phyml →
2:20120412-2 →
armhf → 2013-08-16 13:35:44
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on testbuildd.raspbian.org
╔══════════════════════════════════════════════════════════════════════════════╗
║ phyml 2:20120412-2 (armhf) 16 Aug 2013 13:19 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: phyml
Version: 2:20120412-2
Source Version: 2:20120412-2
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/phyml-qLIho9/phyml-20120412' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/phyml-qLIho9' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-70017ca5-c285-4e90-93aa-f4e24a401f6c' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 jessie-staging Release.gpg [490 B]
Get:2 http://172.17.0.1 jessie-staging Release [10.8 kB]
Get:3 http://172.17.0.1 jessie-staging/main Sources [6708 kB]
Get:4 http://172.17.0.1 jessie-staging/main armhf Packages [7873 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
Fetched 14.6 MB in 47s (309 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
─────────
Checking available source versions...
Download source files with APT
──────────────────────────────
Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'phyml' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/phyml/trunk/
Need to get 4103 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main phyml 2:20120412-2 (dsc) [1378 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main phyml 2:20120412-2 (tar) [4089 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main phyml 2:20120412-2 (diff) [12.1 kB]
Fetched 4103 kB in 3s (1241 kB/s)
Download complete and in download only mode
Check arch
──────────
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-9dX14U/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 47 not upgraded.
Need to get 0 B/704 B of archives.
After this operation, 0 B of additional disk space will be used.
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 11338 files and directories currently installed.)
Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), autotools-dev, dh-autoreconf
Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), autotools-dev, dh-autoreconf
dpkg-deb: building package `sbuild-build-depends-phyml-dummy' in `/«BUILDDIR»/resolver-Zz44C5/apt_archive/sbuild-build-depends-phyml-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install phyml build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf file gettext gettext-base groff-base intltool-debian
libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libmagic1 libpipeline1
libsigsegv2 libtool libunistring0 libxml2 m4 man-db po-debconf
Suggested packages:
autoconf2.13 autoconf-archive gnu-standards autoconf-doc wamerican wordlist
whois vacation dh-make gettext-doc groff libtool-doc automaken gfortran
fortran95-compiler gcj less www-browser libmail-box-perl
Recommended packages:
curl wget lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data
shared-mime-info libltdl-dev xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf file gettext gettext-base groff-base intltool-debian
libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libmagic1 libpipeline1
libsigsegv2 libtool libunistring0 libxml2 m4 man-db po-debconf
sbuild-build-depends-phyml-dummy
0 upgraded, 26 newly installed, 0 to remove and 47 not upgraded.
Need to get 11.1 MB/11.1 MB of archives.
After this operation, 28.3 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.2.4-1 [36.9 kB]
Get:2 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-3 [666 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main bsdmainutils armhf 9.0.5 [206 kB]
Get:4 http://172.17.0.1/private/ jessie-staging/main man-db armhf 2.6.5-2 [949 kB]
Get:5 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.18.3-1 [29.4 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.14-2 [213 kB]
Get:7 http://172.17.0.1/private/ jessie-staging/main libxml2 armhf 2.9.1+dfsg1-3 [836 kB]
Get:8 http://172.17.0.1/private/ jessie-staging/main libffi6 armhf 3.0.13-4 [19.8 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.36.3-3 [1905 kB]
Get:10 http://172.17.0.1/private/ jessie-staging/main libcroco3 armhf 0.6.8-2 [119 kB]
Get:11 http://172.17.0.1/private/ jessie-staging/main libsigsegv2 armhf 2.10-2 [29.2 kB]
Get:12 http://172.17.0.1/private/ jessie-staging/main libunistring0 armhf 0.9.3-5 [408 kB]
Get:13 http://172.17.0.1/private/ jessie-staging/main file armhf 1:5.14-2 [53.8 kB]
Get:14 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.18.3-1 [136 kB]
Get:15 http://172.17.0.1/private/ jessie-staging/main m4 armhf 1.4.16-5 [245 kB]
Get:16 http://172.17.0.1/private/ jessie-staging/main autoconf all 2.69-1 [589 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main autotools-dev all 20130515.1 [73.0 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main automake all 1:1.13.3-1 [758 kB]
Get:19 http://172.17.0.1/private/ jessie-staging/main autopoint all 0.18.3-1 [393 kB]
Get:20 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.18.3-1 [1837 kB]
Get:21 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:22 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu2 [223 kB]
Get:23 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20130630 [710 kB]
Get:24 http://172.17.0.1/private/ jessie-staging/main libtool armhf 2.4.2-1.3 [617 kB]
Get:25 http://172.17.0.1/private/ jessie-staging/main dh-autoreconf all 9 [15.5 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 11.1 MB in 56s (198 kB/s)
Selecting previously unselected package libpipeline1:armhf.
(Reading database ... 11338 files and directories currently installed.)
Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.4-1_armhf.deb) ...
Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.22.2-3_armhf.deb) ...
Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_9.0.5_armhf.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.5-2_armhf.deb) ...
Selecting previously unselected package libasprintf0c2:armhf.
Unpacking libasprintf0c2:armhf (from .../libasprintf0c2_0.18.3-1_armhf.deb) ...
Selecting previously unselected package libmagic1:armhf.
Unpacking libmagic1:armhf (from .../libmagic1_1%3a5.14-2_armhf.deb) ...
Selecting previously unselected package libxml2:armhf.
Unpacking libxml2:armhf (from .../libxml2_2.9.1+dfsg1-3_armhf.deb) ...
Selecting previously unselected package libffi6:armhf.
Unpacking libffi6:armhf (from .../libffi6_3.0.13-4_armhf.deb) ...
Selecting previously unselected package libglib2.0-0:armhf.
Unpacking libglib2.0-0:armhf (from .../libglib2.0-0_2.36.3-3_armhf.deb) ...
Selecting previously unselected package libcroco3:armhf.
Unpacking libcroco3:armhf (from .../libcroco3_0.6.8-2_armhf.deb) ...
Selecting previously unselected package libsigsegv2:armhf.
Unpacking libsigsegv2:armhf (from .../libsigsegv2_2.10-2_armhf.deb) ...
Selecting previously unselected package libunistring0:armhf.
Unpacking libunistring0:armhf (from .../libunistring0_0.9.3-5_armhf.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../file_1%3a5.14-2_armhf.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.3-1_armhf.deb) ...
Selecting previously unselected package m4.
Unpacking m4 (from .../archives/m4_1.4.16-5_armhf.deb) ...
Selecting previously unselected package autoconf.
Unpacking autoconf (from .../autoconf_2.69-1_all.deb) ...
Selecting previously unselected package autotools-dev.
Unpacking autotools-dev (from .../autotools-dev_20130515.1_all.deb) ...
Selecting previously unselected package automake.
Unpacking automake (from .../automake_1%3a1.13.3-1_all.deb) ...
Selecting previously unselected package autopoint.
Unpacking autopoint (from .../autopoint_0.18.3-1_all.deb) ...
Selecting previously unselected package gettext.
Unpacking gettext (from .../gettext_0.18.3-1_armhf.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
Unpacking debhelper (from .../debhelper_9.20130630_all.deb) ...
Selecting previously unselected package libtool.
Unpacking libtool (from .../libtool_2.4.2-1.3_armhf.deb) ...
Selecting previously unselected package dh-autoreconf.
Unpacking dh-autoreconf (from .../dh-autoreconf_9_all.deb) ...
Selecting previously unselected package sbuild-build-depends-phyml-dummy.
Unpacking sbuild-build-depends-phyml-dummy (from .../sbuild-build-depends-phyml-dummy.deb) ...
Setting up libpipeline1:armhf (1.2.4-1) ...
Setting up groff-base (1.22.2-3) ...
Setting up bsdmainutils (9.0.5) ...
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 man-db (2.6.5-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasprintf0c2:armhf (0.18.3-1) ...
Setting up libmagic1:armhf (1:5.14-2) ...
Setting up libxml2:armhf (2.9.1+dfsg1-3) ...
Setting up libffi6:armhf (3.0.13-4) ...
Setting up libglib2.0-0:armhf (2.36.3-3) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.8-2) ...
Setting up libsigsegv2:armhf (2.10-2) ...
Setting up libunistring0:armhf (0.9.3-5) ...
Setting up file (1:5.14-2) ...
Setting up gettext-base (0.18.3-1) ...
Setting up m4 (1.4.16-5) ...
Setting up autoconf (2.69-1) ...
Setting up autotools-dev (20130515.1) ...
Setting up automake (1:1.13.3-1) ...
update-alternatives: using /usr/bin/automake-1.13 to provide /usr/bin/automake (automake) in auto mode
Setting up autopoint (0.18.3-1) ...
Setting up gettext (0.18.3-1) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
Setting up debhelper (9.20130630) ...
Setting up libtool (2.4.2-1.3) ...
Setting up dh-autoreconf (9) ...
Setting up sbuild-build-depends-phyml-dummy (0.invalid.0) ...
Processing triggers for libc-bin ...
ldconfig deferred processing now taking place
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.9.8-imx5 armhf (armv7l)
Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.10 g++-4.6_4.6.4-2+rpi1 gcc-4.6_4.6.4-2+rpi1 libc6-dev_2.17-3 libstdc++6_4.8.0-7+rpi1 libstdc++6-4.6-dev_4.6.4-2+rpi1 linux-libc-dev_3.2.41-2+rpi1
Package versions: apt_0.9.7.8+rpi1 autoconf_2.69-1 automake_1:1.13.3-1 autopoint_0.18.3-1 autotools-dev_20130515.1 base-files_7.2 base-passwd_3.5.26 bash_4.2+dfsg-1 binutils_2.22-8 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.4 build-essential_11.6 bzip2_1.0.6-4 coreutils_8.13-3.5 cpio_2.11+dfsg-1 cpp_4:4.6.3-8 cpp-4.6_4.6.4-2+rpi1 dash_0.5.7-3 debconf_1.5.50 debconf-i18n_1.5.50 debfoster_2.7-1.2 debhelper_9.20130630 debianutils_4.3.4 dh-autoreconf_9 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.5-1.1 e2fsprogs_1.42.5-1.1 fakeroot_1.18.4-2 file_1:5.14-2 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.4-2+rpi1 gcc_4:4.6.3-8 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.4-2+rpi1 gcc-4.6-base_4.6.4-2+rpi1 gcc-4.7-base_4.7.3-4+rpi1 gcc-4.8-base_4.8.0-7+rpi1 gettext_0.18.3-1 gettext-base_0.18.3-1 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.14-2 groff-base_1.22.2-3 gzip_1.5-1.1 hostname_3.12 initramfs-tools_0.112 initscripts_2.88dsf-41 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.1-3.1+rpi1 kmod_9-3 libacl1_2.2.52-1 libapt-pkg4.12_0.9.7.8+rpi1 libasprintf0c2_0.18.3-1 libattr1_1:2.4.47-1 libblkid1_2.20.1-5.4 libbz2-1.0_1.0.6-4 libc-bin_2.17-3 libc-dev-bin_2.17-3 libc6_2.17-3 libc6-dev_2.17-3 libcap2_1:2.22-1.2 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1.1 libcroco3_0.6.8-2 libdb5.1_5.1.29-5 libdbus-1-3_1.6.10-1 libdpkg-perl_1.16.10 libffi6_3.0.13-4 libgc1c2_1:7.1-9.1 libgcc1_1:4.8.0-7+rpi1 libgdbm3_1.8.3-12 libglib2.0-0_2.36.3-3 libgmp10_2:5.1.2+dfsg-1 libgomp1_4.8.0-7+rpi1 libklibc_2.0.1-3.1+rpi1 libkmod2_9-3 liblocale-gettext-perl_1.05-7 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.14-2 libmount1_2.20.1-5.4 libmpc2_0.9-4 libmpc3_1.0.1-1 libmpfr4_3.1.1-1 libncurses5_5.9+20130504-1 libncursesw5_5.9+20130504-1 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpcre3_1:8.31-2 libpipeline1_1.2.4-1 libprocps0_1:3.3.4-2 libreadline6_6.2+dfsg-0.1 libselinux1_2.1.13-2 libsemanage-common_2.1.10-2 libsemanage1_2.1.10-2 libsepol1_2.1.9-2 libsigsegv2_2.10-2 libslang2_2.2.4-15 libss2_1.42.5-1.1 libstdc++6_4.8.0-7+rpi1 libstdc++6-4.6-dev_4.6.4-2+rpi1 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9+20130504-1 libtool_2.4.2-1.3 libudev0_175-7.2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.2 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.4 libxml2_2.9.1+dfsg1-3 linux-libc-dev_3.2.41-2+rpi1 login_1:4.1.5.1-1 lsb-base_4.1+Debian8+rpi1 m4_1.4.16-5 make_3.81-8.2 makedev_2.3.1-93 man-db_2.6.5-2 mawk_1.3.3-17 mount_2.20.1-5.4 multiarch-support_2.17-3 ncurses-base_5.9+20130504-1 ncurses-bin_5.9+20130504-1 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-21+rpi1 perl-base_5.14.2-21+rpi1 perl-modules_5.14.2-21+rpi1 plymouth_0.8.8-6 po-debconf_1.0.16+nmu2 procps_1:3.3.4-2 raspbian-archive-keyring_20120528.2 readline-common_6.2+dfsg-0.1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-phyml-dummy_0.invalid.0 sed_4.2.2-1 sensible-utils_0.0.7 sysv-rc_2.88dsf-41 sysvinit_2.88dsf-41 sysvinit-utils_2.88dsf-41 tar_1.26+dfsg-6 tzdata_2013c-2 udev_175-7.2 util-linux_2.20.1-5.4 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Mon Aug 5 08:01:19 2013 UTC using DSA key ID C09FD35A
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./phyml_20120412-2.dsc
dpkg-source: info: extracting phyml in phyml-20120412
dpkg-source: info: unpacking phyml_20120412.orig.tar.gz
dpkg-source: info: unpacking phyml_20120412-2.debian.tar.gz
dpkg-source: info: applying sse_only_if_supported.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
LANG=en_US.UTF-8
LC_ALL=POSIX
LOGNAME=root
LS_OPTIONS=--color=auto
MAIL=/var/mail/root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/root
SCHROOT_ALIAS_NAME=jessie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=jessie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=111
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-70017ca5-c285-4e90-93aa-f4e24a401f6c
SCHROOT_UID=106
SCHROOT_USER=buildd
SHELL=/bin/sh
SHLVL=1
SSH_CLIENT=192.168.1.2 42903 22
SSH_CONNECTION=192.168.1.2 42903 192.168.1.45 22
SSH_TTY=/dev/pts/0
TERM=xterm
USER=root
XDG_SESSION_COOKIE=106ef489ba27ee071ab233f6518d3bce-1376636543.980417-671366454
_=/etc/init.d/buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package phyml
dpkg-buildpackage: source version 2:20120412-2
dpkg-source --before-build phyml-20120412
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean --with autoreconf
dh_testdir
debian/rules override_dh_auto_clean
make[1]: Entering directory `/«PKGBUILDDIR»'
dh_auto_clean
# remove temporary bin dir for phyml (see above hack)
rm -rf debian/bin
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_autoreconf_clean
dh_clean
debian/rules build-arch
dh build-arch --with autoreconf
dh_testdir -a
debian/rules override_dh_autoreconf
make[1]: Entering directory `/«PKGBUILDDIR»'
dh_autoreconf --as-needed
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
dh_auto_configure
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 for style of include used by make... GNU
checking dependency style of gcc... none
checking dependency style of gcc... (cached) none
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 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 that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/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"
make[2]: Entering directory `/«PKGBUILDDIR»'
make all-recursive
make[3]: Entering directory `/«PKGBUILDDIR»'
Making all in src
make[4]: Entering directory `/«PKGBUILDDIR»/src'
:: Building [phyml]. Version 20130816 ::
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c main.c
main.c: In function 'main':
main.c:43:36: warning: variable 'tree_size' set but not used [-Wunused-but-set-variable]
main.c:43:19: warning: variable 'most_likely_size' set but not used [-Wunused-but-set-variable]
main.c:40:11: warning: variable 'mat' set but not used [-Wunused-but-set-variable]
main.c:39:16: warning: variable 'tree_line_number' set but not used [-Wunused-but-set-variable]
main.c:38:7: warning: variable 'n_otu' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c utilities.c
utilities.c: In function 'Read_Branch_Label':
utilities.c:294:7: warning: variable 'i' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'Write_Tree':
utilities.c:633:16: warning: variable 'last_len' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'Make_Edge_Dirs':
utilities.c:1366:11: warning: variable 'e_root' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'Get_Nexus_Data':
utilities.c:1847:7: warning: variable 'in_comment' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'Traverse_Prefix_Tree':
utilities.c:3411:7: warning: variable 'ret_val' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'NNI':
utilities.c:5117:10: warning: variable 'bl_init' set but not used [-Wunused-but-set-variable]
utilities.c:5113:7: warning: variable 'l_r' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'NNI_Pars':
utilities.c:5382:7: warning: variable 'l_r' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'K80_dist':
utilities.c:6236:10: warning: variable 'unc_len' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'JC69_Dist':
utilities.c:6341:10: warning: variable 'unc_len' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'Hamming_Dist':
utilities.c:6417:10: warning: variable 'unc_len' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'Fast_Br_Len':
utilities.c:9597:23: warning: variable 'new_l' set but not used [-Wunused-but-set-variable]
utilities.c:9597:17: warning: variable 'old_l' set but not used [-Wunused-but-set-variable]
utilities.c:9597:10: warning: variable 'eps_bl' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'Print_Diversity':
utilities.c:11656:7: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c optimiz.c
optimiz.c: In function 'Generic_Brent':
optimiz.c:174:10: warning: variable 'old_lnL' set but not used [-Wunused-but-set-variable]
optimiz.c: In function 'Round_Optimize':
optimiz.c:624:26: warning: variable 'tol' set but not used [-Wunused-but-set-variable]
optimiz.c: In function 'Optimiz_Ext_Br':
optimiz.c:762:10: warning: variable 'lk' set but not used [-Wunused-but-set-variable]
optimiz.c: In function 'Missing_Dist_Brent':
optimiz.c:2102:10: warning: variable 'bestx' set but not used [-Wunused-but-set-variable]
optimiz.c:2101:22: warning: variable 'max_LOGlk' set but not used [-Wunused-but-set-variable]
optimiz.c:2101:10: warning: variable 'init_LOGlk' set but not used [-Wunused-but-set-variable]
optimiz.c: In function 'Optimiz_Alpha_And_Pinv':
optimiz.c:2221:19: warning: variable 'f3' set but not used [-Wunused-but-set-variable]
optimiz.c:2220:19: warning: variable 'lk_final' set but not used [-Wunused-but-set-variable]
optimiz.c:2220:10: warning: variable 'lk_init' set but not used [-Wunused-but-set-variable]
optimiz.c: In function 'Opt_Node_Heights_Recurr_Pre':
optimiz.c:2706:17: warning: variable 't1' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c lk.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c bionj.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c models.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c free.c
free.c: In function 'Free_Tree_Lk':
free.c:305:11: warning: variable 'n' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c help.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c simu.c
simu.c: In function 'Simu':
simu.c:93:7: warning: variable 'recurr' set but not used [-Wunused-but-set-variable]
simu.c:92:7: warning: variable 'opt_free_param' set but not used [-Wunused-but-set-variable]
simu.c: In function 'Select_Edges_To_Swap':
simu.c:297:7: warning: variable 'min' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c eigen.c
eigen.c: In function 'cmatinv':
eigen.c:185:12: warning: variable 'xmax' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c pars.c
pars.c: In function 'Update_P_Pars':
pars.c:246:18: warning: variable 'matches' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c alrt.c
alrt.c: In function 'NNI_Neigh_BL':
alrt.c:321:10: warning: variable 'l1' set but not used [-Wunused-but-set-variable]
alrt.c:315:7: warning: variable 'l_r' set but not used [-Wunused-but-set-variable]
alrt.c: In function 'Make_Target_Swap':
alrt.c:759:10: warning: variable 'bl_init' set but not used [-Wunused-but-set-variable]
alrt.c:757:23: warning: variable 'e4' set but not used [-Wunused-but-set-variable]
alrt.c:757:19: warning: variable 'e3' set but not used [-Wunused-but-set-variable]
alrt.c:757:15: warning: variable 'e2' set but not used [-Wunused-but-set-variable]
alrt.c:757:11: warning: variable 'e1' set but not used [-Wunused-but-set-variable]
alrt.c:755:7: warning: variable 'l_r' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c interface.c
interface.c: In function 'Launch_Interface_Model':
interface.c:798:6: warning: variable 'curr_param' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c cl.c
cl.c: In function 'Read_Command_Line':
cl.c:24:7: warning: variable 'use_gamma' set but not used [-Wunused-but-set-variable]
cl.c:23:7: warning: variable 'open_ps_file' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c spr.c
spr.c: In function 'Est_Lk_Change':
spr.c:1275:37: warning: variable 'u_n' set but not used [-Wunused-but-set-variable]
spr.c: In function 'Best_Lk_Change':
spr.c:1817:37: warning: variable 'u_n' set but not used [-Wunused-but-set-variable]
spr.c: In function 'Spr_Subtree':
spr.c:3164:7: warning: variable 'ret_val' set but not used [-Wunused-but-set-variable]
spr.c: In function 'Test_All_Spr_Targets':
spr.c:3291:18: warning: variable 'approx' set but not used [-Wunused-but-set-variable]
spr.c:3287:38: warning: variable 'n_up' set but not used [-Wunused-but-set-variable]
spr.c: In function 'Test_One_Spr_Target':
spr.c:3458:7: warning: variable 'approx' set but not used [-Wunused-but-set-variable]
spr.c:3457:17: warning: variable 'move_pars' set but not used [-Wunused-but-set-variable]
spr.c: In function 'Speed_Spr_Loop':
spr.c:3548:7: warning: variable 'init_thresh' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c draw.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c stats.c
stats.c: In function 'Rnorm_Trunc_Inverse':
stats.c:253:12: warning: variable 'rz' set but not used [-Wunused-but-set-variable]
stats.c: In function 'Rnorm_Trunc':
stats.c:306:12: warning: variable 'rz' set but not used [-Wunused-but-set-variable]
stats.c:304:10: warning: variable 'u' set but not used [-Wunused-but-set-variable]
stats.c: In function 'Covariance_Matrix':
stats.c:1486:22: warning: variable 'var_min' set but not used [-Wunused-but-set-variable]
stats.c: In function 'Gradient':
stats.c:1951:7: warning: variable 'n_ok_edges' set but not used [-Wunused-but-set-variable]
stats.c: In function 'Hessian_Seo':
stats.c:2098:18: warning: variable 'lnL' set but not used [-Wunused-but-set-variable]
stats.c:2095:7: warning: variable 'n_ok_edges' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c rates.c
rates.c: In function 'RATES_Average_Substitution_Rate':
rates.c:688:20: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Dmu':
rates.c:1123:80: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
rates.c:1123:73: warning: variable 'suminv' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Dmu_One':
rates.c:1178:76: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
rates.c:1178:69: warning: variable 'suminv' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Random_Branch_Lengths':
rates.c:1375:13: warning: variable 'r_d' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Dmu2_And_Mu1_Given_N':
rates.c:1625:36: warning: variable 'texpn' set but not used [-Wunused-but-set-variable]
rates.c:1625:28: warning: variable 'lexpdt2' set but not used [-Wunused-but-set-variable]
rates.c:1625:20: warning: variable 'lexpdt1' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Posterior_One_Rate':
rates.c:1778:21: warning: variable 'cond_cov' set but not used [-Wunused-but-set-variable]
rates.c:1778:11: warning: variable 'cond_mu' set but not used [-Wunused-but-set-variable]
rates.c:1777:14: warning: variable 'is_1' set but not used [-Wunused-but-set-variable]
rates.c:1775:10: warning: variable 'cur_l' set but not used [-Wunused-but-set-variable]
rates.c:1774:22: warning: variable 'nu' set but not used [-Wunused-but-set-variable]
rates.c:1774:13: warning: variable 'ra' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Posterior_Time_Root':
rates.c:2544:38: warning: variable 'new_lnL_rate' set but not used [-Wunused-but-set-variable]
rates.c:2543:16: warning: variable 'cur_l' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Update_Cur_Bl_Pre':
rates.c:2740:19: warning: variable 'nf' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Get_Cov_Matrix_Rooted_Pre':
rates.c:2913:15: warning: variable 'done_left' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Variance_Mu_Pre':
rates.c:3022:10: warning: variable 'dt0' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Check_Lk_Rates':
rates.c:3236:10: warning: variable 'z' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Expected_Tree_Length_Pre':
rates.c:3292:10: warning: variable 'sd' set but not used [-Wunused-but-set-variable]
rates.c:3289:12: warning: variable 'u_anc' set but not used [-Wunused-but-set-variable]
rates.c:3289:10: warning: variable 'u' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Get_Correction_Factor':
rates.c:3588:10: warning: variable 'num' set but not used [-Wunused-but-set-variable]
rates.c: In function 'Sample_Average_Rate':
rates.c:3665:13: warning: variable 'td' set but not used [-Wunused-but-set-variable]
rates.c:3665:10: warning: variable 'ta' set but not used [-Wunused-but-set-variable]
rates.c:3664:13: warning: variable 'rd' set but not used [-Wunused-but-set-variable]
rates.c:3664:10: warning: variable 'ra' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Set_Clock_And_Nu_Max':
rates.c:3812:10: warning: variable 'r_min' set but not used [-Wunused-but-set-variable]
rates.c:3811:10: warning: variable 'a' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c mcmc.c
mcmc.c: In function 'MCMC':
mcmc.c:184:14: warning: variable 'cur_lnL' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_Single_Param_Generic':
mcmc.c:394:12: warning: variable 'mult' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_One_Rate':
mcmc.c:586:13: warning: variable 'cr' set but not used [-Wunused-but-set-variable]
mcmc.c:586:10: warning: variable 'nu' set but not used [-Wunused-but-set-variable]
mcmc.c:583:10: warning: variable 'K' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_Tree_Height':
mcmc.c:1001:16: warning: variable 'max_t' set but not used [-Wunused-but-set-variable]
mcmc.c:1001:10: warning: variable 'min_t' set but not used [-Wunused-but-set-variable]
mcmc.c:1000:22: warning: variable 'new_height' set but not used [-Wunused-but-set-variable]
mcmc.c:1000:10: warning: variable 'cur_height' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_Subtree_Height':
mcmc.c:1223:21: warning: variable 'new_height' set but not used [-Wunused-but-set-variable]
mcmc.c:1223:10: warning: variable 'cur_height' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_Updown_Nu_Cr':
mcmc.c:1597:7: warning: variable 'n_nodes' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_Randomize_Rates':
mcmc.c:2614:16: warning: variable 'r_max' set but not used [-Wunused-but-set-variable]
mcmc.c:2614:10: warning: variable 'r_min' set but not used [-Wunused-but-set-variable]
mcmc.c:2613:10: warning: variable 'u' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_Read_Param_Vals':
mcmc.c:3970:9: warning: variable 'v' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c times.c
times.c: In function 'TIMES_Lk_Yule_Joint':
times.c:853:7: warning: variable 'curr_ts' set but not used [-Wunused-but-set-variable]
times.c:852:10: warning: variable 'eps' set but not used [-Wunused-but-set-variable]
times.c:850:15: warning: variable 'tf' set but not used [-Wunused-but-set-variable]
times.c: In function 'TIMES_Lk_Yule_Order':
times.c:938:11: warning: variable 'ts' set but not used [-Wunused-but-set-variable]
times.c: In function 'TIMES_Lk_Times':
times.c:978:10: warning: variable 'condlogdens' set but not used [-Wunused-but-set-variable]
times.c: In function 'TIMES_Log_Number_Of_Ranked_Labelled_Histories':
times.c:1163:7: warning: variable 'dir1r' set but not used [-Wunused-but-set-variable]
times.c: In function 'TIMES_Log_Number_Of_Ranked_Labelled_Histories_Post':
times.c:1234:11: warning: variable 'dir1d' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c tiporder.c
tiporder.c: In function 'TIPO_Read_One_Taxon_Zscore':
tiporder.c:1175:9: warning: variable 'line' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c mg.c
mg.c: In function 'PART_Map_St_Nodes_In_Gt_Post':
mg.c:1122:9: warning: variable 'dir' set but not used [-Wunused-but-set-variable]
mg.c: In function 'PART_Spr':
mg.c:1384:7: warning: variable 'move' set but not used [-Wunused-but-set-variable]
mg.c:1383:11: warning: variable 'target' set but not used [-Wunused-but-set-variable]
mg.c: In function 'PART_NNI':
mg.c:2107:10: warning: variable 'lk0_init' set but not used [-Wunused-but-set-variable]
mg.c:2106:10: warning: variable 'lk_init' set but not used [-Wunused-but-set-variable]
mg.c: In function 'PART_Br_Len_Brent':
mg.c:2640:14: warning: variable 'bx' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c m4.c
m4.c: In function 'M4_main':
m4.c:29:36: warning: variable 'tree_size' set but not used [-Wunused-but-set-variable]
m4.c:29:19: warning: variable 'most_likely_size' set but not used [-Wunused-but-set-variable]
m4.c:26:11: warning: variable 'mat' set but not used [-Wunused-but-set-variable]
m4.c:25:16: warning: variable 'tree_line_number' set but not used [-Wunused-but-set-variable]
m4.c:24:7: warning: variable 'n_otu' set but not used [-Wunused-but-set-variable]
m4.c: In function 'M4_Post_Prob_H_Class_Edge_Site':
m4.c:771:7: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
m4.c: In function 'M4_Compute_Proba_Hidden_States_On_Edges':
m4.c:897:26: warning: variable 'dwell' set but not used [-Wunused-but-set-variable]
m4.c: In function 'M4_Site_Branch_Classification_Experiment':
m4.c:1229:7: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
m4.c:1224:11: warning: variable 'ori_data' set but not used [-Wunused-but-set-variable]
m4.c: In function 'M4_Detect_Site_Switches_Experiment':
m4.c:1446:16: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
m4.c: In function 'M4_Posterior_Prediction_Experiment':
m4.c:1583:24: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
m4.c:1581:10: warning: variable 'ori_mod' set but not used [-Wunused-but-set-variable]
m4.c: In function 'M4_Copy_M4_Model':
m4.c:1733:7: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
gcc -Wall -O2 -fomit-frame-pointer -funroll-loops -Wl,-z,relro -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 mg.o m4.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/
/usr/bin/make prefix=/«PKGBUILDDIR»/debian install
make[2]: Entering directory `/«PKGBUILDDIR»'
Making install in src
make[3]: Entering directory `/«PKGBUILDDIR»/src'
:: Building [phyml]. Version 20130816 ::
Done.
make[4]: Entering directory `/«PKGBUILDDIR»/src'
/bin/mkdir -p '/«PKGBUILDDIR»/debian/bin'
/usr/bin/install -c phyml '/«PKGBUILDDIR»/debian/bin'
make[4]: Nothing to be done for `install-data-am'.
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»'
/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 -rf ./.deps
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-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 for style of include used by make... GNU
checking dependency style of gcc... none
checking dependency style of gcc... (cached) none
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 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 that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/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"
make[2]: Entering directory `/«PKGBUILDDIR»'
make all-recursive
make[3]: Entering directory `/«PKGBUILDDIR»'
Making all in src
make[4]: Entering directory `/«PKGBUILDDIR»/src'
:: Building [phytime]. Version 20130816 ::
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c main.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c utilities.c
utilities.c: In function 'Read_Branch_Label':
utilities.c:294:7: warning: variable 'i' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'Write_Tree':
utilities.c:633:16: warning: variable 'last_len' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'Make_Edge_Dirs':
utilities.c:1366:11: warning: variable 'e_root' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'Get_Nexus_Data':
utilities.c:1847:7: warning: variable 'in_comment' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'Traverse_Prefix_Tree':
utilities.c:3411:7: warning: variable 'ret_val' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'NNI':
utilities.c:5117:10: warning: variable 'bl_init' set but not used [-Wunused-but-set-variable]
utilities.c:5113:7: warning: variable 'l_r' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'NNI_Pars':
utilities.c:5382:7: warning: variable 'l_r' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'K80_dist':
utilities.c:6236:10: warning: variable 'unc_len' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'JC69_Dist':
utilities.c:6341:10: warning: variable 'unc_len' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'Hamming_Dist':
utilities.c:6417:10: warning: variable 'unc_len' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'Fast_Br_Len':
utilities.c:9597:23: warning: variable 'new_l' set but not used [-Wunused-but-set-variable]
utilities.c:9597:17: warning: variable 'old_l' set but not used [-Wunused-but-set-variable]
utilities.c:9597:10: warning: variable 'eps_bl' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'Print_Diversity':
utilities.c:11656:7: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c optimiz.c
optimiz.c: In function 'Generic_Brent':
optimiz.c:174:10: warning: variable 'old_lnL' set but not used [-Wunused-but-set-variable]
optimiz.c: In function 'Round_Optimize':
optimiz.c:624:26: warning: variable 'tol' set but not used [-Wunused-but-set-variable]
optimiz.c: In function 'Optimiz_Ext_Br':
optimiz.c:762:10: warning: variable 'lk' set but not used [-Wunused-but-set-variable]
optimiz.c: In function 'Missing_Dist_Brent':
optimiz.c:2102:10: warning: variable 'bestx' set but not used [-Wunused-but-set-variable]
optimiz.c:2101:22: warning: variable 'max_LOGlk' set but not used [-Wunused-but-set-variable]
optimiz.c:2101:10: warning: variable 'init_LOGlk' set but not used [-Wunused-but-set-variable]
optimiz.c: In function 'Optimiz_Alpha_And_Pinv':
optimiz.c:2221:19: warning: variable 'f3' set but not used [-Wunused-but-set-variable]
optimiz.c:2220:19: warning: variable 'lk_final' set but not used [-Wunused-but-set-variable]
optimiz.c:2220:10: warning: variable 'lk_init' set but not used [-Wunused-but-set-variable]
optimiz.c: In function 'Opt_Node_Heights_Recurr_Pre':
optimiz.c:2706:17: warning: variable 't1' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c lk.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c bionj.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c models.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c free.c
free.c: In function 'Free_Tree_Lk':
free.c:305:11: warning: variable 'n' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c help.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c simu.c
simu.c: In function 'Simu':
simu.c:93:7: warning: variable 'recurr' set but not used [-Wunused-but-set-variable]
simu.c:92:7: warning: variable 'opt_free_param' set but not used [-Wunused-but-set-variable]
simu.c: In function 'Select_Edges_To_Swap':
simu.c:297:7: warning: variable 'min' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c eigen.c
eigen.c: In function 'cmatinv':
eigen.c:185:12: warning: variable 'xmax' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c pars.c
pars.c: In function 'Update_P_Pars':
pars.c:246:18: warning: variable 'matches' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c alrt.c
alrt.c: In function 'NNI_Neigh_BL':
alrt.c:321:10: warning: variable 'l1' set but not used [-Wunused-but-set-variable]
alrt.c:315:7: warning: variable 'l_r' set but not used [-Wunused-but-set-variable]
alrt.c: In function 'Make_Target_Swap':
alrt.c:759:10: warning: variable 'bl_init' set but not used [-Wunused-but-set-variable]
alrt.c:757:23: warning: variable 'e4' set but not used [-Wunused-but-set-variable]
alrt.c:757:19: warning: variable 'e3' set but not used [-Wunused-but-set-variable]
alrt.c:757:15: warning: variable 'e2' set but not used [-Wunused-but-set-variable]
alrt.c:757:11: warning: variable 'e1' set but not used [-Wunused-but-set-variable]
alrt.c:755:7: warning: variable 'l_r' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c interface.c
interface.c: In function 'Launch_Interface_Model':
interface.c:798:6: warning: variable 'curr_param' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c cl.c
cl.c: In function 'Read_Command_Line':
cl.c:24:7: warning: variable 'use_gamma' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c spr.c
spr.c: In function 'Est_Lk_Change':
spr.c:1275:37: warning: variable 'u_n' set but not used [-Wunused-but-set-variable]
spr.c: In function 'Best_Lk_Change':
spr.c:1817:37: warning: variable 'u_n' set but not used [-Wunused-but-set-variable]
spr.c: In function 'Spr_Subtree':
spr.c:3164:7: warning: variable 'ret_val' set but not used [-Wunused-but-set-variable]
spr.c: In function 'Test_All_Spr_Targets':
spr.c:3291:18: warning: variable 'approx' set but not used [-Wunused-but-set-variable]
spr.c:3287:38: warning: variable 'n_up' set but not used [-Wunused-but-set-variable]
spr.c: In function 'Test_One_Spr_Target':
spr.c:3458:7: warning: variable 'approx' set but not used [-Wunused-but-set-variable]
spr.c:3457:17: warning: variable 'move_pars' set but not used [-Wunused-but-set-variable]
spr.c: In function 'Speed_Spr_Loop':
spr.c:3548:7: warning: variable 'init_thresh' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c times.c
times.c: In function 'TIMES_main':
times.c:35:36: warning: variable 'tree_size' set but not used [-Wunused-but-set-variable]
times.c:35:19: warning: variable 'most_likely_size' set but not used [-Wunused-but-set-variable]
times.c:35:10: warning: variable 'best_lnL' set but not used [-Wunused-but-set-variable]
times.c:32:11: warning: variable 'mat' set but not used [-Wunused-but-set-variable]
times.c:31:16: warning: variable 'tree_line_number' set but not used [-Wunused-but-set-variable]
times.c:30:7: warning: variable 'n_otu' set but not used [-Wunused-but-set-variable]
times.c: In function 'TIMES_Lk_Yule_Joint':
times.c:853:7: warning: variable 'curr_ts' set but not used [-Wunused-but-set-variable]
times.c:852:10: warning: variable 'eps' set but not used [-Wunused-but-set-variable]
times.c:850:15: warning: variable 'tf' set but not used [-Wunused-but-set-variable]
times.c: In function 'TIMES_Lk_Yule_Order':
times.c:938:11: warning: variable 'ts' set but not used [-Wunused-but-set-variable]
times.c: In function 'TIMES_Lk_Times':
times.c:978:10: warning: variable 'condlogdens' set but not used [-Wunused-but-set-variable]
times.c: In function 'TIMES_Log_Number_Of_Ranked_Labelled_Histories':
times.c:1163:7: warning: variable 'dir1r' set but not used [-Wunused-but-set-variable]
times.c: In function 'TIMES_Log_Number_Of_Ranked_Labelled_Histories_Post':
times.c:1234:11: warning: variable 'dir1d' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c m4.c
m4.c: In function 'M4_main':
m4.c:29:36: warning: variable 'tree_size' set but not used [-Wunused-but-set-variable]
m4.c:29:19: warning: variable 'most_likely_size' set but not used [-Wunused-but-set-variable]
m4.c:26:11: warning: variable 'mat' set but not used [-Wunused-but-set-variable]
m4.c:25:16: warning: variable 'tree_line_number' set but not used [-Wunused-but-set-variable]
m4.c:24:7: warning: variable 'n_otu' set but not used [-Wunused-but-set-variable]
m4.c: In function 'M4_Post_Prob_H_Class_Edge_Site':
m4.c:771:7: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
m4.c: In function 'M4_Compute_Proba_Hidden_States_On_Edges':
m4.c:897:26: warning: variable 'dwell' set but not used [-Wunused-but-set-variable]
m4.c: In function 'M4_Site_Branch_Classification_Experiment':
m4.c:1229:7: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
m4.c:1224:11: warning: variable 'ori_data' set but not used [-Wunused-but-set-variable]
m4.c: In function 'M4_Detect_Site_Switches_Experiment':
m4.c:1446:16: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
m4.c: In function 'M4_Posterior_Prediction_Experiment':
m4.c:1583:24: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
m4.c:1581:10: warning: variable 'ori_mod' set but not used [-Wunused-but-set-variable]
m4.c: In function 'M4_Copy_M4_Model':
m4.c:1733:7: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c draw.c
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c rates.c
rates.c: In function 'RATES_Average_Substitution_Rate':
rates.c:688:20: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Dmu':
rates.c:1123:80: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
rates.c:1123:73: warning: variable 'suminv' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Dmu_One':
rates.c:1178:76: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
rates.c:1178:69: warning: variable 'suminv' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Random_Branch_Lengths':
rates.c:1375:13: warning: variable 'r_d' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Dmu2_And_Mu1_Given_N':
rates.c:1625:36: warning: variable 'texpn' set but not used [-Wunused-but-set-variable]
rates.c:1625:28: warning: variable 'lexpdt2' set but not used [-Wunused-but-set-variable]
rates.c:1625:20: warning: variable 'lexpdt1' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Posterior_One_Rate':
rates.c:1778:21: warning: variable 'cond_cov' set but not used [-Wunused-but-set-variable]
rates.c:1778:11: warning: variable 'cond_mu' set but not used [-Wunused-but-set-variable]
rates.c:1777:14: warning: variable 'is_1' set but not used [-Wunused-but-set-variable]
rates.c:1775:10: warning: variable 'cur_l' set but not used [-Wunused-but-set-variable]
rates.c:1774:22: warning: variable 'nu' set but not used [-Wunused-but-set-variable]
rates.c:1774:13: warning: variable 'ra' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Posterior_Time_Root':
rates.c:2544:38: warning: variable 'new_lnL_rate' set but not used [-Wunused-but-set-variable]
rates.c:2543:16: warning: variable 'cur_l' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Update_Cur_Bl_Pre':
rates.c:2740:19: warning: variable 'nf' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Get_Cov_Matrix_Rooted_Pre':
rates.c:2913:15: warning: variable 'done_left' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Variance_Mu_Pre':
rates.c:3022:10: warning: variable 'dt0' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Check_Lk_Rates':
rates.c:3236:10: warning: variable 'z' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Expected_Tree_Length_Pre':
rates.c:3292:10: warning: variable 'sd' set but not used [-Wunused-but-set-variable]
rates.c:3289:12: warning: variable 'u_anc' set but not used [-Wunused-but-set-variable]
rates.c:3289:10: warning: variable 'u' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Get_Correction_Factor':
rates.c:3588:10: warning: variable 'num' set but not used [-Wunused-but-set-variable]
rates.c: In function 'Sample_Average_Rate':
rates.c:3665:13: warning: variable 'td' set but not used [-Wunused-but-set-variable]
rates.c:3665:10: warning: variable 'ta' set but not used [-Wunused-but-set-variable]
rates.c:3664:13: warning: variable 'rd' set but not used [-Wunused-but-set-variable]
rates.c:3664:10: warning: variable 'ra' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Set_Clock_And_Nu_Max':
rates.c:3812:10: warning: variable 'r_min' set but not used [-Wunused-but-set-variable]
rates.c:3811:10: warning: variable 'a' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c mcmc.c
mcmc.c: In function 'MCMC':
mcmc.c:184:14: warning: variable 'cur_lnL' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_Single_Param_Generic':
mcmc.c:394:12: warning: variable 'mult' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_One_Rate':
mcmc.c:586:13: warning: variable 'cr' set but not used [-Wunused-but-set-variable]
mcmc.c:586:10: warning: variable 'nu' set but not used [-Wunused-but-set-variable]
mcmc.c:583:10: warning: variable 'K' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_Tree_Height':
mcmc.c:1001:16: warning: variable 'max_t' set but not used [-Wunused-but-set-variable]
mcmc.c:1001:10: warning: variable 'min_t' set but not used [-Wunused-but-set-variable]
mcmc.c:1000:22: warning: variable 'new_height' set but not used [-Wunused-but-set-variable]
mcmc.c:1000:10: warning: variable 'cur_height' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_Subtree_Height':
mcmc.c:1223:21: warning: variable 'new_height' set but not used [-Wunused-but-set-variable]
mcmc.c:1223:10: warning: variable 'cur_height' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_Updown_Nu_Cr':
mcmc.c:1597:7: warning: variable 'n_nodes' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_Randomize_Rates':
mcmc.c:2614:16: warning: variable 'r_max' set but not used [-Wunused-but-set-variable]
mcmc.c:2614:10: warning: variable 'r_min' set but not used [-Wunused-but-set-variable]
mcmc.c:2613:10: warning: variable 'u' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_Read_Param_Vals':
mcmc.c:3970:9: warning: variable 'v' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c stats.c
stats.c: In function 'Rnorm_Trunc_Inverse':
stats.c:253:12: warning: variable 'rz' set but not used [-Wunused-but-set-variable]
stats.c: In function 'Rnorm_Trunc':
stats.c:306:12: warning: variable 'rz' set but not used [-Wunused-but-set-variable]
stats.c:304:10: warning: variable 'u' set but not used [-Wunused-but-set-variable]
stats.c: In function 'Covariance_Matrix':
stats.c:1486:22: warning: variable 'var_min' set but not used [-Wunused-but-set-variable]
stats.c: In function 'Gradient':
stats.c:1951:7: warning: variable 'n_ok_edges' set but not used [-Wunused-but-set-variable]
stats.c: In function 'Hessian_Seo':
stats.c:2098:18: warning: variable 'lnL' set but not used [-Wunused-but-set-variable]
stats.c:2095:7: warning: variable 'n_ok_edges' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c mg.c
mg.c: In function 'PART_Map_St_Nodes_In_Gt_Post':
mg.c:1122:9: warning: variable 'dir' set but not used [-Wunused-but-set-variable]
mg.c: In function 'PART_Spr':
mg.c:1384:7: warning: variable 'move' set but not used [-Wunused-but-set-variable]
mg.c:1383:11: warning: variable 'target' set but not used [-Wunused-but-set-variable]
mg.c: In function 'PART_NNI':
mg.c:2107:10: warning: variable 'lk0_init' set but not used [-Wunused-but-set-variable]
mg.c:2106:10: warning: variable 'lk_init' set but not used [-Wunused-but-set-variable]
mg.c: In function 'PART_Br_Len_Brent':
mg.c:2640:14: warning: variable 'bx' set but not used [-Wunused-but-set-variable]
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -fomit-frame-pointer -funroll-loops -c tiporder.c
tiporder.c: In function 'TIPO_Read_One_Taxon_Zscore':
tiporder.c:1175:9: warning: variable 'line' set but not used [-Wunused-but-set-variable]
gcc -Wall -O2 -fomit-frame-pointer -funroll-loops -Wl,-z,relro -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 -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»'
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_auto_test -a
make[1]: Entering directory `/«PKGBUILDDIR»'
Making check in src
make[2]: Entering directory `/«PKGBUILDDIR»/src'
:: Building [phytime]. Version 20130816 ::
Done.
make[2]: Leaving directory `/«PKGBUILDDIR»/src'
make[2]: Entering directory `/«PKGBUILDDIR»'
make[2]: Leaving directory `/«PKGBUILDDIR»'
make[1]: Leaving directory `/«PKGBUILDDIR»'
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 `/«PKGBUILDDIR»'
dh_auto_install
make[2]: Entering directory `/«PKGBUILDDIR»'
Making install in src
make[3]: Entering directory `/«PKGBUILDDIR»/src'
:: Building [phytime]. Version 20130816 ::
Done.
make[4]: Entering directory `/«PKGBUILDDIR»/src'
/bin/mkdir -p '/«PKGBUILDDIR»/debian/phyml/usr/bin'
/usr/bin/install -c phytime '/«PKGBUILDDIR»/debian/phyml/usr/bin'
make[4]: Nothing to be done for `install-data-am'.
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
mv /«PKGBUILDDIR»/debian/bin/* /«PKGBUILDDIR»/debian/phyml/usr/bin
make[1]: Leaving directory `/«PKGBUILDDIR»'
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_installman -a
dh_perl -a
dh_link -a
debian/rules override_dh_compress
make[1]: Entering directory `/«PKGBUILDDIR»'
dh_compress --exclude=.pdf
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb -a
dh_gencontrol -a
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' in `../phyml_20120412-2_armhf.deb'.
dpkg-genchanges -B -mRaspbian nitrogen6x test autobuilder <root@raspbian.org> >../phyml_20120412-2_armhf.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build phyml-20120412
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20130816-1333
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
phyml_20120412-2_armhf.changes:
───────────────────────────────
Format: 1.8
Date: Mon, 05 Aug 2013 09:56:27 +0200
Source: phyml
Binary: phyml
Architecture: armhf
Version: 2:20120412-2
Distribution: jessie-staging
Urgency: low
Maintainer: Raspbian nitrogen6x test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
phyml - Phylogenetic estimation using Maximum Likelihood
Closes: 718747
Changes:
phyml (2:20120412-2) unstable; urgency=low
.
* debian/patches/sse_only_if_supported.patch: Check architecture before
deciding to build using -msse
Closes: #718747
Checksums-Sha1:
d58a87f599ea704a9c9b3171555df3b1c8fdce81 1394418 phyml_20120412-2_armhf.deb
Checksums-Sha256:
11018c241bbee3bdfd648c721ddbfbb5ac053fba53c5276786b91d823167d01c 1394418 phyml_20120412-2_armhf.deb
Files:
73296176838840b278636841d18c73c9 1394418 science optional phyml_20120412-2_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
phyml_20120412-2_armhf.deb
──────────────────────────
new debian package, version 2.0.
size 1394418 bytes: control archive=1403 bytes.
1636 bytes, 31 lines control
631 bytes, 10 lines md5sums
Package: phyml
Version: 2:20120412-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2513
Depends: libc6 (>= 2.7)
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 pakcage also includes PhyTime.
drwxr-xr-x root/root 0 2013-08-16 13:33 ./
drwxr-xr-x root/root 0 2013-08-16 13:33 ./usr/
drwxr-xr-x root/root 0 2013-08-16 13:33 ./usr/bin/
-rwxr-xr-x root/root 997120 2013-08-16 13:33 ./usr/bin/phytime
-rwxr-xr-x root/root 993024 2013-08-16 13:33 ./usr/bin/phyml
drwxr-xr-x root/root 0 2013-08-16 13:33 ./usr/share/
drwxr-xr-x root/root 0 2013-08-16 13:33 ./usr/share/doc/
drwxr-xr-x root/root 0 2013-08-16 13:33 ./usr/share/doc/phyml/
-rw-r--r-- root/root 299 2013-07-31 12:03 ./usr/share/doc/phyml/README.Debian
-rw-r--r-- root/root 8681 2013-07-31 06:29 ./usr/share/doc/phyml/copyright
-rw-r--r-- root/root 561368 2011-09-19 01:16 ./usr/share/doc/phyml/phyml_manual.pdf
-rw-r--r-- root/root 1525 2013-08-05 07:59 ./usr/share/doc/phyml/changelog.Debian.gz
-rw-r--r-- root/root 5458 2010-01-09 01:12 ./usr/share/doc/phyml/changelog.gz
drwxr-xr-x root/root 0 2013-08-16 13:33 ./usr/share/doc-base/
-rw-r--r-- root/root 202 2011-12-07 07:37 ./usr/share/doc-base/phyml
drwxr-xr-x root/root 0 2013-08-16 13:33 ./usr/share/man/
drwxr-xr-x root/root 0 2013-08-16 13:33 ./usr/share/man/man1/
-rw-r--r-- root/root 2898 2013-08-16 13:33 ./usr/share/man/man1/phyml.1.gz
-rw-r--r-- root/root 2306 2013-08-16 13:33 ./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: 16356
Build-Time: 557
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 188
Job: phyml_2:20120412-2
Machine Architecture: armhf
Package: phyml
Package-Time: 836
Source-Version: 2:20120412-2
Space: 16356
Status: successful
Version: 2:20120412-2
────────────────────────────────────────────────────────────────────────────────
Finished at 20130816-1333
Build needed 00:13:56, 16356k disc space