phyml →
3:3.2.0+dfsg-4 →
armhf → 2017-01-28 05:57:39
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01
+==============================================================================+
| phyml 3:3.2.0+dfsg-4 (armhf) Sat, 28 Jan 2017 05:36:54 +0000 |
+==============================================================================+
Package: phyml
Version: 3:3.2.0+dfsg-4
Source Version: 3:3.2.0+dfsg-4
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/stretch-staging-armhf-sbuild-c914aaeb-ff6b-46ab-b2d7-90fc46897b7c' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9731 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.7 MB]
Fetched 21.4 MB in 23s (894 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| 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://anonscm.debian.org/git/debian-med/phyml.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/phyml.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1087 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main phyml 3:3.2.0+dfsg-4 (dsc) [2179 B]
Get:2 http://172.17.0.1/private stretch-staging/main phyml 3:3.2.0+dfsg-4 (tar) [1068 kB]
Get:3 http://172.17.0.1/private stretch-staging/main phyml 3:3.2.0+dfsg-4 (diff) [16.2 kB]
Fetched 1087 kB in 0s (7651 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/phyml-CcqVfm/phyml-3.2.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/phyml-CcqVfm' 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-nGAojs/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-nGAojs/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-nGAojs/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-nGAojs/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-nGAojs/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-nGAojs/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-nGAojs/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-nGAojs/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-nGAojs/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (3076 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-nGAojs/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-nGAojs/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
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:
fuse2fs gnupg-l10n libfuse2 manpages
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 62 not upgraded.
Need to get 770 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-nGAojs/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 770 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12988 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) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 10), autotools-dev, dh-autoreconf, pkg-config, libhmsbeagle-dev, libopenmpi-dev, chrpath
Filtered Build-Depends: debhelper (>= 10), autotools-dev, dh-autoreconf, pkg-config, libhmsbeagle-dev, libopenmpi-dev, chrpath
dpkg-deb: building package 'sbuild-build-depends-phyml-dummy' in '/<<BUILDDIR>>/resolver-nGAojs/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-nGAojs/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-nGAojs/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-nGAojs/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-nGAojs/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-nGAojs/apt_archive ./ Sources [533 B]
Get:5 copy:/<<BUILDDIR>>/resolver-nGAojs/apt_archive ./ Packages [616 B]
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Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-nGAojs/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-nGAojs/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
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:
fuse2fs gnupg-l10n libfuse2 manpages
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
intltool-debian libarchive-zip-perl libbsd0 libclang-common-3.9-dev
libclc-amdgcn libclc-dev libclc-r600 libcroco3 libdrm-amdgpu1
libdrm-freedreno1 libdrm-nouveau2 libdrm-radeon1 libedit2 libelf1 libexpat1
libffi6 libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0
libhmsbeagle-dev libhmsbeagle1v5 libhwloc-dev libhwloc-plugins libhwloc5
libibverbs-dev libibverbs1 libicu57 libllvm3.9 libltdl-dev libltdl7
libmagic-mgc libmagic1 libnl-3-200 libnl-route-3-200 libopenmpi-dev
libopenmpi2 libpciaccess0 libpipeline1 libsensors4 libsigsegv2
libtimedate-perl libtool libunistring0 libxml2 m4 man-db mesa-opencl-icd
ocl-icd-libopencl1 openmpi-common pkg-config po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libhwloc-contrib-plugins libtool-doc openmpi-doc pciutils lm-sensors
gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
openmpi-bin xml-core 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
intltool-debian libarchive-zip-perl libbsd0 libclang-common-3.9-dev
libclc-amdgcn libclc-dev libclc-r600 libcroco3 libdrm-amdgpu1
libdrm-freedreno1 libdrm-nouveau2 libdrm-radeon1 libedit2 libelf1 libexpat1
libffi6 libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0
libhmsbeagle-dev libhmsbeagle1v5 libhwloc-dev libhwloc-plugins libhwloc5
libibverbs-dev libibverbs1 libicu57 libllvm3.9 libltdl-dev libltdl7
libmagic-mgc libmagic1 libnl-3-200 libnl-route-3-200 libopenmpi-dev
libopenmpi2 libpciaccess0 libpipeline1 libsensors4 libsigsegv2
libtimedate-perl libtool libunistring0 libxml2 m4 man-db mesa-opencl-icd
ocl-icd-libopencl1 openmpi-common pkg-config po-debconf
sbuild-build-depends-phyml-dummy
0 upgraded, 65 newly installed, 0 to remove and 62 not upgraded.
Need to get 58.5 MB/58.6 MB of archives.
After this operation, 260 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-nGAojs/apt_archive ./ sbuild-build-depends-phyml-dummy 0.invalid.0 [820 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.12 [178 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.29-2 [221 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.29-2 [104 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.29-2 [63.1 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libedit2 armhf 3.1-20160903-2 [68.7 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-5 [7427 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2.1 [804 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-5 [733 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf chrpath armhf 0.16-2 [15.4 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 13 [15.8 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.029-2 [15.3 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.029-2 [9330 B]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.2-2 [2527 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.3 [829 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libllvm3.9 armhf 1:3.9.1-1+rpi1 [9681 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libclang-common-3.9-dev armhf 1:3.9.1-1+rpi1 [1141 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libdrm-amdgpu1 armhf 2.4.74-1 [25.0 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libdrm-freedreno1 armhf 2.4.74-1 [23.8 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libdrm-nouveau2 armhf 2.4.74-1 [23.5 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libdrm-radeon1 armhf 2.4.74-1 [27.7 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libelf1 armhf 0.168-0.2 [154 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.2.0-2 [62.2 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 6.2.1-5+rpi1 [166 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf ocl-icd-libopencl1 armhf 2.2.10-2 [34.9 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libclc-dev all 0.2.0+git20160907-3 [23.9 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libclc-r600 all 0.2.0+git20160907-3 [9207 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libclc-amdgcn all 0.2.0+git20160907-3 [8325 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libsensors4 armhf 1:3.4.0-3 [50.4 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf mesa-opencl-icd armhf 13.0.3-1 [5932 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libhmsbeagle1v5 armhf 2.1.2+20160831-5+b2 [89.7 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libhmsbeagle-dev armhf 2.1.2+20160831-5+b2 [150 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libltdl7 armhf 2.4.6-2 [386 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libltdl-dev armhf 2.4.6-2 [159 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libnl-3-200 armhf 3.2.27-1 [53.4 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libnl-route-3-200 armhf 3.2.27-1 [111 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf libpciaccess0 armhf 0.13.4-1 [47.4 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libhwloc5 armhf 1.11.5-1+rpi1 [83.2 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libhwloc-dev armhf 1.11.5-1+rpi1 [136 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libhwloc-plugins armhf 1.11.5-1+rpi1 [14.9 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf libibverbs1 armhf 1.2.1-2 [35.4 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf libibverbs-dev armhf 1.2.1-2 [104 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libopenmpi2 armhf 2.0.2~git.20161225-9 [1964 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf openmpi-common all 2.0.2~git.20161225-9 [148 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf libopenmpi-dev armhf 2.0.2~git.20161225-9 [1053 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking sbuild-build-depends-phyml-dummy (0.invalid.0) ...
Setting up chrpath (0.16-2) ...
Setting up libexpat1:armhf (2.2.0-2) ...
Setting up libarchive-zip-perl (1.59-1) ...
Setting up libdrm-amdgpu1:armhf (2.4.74-1) ...
Setting up libdrm-freedreno1:armhf (2.4.74-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up libelf1:armhf (0.168-0.2) ...
Setting up libgfortran3:armhf (6.2.1-5+rpi1) ...
Setting up groff-base (1.22.3-9) ...
Setting up gettext-base (0.19.8.1-1) ...
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up m4 (1.4.18-1) ...
Setting up libicu57:armhf (57.1-5) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-2.1) ...
Setting up libmagic-mgc (1:5.29-2) ...
Setting up libmagic1:armhf (1:5.29-2) ...
Setting up openmpi-common (2.0.2~git.20161225-9) ...
Processing triggers for libc-bin (2.24-7+rpi1) ...
Setting up autotools-dev (20161112.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up libltdl7:armhf (2.4.6-2) ...
Setting up libpciaccess0:armhf (0.13.4-1) ...
Setting up libsensors4:armhf (1:3.4.0-3) ...
Setting up libffi6:armhf (3.2.1-6) ...
Setting up libdrm-radeon1:armhf (2.4.74-1) ...
Setting up ocl-icd-libopencl1:armhf (2.2.10-2) ...
Setting up libdrm-nouveau2:armhf (2.4.74-1) ...
Setting up bsdmainutils (9.0.12) ...
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 (3.2.27-1) ...
Setting up libclc-dev (0.2.0+git20160907-3) ...
Setting up autopoint (0.19.8.1-1) ...
Setting up libfile-stripnondeterminism-perl (0.029-2) ...
Setting up libedit2:armhf (3.1-20160903-2) ...
Setting up libltdl-dev:armhf (2.4.6-2) ...
Setting up libglib2.0-0:armhf (2.50.2-2) ...
No schema files found: doing nothing.
Setting up libllvm3.9:armhf (1:3.9.1-1+rpi1) ...
Setting up libnl-route-3-200:armhf (3.2.27-1) ...
Setting up autoconf (2.69-10) ...
Setting up file (1:5.29-2) ...
Setting up libhwloc5:armhf (1.11.5-1+rpi1) ...
Setting up libclang-common-3.9-dev (1:3.9.1-1+rpi1) ...
Setting up libcroco3:armhf (0.6.11-2) ...
Setting up libhwloc-plugins (1.11.5-1+rpi1) ...
Setting up pkg-config (0.29-4) ...
Setting up libclc-amdgcn (0.2.0+git20160907-3) ...
Setting up automake (1:1.15-5) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-2) ...
Setting up libibverbs1 (1.2.1-2) ...
Setting up libclc-r600 (0.2.0+git20160907-3) ...
Setting up libhwloc-dev:armhf (1.11.5-1+rpi1) ...
Setting up gettext (0.19.8.1-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libopenmpi2:armhf (2.0.2~git.20161225-9) ...
Setting up libibverbs-dev (1.2.1-2) ...
Setting up mesa-opencl-icd:armhf (13.0.3-1) ...
Setting up po-debconf (1.0.20) ...
Setting up libopenmpi-dev (2.0.2~git.20161225-9) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/mpi (mpi) in auto mode
Setting up libhmsbeagle1v5 (2.1.2+20160831-5+b2) ...
Setting up libhmsbeagle-dev (2.1.2+20160831-5+b2) ...
Setting up dh-autoreconf (13) ...
Setting up dh-strip-nondeterminism (0.029-2) ...
Setting up debhelper (10.2.3) ...
Setting up sbuild-build-depends-phyml-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-7+rpi1) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.6.0-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.27.51.20161127-1 dpkg-dev_1.18.15 g++-6_6.2.1-5+rpi1 gcc-6_6.2.1-5+rpi1 libc6-dev_2.24-7+rpi1 libstdc++-6-dev_6.2.1-5+rpi1 libstdc++6_6.2.1-5+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.4~beta1 autoconf_2.69-10 automake_1:1.15-5 autopoint_0.19.8.1-1 autotools-dev_20161112.1 base-files_9.7+rpi1 base-passwd_3.5.41 bash_4.4-2 binutils_2.27.51.20161127-1 bsdmainutils_9.0.12 bsdutils_1:2.29-1 build-essential_12.2 bzip2_1.0.6-8 chrpath_0.16-2 coreutils_8.25-2 cpio_2.11+dfsg-6 cpp_4:6.1.1-1 cpp-6_6.2.1-5+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10.2.3 debianutils_4.8.1 dh-autoreconf_13 dh-strip-nondeterminism_0.029-2 diffutils_1:3.5-1 dmsetup_2:1.02.136-1 dpkg_1.18.15 dpkg-dev_1.18.15 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-2 file_1:5.29-2 findutils_4.6.0+git+20161106-1 fuse2fs_1.43.3-1 g++_4:6.1.1-1 g++-6_6.2.1-5+rpi1 gcc_4:6.1.1-1 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_4.9.3-14 gcc-6_6.2.1-5+rpi1 gcc-6-base_6.2.1-5+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gnupg_2.1.16-2 gnupg-agent_2.1.16-2 gnupg-l10n_2.1.16-2 gpgv_2.1.16-2 grep_2.26-1 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 init_1.46 init-system-helpers_1.46 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_23-1 libacl1_2.2.52-3 libapparmor1_2.10.95-6 libapt-pkg5.0_1.4~beta1 libarchive-zip-perl_1.59-1 libasan3_6.2.1-5+rpi1 libassuan0_2.4.3-2 libatomic1_6.2.1-5+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-1 libaudit1_1:2.6.7-1 libblkid1_2.29-1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.24-7+rpi1 libc-dev-bin_2.24-7+rpi1 libc6_2.24-7+rpi1 libc6-dev_2.24-7+rpi1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.2.1-5+rpi1 libclang-common-3.9-dev_1:3.9.1-1+rpi1 libclc-amdgcn_0.2.0+git20160907-3 libclc-dev_0.2.0+git20160907-3 libclc-r600_0.2.0+git20160907-3 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.3-2 libdb5.3_5.3.28-12 libdbus-1-3_1.10.14-1 libdebconfclient0_0.218 libdevmapper1.02.1_2:1.02.136-1 libdpkg-perl_1.18.15 libdrm-amdgpu1_2.4.74-1 libdrm-freedreno1_2.4.74-1 libdrm-nouveau2_2.4.74-1 libdrm-radeon1_2.4.74-1 libdrm2_2.4.74-1 libedit2_3.1-20160903-2 libelf1_0.168-0.2 libexpat1_2.2.0-2 libfakeroot_1.21-2 libfdisk1_2.29-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.029-2 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.2.1-5+rpi1 libgcc1_1:6.2.1-5+rpi1 libgcrypt20_1.7.3-2 libgdbm3_1.8.3-14 libgfortran3_6.2.1-5+rpi1 libglib2.0-0_2.50.2-2 libgmp10_2:6.1.1+dfsg-1 libgomp1_6.2.1-5+rpi1 libgpg-error0_1.25-1 libhmsbeagle-dev_2.1.2+20160831-5+b2 libhmsbeagle1v5_2.1.2+20160831-5+b2 libhwloc-dev_1.11.5-1+rpi1 libhwloc-plugins_1.11.5-1+rpi1 libhwloc5_1.11.5-1+rpi1 libibverbs-dev_1.2.1-2 libibverbs1_1.2.1-2 libicu57_57.1-5 libidn11_1.33-1 libip4tc0_1.6.0-4 libisl15_0.17.1-1 libklibc_2.0.4-9+rpi1 libkmod2_23-1 libksba8_1.3.5-2 libllvm3.9_1:3.9.1-1+rpi1 libltdl-dev_2.4.6-2 libltdl7_2.4.6-2 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.29-2 libmagic1_1:5.29-2 libmount1_2.29-1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160917-1 libncursesw5_6.0+20160917-1 libnl-3-200_3.2.27-1 libnl-route-3-200_3.2.27-1 libnpth0_1.3-1 libopenmpi-dev_2.0.2~git.20161225-9 libopenmpi2_2.0.2~git.20161225-9 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpciaccess0_0.13.4-1 libpcre3_2:8.39-2 libperl5.24_5.24.1~rc4-1 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6 libprocps6_2:3.3.12-3 libreadline7_7.0-1 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-1 libsemanage1_2.6-1 libsensors4_1:3.4.0-3 libsepol1_2.6-1 libsigsegv2_2.10-5 libsmartcols1_2.29-1 libsqlite3-0_3.15.2-1 libss2_1.43.3-1 libstdc++-6-dev_6.2.1-5+rpi1 libstdc++6_6.2.1-5+rpi1 libsystemd0_232-6 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160917-1 libtool_2.4.6-2 libubsan0_6.2.1-5+rpi1 libudev1_232-6 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-6 libuuid1_2.29-1 libxml2_2.9.4+dfsg1-2.1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.3 lsb-base_9.20161125+rpi1 m4_1.4.18-1 make_4.1-9 makedev_2.3.1-93 man-db_2.7.6.1-2 manpages_4.08-1 mawk_1.3.3-17 mesa-opencl-icd_13.0.3-1 mount_2.29-1 multiarch-support_2.24-7+rpi1 nano_2.7.1-1 ncurses-base_6.0+20160917-1 ncurses-bin_6.0+20160917-1 ocl-icd-libopencl1_2.2.10-2 openmpi-common_2.0.2~git.20161225-9 passwd_1:4.2-3.3 patch_2.7.5-1 perl_5.24.1~rc4-1 perl-base_5.24.1~rc4-1 perl-modules-5.24_5.24.1~rc4-1 pinentry-curses_0.9.7-9 pkg-config_0.29-4 po-debconf_1.0.20 procps_2:3.3.12-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-phyml-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_232-6 systemd-sysv_232-6 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1.1 tzdata_2016j-2 udev_232-6 util-linux_2.29-1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| 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 Jan 16 09:31:01 2017 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_3.2.0+dfsg-4.dsc
dpkg-source: info: extracting phyml in /<<BUILDDIR>>/phyml-3.2.0+dfsg
dpkg-source: info: unpacking phyml_3.2.0+dfsg.orig.tar.gz
dpkg-source: info: unpacking phyml_3.2.0+dfsg-4.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
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=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-c914aaeb-ff6b-46ab-b2d7-90fc46897b7c
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package phyml
dpkg-buildpackage: info: source version 3:3.2.0+dfsg-4
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build phyml-3.2.0+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --with autoreconf
dh_testdir
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+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-3.2.0+dfsg'
dh_autoreconf_clean
dh_clean
debian/rules build-arch
dh build-arch --with autoreconf
dh_testdir -a
dh_update_autotools_config -a
debian/rules override_dh_autoreconf
make[1]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
dh_autoreconf --as-needed
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.ac,
libtoolize: and rerunning libtoolize and aclocal.
libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am.
configure.ac:17: installing './compile'
configure.ac:15: installing './config.guess'
configure.ac:15: installing './config.sub'
configure.ac:5: installing './install-sh'
configure.ac:5: installing './missing'
src/Makefile.am: installing './depcomp'
patching file ./ltmain.sh
make[1]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
# According to README you need different configure options to get different executables
# Here we hack in a full build process for phyml executable
dh_auto_configure -- --enable-beagle
./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 --disable-maintainer-mode --disable-dependency-tracking --enable-beagle
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 whether make supports nested variables... (cached) 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
configure: "Do not use MSSE = because not available on arch arm-unknown-linux-gnueabihf"
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop
checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for BEAGLE... 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
config.status: executing libtool commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
dh_auto_build -- LDFLAGS="-specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,now"
make -j4 "LDFLAGS=-specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,now"
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make all-recursive
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
Making all in src
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o main.o main.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o utilities.o utilities.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o optimiz.o optimiz.c
.: Building [phyml-beagle]. Version 3:3.2.0+dfsg-4 :.
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o lk.o lk.c
utilities.c: In function 'K80_dist':
utilities.c:2129:7: warning: unused variable 'temp' [-Wunused-variable]
int temp;
^~~~
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o bionj.o bionj.c
utilities.c: In function 'Get_Edge_Binary_Coding_Number':
utilities.c:9526:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(b->left->bip_node[b->l_r][j]->id_rank > max_left)
^~
utilities.c:9529:7: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
max_rght = 0;
^~~~~~~~
utilities.c:9531:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(b->rght->bip_node[b->r_l][j]->id_rank > max_rght)
^~
utilities.c:9535:7: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if(max_left < max_rght)
^~
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o models.o models.c
models.c: In function 'General_Dist':
models.c:1171:79: warning: comparison of constant '0' with boolean expression is always false [-Wbool-compare]
if(!Matinv(eigen_struct->l_e_vect,eigen_struct->size,eigen_struct->size,YES)<0)
^
models.c:1171:79: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses]
models.c: In function 'GTR_Dist':
models.c:1273:79: warning: comparison of constant '0' with boolean expression is always false [-Wbool-compare]
if(!Matinv(eigen_struct->l_e_vect,eigen_struct->size,eigen_struct->size,YES)<0) {Free(pi); return -1.;}
^
models.c:1273:79: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses]
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o free.o free.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o help.o help.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o simu.o simu.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o eigen.o eigen.c
simu.c: In function 'Simu':
simu.c:113:11: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(tree->io->print_site_lnl) Print_Site_Lk(tree,tree->io->fp_out_lk); fflush(tree->io->fp_out_lk);
^~
simu.c:113:81: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if(tree->io->print_site_lnl) Print_Site_Lk(tree,tree->io->fp_out_lk); fflush(tree->io->fp_out_lk);
^~~~~~
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o pars.o pars.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o alrt.o alrt.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o interface.o interface.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o cl.o cl.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o spr.o spr.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o draw.o draw.c
spr.c: In function 'Speed_Spr':
spr.c:3795:11: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if((tree->io->print_site_lnl) && (!tree->mod->s_opt->spr_pars)) Print_Site_Lk(tree,tree->io->fp_out_lk); fflush(tree->io->fp_out_lk);
^~
spr.c:3795:116: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if((tree->io->print_site_lnl) && (!tree->mod->s_opt->spr_pars)) Print_Site_Lk(tree,tree->io->fp_out_lk); fflush(tree->io->fp_out_lk);
^~~~~~
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o stats.o stats.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o rates.o rates.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o mcmc.o mcmc.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o times.o times.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o tiporder.o tiporder.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o mg.o mg.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o m4.o m4.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o io.o io.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o make.o make.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o nexus.o nexus.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o init.o init.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o xml.o xml.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o mixt.o mixt.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o beagle_utils.o beagle_utils.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,now -o phyml-beagle 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 beagle_utils.o -lm -lhmsbeagle -lm
libtool: link: gcc -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z -Wl,relro -Wl,-z -Wl,now -o phyml-beagle 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 beagle_utils.o -ldl -lhmsbeagle -lm
Done.
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
# move phyml binary to temporary dir inside debian/
mkdir -p /<<BUILDDIR>>/phyml-3.2.0+dfsg/debian/bin
mv src/phyml-beagle /<<BUILDDIR>>/phyml-3.2.0+dfsg/debian/bin/phyml
mv doc/phyml-manual.pdf .
/usr/bin/make distclean
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
Making distclean in src
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
rm -f phyml-beagle
test -z "" || rm -f
rm -rf .libs _libs
rm -f *.o
rm -f *.lo
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-3.2.0+dfsg/src'
Making distclean in doc
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/doc'
test -z "phyml-manual.pdf phyml-manual.log phyml-manual.idx phyml-manual.out phyml-manual.toc phyml-manual.aux phyml-manual.ilg phyml-manual.ind phyml-manual.dvi " || rm -f phyml-manual.pdf phyml-manual.log phyml-manual.idx phyml-manual.out phyml-manual.toc phyml-manual.aux phyml-manual.ilg phyml-manual.ind phyml-manual.dvi
rm -rf .libs _libs
rm -f *.lo
test -z "" || rm -f
test . = "." || test -z "" || rm -f
rm -f Makefile
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/doc'
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
rm -rf .libs _libs
rm -f *.lo
test -z "" || rm -f
test . = "." || test -z "" || rm -f
rm -f config.h stamp-h1
rm -f libtool config.lt
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-3.2.0+dfsg'
rm -f config.status config.cache config.log configure.lineno config.status.lineno
rm -f Makefile
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
mv phyml-manual.pdf doc
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 --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 whether make supports nested variables... (cached) 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
configure: "Do not use MSSE = because not available on arch arm-unknown-linux-gnueabihf"
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop
checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... 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
config.status: executing libtool commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
dh_auto_build -- LDFLAGS="-specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,now"
make -j4 "LDFLAGS=-specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,now"
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make all-recursive
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
Making all in src
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o main.o main.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o utilities.o utilities.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o optimiz.o optimiz.c
.: Building [phyml-mpi]. Version 3:3.2.0+dfsg-4 :.
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o lk.o lk.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o bionj.o bionj.c
utilities.c: In function 'Get_Edge_Binary_Coding_Number':
utilities.c:9526:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(b->left->bip_node[b->l_r][j]->id_rank > max_left)
^~
utilities.c:9529:7: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
max_rght = 0;
^~~~~~~~
utilities.c:9531:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(b->rght->bip_node[b->r_l][j]->id_rank > max_rght)
^~
utilities.c:9535:7: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if(max_left < max_rght)
^~
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o models.o models.c
models.c: In function 'General_Dist':
models.c:1171:79: warning: comparison of constant '0' with boolean expression is always false [-Wbool-compare]
if(!Matinv(eigen_struct->l_e_vect,eigen_struct->size,eigen_struct->size,YES)<0)
^
models.c:1171:79: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses]
models.c: In function 'GTR_Dist':
models.c:1273:79: warning: comparison of constant '0' with boolean expression is always false [-Wbool-compare]
if(!Matinv(eigen_struct->l_e_vect,eigen_struct->size,eigen_struct->size,YES)<0) {Free(pi); return -1.;}
^
models.c:1273:79: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses]
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o free.o free.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o help.o help.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o simu.o simu.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o eigen.o eigen.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o pars.o pars.c
simu.c: In function 'Simu':
simu.c:113:11: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(tree->io->print_site_lnl) Print_Site_Lk(tree,tree->io->fp_out_lk); fflush(tree->io->fp_out_lk);
^~
simu.c:113:81: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if(tree->io->print_site_lnl) Print_Site_Lk(tree,tree->io->fp_out_lk); fflush(tree->io->fp_out_lk);
^~~~~~
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o alrt.o alrt.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o interface.o interface.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o cl.o cl.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o spr.o spr.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o draw.o draw.c
spr.c: In function 'Speed_Spr':
spr.c:3795:11: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if((tree->io->print_site_lnl) && (!tree->mod->s_opt->spr_pars)) Print_Site_Lk(tree,tree->io->fp_out_lk); fflush(tree->io->fp_out_lk);
^~
spr.c:3795:116: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if((tree->io->print_site_lnl) && (!tree->mod->s_opt->spr_pars)) Print_Site_Lk(tree,tree->io->fp_out_lk); fflush(tree->io->fp_out_lk);
^~~~~~
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o stats.o stats.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o rates.o rates.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o mcmc.o mcmc.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o times.o times.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o tiporder.o tiporder.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o mg.o mg.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o m4.o m4.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o io.o io.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o make.o make.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o nexus.o nexus.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o init.o init.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o xml.o xml.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o mixt.o mixt.c
mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o mpi_boot.o mpi_boot.c
/bin/bash ../libtool --tag=CC --mode=link mpicc -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -specs=/usr/share/dpkg/no-pie-link.specs -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 mpi_boot.o -lm -lm
libtool: link: mpicc -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z -Wl,relro -Wl,-z -Wl,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 mpi_boot.o -lm
Done.
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
# move phyml binary to temporary dir inside debian/
# mkdir -p /<<BUILDDIR>>/phyml-3.2.0+dfsg/debian/bin
mv src/phyml-mpi /<<BUILDDIR>>/phyml-3.2.0+dfsg/debian/bin/phyml-mpi
mv doc/phyml-manual.pdf .
/usr/bin/make distclean
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
Making distclean in src
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
rm -f phyml-mpi
test -z "" || rm -f
rm -rf .libs _libs
rm -f *.o
rm -f *.lo
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-3.2.0+dfsg/src'
Making distclean in doc
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/doc'
test -z "phyml-manual.pdf phyml-manual.log phyml-manual.idx phyml-manual.out phyml-manual.toc phyml-manual.aux phyml-manual.ilg phyml-manual.ind phyml-manual.dvi " || rm -f phyml-manual.pdf phyml-manual.log phyml-manual.idx phyml-manual.out phyml-manual.toc phyml-manual.aux phyml-manual.ilg phyml-manual.ind phyml-manual.dvi
rm -rf .libs _libs
rm -f *.lo
test -z "" || rm -f
test . = "." || test -z "" || rm -f
rm -f Makefile
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/doc'
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
rm -rf .libs _libs
rm -f *.lo
test -z "" || rm -f
test . = "." || test -z "" || rm -f
rm -f config.h stamp-h1
rm -f libtool config.lt
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-3.2.0+dfsg'
rm -f config.status config.cache config.log configure.lineno config.status.lineno
rm -f Makefile
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
mv phyml-manual.pdf doc
dh_auto_configure -- --enable-phytime
./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 --disable-maintainer-mode --disable-dependency-tracking --enable-phytime
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 whether make supports nested variables... (cached) 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
configure: "Do not use MSSE = because not available on arch arm-unknown-linux-gnueabihf"
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop
checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... 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
config.status: executing libtool commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
dh_auto_build -- LDFLAGS="-specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,now" CPPFLAGS="-DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2"
make -j4 "LDFLAGS=-specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,now" "CPPFLAGS=-DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2"
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make all-recursive
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
Making all in src
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o main.o main.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o utilities.o utilities.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o optimiz.o optimiz.c
.: Building [phytime]. Version 3:3.2.0+dfsg-4 :.
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o lk.o lk.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o bionj.o bionj.c
utilities.c: In function 'Get_Edge_Binary_Coding_Number':
utilities.c:9526:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(b->left->bip_node[b->l_r][j]->id_rank > max_left)
^~
utilities.c:9529:7: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
max_rght = 0;
^~~~~~~~
utilities.c:9531:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(b->rght->bip_node[b->r_l][j]->id_rank > max_rght)
^~
utilities.c:9535:7: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if(max_left < max_rght)
^~
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o models.o models.c
models.c: In function 'General_Dist':
models.c:1171:79: warning: comparison of constant '0' with boolean expression is always false [-Wbool-compare]
if(!Matinv(eigen_struct->l_e_vect,eigen_struct->size,eigen_struct->size,YES)<0)
^
models.c:1171:79: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses]
models.c: In function 'GTR_Dist':
models.c:1273:79: warning: comparison of constant '0' with boolean expression is always false [-Wbool-compare]
if(!Matinv(eigen_struct->l_e_vect,eigen_struct->size,eigen_struct->size,YES)<0) {Free(pi); return -1.;}
^
models.c:1273:79: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses]
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o free.o free.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o help.o help.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o simu.o simu.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o eigen.o eigen.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o pars.o pars.c
simu.c: In function 'Simu':
simu.c:113:11: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if(tree->io->print_site_lnl) Print_Site_Lk(tree,tree->io->fp_out_lk); fflush(tree->io->fp_out_lk);
^~
simu.c:113:81: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if(tree->io->print_site_lnl) Print_Site_Lk(tree,tree->io->fp_out_lk); fflush(tree->io->fp_out_lk);
^~~~~~
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o alrt.o alrt.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o interface.o interface.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o cl.o cl.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o spr.o spr.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o times.o times.c
spr.c: In function 'Speed_Spr':
spr.c:3795:11: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if((tree->io->print_site_lnl) && (!tree->mod->s_opt->spr_pars)) Print_Site_Lk(tree,tree->io->fp_out_lk); fflush(tree->io->fp_out_lk);
^~
spr.c:3795:116: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
if((tree->io->print_site_lnl) && (!tree->mod->s_opt->spr_pars)) Print_Site_Lk(tree,tree->io->fp_out_lk); fflush(tree->io->fp_out_lk);
^~~~~~
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o m4.o m4.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o draw.o draw.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o rates.o rates.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o mcmc.o mcmc.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o stats.o stats.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o mg.o mg.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o tiporder.o tiporder.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o io.o io.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o make.o make.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o mixt.o mixt.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o init.o init.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o nexus.o nexus.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o xml.o xml.c
gcc -I. -I.. -DPHYREX -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -c -o phyrex.o phyrex.c
phyrex.c: In function 'PHYREX_Main_Simulate':
phyrex.c:137:7: warning: variable 'n_otus' set but not used [-Wunused-but-set-variable]
int n_otus, n_sites;
^~~~~~
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,now -o phytime 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 times.o m4.o draw.o rates.o mcmc.o stats.o mg.o tiporder.o io.o make.o mixt.o init.o nexus.o xml.o phyrex.o -lm -lm
libtool: link: gcc -Wall -O2 -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z -Wl,relro -Wl,-z -Wl,now -o phytime 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 times.o m4.o draw.o rates.o mcmc.o stats.o mg.o tiporder.o io.o make.o mixt.o init.o nexus.o xml.o phyrex.o -lm
Done.
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
dh_auto_test -a
make -j4 check VERBOSE=1
make[1]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
Making check in src
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
.: Building [phytime]. Version 3:3.2.0+dfsg-4 :.
Done.
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
fakeroot debian/rules binary-arch
dh binary-arch --with autoreconf
dh_testroot -a
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
dh_auto_install
make -j4 install DESTDIR=/<<BUILDDIR>>/phyml-3.2.0\+dfsg/debian/phyml AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
Making install in src
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
.: Building [phytime]. Version 3:3.2.0+dfsg-4 :.
Done.
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<BUILDDIR>>/phyml-3.2.0+dfsg/debian/phyml/usr/bin'
/bin/bash ../libtool --mode=install /usr/bin/install -c phytime '/<<BUILDDIR>>/phyml-3.2.0+dfsg/debian/phyml/usr/bin'
libtool: install: /usr/bin/install -c phytime /<<BUILDDIR>>/phyml-3.2.0+dfsg/debian/phyml/usr/bin/phytime
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[4]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[3]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
# install phyml binary we have kept safe above
mkdir -p /<<BUILDDIR>>/phyml-3.2.0+dfsg/debian/phyml/usr/lib/phyml/bin
mv /<<BUILDDIR>>/phyml-3.2.0+dfsg/debian/bin/* /<<BUILDDIR>>/phyml-3.2.0+dfsg/debian/phyml/usr/lib/phyml/bin
chrpath --delete debian/phyml/usr/lib/phyml/bin/phyml*
make[1]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
dh_install -a
debian/rules override_dh_installdocs
make[1]: Entering directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
dh_installdocs
mv /<<BUILDDIR>>/phyml-3.2.0+dfsg/debian/phyml/usr/share/doc/phyml/phyml-manual.pdf /<<BUILDDIR>>/phyml-3.2.0+dfsg/debian/phyml/usr/share/doc/phyml/phyml_manual.pdf
make[1]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+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-3.2.0+dfsg'
dh_compress --exclude=.pdf
make[1]: Leaving directory '/<<BUILDDIR>>/phyml-3.2.0+dfsg'
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phyml/usr/lib/phyml/bin/phyml was not linked against libdl.so.2 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'phyml-dbgsym' in '../phyml-dbgsym_3.2.0+dfsg-4_armhf.deb'.
dpkg-deb: building package 'phyml' in '../phyml_3.2.0+dfsg-4_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genbuildinfo: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../phyml_3.2.0+dfsg-4_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build phyml-3.2.0+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-01-28T05:56:44Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
phyml_3.2.0+dfsg-4_armhf.changes:
---------------------------------
Format: 1.8
Date: Mon, 16 Jan 2017 10:22:34 +0100
Source: phyml
Binary: phyml
Architecture: armhf
Version: 3:3.2.0+dfsg-4
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
phyml - Phylogenetic estimation using Maximum Likelihood
Changes:
phyml (3:3.2.0+dfsg-4) unstable; urgency=medium
.
* Add pocl-opencl-icd to autopkgtest dependencies to emulate CPU-based ICD
* debhelper 10
* d/watch: version=4
* Use chrpath to remove RPATH from binary
* Use "OMPI_MCA_plm_rsh_agent=/bin/false" in test (see #494046)
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Files:
86a1070acfd90ba55033db6d60408dec 56618 debug extra phyml-dbgsym_3.2.0+dfsg-4_armhf.deb
50767652270e092ada6d5f5aa00770d8 5504 science optional phyml_3.2.0+dfsg-4_armhf.buildinfo
033f636b4616e8684138aaa8b9782df4 1036326 science optional phyml_3.2.0+dfsg-4_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
phyml-dbgsym_3.2.0+dfsg-4_armhf.deb
-----------------------------------
new debian package, version 2.0.
size 56618 bytes: control archive=609 bytes.
502 bytes, 13 lines control
318 bytes, 3 lines md5sums
Package: phyml-dbgsym
Source: phyml
Version: 3:3.2.0+dfsg-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 271
Depends: phyml (= 3:3.2.0+dfsg-4)
Section: debug
Priority: extra
Homepage: http://www.atgc-montpellier.fr/phyml
Description: Debug symbols for phyml
Auto-Built-Package: debug-symbols
Build-Ids: 0eed1bc0e327317619ceb242391cd99fc232839f 22c294c0d9fde7db15a91a298a589d1253325199 cc98ab3b46e650648fbfffc64ccc686f5c95899f
drwxr-xr-x root/root 0 2017-01-16 09:22 ./
drwxr-xr-x root/root 0 2017-01-16 09:22 ./usr/
drwxr-xr-x root/root 0 2017-01-16 09:22 ./usr/lib/
drwxr-xr-x root/root 0 2017-01-16 09:22 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-01-16 09:22 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-01-16 09:22 ./usr/lib/debug/.build-id/0e/
-rw-r--r-- root/root 85184 2017-01-16 09:22 ./usr/lib/debug/.build-id/0e/ed1bc0e327317619ceb242391cd99fc232839f.debug
drwxr-xr-x root/root 0 2017-01-16 09:22 ./usr/lib/debug/.build-id/22/
-rw-r--r-- root/root 84472 2017-01-16 09:22 ./usr/lib/debug/.build-id/22/c294c0d9fde7db15a91a298a589d1253325199.debug
drwxr-xr-x root/root 0 2017-01-16 09:22 ./usr/lib/debug/.build-id/cc/
-rw-r--r-- root/root 94152 2017-01-16 09:22 ./usr/lib/debug/.build-id/cc/98ab3b46e650648fbfffc64ccc686f5c95899f.debug
drwxr-xr-x root/root 0 2017-01-16 09:22 ./usr/share/
drwxr-xr-x root/root 0 2017-01-16 09:22 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-01-16 09:22 ./usr/share/doc/phyml-dbgsym -> phyml
phyml_3.2.0+dfsg-4_armhf.deb
----------------------------
new debian package, version 2.0.
size 1036326 bytes: control archive=1842 bytes.
1681 bytes, 31 lines control
1711 bytes, 24 lines md5sums
Package: phyml
Version: 3:3.2.0+dfsg-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3802
Depends: libc6 (>= 2.7), libhmsbeagle1v5, libopenmpi2, 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.
drwxr-xr-x root/root 0 2017-01-16 09:22 ./
drwxr-xr-x root/root 0 2017-01-16 09:22 ./usr/
drwxr-xr-x root/root 0 2017-01-16 09:22 ./usr/bin/
-rwxr-xr-x root/root 331 2017-01-16 09:22 ./usr/bin/phyml
-rwxr-xr-x root/root 1205808 2017-01-16 09:22 ./usr/bin/phytime
drwxr-xr-x root/root 0 2017-01-16 09:22 ./usr/lib/
drwxr-xr-x root/root 0 2017-01-16 09:22 ./usr/lib/phyml/
drwxr-xr-x root/root 0 2017-01-16 09:22 ./usr/lib/phyml/bin/
-rwxr-xr-x root/root 1095216 2017-01-16 09:22 ./usr/lib/phyml/bin/phyml
-rwxr-xr-x root/root 1107504 2017-01-16 09:22 ./usr/lib/phyml/bin/phyml-mpi
drwxr-xr-x root/root 0 2017-01-16 09:22 ./usr/share/
drwxr-xr-x root/root 0 2017-01-16 09:22 ./usr/share/doc-base/
-rw-r--r-- root/root 202 2017-01-16 09:22 ./usr/share/doc-base/phyml
drwxr-xr-x root/root 0 2017-01-16 09:22 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-01-16 09:22 ./usr/share/doc/phyml/
-rw-r--r-- root/root 1922 2017-01-16 09:22 ./usr/share/doc/phyml/README.Debian
-rw-r--r-- root/root 2239 2017-01-16 09:22 ./usr/share/doc/phyml/changelog.Debian.gz
-rw-r--r-- root/root 5458 2015-12-17 10:01 ./usr/share/doc/phyml/changelog.gz
-rw-r--r-- root/root 2025 2017-01-16 09:22 ./usr/share/doc/phyml/copyright
drwxr-xr-x root/root 0 2017-01-16 09:22 ./usr/share/doc/phyml/examples/
-rw-r--r-- root/root 5082 2017-01-16 09:22 ./usr/share/doc/phyml/examples/example.nex.gz
drwxr-xr-x root/root 0 2015-12-17 10:01 ./usr/share/doc/phyml/examples/lg4x/
-rw-r--r-- root/root 1900 2015-12-17 10:01 ./usr/share/doc/phyml/examples/lg4x/X1.mat
-rw-r--r-- root/root 1899 2015-12-17 10:01 ./usr/share/doc/phyml/examples/lg4x/X2.mat
-rw-r--r-- root/root 1893 2015-12-17 10:01 ./usr/share/doc/phyml/examples/lg4x/X3.mat
-rw-r--r-- root/root 1895 2015-12-17 10:01 ./usr/share/doc/phyml/examples/lg4x/X4.mat
-rw-r--r-- root/root 1994 2015-12-17 10:01 ./usr/share/doc/phyml/examples/lg4x/lg4x.xml
-rw-r--r-- root/root 2175 2015-12-17 10:01 ./usr/share/doc/phyml/examples/nexus_example.nxs
-rw-r--r-- root/root 3543 2015-12-17 10:01 ./usr/share/doc/phyml/examples/nucleic.gz
drwxr-xr-x root/root 0 2017-01-16 09:22 ./usr/share/doc/phyml/examples/phytime_input_files/
-rw-r--r-- root/root 1933 2015-12-17 10:01 ./usr/share/doc/phyml/examples/phytime_input_files/p1.calib
-rw-r--r-- root/root 2055 2015-12-17 10:01 ./usr/share/doc/phyml/examples/phytime_input_files/p1.nxs.gz
-rw-r--r-- root/root 3249 2015-12-17 10:01 ./usr/share/doc/phyml/examples/phytime_input_files/p1.tree
-rw-r--r-- root/root 5114 2015-12-17 10:01 ./usr/share/doc/phyml/examples/proteic.gz
-rw-r--r-- root/root 407931 2015-12-17 10:01 ./usr/share/doc/phyml/phyml_manual.pdf
drwxr-xr-x root/root 0 2017-01-16 09:22 ./usr/share/man/
drwxr-xr-x root/root 0 2017-01-16 09:22 ./usr/share/man/man1/
-rw-r--r-- root/root 2898 2017-01-16 09:22 ./usr/share/man/man1/phyml.1.gz
-rw-r--r-- root/root 2306 2017-01-16 09:22 ./usr/share/man/man1/phytime.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 15732
Build-Time: 598
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 544
Job: phyml_3:3.2.0+dfsg-4
Machine Architecture: armhf
Package: phyml
Package-Time: 1190
Source-Version: 3:3.2.0+dfsg-4
Space: 15732
Status: successful
Version: 3:3.2.0+dfsg-4
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Finished at 2017-01-28T05:56:44Z
Build needed 00:19:50, 15732k disc space