.o avx.o tbe.o mixt.o -lm -lm
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
Done.
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
# move phyml binary to temporary dir inside debian/
mkdir -p /<<BUILDDIR>>/phyml-3.3.20180214+dfsg/debian/bin
mv src/phyml /<<BUILDDIR>>/phyml-3.3.20180214+dfsg/debian/bin/phyml
/usr/bin/make distclean
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg'
Making distclean in src
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
test -z "phyml" || rm -f phyml
rm -f *.o
rm -f *.tab.c
test -z "" || rm -f
test . = "." || test -z "" || rm -f
rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
rm -rf ./.deps
rm -f Makefile
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg'
test -z "" || rm -f
test . = "." || test -z "" || rm -f
rm -f config.h stamp-h1
rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
rm -f cscope.out cscope.in.out cscope.po.out cscope.files
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg'
rm -f config.status config.cache config.log configure.lineno config.status.lineno
rm -f Makefile
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg'
dh_auto_configure -- --enable-mpi
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-mpi
configure: WARNING: unrecognized options: --disable-maintainer-mode
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 build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
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 for style of include used by make... GNU
checking dependency style of gcc... none
checking dependency style of gcc... (cached) none
configure: "Do not use MSSE = because not available on arch arm-unknown-linux-gnueabihf"
checking for log 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
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
checking for pdflatex... no
checking for latex... no
configure: WARNING: Documentation will not be built!
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for vprintf... yes
checking for _doprnt... no
checking for floor... yes
checking for pow... yes
checking for rint... yes
checking for sqrt... yes
checking for strchr... yes
checking for strstr... yes
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating doc/Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
dh_auto_build -- LDFLAGS="-Wl,-z,relro -Wl,-z,now"
make -j4 -Oline "LDFLAGS=-Wl,-z,relro -Wl,-z,now"
make all-recursive
Making all in src
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
.: Building [phyml-mpi]. Version 3.3.3:3.3.20180214+dfsg-1 :.
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o main.o main.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o bionj.o bionj.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o models.o models.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o optimiz.o optimiz.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o lk.o lk.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o free.o free.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o help.o help.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o simu.o simu.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o pars.o pars.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o alrt.o alrt.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o eigen.o eigen.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o interface.o interface.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o cl.o cl.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o draw.o draw.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o spr.o spr.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o utilities.o utilities.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o rates.o rates.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o times.o times.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o mg.o mg.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o mcmc.o mcmc.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o tiporder.o tiporder.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o stats.o stats.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o make.o make.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o nexus.o nexus.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o m4.o m4.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o xml.o xml.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o tbe.o tbe.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o io.o io.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o sse.o sse.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o mixt.o mixt.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o avx.o avx.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o date.o date.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o mpi_boot.o mpi_boot.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o init.o init.c
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -Wl,-z,relro -Wl,-z,now -o phyml-mpi main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o rates.o mcmc.o times.o tiporder.o mg.o m4.o io.o make.o nexus.o init.o xml.o mixt.o tbe.o date.o sse.o avx.o mpi_boot.o -lm -lm
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
Done.
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
# move phyml binary to temporary dir inside debian/
# mkdir -p /<<BUILDDIR>>/phyml-3.3.20180214+dfsg/debian/bin
mv src/phyml-mpi /<<BUILDDIR>>/phyml-3.3.20180214+dfsg/debian/bin/phyml-mpi
mv phyml-manual.pdf doc
make[1]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg'
dh_auto_test -a
make -j4 -Oline check VERBOSE=1
Making check in src
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
.: Building [phyml-mpi]. Version 3.3.3:3.3.20180214+dfsg-1 :.
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
mpicc -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -o phyml-mpi main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o rates.o mcmc.o times.o tiporder.o mg.o m4.o io.o make.o nexus.o init.o xml.o mixt.o tbe.o date.o sse.o avx.o mpi_boot.o -lm -lm
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
Done.
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg'
dh_auto_install
make -j4 -Oline install DESTDIR=/<<BUILDDIR>>/phyml-3.3.20180214\+dfsg/debian/phyml AM_UPDATE_INFO_DIR=no
Making install in src
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
.: Building [phyml-mpi]. Version 3.3.3:3.3.20180214+dfsg-1 :.
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
Done.
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
/bin/mkdir -p '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/debian/phyml/usr/bin'
/usr/bin/install -c phyml-mpi '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/debian/phyml/usr/bin'
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg/src'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
# install phyml binary we have kept safe above
mkdir -p /<<BUILDDIR>>/phyml-3.3.20180214+dfsg/debian/phyml/usr/lib/phyml/bin
mv /<<BUILDDIR>>/phyml-3.3.20180214+dfsg/debian/bin/* /<<BUILDDIR>>/phyml-3.3.20180214+dfsg/debian/phyml/usr/lib/phyml/bin
chrpath --delete debian/phyml/usr/lib/phyml/bin/phyml*
make[1]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg'
dh_install -a
debian/rules override_dh_installdocs
make[1]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg'
dh_installdocs
mv /<<BUILDDIR>>/phyml-3.3.20180214+dfsg/debian/phyml/usr/share/doc/phyml/phyml-manual.pdf /<<BUILDDIR>>/phyml-3.3.20180214+dfsg/debian/phyml/usr/share/doc/phyml/phyml_manual.pdf
make[1]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg'
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
debian/rules override_dh_compress
make[1]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg'
dh_compress --exclude=.pdf
make[1]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg'
debian/rules override_dh_fixperms
make[1]: Entering directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg'
dh_fixperms
find debian/*/usr/share/doc -name "*.nxs" -exec chmod -x \{\} \;
find debian/*/usr/share/doc -name "*.xml" -exec chmod -x \{\} \;
find debian/*/usr/share/doc -name "*.mat" -exec chmod -x \{\} \;
find debian/*/usr/share/doc -name "*.txt" -exec chmod -x \{\} \;
make[1]: Leaving directory '/<<BUILDDIR>>/phyml-3.3.20180214+dfsg'
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'phyml' in '../phyml_3.3.20180214+dfsg-1_armhf.deb'.
dpkg-deb: building package 'phyml-dbgsym' in '../phyml-dbgsym_3.3.20180214+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../phyml_3.3.20180214+dfsg-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build phyml-3.3.20180214+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-05-02T16:46:46Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
phyml_3.3.20180214+dfsg-1_armhf.changes:
----------------------------------------
Format: 1.8
Date: Fri, 27 Apr 2018 08:09:18 +0200
Source: phyml
Binary: phyml
Architecture: armhf
Version: 3:3.3.20180214+dfsg-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
phyml - Phylogenetic estimation using Maximum Likelihood
Changes:
phyml (3:3.3.20180214+dfsg-1) unstable; urgency=medium
.
[ Steffen Moeller ]
* debian/upstream/metadata: Added refs to registries
.
[ Andreas Tille ]
* New upstream version
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.4
* debhelper 11
* Fix file permissions of example files
Checksums-Sha1:
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bb28bee7d547cdaeb5372e486076188181abdb63 5587 phyml_3.3.20180214+dfsg-1_armhf.buildinfo
0f84859058fec386dc6a8cdd613bce2756966ba7 1554712 phyml_3.3.20180214+dfsg-1_armhf.deb
Checksums-Sha256:
e09052a1ee1175e7738c74db7990e22e8dcab62b743db247958870ece386bb67 40008 phyml-dbgsym_3.3.20180214+dfsg-1_armhf.deb
90c32bea8c05eff97143b2b4562747ef6de05895a48aba4b818145367b31b812 5587 phyml_3.3.20180214+dfsg-1_armhf.buildinfo
237aedc5ac4692217e5a2b4a50a670fa99642ba36582593f5c7c849e2dda5cd4 1554712 phyml_3.3.20180214+dfsg-1_armhf.deb
Files:
1da453aa922b43e1daae525754017947 40008 debug optional phyml-dbgsym_3.3.20180214+dfsg-1_armhf.deb
d3ad0f6f77ef4505060169b4202b251a 5587 science optional phyml_3.3.20180214+dfsg-1_armhf.buildinfo
9de00a61dea998097b98046e35993413 1554712 science optional phyml_3.3.20180214+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
phyml-dbgsym_3.3.20180214+dfsg-1_armhf.deb
------------------------------------------
new Debian package, version 2.0.
size 40008 bytes: control archive=656 bytes.
472 bytes, 12 lines control
318 bytes, 3 lines md5sums
Package: phyml-dbgsym
Source: phyml
Version: 3:3.3.20180214+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 275
Depends: phyml (= 3:3.3.20180214+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for phyml
Build-Ids: 42fd2c9a6367a785f5555005c93dc3f502335c71 ea903a4b7e8febaeb73cde1cd1f0fe7804238f5c f76e2916afb7cac61e8e35d848bbd2ea3227459f
drwxr-xr-x root/root 0 2018-04-27 06:09 ./
drwxr-xr-x root/root 0 2018-04-27 06:09 ./usr/
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phyml_3.3.20180214+dfsg-1_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 1554712 bytes: control archive=1892 bytes.
1671 bytes, 31 lines control
1732 bytes, 24 lines md5sums
Package: phyml
Version: 3:3.3.20180214+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4333
Depends: libc6 (>= 2.7), libopenmpi3, openmpi-bin
Section: science
Priority: optional
Homepage: http://www.atgc-montpellier.fr/phyml
Description: Phylogenetic estimation using Maximum Likelihood
PhyML is a software that estimates maximum likelihood phylogenies from
alignments of nucleotide or amino acid sequences. It provides a wide
range of options that were designed to facilitate standard phylogenetic
analyses. The main strengths of PhyML lies in the large number of
substitution models coupled to various options to search the space of
phylogenetic tree topologies, going from very fast and efficient methods
to slower but generally more accurate approaches. It also implements
two methods to evaluate branch supports in a sound statistical framework
(the non-parametric bootstrap and the approximate likelihood ratio test).
.
PhyML was designed to process moderate to large data sets. In theory,
alignments with up to 4,000 sequences 2,000,000 character-long can
be analyzed. In practice however, the amount of memory required to process
a data set is proportional of the product of the number of sequences by their
length. Hence, a large number of sequences can only be processed provided
that they are short. Also, PhyML can handle long sequences provided that
they are not numerous. With most standard personal computers, the “comfort
zone” for PhyML generally lies around 3 to 500 sequences less than 2,000
character long.
.
This package also includes PhyTime.
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drwxr-xr-x root/root 0 2018-04-27 06:09 ./usr/bin/
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-rwxr-xr-x root/root 1099584 2018-04-27 06:09 ./usr/bin/phyml-mpi
drwxr-xr-x root/root 0 2018-04-27 06:09 ./usr/lib/
drwxr-xr-x root/root 0 2018-04-27 06:09 ./usr/lib/phyml/
drwxr-xr-x root/root 0 2018-04-27 06:09 ./usr/lib/phyml/bin/
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-rwxr-xr-x root/root 1099268 2018-04-27 06:09 ./usr/lib/phyml/bin/phyml-mpi
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drwxr-xr-x root/root 0 2018-04-27 06:09 ./usr/share/doc-base/
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drwxr-xr-x root/root 0 2018-04-27 06:09 ./usr/share/doc/phyml/
-rw-r--r-- root/root 2446 2018-04-27 06:09 ./usr/share/doc/phyml/README.Debian
-rw-r--r-- root/root 2767 2018-04-27 06:09 ./usr/share/doc/phyml/changelog.Debian.gz
-rw-r--r-- root/root 2025 2018-04-27 06:09 ./usr/share/doc/phyml/copyright
drwxr-xr-x root/root 0 2018-04-27 06:09 ./usr/share/doc/phyml/examples/
-rw-r--r-- root/root 5082 2018-04-27 06:09 ./usr/share/doc/phyml/examples/example.nex.gz
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-rw-r--r-- root/root 1784 2018-02-14 10:54 ./usr/share/doc/phyml/examples/phyrex/usa_coord.txt
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-rw-r--r-- root/root 1056596 2018-02-14 10:54 ./usr/share/doc/phyml/phyml_manual.pdf
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drwxr-xr-x root/root 0 2018-04-27 06:09 ./usr/share/man/man1/
-rw-r--r-- root/root 2899 2018-04-27 06:09 ./usr/share/man/man1/phyml.1.gz
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 16616
Build-Time: 85
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 233
Job: phyml_3:3.3.20180214+dfsg-1
Machine Architecture: armhf
Package: phyml
Package-Time: 338
Source-Version: 3:3.3.20180214+dfsg-1
Space: 16616
Status: successful
Version: 3:3.3.20180214+dfsg-1
--------------------------------------------------------------------------------
Finished at 2018-05-02T16:46:46Z
Build needed 00:05:38, 16616k disk space