phyml →
3:3.3.20190321-2 →
armhf → 2019-08-27 07:01:10
sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on test2019
+==============================================================================+
| phyml 3:3.3.20190321-2 (armhf) Tue, 27 Aug 2019 06:45:08 +0000 |
+==============================================================================+
Package: phyml
Version: 3:3.3.20190321-2
Source Version: 3:3.3.20190321-2
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bullseye-staging-armhf-sbuild-e5ee8acf-1c6a-40c1-b318-5d3d291d9d96' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.1 MB]
Fetched 24.6 MB in 32s (779 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://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 2243 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main phyml 3:3.3.20190321-2 (dsc) [2094 B]
Get:2 http://172.17.0.1/private bullseye-staging/main phyml 3:3.3.20190321-2 (tar) [2223 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main phyml 3:3.3.20190321-2 (diff) [17.1 kB]
Fetched 2243 kB in 1s (1925 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/phyml-uU2O4I/phyml-3.3.20190321' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/phyml-uU2O4I' 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-Cap11e/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-Cap11e/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-Cap11e/gpg/trustdb.gpg: trustdb created
gpg: key E70254B6505CF8F7: 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 E70254B6505CF8F7: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key E70254B6505CF8F7: 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-Cap11e/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Cap11e/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Cap11e/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-Cap11e/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-Cap11e/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-Cap11e/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2302 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-Cap11e/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-Cap11e/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY E70254B6505CF8F7
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 90 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-Cap11e/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12044 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-compat (= 12), pkg-config, libopenmpi-dev, chrpath
Filtered Build-Depends: debhelper-compat (= 12), pkg-config, libopenmpi-dev, chrpath
dpkg-deb: building package 'sbuild-build-depends-phyml-dummy' in '/<<BUILDDIR>>/resolver-Cap11e/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-Cap11e/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Cap11e/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Cap11e/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-Cap11e/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-Cap11e/apt_archive ./ Sources [514 B]
Get:5 copy:/<<BUILDDIR>>/resolver-Cap11e/apt_archive ./ Packages [594 B]
Fetched 2441 B in 1s (2807 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-Cap11e/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-Cap11e/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY E70254B6505CF8F7
Reading package lists...
Install phyml build dependencies (apt-based resolver)
-----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils chrpath debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gcc-9-base gettext
gettext-base groff-base ibverbs-providers intltool-debian
libarchive-zip-perl libbsd0 libcroco3 libedit2 libelf1 libevent-2.1-6
libevent-core-2.1-6 libevent-pthreads-2.1-6 libfile-stripnondeterminism-perl
libgfortran5 libglib2.0-0 libgssapi-krb5-2 libhwloc-dev libhwloc-plugins
libhwloc5 libibverbs-dev libibverbs1 libicu63 libk5crypto3 libkeyutils1
libkrb5-3 libkrb5support0 libltdl-dev libltdl7 libmagic-mgc libmagic1
libncurses6 libncursesw6 libnl-3-200 libnl-3-dev libnl-route-3-200
libnl-route-3-dev libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1
libpmix2 libsigsegv2 libssl1.1 libsub-override-perl libtinfo5 libtinfo6
libtool libuchardet0 libxml2 m4 man-db ocl-icd-libopencl1 openmpi-bin
openmpi-common openssh-client pkg-config po-debconf sensible-utils
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make 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 | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass
libmail-box-perl
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales libgpm2 libcoarrays-openmpi-dev xauth
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils chrpath debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gcc-9-base gettext
gettext-base groff-base ibverbs-providers intltool-debian
libarchive-zip-perl libbsd0 libcroco3 libedit2 libelf1 libevent-2.1-6
libevent-core-2.1-6 libevent-pthreads-2.1-6 libfile-stripnondeterminism-perl
libgfortran5 libglib2.0-0 libgssapi-krb5-2 libhwloc-dev libhwloc-plugins
libhwloc5 libibverbs-dev libibverbs1 libicu63 libk5crypto3 libkeyutils1
libkrb5-3 libkrb5support0 libltdl-dev libltdl7 libmagic-mgc libmagic1
libncurses6 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev
libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix2 libsigsegv2
libssl1.1 libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4
man-db ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client
pkg-config po-debconf sbuild-build-depends-phyml-dummy sensible-utils
The following packages will be upgraded:
libncursesw6 libtinfo6
2 upgraded, 70 newly installed, 0 to remove and 88 not upgraded.
Need to get 27.5 MB of archives.
After this operation, 97.0 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-Cap11e/apt_archive ./ sbuild-build-depends-phyml-dummy 0.invalid.0 [884 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20190803-1 [314 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-3 [782 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.1-2 [26.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.8.6.1-1 [1248 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libtinfo6 armhf 6.1+20190803-1 [318 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libncursesw6 armhf 6.1+20190803-1 [104 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf gcc-9-base armhf 9.1.0-10+rpi1 [190 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12 [15.8 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.37-5 [253 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.37-5 [111 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.37-5 [66.2 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libevent-2.1-6 armhf 2.1.8-stable-4 [156 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libedit2 armhf 3.1-20190324-1 [78.9 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6-6 [14.0 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-6+b1 [61.5 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-6+b1 [112 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1c-1 [1259 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-6+b1 [316 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-6+b1 [134 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf openssh-client armhf 1:8.0p1-4 [692 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf chrpath armhf 0.16-2 [15.4 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-9 [547 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.5.0-1 [22.8 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.5.0-1 [14.1 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-1 [69.7 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.60.6-2 [1109 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b2 [571 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20190803-1 [79.3 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.5.3 [1036 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libnl-3-200 armhf 3.4.0-1 [55.0 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libnl-route-3-200 armhf 3.4.0-1 [132 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libibverbs1 armhf 24.0-2 [44.1 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf ibverbs-providers armhf 24.0-2 [20.5 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libevent-core-2.1-6 armhf 2.1.8-stable-4 [117 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libevent-pthreads-2.1-6 armhf 2.1.8-stable-4 [47.6 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 9.1.0-10+rpi1 [230 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libltdl7 armhf 2.4.6-9 [387 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libhwloc5 armhf 1.11.13-1+rpi1 [87.4 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libltdl-dev armhf 2.4.6-9 [159 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libhwloc-dev armhf 1.11.13-1+rpi1 [143 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libpciaccess0 armhf 0.14-1 [51.0 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf ocl-icd-libopencl1 armhf 2.2.12-2 [35.7 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libhwloc-plugins armhf 1.11.13-1+rpi1 [16.1 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libnl-3-dev armhf 3.4.0-1 [92.4 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libnl-route-3-dev armhf 3.4.0-1 [145 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libibverbs-dev armhf 24.0-2 [187 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libpmix2 armhf 3.1.4-1 [433 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libopenmpi3 armhf 3.1.3-11+rpi1 [1813 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf openmpi-common all 3.1.3-11+rpi1 [164 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf openmpi-bin armhf 3.1.3-11+rpi1 [197 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libopenmpi-dev armhf 3.1.3-11+rpi1 [964 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29-6 [59.8 kB]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 12044 files and directories currently installed.)
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Setting up libtinfo6:armhf (6.1+20190803-1) ...
(Reading database ... 12685 files and directories currently installed.)
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Setting up ocl-icd-libopencl1:armhf (2.2.12-2) ...
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Setting up chrpath (0.16-2) ...
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Setting up libhwloc5:armhf (1.11.13-1+rpi1) ...
Setting up libedit2:armhf (3.1-20190324-1) ...
Setting up m4 (1.4.18-2) ...
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Setting up libnl-route-3-200:armhf (3.4.0-1) ...
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 libgssapi-krb5-2:armhf (1.17-6+b1) ...
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Setting up groff-base (1.22.4-3) ...
Setting up automake (1:1.16.1-4) ...
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Setting up gettext (0.19.8.1-9) ...
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Setting up openssh-client (1:8.0p1-4) ...
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Setting up man-db (2.8.6.1-1) ...
Not building database; man-db/auto-update is not 'true'.
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Setting up libltdl-dev:armhf (2.4.6-9) ...
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Setting up openmpi-bin (3.1.3-11+rpi1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up po-debconf (1.0.21) ...
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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-strip-nondeterminism (1.5.0-1) ...
Setting up debhelper (12.5.3) ...
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Processing triggers for libc-bin (2.28-10+rpi1) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ armhf (armv7l)
Toolchain package versions: binutils_2.31.1-16+rpi1 dpkg-dev_1.19.7 g++-8_8.3.0-6+rpi1 gcc-8_8.3.0-6+rpi1 libc6-dev_2.28-10+rpi1 libstdc++-8-dev_8.3.0-6+rpi1 libstdc++6_8.3.0-6+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.2 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.3+rpi1 base-passwd_3.5.46 bash_5.0-4 binutils_2.31.1-16+rpi1 binutils-arm-linux-gnueabihf_2.31.1-16+rpi1 binutils-common_2.31.1-16+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33.1-0.1 build-essential_12.6 bzip2_1.0.6-9.1 chrpath_0.16-2 coreutils_8.30-3 cpp_4:8.3.0-1+rpi2 cpp-8_8.3.0-6+rpi1 dash_0.5.10.2-5 debconf_1.5.71 debhelper_12.5.3 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.5.0-1 diffutils_1:3.7-3 dirmngr_2.2.12-1+rpi1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-1 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.37-5 findutils_4.6.0+git+20190209-2 g++_4:8.3.0-1+rpi2 g++-8_8.3.0-6+rpi1 gcc_4:8.3.0-1+rpi2 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-6-base_6.5.0-1+rpi1+b1 gcc-7-base_7.3.0-19 gcc-8_8.3.0-6+rpi1 gcc-8-base_8.3.0-6+rpi1 gcc-9-base_9.1.0-10+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hostname_3.21 ibverbs-providers_24.0-2 init-system-helpers_1.56+nmu1 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libapt-pkg5.0_1.8.2 libarchive-zip-perl_1.64-1 libasan5_8.3.0-6+rpi1 libassuan0_2.5.2-1 libatomic1_8.3.0-6+rpi1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.4-3 libaudit1_1:2.8.4-3 libbinutils_2.31.1-16+rpi1 libblkid1_2.33.1-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.6-9.1 libc-bin_2.28-10+rpi1 libc-dev-bin_2.28-10+rpi1 libc6_2.28-10+rpi1 libc6-dev_2.28-10+rpi1 libcap-ng0_0.7.9-2 libcc1-0_8.3.0-6+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.13-1 libdb5.3_5.3.28+dfsg1-0.5 libdebconfclient0_0.249 libdpkg-perl_1.19.7 libedit2_3.1-20190324-1 libelf1_0.176-1.1 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 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.5.0-1 libgcc-8-dev_8.3.0-6+rpi1 libgcc1_1:8.3.0-6+rpi1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-4 libgdbm6_1.18.1-4 libgfortran5_9.1.0-10+rpi1 libglib2.0-0_2.60.6-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.7-4 libgomp1_8.3.0-6+rpi1 libgpg-error0_1.35-1 libgssapi-krb5-2_1.17-6+b1 libhogweed4_3.4.1-1 libhwloc-dev_1.11.13-1+rpi1 libhwloc-plugins_1.11.13-1+rpi1 libhwloc5_1.11.13-1+rpi1 libibverbs-dev_24.0-2 libibverbs1_24.0-2 libicu63_63.2-2 libidn2-0_2.0.5-1 libisl19_0.20-2 libk5crypto3_1.17-6+b1 libkeyutils1_1.6-6 libkrb5-3_1.17-6+b1 libkrb5support0_1.17-6+b1 libksba8_1.3.5-2 libldap-2.4-2_2.4.47+dfsg-3+rpi1 libldap-common_2.4.47+dfsg-3+rpi1 liblocale-gettext-perl_1.07-3+b3 libltdl-dev_2.4.6-9 libltdl7_2.4.6-9 liblz4-1_1.8.3-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-5 libmagic1_1:5.37-5 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses6_6.1+20190803-1 libncursesw6_6.1+20190803-1 libnettle6_3.4.1-1 libnl-3-200_3.4.0-1 libnl-3-dev_3.4.0-1 libnl-route-3-200_3.4.0-1 libnl-route-3-dev_3.4.0-1 libnpth0_1.6-1 libopenmpi-dev_3.1.3-11+rpi1 libopenmpi3_3.1.3-11+rpi1 libp11-kit0_0.23.15-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpciaccess0_0.14-1 libpcre3_2:8.39-12 libperl5.28_5.28.1-6 libpipeline1_1.5.1-2 libpmix2_3.1.4-1 libreadline7_7.0-5 libsasl2-2_2.1.27+dfsg-1+b1 libsasl2-modules-db_2.1.27+dfsg-1+b1 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libsqlite3-0_3.27.2-3 libss2_1.44.5-1 libssl1.1_1.1.1c-1 libstdc++-8-dev_8.3.0-6+rpi1 libstdc++6_8.3.0-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_241-5+rpi1 libtasn1-6_4.13-3 libtext-charwidth-perl_0.04-7.1+b1 libtext-iconv-perl_1.7-5+b10 libtext-wrapi18n-perl_0.06-7.1 libtinfo5_6.1+20190803-1 libtinfo6_6.1+20190803-1 libtool_2.4.6-9 libubsan1_8.3.0-6+rpi1 libuchardet0_0.0.6-3 libudev1_241-5+rpi1 libunistring2_0.9.10-1 libuuid1_2.33.1-0.1 libxml2_2.9.4+dfsg1-7+b2 libzstd1_1.3.8+dfsg-3+rpi1 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2019051400+rpi1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.6.1-1 mawk_1.3.3-17 mount_2.33.1-0.1 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 ocl-icd-libopencl1_2.2.12-2 openmpi-bin_3.1.3-11+rpi1 openmpi-common_3.1.3-11+rpi1 openssh-client_1:8.0p1-4 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 pinentry-curses_1.1.0-2 pkg-config_0.29-6 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-phyml-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.93-8 tar_1.30+dfsg-6 tzdata_2019a-1 util-linux_2.33.1-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sat Aug 24 14:17:32 2019 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_3.3.20190321-2.dsc
dpkg-source: info: extracting phyml in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking phyml_3.3.20190321.orig.tar.gz
dpkg-source: info: unpacking phyml_3.3.20190321-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
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
dpkg-source: info: applying cross.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
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
PWD=/build/buildd
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=116
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-e5ee8acf-1c6a-40c1-b318-5d3d291d9d96
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_ID=c46778
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package phyml
dpkg-buildpackage: info: source version 3:3.3.20190321-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# 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 '/<<PKGBUILDDIR>>'
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
debian/rules override_dh_autoreconf
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# 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 --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 whether make supports the include directive... yes (GNU style)
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 "LDFLAGS=-Wl,-z,relro -Wl,-z,now"
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make all-recursive
make[3]: Entering directory '/<<PKGBUILDDIR>>'
Making all in src
make[4]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o main.o main.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o utilities.o utilities.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o optimiz.o optimiz.c
.: Building [phyml]. Version 3.3.3:3.3.20190321-2 :.
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o lk.o lk.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o bionj.o bionj.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o models.o models.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o free.o free.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o help.o help.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o simu.o simu.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o eigen.o eigen.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o pars.o pars.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o alrt.o alrt.c
utilities.c: In function 'Assign_State_With_Ambiguity':
utilities.c:3033:29: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=]
sprintf(format,"%%%dd",stepsize);
^~
utilities.c:3033:26: note: directive argument in the range [0, 2147483647]
sprintf(format,"%%%dd",stepsize);
^~~~~~~
In file included from /usr/include/stdio.h:873,
from utilities.h:19,
from utilities.c:12:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 4 and 13 bytes into a destination of size 6
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o interface.o interface.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o cl.o cl.c
utilities.c: In function 'Are_Compatible':
utilities.c:4863:29: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=]
sprintf(format,"%%%dd",stepsize);
^~
utilities.c:4863:26: note: directive argument in the range [0, 2147483647]
sprintf(format,"%%%dd",stepsize);
^~~~~~~
In file included from /usr/include/stdio.h:873,
from utilities.h:19,
from utilities.c:12:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 4 and 13 bytes into a destination of size 6
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o spr.o spr.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o draw.o draw.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o stats.o stats.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o rates.o rates.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o mcmc.o mcmc.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o times.o times.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o tiporder.o tiporder.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o m4.o m4.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o io.o io.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o make.o make.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o nexus.o nexus.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o init.o init.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o xml.o xml.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o date.o date.c
io.c: In function 'Print_Fp_Out':
io.c:2744:47: warning: '%d' directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=]
if (precision > 0) snprintf (format, 8, "%%.%df", precision);
^~
io.c:2744:43: note: directive argument in the range [1, 2147483647]
if (precision > 0) snprintf (format, 8, "%%.%df", precision);
^~~~~~~~
In file included from /usr/include/stdio.h:873,
from utilities.h:19,
from io.h:18,
from io.c:13:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 5 and 14 bytes into a destination of size 8
return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o sse.o sse.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o avx.o avx.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o tbe.o tbe.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o ancestral.o ancestral.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o mixt.o mixt.c
gcc -std=c99 -O3 -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 ancestral.o mixt.o -lm -lm
Done.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[4]: Entering directory '/<<PKGBUILDDIR>>'
make[4]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
# move phyml binary to temporary dir inside debian/
mkdir -p /<<PKGBUILDDIR>>/debian/bin
mv src/phyml /<<PKGBUILDDIR>>/debian/bin/phyml
/usr/bin/make distclean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making distclean in src
make[3]: Entering directory '/<<PKGBUILDDIR>>/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 -f ./.deps/alrt.Po
rm -f ./.deps/ancestral.Po
rm -f ./.deps/avx.Po
rm -f ./.deps/beagle_utils.Po
rm -f ./.deps/bionj.Po
rm -f ./.deps/checkpoint.Po
rm -f ./.deps/cl.Po
rm -f ./.deps/date.Po
rm -f ./.deps/draw.Po
rm -f ./.deps/eigen.Po
rm -f ./.deps/free.Po
rm -f ./.deps/geo.Po
rm -f ./.deps/help.Po
rm -f ./.deps/init.Po
rm -f ./.deps/interface.Po
rm -f ./.deps/invitee.Po
rm -f ./.deps/io.Po
rm -f ./.deps/lk.Po
rm -f ./.deps/m4.Po
rm -f ./.deps/main.Po
rm -f ./.deps/make.Po
rm -f ./.deps/mcmc.Po
rm -f ./.deps/mg.Po
rm -f ./.deps/mixt.Po
rm -f ./.deps/models.Po
rm -f ./.deps/nexus.Po
rm -f ./.deps/optimiz.Po
rm -f ./.deps/pars.Po
rm -f ./.deps/phyml_mpi-alrt.Po
rm -f ./.deps/phyml_mpi-ancestral.Po
rm -f ./.deps/phyml_mpi-avx.Po
rm -f ./.deps/phyml_mpi-bionj.Po
rm -f ./.deps/phyml_mpi-cl.Po
rm -f ./.deps/phyml_mpi-date.Po
rm -f ./.deps/phyml_mpi-draw.Po
rm -f ./.deps/phyml_mpi-eigen.Po
rm -f ./.deps/phyml_mpi-free.Po
rm -f ./.deps/phyml_mpi-help.Po
rm -f ./.deps/phyml_mpi-init.Po
rm -f ./.deps/phyml_mpi-interface.Po
rm -f ./.deps/phyml_mpi-io.Po
rm -f ./.deps/phyml_mpi-lk.Po
rm -f ./.deps/phyml_mpi-m4.Po
rm -f ./.deps/phyml_mpi-main.Po
rm -f ./.deps/phyml_mpi-make.Po
rm -f ./.deps/phyml_mpi-mcmc.Po
rm -f ./.deps/phyml_mpi-mg.Po
rm -f ./.deps/phyml_mpi-mixt.Po
rm -f ./.deps/phyml_mpi-models.Po
rm -f ./.deps/phyml_mpi-mpi_boot.Po
rm -f ./.deps/phyml_mpi-nexus.Po
rm -f ./.deps/phyml_mpi-optimiz.Po
rm -f ./.deps/phyml_mpi-pars.Po
rm -f ./.deps/phyml_mpi-rates.Po
rm -f ./.deps/phyml_mpi-simu.Po
rm -f ./.deps/phyml_mpi-spr.Po
rm -f ./.deps/phyml_mpi-sse.Po
rm -f ./.deps/phyml_mpi-stats.Po
rm -f ./.deps/phyml_mpi-tbe.Po
rm -f ./.deps/phyml_mpi-times.Po
rm -f ./.deps/phyml_mpi-tiporder.Po
rm -f ./.deps/phyml_mpi-utilities.Po
rm -f ./.deps/phyml_mpi-xml.Po
rm -f ./.deps/phyrex.Po
rm -f ./.deps/rates.Po
rm -f ./.deps/simu.Po
rm -f ./.deps/spr.Po
rm -f ./.deps/sse.Po
rm -f ./.deps/stats.Po
rm -f ./.deps/tbe.Po
rm -f ./.deps/times.Po
rm -f ./.deps/tiporder.Po
rm -f ./.deps/utilities.Po
rm -f ./.deps/xml.Po
rm -f Makefile
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
rm -f config.status config.cache config.log configure.lineno config.status.lineno
rm -f Makefile
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 --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 whether make supports the include directive... yes (GNU style)
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 for MPI_C... 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 "LDFLAGS=-Wl,-z,relro -Wl,-z,now"
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make all-recursive
make[3]: Entering directory '/<<PKGBUILDDIR>>'
Making all in src
make[4]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-main.o `test -f 'main.c' || echo './'`main.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-utilities.o `test -f 'utilities.c' || echo './'`utilities.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-optimiz.o `test -f 'optimiz.c' || echo './'`optimiz.c
.: Building [phyml-mpi]. Version 3.3.3:3.3.20190321-2 :.
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-lk.o `test -f 'lk.c' || echo './'`lk.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-bionj.o `test -f 'bionj.c' || echo './'`bionj.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-models.o `test -f 'models.c' || echo './'`models.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-free.o `test -f 'free.c' || echo './'`free.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-help.o `test -f 'help.c' || echo './'`help.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-simu.o `test -f 'simu.c' || echo './'`simu.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-eigen.o `test -f 'eigen.c' || echo './'`eigen.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-pars.o `test -f 'pars.c' || echo './'`pars.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-alrt.o `test -f 'alrt.c' || echo './'`alrt.c
utilities.c: In function 'Assign_State_With_Ambiguity':
utilities.c:3033:29: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=]
sprintf(format,"%%%dd",stepsize);
^~
utilities.c:3033:26: note: directive argument in the range [0, 2147483647]
sprintf(format,"%%%dd",stepsize);
^~~~~~~
In file included from /usr/include/stdio.h:873,
from utilities.h:19,
from utilities.c:12:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 4 and 13 bytes into a destination of size 6
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-interface.o `test -f 'interface.c' || echo './'`interface.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-cl.o `test -f 'cl.c' || echo './'`cl.c
utilities.c: In function 'Are_Compatible':
utilities.c:4863:29: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=]
sprintf(format,"%%%dd",stepsize);
^~
utilities.c:4863:26: note: directive argument in the range [0, 2147483647]
sprintf(format,"%%%dd",stepsize);
^~~~~~~
In file included from /usr/include/stdio.h:873,
from utilities.h:19,
from utilities.c:12:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 4 and 13 bytes into a destination of size 6
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-spr.o `test -f 'spr.c' || echo './'`spr.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-draw.o `test -f 'draw.c' || echo './'`draw.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-stats.o `test -f 'stats.c' || echo './'`stats.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-rates.o `test -f 'rates.c' || echo './'`rates.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-mcmc.o `test -f 'mcmc.c' || echo './'`mcmc.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-times.o `test -f 'times.c' || echo './'`times.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-tiporder.o `test -f 'tiporder.c' || echo './'`tiporder.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-mg.o `test -f 'mg.c' || echo './'`mg.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-m4.o `test -f 'm4.c' || echo './'`m4.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-io.o `test -f 'io.c' || echo './'`io.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-make.o `test -f 'make.c' || echo './'`make.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-nexus.o `test -f 'nexus.c' || echo './'`nexus.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-init.o `test -f 'init.c' || echo './'`init.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-xml.o `test -f 'xml.c' || echo './'`xml.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-mixt.o `test -f 'mixt.c' || echo './'`mixt.c
io.c: In function 'Print_Fp_Out':
io.c:2744:47: warning: '%d' directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=]
if (precision > 0) snprintf (format, 8, "%%.%df", precision);
^~
io.c:2744:43: note: directive argument in the range [1, 2147483647]
if (precision > 0) snprintf (format, 8, "%%.%df", precision);
^~~~~~~~
In file included from /usr/include/stdio.h:873,
from utilities.h:19,
from io.h:18,
from io.c:13:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 5 and 14 bytes into a destination of size 8
return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-tbe.o `test -f 'tbe.c' || echo './'`tbe.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-date.o `test -f 'date.c' || echo './'`date.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-sse.o `test -f 'sse.c' || echo './'`sse.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-avx.o `test -f 'avx.c' || echo './'`avx.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-ancestral.o `test -f 'ancestral.c' || echo './'`ancestral.c
gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-mpi_boot.o `test -f 'mpi_boot.c' || echo './'`mpi_boot.c
gcc -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -Wl,-z,relro -Wl,-z,now -o phyml-mpi phyml_mpi-main.o phyml_mpi-utilities.o phyml_mpi-optimiz.o phyml_mpi-lk.o phyml_mpi-bionj.o phyml_mpi-models.o phyml_mpi-free.o phyml_mpi-help.o phyml_mpi-simu.o phyml_mpi-eigen.o phyml_mpi-pars.o phyml_mpi-alrt.o phyml_mpi-interface.o phyml_mpi-cl.o phyml_mpi-spr.o phyml_mpi-draw.o phyml_mpi-stats.o phyml_mpi-rates.o phyml_mpi-mcmc.o phyml_mpi-times.o phyml_mpi-tiporder.o phyml_mpi-mg.o phyml_mpi-m4.o phyml_mpi-io.o phyml_mpi-make.o phyml_mpi-nexus.o phyml_mpi-init.o phyml_mpi-xml.o phyml_mpi-mixt.o phyml_mpi-tbe.o phyml_mpi-date.o phyml_mpi-sse.o phyml_mpi-avx.o phyml_mpi-ancestral.o phyml_mpi-mpi_boot.o -lm -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -lmpi -lm
Done.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[4]: Entering directory '/<<PKGBUILDDIR>>'
make[4]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
# move phyml binary to temporary dir inside debian/
# mkdir -p /<<PKGBUILDDIR>>/debian/bin
mv src/phyml-mpi /<<PKGBUILDDIR>>/debian/bin/phyml-mpi
mv phyml-manual.pdf doc
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
make -j4 check VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making check in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -o phyml-mpi phyml_mpi-main.o phyml_mpi-utilities.o phyml_mpi-optimiz.o phyml_mpi-lk.o phyml_mpi-bionj.o phyml_mpi-models.o phyml_mpi-free.o phyml_mpi-help.o phyml_mpi-simu.o phyml_mpi-eigen.o phyml_mpi-pars.o phyml_mpi-alrt.o phyml_mpi-interface.o phyml_mpi-cl.o phyml_mpi-spr.o phyml_mpi-draw.o phyml_mpi-stats.o phyml_mpi-rates.o phyml_mpi-mcmc.o phyml_mpi-times.o phyml_mpi-tiporder.o phyml_mpi-mg.o phyml_mpi-m4.o phyml_mpi-io.o phyml_mpi-make.o phyml_mpi-nexus.o phyml_mpi-init.o phyml_mpi-xml.o phyml_mpi-mixt.o phyml_mpi-tbe.o phyml_mpi-date.o phyml_mpi-sse.o phyml_mpi-avx.o phyml_mpi-ancestral.o phyml_mpi-mpi_boot.o -lm -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -lmpi -lm
.: Building [phyml-mpi]. Version 3.3.3:3.3.20190321-2 :.
Done.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
dh_auto_install
make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/phyml AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making install in src
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
.: Building [phyml-mpi]. Version 3.3.3:3.3.20190321-2 :.
Done.
make[4]: Entering directory '/<<PKGBUILDDIR>>/src'
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/phyml/usr/bin'
/usr/bin/install -c phyml-mpi '/<<PKGBUILDDIR>>/debian/phyml/usr/bin'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[4]: Entering directory '/<<PKGBUILDDIR>>'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
# install phyml binary we have kept safe above
mkdir -p /<<PKGBUILDDIR>>/debian/phyml/usr/lib/phyml/bin
mv /<<PKGBUILDDIR>>/debian/bin/* /<<PKGBUILDDIR>>/debian/phyml/usr/lib/phyml/bin
chrpath --delete debian/phyml/usr/lib/phyml/bin/phyml*
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_install -a
debian/rules override_dh_installdocs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installdocs
mv /<<PKGBUILDDIR>>/debian/phyml/usr/share/doc/phyml/phyml-manual.pdf /<<PKGBUILDDIR>>/debian/phyml/usr/share/doc/phyml/phyml_manual.pdf
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
dh_compress --exclude=.pdf
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_fixperms
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
dh_missing -a
debian/rules override_dh_dwz
make[1]: Entering directory '/<<PKGBUILDDIR>>'
echo "Do not run dh_dwz"
Do not run dh_dwz
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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_3.3.20190321-2_armhf.deb'.
dpkg-deb: building package 'phyml-dbgsym' in '../phyml-dbgsym_3.3.20190321-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian 2019 test autobuilder <root@raspbian.org> >../phyml_3.3.20190321-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2019-08-27T07:00:40Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
phyml_3.3.20190321-2_armhf.changes:
-----------------------------------
Format: 1.8
Date: Sat, 24 Aug 2019 16:08:44 +0200
Source: phyml
Binary: phyml phyml-dbgsym
Architecture: armhf
Version: 3:3.3.20190321-2
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian 2019 test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
phyml - Phylogenetic estimation using Maximum Likelihood
Closes: 935598
Changes:
phyml (3:3.3.20190321-2) unstable; urgency=medium
.
* Fix autopkgtest
Closes: #935598
* Secure URI in copyright format
* Remove trailing whitespace in debian/changelog
* Remove obsolete fields Name, Contact from debian/upstream/metadata.
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Files:
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b759286f814c16253c1c6266f799a3e3 5663 science optional phyml_3.3.20190321-2_armhf.buildinfo
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+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: phyml
Binary: phyml
Architecture: armhf
Version: 3:3.3.20190321-2
Checksums-Md5:
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Checksums-Sha256:
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1c5a93650ce9c8960a2af065879b5c2a3c07a5e07f5c080b1634c094a6e6c890 1527232 phyml_3.3.20190321-2_armhf.deb
Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Tue, 27 Aug 2019 07:00:37 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
adduser (= 3.118),
autoconf (= 2.69-11),
automake (= 1:1.16.1-4),
autopoint (= 0.19.8.1-9),
autotools-dev (= 20180224.1),
base-files (= 10.3+rpi1),
base-passwd (= 3.5.46),
bash (= 5.0-4),
binutils (= 2.31.1-16+rpi1),
binutils-arm-linux-gnueabihf (= 2.31.1-16+rpi1),
binutils-common (= 2.31.1-16+rpi1),
bsdmainutils (= 11.1.2),
bsdutils (= 1:2.33.1-0.1),
build-essential (= 12.6),
bzip2 (= 1.0.6-9.1),
chrpath (= 0.16-2),
coreutils (= 8.30-3),
cpp (= 4:8.3.0-1+rpi2),
cpp-8 (= 8.3.0-6+rpi1),
dash (= 0.5.10.2-5),
debconf (= 1.5.71),
debhelper (= 12.5.3),
debianutils (= 4.8.6.1),
dh-autoreconf (= 19),
dh-strip-nondeterminism (= 1.5.0-1),
diffutils (= 1:3.7-3),
dpkg (= 1.19.7),
dpkg-dev (= 1.19.7),
dwz (= 0.13-1),
fdisk (= 2.33.1-0.1),
file (= 1:5.37-5),
findutils (= 4.6.0+git+20190209-2),
g++ (= 4:8.3.0-1+rpi2),
g++-8 (= 8.3.0-6+rpi1),
gcc (= 4:8.3.0-1+rpi2),
gcc-8 (= 8.3.0-6+rpi1),
gcc-8-base (= 8.3.0-6+rpi1),
gcc-9-base (= 9.1.0-10+rpi1),
gettext (= 0.19.8.1-9),
gettext-base (= 0.19.8.1-9),
grep (= 3.3-1),
groff-base (= 1.22.4-3),
gzip (= 1.9-3),
hostname (= 3.21),
ibverbs-providers (= 24.0-2),
init-system-helpers (= 1.56+nmu1),
intltool-debian (= 0.35.0+20060710.5),
libacl1 (= 2.2.53-4),
libarchive-zip-perl (= 1.64-1),
libasan5 (= 8.3.0-6+rpi1),
libatomic1 (= 8.3.0-6+rpi1),
libattr1 (= 1:2.4.48-4),
libaudit-common (= 1:2.8.4-3),
libaudit1 (= 1:2.8.4-3),
libbinutils (= 2.31.1-16+rpi1),
libblkid1 (= 2.33.1-0.1),
libbsd0 (= 0.10.0-1),
libbz2-1.0 (= 1.0.6-9.1),
libc-bin (= 2.28-10+rpi1),
libc-dev-bin (= 2.28-10+rpi1),
libc6 (= 2.28-10+rpi1),
libc6-dev (= 2.28-10+rpi1),
libcap-ng0 (= 0.7.9-2),
libcc1-0 (= 8.3.0-6+rpi1),
libcom-err2 (= 1.44.5-1),
libcroco3 (= 0.6.13-1),
libdb5.3 (= 5.3.28+dfsg1-0.5),
libdebconfclient0 (= 0.249),
libdpkg-perl (= 1.19.7),
libedit2 (= 3.1-20190324-1),
libelf1 (= 0.176-1.1),
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),
libfdisk1 (= 2.33.1-0.1),
libffi6 (= 3.2.1-9),
libfile-stripnondeterminism-perl (= 1.5.0-1),
libgcc-8-dev (= 8.3.0-6+rpi1),
libgcc1 (= 1:8.3.0-6+rpi1),
libgcrypt20 (= 1.8.4-5),
libgdbm-compat4 (= 1.18.1-4),
libgdbm6 (= 1.18.1-4),
libgfortran5 (= 9.1.0-10+rpi1),
libglib2.0-0 (= 2.60.6-2),
libgmp10 (= 2:6.1.2+dfsg-4),
libgomp1 (= 8.3.0-6+rpi1),
libgpg-error0 (= 1.35-1),
libgssapi-krb5-2 (= 1.17-6+b1),
libhwloc-dev (= 1.11.13-1+rpi1),
libhwloc-plugins (= 1.11.13-1+rpi1),
libhwloc5 (= 1.11.13-1+rpi1),
libibverbs-dev (= 24.0-2),
libibverbs1 (= 24.0-2),
libicu63 (= 63.2-2),
libisl19 (= 0.20-2),
libk5crypto3 (= 1.17-6+b1),
libkeyutils1 (= 1.6-6),
libkrb5-3 (= 1.17-6+b1),
libkrb5support0 (= 1.17-6+b1),
libltdl-dev (= 2.4.6-9),
libltdl7 (= 2.4.6-9),
liblz4-1 (= 1.8.3-1),
liblzma5 (= 5.2.4-1),
libmagic-mgc (= 1:5.37-5),
libmagic1 (= 1:5.37-5),
libmount1 (= 2.33.1-0.1),
libmpc3 (= 1.1.0-1),
libmpfr6 (= 4.0.2-1),
libncurses6 (= 6.1+20190803-1),
libncursesw6 (= 6.1+20190803-1),
libnl-3-200 (= 3.4.0-1),
libnl-3-dev (= 3.4.0-1),
libnl-route-3-200 (= 3.4.0-1),
libnl-route-3-dev (= 3.4.0-1),
libopenmpi-dev (= 3.1.3-11+rpi1),
libopenmpi3 (= 3.1.3-11+rpi1),
libpam-modules (= 1.3.1-5),
libpam-modules-bin (= 1.3.1-5),
libpam-runtime (= 1.3.1-5),
libpam0g (= 1.3.1-5),
libpciaccess0 (= 0.14-1),
libpcre3 (= 2:8.39-12),
libperl5.28 (= 5.28.1-6),
libpipeline1 (= 1.5.1-2),
libpmix2 (= 3.1.4-1),
libseccomp2 (= 2.3.3-4),
libselinux1 (= 2.8-1+b1),
libsemanage-common (= 2.8-2),
libsemanage1 (= 2.8-2),
libsepol1 (= 2.8-1),
libsigsegv2 (= 2.12-2),
libsmartcols1 (= 2.33.1-0.1),
libssl1.1 (= 1.1.1c-1),
libstdc++-8-dev (= 8.3.0-6+rpi1),
libstdc++6 (= 8.3.0-6+rpi1),
libsub-override-perl (= 0.09-2),
libsystemd0 (= 241-5+rpi1),
libtinfo5 (= 6.1+20190803-1),
libtinfo6 (= 6.1+20190803-1),
libtool (= 2.4.6-9),
libubsan1 (= 8.3.0-6+rpi1),
libuchardet0 (= 0.0.6-3),
libudev1 (= 241-5+rpi1),
libunistring2 (= 0.9.10-1),
libuuid1 (= 2.33.1-0.1),
libxml2 (= 2.9.4+dfsg1-7+b2),
linux-libc-dev (= 4.18.20-2+rpi1),
login (= 1:4.5-1.1),
m4 (= 1.4.18-2),
make (= 4.2.1-1.2),
man-db (= 2.8.6.1-1),
mawk (= 1.3.3-17),
ncurses-base (= 6.1+20181013-2),
ncurses-bin (= 6.1+20181013-2),
ocl-icd-libopencl1 (= 2.2.12-2),
openmpi-bin (= 3.1.3-11+rpi1),
openmpi-common (= 3.1.3-11+rpi1),
openssh-client (= 1:8.0p1-4),
passwd (= 1:4.5-1.1),
patch (= 2.7.6-3),
perl (= 5.28.1-6),
perl-base (= 5.28.1-6),
perl-modules-5.28 (= 5.28.1-6),
pkg-config (= 0.29-6),
po-debconf (= 1.0.21),
sed (= 4.7-1),
sensible-utils (= 0.0.12),
sysvinit-utils (= 2.93-8),
tar (= 1.30+dfsg-6),
util-linux (= 2.33.1-0.1),
xz-utils (= 5.2.4-1),
zlib1g (= 1:1.2.11.dfsg-1)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LC_ALL="POSIX"
SOURCE_DATE_EPOCH="1566655724"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
phyml-dbgsym_3.3.20190321-2_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 43636 bytes: control archive=656 bytes.
462 bytes, 12 lines control
318 bytes, 3 lines md5sums
Package: phyml-dbgsym
Source: phyml
Version: 3:3.3.20190321-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 308
Depends: phyml (= 3:3.3.20190321-2)
Section: debug
Priority: optional
Description: debug symbols for phyml
Build-Ids: 0510e1e0725f466e20626ccbe4d15b94cdb88ee5 5822fc6adfadab86b8061652efe4ebd7ebb55caa dec429240a86536b6ff49e34d842f7b00784c671
drwxr-xr-x root/root 0 2019-08-24 14:08 ./
drwxr-xr-x root/root 0 2019-08-24 14:08 ./usr/
drwxr-xr-x root/root 0 2019-08-24 14:08 ./usr/lib/
drwxr-xr-x root/root 0 2019-08-24 14:08 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-08-24 14:08 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-08-24 14:08 ./usr/lib/debug/.build-id/05/
-rw-r--r-- root/root 100688 2019-08-24 14:08 ./usr/lib/debug/.build-id/05/10e1e0725f466e20626ccbe4d15b94cdb88ee5.debug
drwxr-xr-x root/root 0 2019-08-24 14:08 ./usr/lib/debug/.build-id/58/
-rw-r--r-- root/root 99836 2019-08-24 14:08 ./usr/lib/debug/.build-id/58/22fc6adfadab86b8061652efe4ebd7ebb55caa.debug
drwxr-xr-x root/root 0 2019-08-24 14:08 ./usr/lib/debug/.build-id/de/
-rw-r--r-- root/root 100688 2019-08-24 14:08 ./usr/lib/debug/.build-id/de/c429240a86536b6ff49e34d842f7b00784c671.debug
drwxr-xr-x root/root 0 2019-08-24 14:08 ./usr/share/
drwxr-xr-x root/root 0 2019-08-24 14:08 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-08-24 14:08 ./usr/share/doc/phyml-dbgsym -> phyml
phyml_3.3.20190321-2_armhf.deb
------------------------------
new Debian package, version 2.0.
size 1527232 bytes: control archive=1880 bytes.
1666 bytes, 31 lines control
1695 bytes, 24 lines md5sums
Package: phyml
Version: 3:3.3.20190321-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5034
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.
drwxr-xr-x root/root 0 2019-08-24 14:08 ./
drwxr-xr-x root/root 0 2019-08-24 14:08 ./usr/
drwxr-xr-x root/root 0 2019-08-24 14:08 ./usr/bin/
-rwxr-xr-x root/root 579 2019-08-24 14:08 ./usr/bin/phyml
-rwxr-xr-x root/root 1288008 2019-08-24 14:08 ./usr/bin/phyml-mpi
drwxr-xr-x root/root 0 2019-08-24 14:08 ./usr/lib/
drwxr-xr-x root/root 0 2019-08-24 14:08 ./usr/lib/phyml/
drwxr-xr-x root/root 0 2019-08-24 14:08 ./usr/lib/phyml/bin/
-rwxr-xr-x root/root 1279492 2019-08-24 14:08 ./usr/lib/phyml/bin/phyml
-rwxr-xr-x root/root 1287684 2019-08-24 14:08 ./usr/lib/phyml/bin/phyml-mpi
drwxr-xr-x root/root 0 2019-08-24 14:08 ./usr/share/
drwxr-xr-x root/root 0 2019-08-24 14:08 ./usr/share/doc-base/
-rw-r--r-- root/root 202 2019-08-24 14:08 ./usr/share/doc-base/phyml
drwxr-xr-x root/root 0 2019-08-24 14:08 ./usr/share/doc/
drwxr-xr-x root/root 0 2019-08-24 14:08 ./usr/share/doc/phyml/
-rw-r--r-- root/root 2446 2019-08-24 14:08 ./usr/share/doc/phyml/README.Debian
-rw-r--r-- root/root 3072 2019-08-24 14:08 ./usr/share/doc/phyml/changelog.Debian.gz
-rw-r--r-- root/root 1490 2019-08-24 14:08 ./usr/share/doc/phyml/copyright
drwxr-xr-x root/root 0 2019-08-24 14:08 ./usr/share/doc/phyml/examples/
-rw-r--r-- root/root 20905 2019-08-24 14:08 ./usr/share/doc/phyml/examples/example.nex
drwxr-xr-x root/root 0 2019-04-04 07:13 ./usr/share/doc/phyml/examples/lg4x/
-rw-r--r-- root/root 1900 2019-04-04 07:13 ./usr/share/doc/phyml/examples/lg4x/X1.mat
-rw-r--r-- root/root 1899 2019-04-04 07:13 ./usr/share/doc/phyml/examples/lg4x/X2.mat
-rw-r--r-- root/root 1893 2019-04-04 07:13 ./usr/share/doc/phyml/examples/lg4x/X3.mat
-rw-r--r-- root/root 1895 2019-04-04 07:13 ./usr/share/doc/phyml/examples/lg4x/X4.mat
-rw-r--r-- root/root 1994 2019-04-04 07:13 ./usr/share/doc/phyml/examples/lg4x/lg4x.xml
-rw-r--r-- root/root 2175 2019-04-04 07:13 ./usr/share/doc/phyml/examples/nexus_example.nxs
-rwxr-xr-x root/root 60771 2019-04-04 07:13 ./usr/share/doc/phyml/examples/nucleic
drwxr-xr-x root/root 0 2019-04-04 07:13 ./usr/share/doc/phyml/examples/phyrex/
-rw-r--r-- root/root 70310 2019-04-04 07:13 ./usr/share/doc/phyml/examples/phyrex/h1n1.nxs
-rw-r--r-- root/root 1784 2019-04-04 07:13 ./usr/share/doc/phyml/examples/phyrex/usa_coord.txt
drwxr-xr-x root/root 0 2019-04-04 07:13 ./usr/share/doc/phyml/examples/phytime/
-rw-r--r-- root/root 2189 2019-04-04 07:13 ./usr/share/doc/phyml/examples/phytime/dating_example.xml
-rw-r--r-- root/root 100171 2019-04-04 07:13 ./usr/share/doc/phyml/examples/phytime/seq.txt
-rwxr-xr-x root/root 25990 2019-04-04 07:13 ./usr/share/doc/phyml/examples/proteic
-rw-r--r-- root/root 965863 2019-04-04 07:13 ./usr/share/doc/phyml/phyml_manual.pdf
-rw-r--r-- root/root 1257 2019-08-24 14:08 ./usr/share/doc/phyml/run-unit-test
drwxr-xr-x root/root 0 2019-08-24 14:08 ./usr/share/man/
drwxr-xr-x root/root 0 2019-08-24 14:08 ./usr/share/man/man1/
-rw-r--r-- root/root 2899 2019-08-24 14:08 ./usr/share/man/man1/phyml.1.gz
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Build Architecture: armhf
Build Type: any
Build-Space: 17660
Build-Time: 418
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 438
Job: phyml_3:3.3.20190321-2
Machine Architecture: armhf
Package: phyml
Package-Time: 932
Source-Version: 3:3.3.20190321-2
Space: 17660
Status: successful
Version: 3:3.3.20190321-2
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Finished at 2019-08-27T07:00:40Z
Build needed 00:15:32, 17660k disk space