[Debian-med-packaging] phyml_20110526-1_amd64.changes ACCEPTED into unstable

Sun Jun 26 13:25:30 UTC 2011

Le Sun, Jun 26, 2011 at 10:45:11AM +0000, Debian FTP Masters a écrit :
> 
> Accepted:
> phyml_20110526-1.debian.tar.gz
>   to main/p/phyml/phyml_20110526-1.debian.tar.gz
> phyml_20110526-1.dsc
>   to main/p/phyml/phyml_20110526-1.dsc
> phyml_20110526-1_amd64.deb
>   to main/p/phyml/phyml_20110526-1_amd64.deb
> phyml_20110526.orig.tar.gz
>   to main/p/phyml/phyml_20110526.orig.tar.gz

Build logs…

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
-------------- next part --------------
sbuild (Debian sbuild) 0.62.4 (25 Jun 2011) on aqwa.igloo

╔══════════════════════════════════════════════════════════════════════════════╗
║ phyml 20110526-1 (amd64)                                  26 juin 2011 13:18 ║
╚══════════════════════════════════════════════════════════════════════════════╝

Package: phyml
Version: 20110526-1
Source Version: 20110526-1
Distribution: unstable
Architecture: amd64

I: NOTICE: Log filtering will replace 'build/phyml-CcgVor/phyml-20110526' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/phyml-CcgVor' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-99866d65-9f43-4082-a65d-3afaf42a1462' with '«CHROOT»'

┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot                                                                │
└──────────────────────────────────────────────────────────────────────────────┘

Hit ftp://ftp.jaist.ac.jp sid InRelease
Hit ftp://ftp.jaist.ac.jp sid/main Sources/DiffIndex
Hit ftp://ftp.jaist.ac.jp sid/main amd64 Packages/DiffIndex
Hit ftp://ftp.jaist.ac.jp sid/main TranslationIndex
Hit ftp://ftp.jaist.ac.jp sid/main Translation-fr
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files                                                           │
└──────────────────────────────────────────────────────────────────────────────┘

Local sources
─────────────

phyml_20110526-1.dsc exists in .; copying to chroot

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-aXa2L3/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 0 not upgraded.
Need to get 0 B/716 B of archives.
After this operation, 0 B of additional disk space will be used.
Selecting previously deselected package sbuild-build-depends-core-dummy.
(Reading database ... 10824 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, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), automake, autoconf
Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), automake, autoconf
dpkg-deb: building package `sbuild-build-depends-phyml-dummy' in `/«BUILDDIR»/resolver-N3Pb8i/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 autotools-dev bsdmainutils debhelper file gettext
  gettext-base groff-base html2text intltool-debian libcroco3 libglib2.0-0
  libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 m4 man-db po-debconf
Suggested packages:
  autoconf2.13 autoconf-archive gnu-standards autoconf-doc libtool wamerican
  wordlist whois vacation dh-make gettext-doc groff less www-browser
  libmail-box-perl
Recommended packages:
  curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core
  libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autotools-dev bsdmainutils debhelper file gettext
  gettext-base groff-base html2text intltool-debian libcroco3 libglib2.0-0
  libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 m4 man-db po-debconf
  sbuild-build-depends-phyml-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded.
Need to get 0 B/11.0 MB of archives.
After this operation, 32.0 MB of additional disk space will be used.
Selecting previously deselected package libpipeline1.
(Reading database ... 10824 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_amd64.deb) ...
Selecting previously deselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_amd64.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_amd64.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-1_amd64.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_amd64.deb) ...
Selecting previously deselected package file.
Unpacking file (from .../file_5.04-5+b1_amd64.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_amd64.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-3_amd64.deb) ...
Selecting previously deselected package libxml2.
Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_amd64.deb) ...
Selecting previously deselected package m4.
Unpacking m4 (from .../archives/m4_1.4.16-1_amd64.deb) ...
Selecting previously deselected package autoconf.
Unpacking autoconf (from .../autoconf_2.68-1_all.deb) ...
Selecting previously deselected package autotools-dev.
Unpacking autotools-dev (from .../autotools-dev_20110511.1_all.deb) ...
Selecting previously deselected package automake.
Unpacking automake (from .../automake_1%3a1.11.1-1_all.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ...
Selecting previously deselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_amd64.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_amd64.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_amd64.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_amd64.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
Unpacking debhelper (from .../debhelper_8.9.0_all.deb) ...
Selecting previously deselected package sbuild-build-depends-phyml-dummy.
Unpacking sbuild-build-depends-phyml-dummy (from .../sbuild-build-depends-phyml-dummy.deb) ...
Setting up libpipeline1 (1.2.0-3) ...
Setting up bsdmainutils (8.2.3) ...
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 groff-base (1.21-6) ...
Setting up man-db (2.6.0.2-1) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5+b1) ...
Setting up file (5.04-5+b1) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
Setting up libxml2 (2.7.8.dfsg-3) ...
Setting up m4 (1.4.16-1) ...
Setting up autoconf (2.68-1) ...
Setting up autotools-dev (20110511.1) ...
Setting up automake (1:1.11.1-1) ...
update-alternatives: using /usr/bin/automake-1.11 to provide /usr/bin/automake (automake) in auto mode.
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.9.0) ...
Setting up sbuild-build-depends-phyml-dummy (0.invalid.0) ...

┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment                                                            │
└──────────────────────────────────────────────────────────────────────────────┘

Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64)
Toolchain package versions: binutils_2.21.52.20110606-2 dpkg-dev_1.16.0.3 g++-4.6_4.6.0-14 gcc-4.6_4.6.0-14 libc6-dev_2.13-7 libstdc++6_4.6.0-14 libstdc++6-4.6-dev_4.6.0-14 linux-libc-dev_2.6.39-2
Package versions: apt_0.8.14.1 autoconf_2.68-1 automake_1:1.11.1-1 autotools-dev_20110511.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110606-2 bsdmainutils_8.2.3 bsdutils_1:2.19.1-2 build-essential_11.5 bzip2_1.0.5-6 coreutils_8.5-1 cpp_4:4.6.0-6 cpp-4.6_4.6.0-14 dash_0.5.5.1-7.4 debconf_1.5.40 debconf-i18n_1.5.40 debfoster_2.7-1.1 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4stable1 e2fsprogs_1.41.12-4stable1 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-6 g++-4.6_4.6.0-14 gcc_4:4.6.0-6 gcc-4.6_4.6.0-14 gcc-4.6-base_4.6.0-14 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-1 libattr1_1:2.4.46-1 libblkid1_2.19.1-2 libbz2-1.0_1.0.5-6 libc-bin_2.13-7 libc-dev-bin_2.13-7 libc6_2.13-7 libc6-dev_2.13-7 libclass-isa-perl_0.36-1 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4stable1 libcroco3_0.6.2-1 libdb4.7_4.7.25-20 libdb4.8_4.8.30-8 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.0-14 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmp3c2_2:4.3.2+dfsg-2 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-14 liblocale-gettext-perl_1.05-6+b1 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmount1_2.19.1-2 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-3 libpipeline1_1.2.0-3 libpod-plainer-perl_1.03-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libquadmath0_4.6.0-14 libreadline6_6.2-2 libselinux1_2.0.98-1.1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-4stable1 libstdc++6_4.6.0-14 libstdc++6-4.6-dev_4.6.0-14 libswitch-perl_2.16-1 libtext-charwidth-perl_0.04-6+b1 libtext-iconv-perl_1.7-2+b1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.19.1-2 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 m4_1.4.16-1 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.19.1-2 multiarch-support_2.13-7 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.3-7+b1 perl-base_5.12.3-7+b1 perl-modules_5.12.3-7 po-debconf_1.0.16+nmu1 readline-common_6.2-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-phyml-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-3 tzdata_2011g-1 util-linux_2.19.1-2 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3

┌──────────────────────────────────────────────────────────────────────────────┐
│ Build                                                                        │
└──────────────────────────────────────────────────────────────────────────────┘

Unpack source
─────────────

dpkg-source: warning: extracting unsigned source package (phyml_20110526-1.dsc)
dpkg-source: info: extracting phyml in phyml-20110526
dpkg-source: info: unpacking phyml_20110526.orig.tar.gz
dpkg-source: info: unpacking phyml_20110526-1.debian.tar.gz

Check disc space
────────────────

Sufficient free space for build

User Environment
────────────────

HOME=/sbuild-nonexistent
LOGNAME=charles
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_CHROOT_NAME=sid-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=charles
SCHROOT_SESSION_ID=sid-amd64-sbuild-99866d65-9f43-4082-a65d-3afaf42a1462
SCHROOT_UID=1000
SCHROOT_USER=charles
SHELL=/bin/sh
TERM=xterm
USER=charles
USERNAME=charles

dpkg-buildpackage
─────────────────

dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor): 
dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor): 
dpkg-buildpackage: source package phyml
dpkg-buildpackage: source version 2:20110526-1
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
 dpkg-source --before-build phyml-20110526
dpkg-buildpackage: host architecture amd64
 fakeroot debian/rules clean
dh clean
   dh_testdir
   dh_auto_clean
   dh_clean
 dpkg-source -b phyml-20110526
dpkg-source: info: using source format `3.0 (quilt)'
dpkg-source: info: building phyml using existing ./phyml_20110526.orig.tar.gz
dpkg-source: info: building phyml in phyml_20110526-1.debian.tar.gz
dpkg-source: info: building phyml in phyml_20110526-1.dsc
 debian/rules build
dh build
   dh_testdir
   # Skipping dh_auto_configure - empty override
   debian/rules override_dh_auto_build
make[1]: Entering directory `/«PKGBUILDDIR»'
dh_testdir
aclocal ; autoconf -f ; automake -f ; ./configure --prefix=/usr
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 build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
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... gcc3
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: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands
/usr/bin/make CFLAGS="-Wall -g -O2"
make[2]: Entering directory `/«PKGBUILDDIR»'
(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /«PKGBUILDDIR»/missing --run autoheader)
rm -f stamp-h1
touch config.h.in
/usr/bin/make  all-recursive
make[3]: Entering directory `/«PKGBUILDDIR»'
Making all in src
make[4]: Entering directory `/«PKGBUILDDIR»/src'

:: Building PHYML. Version 20110626 ::

gcc -DUNIX -DPHYML -DDEBUG  -I. -I..     -Wall -g -O2 -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o 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]
mv -f .deps/main.Tpo .deps/main.Po
gcc -DUNIX -DPHYML -DDEBUG  -I. -I..     -Wall -g -O2 -MT utilities.o -MD -MP -MF .deps/utilities.Tpo -c -o utilities.o utilities.c
utilities.c: In function 'Get_Nexus_Data':
utilities.c:1369:7: warning: variable 'in_comment' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'Traverse_Prefix_Tree':
utilities.c:2842:7: warning: variable 'ret_val' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'NNI':
utilities.c:4153:10: warning: variable 'bl_init' set but not used [-Wunused-but-set-variable]
utilities.c:4149:7: warning: variable 'l_r' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'NNI_Pars':
utilities.c:4416:7: warning: variable 'l_r' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'K80_dist':
utilities.c:5232:10: warning: variable 'unc_len' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'JC69_Dist':
utilities.c:5335:10: warning: variable 'unc_len' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'Hamming_Dist':
utilities.c:5409:10: warning: variable 'unc_len' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'Fast_Br_Len':
utilities.c:8326:23: warning: variable 'new_l' set but not used [-Wunused-but-set-variable]
utilities.c:8326:17: warning: variable 'old_l' set but not used [-Wunused-but-set-variable]
utilities.c:8326:10: warning: variable 'eps_bl' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'Print_Diversity':
utilities.c:10195:7: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
mv -f .deps/utilities.Tpo .deps/utilities.Po
gcc -DUNIX -DPHYML -DDEBUG  -I. -I..     -Wall -g -O2 -MT optimiz.o -MD -MP -MF .deps/optimiz.Tpo -c -o optimiz.o optimiz.c
optimiz.c: In function 'Generic_Brent':
optimiz.c:169:10: warning: variable 'old_lnL' set but not used [-Wunused-but-set-variable]
optimiz.c: In function 'Round_Optimize':
optimiz.c:607:26: warning: variable 'tol' set but not used [-Wunused-but-set-variable]
optimiz.c: In function 'Optimiz_Ext_Br':
optimiz.c:727:10: warning: variable 'lk' set but not used [-Wunused-but-set-variable]
optimiz.c: In function 'Missing_Dist_Brent':
optimiz.c:2026:10: warning: variable 'bestx' set but not used [-Wunused-but-set-variable]
optimiz.c:2025:22: warning: variable 'max_LOGlk' set but not used [-Wunused-but-set-variable]
optimiz.c:2025:10: warning: variable 'init_LOGlk' set but not used [-Wunused-but-set-variable]
optimiz.c: In function 'Optimiz_Alpha_And_Pinv':
optimiz.c:2141:19: warning: variable 'f3' set but not used [-Wunused-but-set-variable]
optimiz.c:2140:19: warning: variable 'lk_final' set but not used [-Wunused-but-set-variable]
optimiz.c:2140:10: warning: variable 'lk_init' set but not used [-Wunused-but-set-variable]
optimiz.c: In function 'Opt_Node_Heights_Recurr_Pre':
optimiz.c:2611:17: warning: variable 't1' set but not used [-Wunused-but-set-variable]
mv -f .deps/optimiz.Tpo .deps/optimiz.Po
gcc -DUNIX -DPHYML -DDEBUG  -I. -I..     -Wall -g -O2 -MT lk.o -MD -MP -MF .deps/lk.Tpo -c -o lk.o lk.c
mv -f .deps/lk.Tpo .deps/lk.Po
gcc -DUNIX -DPHYML -DDEBUG  -I. -I..     -Wall -g -O2 -MT bionj.o -MD -MP -MF .deps/bionj.Tpo -c -o bionj.o bionj.c
mv -f .deps/bionj.Tpo .deps/bionj.Po
gcc -DUNIX -DPHYML -DDEBUG  -I. -I..     -Wall -g -O2 -MT models.o -MD -MP -MF .deps/models.Tpo -c -o models.o models.c
mv -f .deps/models.Tpo .deps/models.Po
gcc -DUNIX -DPHYML -DDEBUG  -I. -I..     -Wall -g -O2 -MT free.o -MD -MP -MF .deps/free.Tpo -c -o free.o free.c
free.c: In function 'Free_Tree_Lk':
free.c:256:11: warning: variable 'n' set but not used [-Wunused-but-set-variable]
mv -f .deps/free.Tpo .deps/free.Po
gcc -DUNIX -DPHYML -DDEBUG  -I. -I..     -Wall -g -O2 -MT help.o -MD -MP -MF .deps/help.Tpo -c -o help.o help.c
mv -f .deps/help.Tpo .deps/help.Po
gcc -DUNIX -DPHYML -DDEBUG  -I. -I..     -Wall -g -O2 -MT simu.o -MD -MP -MF .deps/simu.Tpo -c -o simu.o simu.c
simu.c: In function 'Simu':
simu.c:54:7: warning: variable 'recurr' set but not used [-Wunused-but-set-variable]
simu.c:53:7: warning: variable 'opt_free_param' set but not used [-Wunused-but-set-variable]
simu.c: In function 'Select_Edges_To_Swap':
simu.c:253:7: warning: variable 'min' set but not used [-Wunused-but-set-variable]
mv -f .deps/simu.Tpo .deps/simu.Po
gcc -DUNIX -DPHYML -DDEBUG  -I. -I..     -Wall -g -O2 -MT eigen.o -MD -MP -MF .deps/eigen.Tpo -c -o eigen.o eigen.c
eigen.c: In function 'cmatinv':
eigen.c:185:12: warning: variable 'xmax' set but not used [-Wunused-but-set-variable]
mv -f .deps/eigen.Tpo .deps/eigen.Po
gcc -DUNIX -DPHYML -DDEBUG  -I. -I..     -Wall -g -O2 -MT pars.o -MD -MP -MF .deps/pars.Tpo -c -o pars.o pars.c
pars.c: In function 'Update_P_Pars':
pars.c:246:18: warning: variable 'matches' set but not used [-Wunused-but-set-variable]
mv -f .deps/pars.Tpo .deps/pars.Po
gcc -DUNIX -DPHYML -DDEBUG  -I. -I..     -Wall -g -O2 -MT alrt.o -MD -MP -MF .deps/alrt.Tpo -c -o alrt.o alrt.c
alrt.c: In function 'NNI_Neigh_BL':
alrt.c:310:10: warning: variable 'l1' set but not used [-Wunused-but-set-variable]
alrt.c:304:7: warning: variable 'l_r' set but not used [-Wunused-but-set-variable]
alrt.c: In function 'Make_Target_Swap':
alrt.c:747:10: warning: variable 'bl_init' set but not used [-Wunused-but-set-variable]
alrt.c:745:23: warning: variable 'e4' set but not used [-Wunused-but-set-variable]
alrt.c:745:19: warning: variable 'e3' set but not used [-Wunused-but-set-variable]
alrt.c:745:15: warning: variable 'e2' set but not used [-Wunused-but-set-variable]
alrt.c:745:11: warning: variable 'e1' set but not used [-Wunused-but-set-variable]
alrt.c:743:7: warning: variable 'l_r' set but not used [-Wunused-but-set-variable]
mv -f .deps/alrt.Tpo .deps/alrt.Po
gcc -DUNIX -DPHYML -DDEBUG  -I. -I..     -Wall -g -O2 -MT interface.o -MD -MP -MF .deps/interface.Tpo -c -o interface.o interface.c
interface.c: In function 'Launch_Interface_Model':
interface.c:787:6: warning: variable 'curr_param' set but not used [-Wunused-but-set-variable]
mv -f .deps/interface.Tpo .deps/interface.Po
gcc -DUNIX -DPHYML -DDEBUG  -I. -I..     -Wall -g -O2 -MT cl.o -MD -MP -MF .deps/cl.Tpo -c -o cl.o 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]
mv -f .deps/cl.Tpo .deps/cl.Po
gcc -DUNIX -DPHYML -DDEBUG  -I. -I..     -Wall -g -O2 -MT spr.o -MD -MP -MF .deps/spr.Tpo -c -o spr.o 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:3261:18: warning: variable 'approx' set but not used [-Wunused-but-set-variable]
spr.c:3257:38: warning: variable 'n_up' set but not used [-Wunused-but-set-variable]
spr.c: In function 'Test_One_Spr_Target':
spr.c:3427:7: warning: variable 'approx' set but not used [-Wunused-but-set-variable]
spr.c:3426:17: warning: variable 'move_pars' set but not used [-Wunused-but-set-variable]
spr.c: In function 'Speed_Spr_Loop':
spr.c:3519:7: warning: variable 'init_thresh' set but not used [-Wunused-but-set-variable]
mv -f .deps/spr.Tpo .deps/spr.Po
gcc -DUNIX -DPHYML -DDEBUG  -I. -I..     -Wall -g -O2 -MT draw.o -MD -MP -MF .deps/draw.Tpo -c -o draw.o draw.c
mv -f .deps/draw.Tpo .deps/draw.Po
gcc -DUNIX -DPHYML -DDEBUG  -I. -I..     -Wall -g -O2 -MT mpi_boot.o -MD -MP -MF .deps/mpi_boot.Tpo -c -o mpi_boot.o mpi_boot.c
mv -f .deps/mpi_boot.Tpo .deps/mpi_boot.Po
gcc -DUNIX -DPHYML -DDEBUG  -I. -I..     -Wall -g -O2 -MT stats.o -MD -MP -MF .deps/stats.Tpo -c -o stats.o stats.c
stats.c: In function 'Rnorm_Trunc_Inverse':
stats.c:237:12: warning: variable 'rz' set but not used [-Wunused-but-set-variable]
stats.c: In function 'Rnorm_Trunc':
stats.c:288:12: warning: variable 'rz' set but not used [-Wunused-but-set-variable]
stats.c:286:10: warning: variable 'u' set but not used [-Wunused-but-set-variable]
stats.c: In function 'Covariance_Matrix':
stats.c:1396:22: warning: variable 'var_min' set but not used [-Wunused-but-set-variable]
stats.c: In function 'Gradient':
stats.c:1857:7: warning: variable 'n_ok_edges' set but not used [-Wunused-but-set-variable]
stats.c: In function 'Hessian_Seo':
stats.c:2002:18: warning: variable 'lnL' set but not used [-Wunused-but-set-variable]
stats.c:1999:7: warning: variable 'n_ok_edges' set but not used [-Wunused-but-set-variable]
mv -f .deps/stats.Tpo .deps/stats.Po
gcc -DUNIX -DPHYML -DDEBUG  -I. -I..     -Wall -g -O2 -MT rates.o -MD -MP -MF .deps/rates.Tpo -c -o rates.o rates.c
rates.c: In function 'RATES_Lk_Rates_Core':
rates.c:343:9: warning: variable 'cr' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Average_Substitution_Rate':
rates.c:618:20: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Dmu':
rates.c:973:80: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
rates.c:973:73: warning: variable 'suminv' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Dmu_One':
rates.c:1026:76: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
rates.c:1026:69: warning: variable 'suminv' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Random_Branch_Lengths':
rates.c:1218:13: warning: variable 'r_d' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Dmu2_And_Mu1_Given_N':
rates.c:1454:36: warning: variable 'texpn' set but not used [-Wunused-but-set-variable]
rates.c:1454:28: warning: variable 'lexpdt2' set but not used [-Wunused-but-set-variable]
rates.c:1454:20: warning: variable 'lexpdt1' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Posterior_One_Rate':
rates.c:1595:21: warning: variable 'cond_cov' set but not used [-Wunused-but-set-variable]
rates.c:1595:11: warning: variable 'cond_mu' set but not used [-Wunused-but-set-variable]
rates.c:1594:14: warning: variable 'is_1' set but not used [-Wunused-but-set-variable]
rates.c:1592:10: warning: variable 'cur_l' set but not used [-Wunused-but-set-variable]
rates.c:1591:22: warning: variable 'nu' set but not used [-Wunused-but-set-variable]
rates.c:1591:13: warning: variable 'ra' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Posterior_Time_Root':
rates.c:2357:38: warning: variable 'new_lnL_rate' set but not used [-Wunused-but-set-variable]
rates.c:2356:16: warning: variable 'cur_l' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Update_Cur_Bl_Pre':
rates.c:2547:19: warning: variable 'nf' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Get_Cov_Matrix_Rooted_Pre':
rates.c:2725:15: warning: variable 'done_left' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Variance_Mu_Pre':
rates.c:2830:10: warning: variable 'dt0' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Check_Lk_Rates':
rates.c:3032:10: warning: variable 'z' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Expected_Tree_Length_Pre':
rates.c:3084:10: warning: variable 'sd' set but not used [-Wunused-but-set-variable]
rates.c:3081:12: warning: variable 'u_anc' set but not used [-Wunused-but-set-variable]
rates.c:3081:10: warning: variable 'u' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Get_Correction_Factor':
rates.c:3366:10: warning: variable 'num' set but not used [-Wunused-but-set-variable]
rates.c: In function 'Sample_Average_Rate':
rates.c:3441:13: warning: variable 'td' set but not used [-Wunused-but-set-variable]
rates.c:3441:10: warning: variable 'ta' set but not used [-Wunused-but-set-variable]
rates.c:3440:13: warning: variable 'rd' set but not used [-Wunused-but-set-variable]
rates.c:3440:10: warning: variable 'ra' set but not used [-Wunused-but-set-variable]
mv -f .deps/rates.Tpo .deps/rates.Po
gcc -DUNIX -DPHYML -DDEBUG  -I. -I..     -Wall -g -O2 -MT mcmc.o -MD -MP -MF .deps/mcmc.Tpo -c -o mcmc.o mcmc.c
mcmc.c: In function 'MCMC':
mcmc.c:114:14: warning: variable 'cur_lnL' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_Single_Param_Generic':
mcmc.c:261:12: warning: variable 'mult' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_One_Rate':
mcmc.c:447:13: warning: variable 'cr' set but not used [-Wunused-but-set-variable]
mcmc.c:447:10: warning: variable 'nu' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_Tree_Height':
mcmc.c:829:22: warning: variable 'new_height' set but not used [-Wunused-but-set-variable]
mcmc.c:829:10: warning: variable 'cur_height' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_Subtree_Height':
mcmc.c:921:21: warning: variable 'new_height' set but not used [-Wunused-but-set-variable]
mcmc.c:921:10: warning: variable 'cur_height' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_Updown_Nu_Cr':
mcmc.c:1276:7: warning: variable 'n_nodes' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_Randomize_Rates':
mcmc.c:2090:16: warning: variable 'r_max' set but not used [-Wunused-but-set-variable]
mcmc.c:2090:10: warning: variable 'r_min' set but not used [-Wunused-but-set-variable]
mcmc.c:2089:10: warning: variable 'u' set but not used [-Wunused-but-set-variable]
mv -f .deps/mcmc.Tpo .deps/mcmc.Po
gcc -DUNIX -DPHYML -DDEBUG  -I. -I..     -Wall -g -O2 -MT times.o -MD -MP -MF .deps/times.Tpo -c -o times.o times.c
mv -f .deps/times.Tpo .deps/times.Po
gcc -DUNIX -DPHYML -DDEBUG  -I. -I..     -Wall -g -O2 -MT tiporder.o -MD -MP -MF .deps/tiporder.Tpo -c -o tiporder.o tiporder.c
tiporder.c: In function 'TIPO_Read_One_Taxon_Zscore':
tiporder.c:1135:9: warning: variable 'line' set but not used [-Wunused-but-set-variable]
mv -f .deps/tiporder.Tpo .deps/tiporder.Po
gcc -DUNIX -DPHYML -DDEBUG  -I. -I..     -Wall -g -O2 -MT mg.o -MD -MP -MF .deps/mg.Tpo -c -o mg.o mg.c
mg.c: In function 'PART_Map_St_Nodes_In_Gt_Post':
mg.c:1090:9: warning: variable 'dir' set but not used [-Wunused-but-set-variable]
mg.c: In function 'PART_Spr':
mg.c:1340:7: warning: variable 'move' set but not used [-Wunused-but-set-variable]
mg.c:1339:11: warning: variable 'target' set but not used [-Wunused-but-set-variable]
mg.c: In function 'PART_NNI':
mg.c:2047:10: warning: variable 'lk0_init' set but not used [-Wunused-but-set-variable]
mg.c:2046:10: warning: variable 'lk_init' set but not used [-Wunused-but-set-variable]
mg.c: In function 'PART_Br_Len_Brent':
mg.c:2562:14: warning: variable 'bx' set but not used [-Wunused-but-set-variable]
mv -f .deps/mg.Tpo .deps/mg.Po
gcc -DUNIX -DPHYML -DDEBUG  -I. -I..     -Wall -g -O2 -MT m4.o -MD -MP -MF .deps/m4.Tpo -c -o m4.o 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:742:7: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
m4.c: In function 'M4_Compute_Proba_Hidden_States_On_Edges':
m4.c:866:26: warning: variable 'dwell' set but not used [-Wunused-but-set-variable]
m4.c: In function 'M4_Site_Branch_Classification_Experiment':
m4.c:1192:7: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
m4.c:1187:11: warning: variable 'ori_data' set but not used [-Wunused-but-set-variable]
m4.c: In function 'M4_Detect_Site_Switches_Experiment':
m4.c:1403:16: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
m4.c: In function 'M4_Posterior_Prediction_Experiment':
m4.c:1538:24: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
m4.c:1536:10: warning: variable 'ori_mod' set but not used [-Wunused-but-set-variable]
m4.c: In function 'M4_Copy_M4_Model':
m4.c:1686:7: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
mv -f .deps/m4.Tpo .deps/m4.Po
gcc  -Wall -g -O2   -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 mpi_boot.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»'
cd . && /bin/bash ./config.status config.h
config.status: creating config.h
config.status: config.h is unchanged
make[4]: Leaving directory `/«PKGBUILDDIR»'
make[3]: Leaving directory `/«PKGBUILDDIR»'
make[2]: Leaving directory `/«PKGBUILDDIR»'
/usr/bin/make prefix=`pwd`/debian/`dh_listpackages`/usr install
make[2]: Entering directory `/«PKGBUILDDIR»'
Making install in src
make[3]: Entering directory `/«PKGBUILDDIR»/src'

:: Building PHYML. Version 20110626 ::

Done.
make[4]: Entering directory `/«PKGBUILDDIR»/src'
test -z "/«PKGBUILDDIR»/debian/phyml/usr/bin" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/phyml/usr/bin"
  /usr/bin/install -c phyml '/«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»'
/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'
Making distclean in .
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
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»'
aclocal ; autoconf -f ; automake -f ; ./configure --prefix=/usr --enable-phytime
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 build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
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... gcc3
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: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands
/usr/bin/make CFLAGS="-Wall -g -O2"
make[2]: Entering directory `/«PKGBUILDDIR»'
/usr/bin/make  all-recursive
make[3]: Entering directory `/«PKGBUILDDIR»'
Making all in src
make[4]: Entering directory `/«PKGBUILDDIR»/src'

:: Building PHYTIME. Version 20110626 ::

gcc -DUNIX -DPHYTIME -DDEBUG  -I. -I..     -Wall -g -O2 -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.c
mv -f .deps/main.Tpo .deps/main.Po
gcc -DUNIX -DPHYTIME -DDEBUG  -I. -I..     -Wall -g -O2 -MT utilities.o -MD -MP -MF .deps/utilities.Tpo -c -o utilities.o utilities.c
utilities.c: In function 'Get_Nexus_Data':
utilities.c:1369:7: warning: variable 'in_comment' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'Traverse_Prefix_Tree':
utilities.c:2842:7: warning: variable 'ret_val' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'NNI':
utilities.c:4153:10: warning: variable 'bl_init' set but not used [-Wunused-but-set-variable]
utilities.c:4149:7: warning: variable 'l_r' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'NNI_Pars':
utilities.c:4416:7: warning: variable 'l_r' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'K80_dist':
utilities.c:5232:10: warning: variable 'unc_len' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'JC69_Dist':
utilities.c:5335:10: warning: variable 'unc_len' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'Hamming_Dist':
utilities.c:5409:10: warning: variable 'unc_len' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'Fast_Br_Len':
utilities.c:8326:23: warning: variable 'new_l' set but not used [-Wunused-but-set-variable]
utilities.c:8326:17: warning: variable 'old_l' set but not used [-Wunused-but-set-variable]
utilities.c:8326:10: warning: variable 'eps_bl' set but not used [-Wunused-but-set-variable]
utilities.c: In function 'Print_Diversity':
utilities.c:10195:7: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
mv -f .deps/utilities.Tpo .deps/utilities.Po
gcc -DUNIX -DPHYTIME -DDEBUG  -I. -I..     -Wall -g -O2 -MT optimiz.o -MD -MP -MF .deps/optimiz.Tpo -c -o optimiz.o optimiz.c
optimiz.c: In function 'Generic_Brent':
optimiz.c:169:10: warning: variable 'old_lnL' set but not used [-Wunused-but-set-variable]
optimiz.c: In function 'Round_Optimize':
optimiz.c:607:26: warning: variable 'tol' set but not used [-Wunused-but-set-variable]
optimiz.c: In function 'Optimiz_Ext_Br':
optimiz.c:727:10: warning: variable 'lk' set but not used [-Wunused-but-set-variable]
optimiz.c: In function 'Missing_Dist_Brent':
optimiz.c:2026:10: warning: variable 'bestx' set but not used [-Wunused-but-set-variable]
optimiz.c:2025:22: warning: variable 'max_LOGlk' set but not used [-Wunused-but-set-variable]
optimiz.c:2025:10: warning: variable 'init_LOGlk' set but not used [-Wunused-but-set-variable]
optimiz.c: In function 'Optimiz_Alpha_And_Pinv':
optimiz.c:2141:19: warning: variable 'f3' set but not used [-Wunused-but-set-variable]
optimiz.c:2140:19: warning: variable 'lk_final' set but not used [-Wunused-but-set-variable]
optimiz.c:2140:10: warning: variable 'lk_init' set but not used [-Wunused-but-set-variable]
optimiz.c: In function 'Opt_Node_Heights_Recurr_Pre':
optimiz.c:2611:17: warning: variable 't1' set but not used [-Wunused-but-set-variable]
mv -f .deps/optimiz.Tpo .deps/optimiz.Po
gcc -DUNIX -DPHYTIME -DDEBUG  -I. -I..     -Wall -g -O2 -MT lk.o -MD -MP -MF .deps/lk.Tpo -c -o lk.o lk.c
mv -f .deps/lk.Tpo .deps/lk.Po
gcc -DUNIX -DPHYTIME -DDEBUG  -I. -I..     -Wall -g -O2 -MT bionj.o -MD -MP -MF .deps/bionj.Tpo -c -o bionj.o bionj.c
mv -f .deps/bionj.Tpo .deps/bionj.Po
gcc -DUNIX -DPHYTIME -DDEBUG  -I. -I..     -Wall -g -O2 -MT models.o -MD -MP -MF .deps/models.Tpo -c -o models.o models.c
mv -f .deps/models.Tpo .deps/models.Po
gcc -DUNIX -DPHYTIME -DDEBUG  -I. -I..     -Wall -g -O2 -MT free.o -MD -MP -MF .deps/free.Tpo -c -o free.o free.c
free.c: In function 'Free_Tree_Lk':
free.c:256:11: warning: variable 'n' set but not used [-Wunused-but-set-variable]
mv -f .deps/free.Tpo .deps/free.Po
gcc -DUNIX -DPHYTIME -DDEBUG  -I. -I..     -Wall -g -O2 -MT help.o -MD -MP -MF .deps/help.Tpo -c -o help.o help.c
mv -f .deps/help.Tpo .deps/help.Po
gcc -DUNIX -DPHYTIME -DDEBUG  -I. -I..     -Wall -g -O2 -MT simu.o -MD -MP -MF .deps/simu.Tpo -c -o simu.o simu.c
simu.c: In function 'Simu':
simu.c:54:7: warning: variable 'recurr' set but not used [-Wunused-but-set-variable]
simu.c:53:7: warning: variable 'opt_free_param' set but not used [-Wunused-but-set-variable]
simu.c: In function 'Select_Edges_To_Swap':
simu.c:253:7: warning: variable 'min' set but not used [-Wunused-but-set-variable]
mv -f .deps/simu.Tpo .deps/simu.Po
gcc -DUNIX -DPHYTIME -DDEBUG  -I. -I..     -Wall -g -O2 -MT eigen.o -MD -MP -MF .deps/eigen.Tpo -c -o eigen.o eigen.c
eigen.c: In function 'cmatinv':
eigen.c:185:12: warning: variable 'xmax' set but not used [-Wunused-but-set-variable]
mv -f .deps/eigen.Tpo .deps/eigen.Po
gcc -DUNIX -DPHYTIME -DDEBUG  -I. -I..     -Wall -g -O2 -MT pars.o -MD -MP -MF .deps/pars.Tpo -c -o pars.o pars.c
pars.c: In function 'Update_P_Pars':
pars.c:246:18: warning: variable 'matches' set but not used [-Wunused-but-set-variable]
mv -f .deps/pars.Tpo .deps/pars.Po
gcc -DUNIX -DPHYTIME -DDEBUG  -I. -I..     -Wall -g -O2 -MT alrt.o -MD -MP -MF .deps/alrt.Tpo -c -o alrt.o alrt.c
alrt.c: In function 'NNI_Neigh_BL':
alrt.c:310:10: warning: variable 'l1' set but not used [-Wunused-but-set-variable]
alrt.c:304:7: warning: variable 'l_r' set but not used [-Wunused-but-set-variable]
alrt.c: In function 'Make_Target_Swap':
alrt.c:747:10: warning: variable 'bl_init' set but not used [-Wunused-but-set-variable]
alrt.c:745:23: warning: variable 'e4' set but not used [-Wunused-but-set-variable]
alrt.c:745:19: warning: variable 'e3' set but not used [-Wunused-but-set-variable]
alrt.c:745:15: warning: variable 'e2' set but not used [-Wunused-but-set-variable]
alrt.c:745:11: warning: variable 'e1' set but not used [-Wunused-but-set-variable]
alrt.c:743:7: warning: variable 'l_r' set but not used [-Wunused-but-set-variable]
mv -f .deps/alrt.Tpo .deps/alrt.Po
gcc -DUNIX -DPHYTIME -DDEBUG  -I. -I..     -Wall -g -O2 -MT interface.o -MD -MP -MF .deps/interface.Tpo -c -o interface.o interface.c
interface.c: In function 'Launch_Interface_Model':
interface.c:787:6: warning: variable 'curr_param' set but not used [-Wunused-but-set-variable]
mv -f .deps/interface.Tpo .deps/interface.Po
gcc -DUNIX -DPHYTIME -DDEBUG  -I. -I..     -Wall -g -O2 -MT cl.o -MD -MP -MF .deps/cl.Tpo -c -o cl.o 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]
mv -f .deps/cl.Tpo .deps/cl.Po
gcc -DUNIX -DPHYTIME -DDEBUG  -I. -I..     -Wall -g -O2 -MT spr.o -MD -MP -MF .deps/spr.Tpo -c -o spr.o 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:3261:18: warning: variable 'approx' set but not used [-Wunused-but-set-variable]
spr.c:3257:38: warning: variable 'n_up' set but not used [-Wunused-but-set-variable]
spr.c: In function 'Test_One_Spr_Target':
spr.c:3427:7: warning: variable 'approx' set but not used [-Wunused-but-set-variable]
spr.c:3426:17: warning: variable 'move_pars' set but not used [-Wunused-but-set-variable]
spr.c: In function 'Speed_Spr_Loop':
spr.c:3519:7: warning: variable 'init_thresh' set but not used [-Wunused-but-set-variable]
mv -f .deps/spr.Tpo .deps/spr.Po
gcc -DUNIX -DPHYTIME -DDEBUG  -I. -I..     -Wall -g -O2 -MT times.o -MD -MP -MF .deps/times.Tpo -c -o times.o times.c
times.c: In function 'TIMES_main':
times.c:33:36: warning: variable 'tree_size' set but not used [-Wunused-but-set-variable]
times.c:33:19: warning: variable 'most_likely_size' set but not used [-Wunused-but-set-variable]
times.c:33:10: warning: variable 'best_lnL' set but not used [-Wunused-but-set-variable]
times.c:30:11: warning: variable 'mat' set but not used [-Wunused-but-set-variable]
times.c:29:16: warning: variable 'tree_line_number' set but not used [-Wunused-but-set-variable]
times.c:28:7: warning: variable 'n_otu' set but not used [-Wunused-but-set-variable]
mv -f .deps/times.Tpo .deps/times.Po
gcc -DUNIX -DPHYTIME -DDEBUG  -I. -I..     -Wall -g -O2 -MT m4.o -MD -MP -MF .deps/m4.Tpo -c -o m4.o 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:742:7: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
m4.c: In function 'M4_Compute_Proba_Hidden_States_On_Edges':
m4.c:866:26: warning: variable 'dwell' set but not used [-Wunused-but-set-variable]
m4.c: In function 'M4_Site_Branch_Classification_Experiment':
m4.c:1192:7: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
m4.c:1187:11: warning: variable 'ori_data' set but not used [-Wunused-but-set-variable]
m4.c: In function 'M4_Detect_Site_Switches_Experiment':
m4.c:1403:16: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
m4.c: In function 'M4_Posterior_Prediction_Experiment':
m4.c:1538:24: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
m4.c:1536:10: warning: variable 'ori_mod' set but not used [-Wunused-but-set-variable]
m4.c: In function 'M4_Copy_M4_Model':
m4.c:1686:7: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
mv -f .deps/m4.Tpo .deps/m4.Po
gcc -DUNIX -DPHYTIME -DDEBUG  -I. -I..     -Wall -g -O2 -MT draw.o -MD -MP -MF .deps/draw.Tpo -c -o draw.o draw.c
mv -f .deps/draw.Tpo .deps/draw.Po
gcc -DUNIX -DPHYTIME -DDEBUG  -I. -I..     -Wall -g -O2 -MT rates.o -MD -MP -MF .deps/rates.Tpo -c -o rates.o rates.c
rates.c: In function 'RATES_Lk_Rates_Core':
rates.c:343:9: warning: variable 'cr' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Average_Substitution_Rate':
rates.c:618:20: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Dmu':
rates.c:973:80: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
rates.c:973:73: warning: variable 'suminv' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Dmu_One':
rates.c:1026:76: warning: variable 'b2' set but not used [-Wunused-but-set-variable]
rates.c:1026:69: warning: variable 'suminv' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Random_Branch_Lengths':
rates.c:1218:13: warning: variable 'r_d' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Dmu2_And_Mu1_Given_N':
rates.c:1454:36: warning: variable 'texpn' set but not used [-Wunused-but-set-variable]
rates.c:1454:28: warning: variable 'lexpdt2' set but not used [-Wunused-but-set-variable]
rates.c:1454:20: warning: variable 'lexpdt1' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Posterior_One_Rate':
rates.c:1595:21: warning: variable 'cond_cov' set but not used [-Wunused-but-set-variable]
rates.c:1595:11: warning: variable 'cond_mu' set but not used [-Wunused-but-set-variable]
rates.c:1594:14: warning: variable 'is_1' set but not used [-Wunused-but-set-variable]
rates.c:1592:10: warning: variable 'cur_l' set but not used [-Wunused-but-set-variable]
rates.c:1591:22: warning: variable 'nu' set but not used [-Wunused-but-set-variable]
rates.c:1591:13: warning: variable 'ra' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Posterior_Time_Root':
rates.c:2357:38: warning: variable 'new_lnL_rate' set but not used [-Wunused-but-set-variable]
rates.c:2356:16: warning: variable 'cur_l' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Update_Cur_Bl_Pre':
rates.c:2547:19: warning: variable 'nf' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Get_Cov_Matrix_Rooted_Pre':
rates.c:2725:15: warning: variable 'done_left' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Variance_Mu_Pre':
rates.c:2830:10: warning: variable 'dt0' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Check_Lk_Rates':
rates.c:3032:10: warning: variable 'z' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Expected_Tree_Length_Pre':
rates.c:3084:10: warning: variable 'sd' set but not used [-Wunused-but-set-variable]
rates.c:3081:12: warning: variable 'u_anc' set but not used [-Wunused-but-set-variable]
rates.c:3081:10: warning: variable 'u' set but not used [-Wunused-but-set-variable]
rates.c: In function 'RATES_Get_Correction_Factor':
rates.c:3366:10: warning: variable 'num' set but not used [-Wunused-but-set-variable]
rates.c: In function 'Sample_Average_Rate':
rates.c:3441:13: warning: variable 'td' set but not used [-Wunused-but-set-variable]
rates.c:3441:10: warning: variable 'ta' set but not used [-Wunused-but-set-variable]
rates.c:3440:13: warning: variable 'rd' set but not used [-Wunused-but-set-variable]
rates.c:3440:10: warning: variable 'ra' set but not used [-Wunused-but-set-variable]
mv -f .deps/rates.Tpo .deps/rates.Po
gcc -DUNIX -DPHYTIME -DDEBUG  -I. -I..     -Wall -g -O2 -MT mcmc.o -MD -MP -MF .deps/mcmc.Tpo -c -o mcmc.o mcmc.c
mcmc.c: In function 'MCMC':
mcmc.c:114:14: warning: variable 'cur_lnL' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_Single_Param_Generic':
mcmc.c:261:12: warning: variable 'mult' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_One_Rate':
mcmc.c:447:13: warning: variable 'cr' set but not used [-Wunused-but-set-variable]
mcmc.c:447:10: warning: variable 'nu' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_Tree_Height':
mcmc.c:829:22: warning: variable 'new_height' set but not used [-Wunused-but-set-variable]
mcmc.c:829:10: warning: variable 'cur_height' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_Subtree_Height':
mcmc.c:921:21: warning: variable 'new_height' set but not used [-Wunused-but-set-variable]
mcmc.c:921:10: warning: variable 'cur_height' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_Updown_Nu_Cr':
mcmc.c:1276:7: warning: variable 'n_nodes' set but not used [-Wunused-but-set-variable]
mcmc.c: In function 'MCMC_Randomize_Rates':
mcmc.c:2090:16: warning: variable 'r_max' set but not used [-Wunused-but-set-variable]
mcmc.c:2090:10: warning: variable 'r_min' set but not used [-Wunused-but-set-variable]
mcmc.c:2089:10: warning: variable 'u' set but not used [-Wunused-but-set-variable]
mv -f .deps/mcmc.Tpo .deps/mcmc.Po
gcc -DUNIX -DPHYTIME -DDEBUG  -I. -I..     -Wall -g -O2 -MT stats.o -MD -MP -MF .deps/stats.Tpo -c -o stats.o stats.c
stats.c: In function 'Rnorm_Trunc_Inverse':
stats.c:237:12: warning: variable 'rz' set but not used [-Wunused-but-set-variable]
stats.c: In function 'Rnorm_Trunc':
stats.c:288:12: warning: variable 'rz' set but not used [-Wunused-but-set-variable]
stats.c:286:10: warning: variable 'u' set but not used [-Wunused-but-set-variable]
stats.c: In function 'Covariance_Matrix':
stats.c:1396:22: warning: variable 'var_min' set but not used [-Wunused-but-set-variable]
stats.c: In function 'Gradient':
stats.c:1857:7: warning: variable 'n_ok_edges' set but not used [-Wunused-but-set-variable]
stats.c: In function 'Hessian_Seo':
stats.c:2002:18: warning: variable 'lnL' set but not used [-Wunused-but-set-variable]
stats.c:1999:7: warning: variable 'n_ok_edges' set but not used [-Wunused-but-set-variable]
mv -f .deps/stats.Tpo .deps/stats.Po
gcc -DUNIX -DPHYTIME -DDEBUG  -I. -I..     -Wall -g -O2 -MT mg.o -MD -MP -MF .deps/mg.Tpo -c -o mg.o mg.c
mg.c: In function 'PART_Map_St_Nodes_In_Gt_Post':
mg.c:1090:9: warning: variable 'dir' set but not used [-Wunused-but-set-variable]
mg.c: In function 'PART_Spr':
mg.c:1340:7: warning: variable 'move' set but not used [-Wunused-but-set-variable]
mg.c:1339:11: warning: variable 'target' set but not used [-Wunused-but-set-variable]
mg.c: In function 'PART_NNI':
mg.c:2047:10: warning: variable 'lk0_init' set but not used [-Wunused-but-set-variable]
mg.c:2046:10: warning: variable 'lk_init' set but not used [-Wunused-but-set-variable]
mg.c: In function 'PART_Br_Len_Brent':
mg.c:2562:14: warning: variable 'bx' set but not used [-Wunused-but-set-variable]
mv -f .deps/mg.Tpo .deps/mg.Po
gcc -DUNIX -DPHYTIME -DDEBUG  -I. -I..     -Wall -g -O2 -MT tiporder.o -MD -MP -MF .deps/tiporder.Tpo -c -o tiporder.o tiporder.c
tiporder.c: In function 'TIPO_Read_One_Taxon_Zscore':
tiporder.c:1135:9: warning: variable 'line' set but not used [-Wunused-but-set-variable]
mv -f .deps/tiporder.Tpo .deps/tiporder.Po
gcc  -Wall -g -O2   -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]: Nothing to be done for `all-am'.
make[4]: Leaving directory `/«PKGBUILDDIR»'
make[3]: Leaving directory `/«PKGBUILDDIR»'
make[2]: Leaving directory `/«PKGBUILDDIR»'
/usr/bin/make prefix=`pwd`/debian/`dh_listpackages`/usr install
make[2]: Entering directory `/«PKGBUILDDIR»'
Making install in src
make[3]: Entering directory `/«PKGBUILDDIR»/src'

:: Building PHYTIME. Version 20110626 ::

Done.
make[4]: Entering directory `/«PKGBUILDDIR»/src'
test -z "/«PKGBUILDDIR»/debian/phyml/usr/bin" || /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»'
touch build-stamp
make[1]: Leaving directory `/«PKGBUILDDIR»'
   dh_auto_test
make[1]: Entering directory `/«PKGBUILDDIR»'
Making check in src
make[2]: Entering directory `/«PKGBUILDDIR»/src'

:: Building PHYTIME. Version 20110626 ::

Done.
make[2]: Leaving directory `/«PKGBUILDDIR»/src'
make[2]: Entering directory `/«PKGBUILDDIR»'
make[2]: Nothing to be done for `check-am'.
make[2]: Leaving directory `/«PKGBUILDDIR»'
make[1]: Leaving directory `/«PKGBUILDDIR»'
 fakeroot debian/rules binary
dh binary-indep
dh binary-arch
   dh_testroot -a
   debian/rules override_dh_prep
make[1]: Entering directory `/«PKGBUILDDIR»'
dh_prep -X debian/phyml
make[1]: Leaving directory `/«PKGBUILDDIR»'
   dh_installdirs -a
   # Skipping dh_auto_install - empty override
   dh_install -a
   dh_installdocs -a
   dh_installchangelogs -a
   dh_installexamples -a
   dh_installman -a
   dh_installcatalogs -a
   dh_installcron -a
   dh_installdebconf -a
   dh_installemacsen -a
   dh_installifupdown -a
   dh_installinfo -a
   dh_installinit -a
   dh_installmenu -a
   dh_installmime -a
   dh_installmodules -a
   dh_installlogcheck -a
   dh_installlogrotate -a
   dh_installpam -a
   dh_installppp -a
   dh_installudev -a
   dh_installwm -a
   dh_installxfonts -a
   dh_installgsettings -a
   dh_bugfiles -a
   dh_ucf -a
   dh_lintian -a
   dh_gconf -a
   dh_icons -a
   dh_perl -a
   dh_usrlocal -a
   dh_link -a
   dh_compress -a
   dh_fixperms -a
   dh_strip -a
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dpkg-deb: building package `phyml' in `../phyml_20110526-1_amd64.deb'.
 dpkg-genchanges  >../phyml_20110526-1_amd64.changes
dpkg-genchanges: including full source code in upload
 dpkg-source --after-build phyml-20110526
dpkg-buildpackage: full upload (original source is included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20110626-1320

Finished
────────

I: Built successfully

┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘

phyml_20110526-1_amd64.changes:
───────────────────────────────

Format: 1.8
Date: Sun, 26 Jun 2011 12:14:54 +0900
Source: phyml
Binary: phyml
Architecture: source amd64
Version: 2:20110526-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description: 
 phyml      - Phylogenetic estimation using Maximum Likelihood
Changes: 
 phyml (2:20110526-1) unstable; urgency=low
 .
   * New upstream version.
   * debian/control:
     - Corrected VCS URLs.
     - Using debhelper 8 (debian/compat).
     - Enhances bioperl-run (that has a PhyML wrapper).
     - Standards-Version incremented to reflect compliance with Policy 3.9.2.
   * Added build-arch and build-indep targets to debian/rules.
   * Build and distribute PhyTime (debian/rules, debian/control).
Checksums-Sha1: 
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 e0c15c0c0a90ff668d2c5a29177cade2e27937fc 2746094 phyml_20110526.orig.tar.gz
 d004ce1a4e577f1d5bb8a935de16c593dde8efbb 9449 phyml_20110526-1.debian.tar.gz
 9d45ad0edf5be119daee6ab7e6b3368454fbc885 1011470 phyml_20110526-1_amd64.deb
Checksums-Sha256: 
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 2cf0bdb87b0be02a9c6fdad04f205cef6809fd6bf0e8e02127ba70be2abde5a3 2746094 phyml_20110526.orig.tar.gz
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 d16ded7d938390da72eaf0d33c61c42e62a80fda197f3a61c4726f650e2178f3 1011470 phyml_20110526-1_amd64.deb
Files: 
 e59cf423dcd2761eff70e40ee505c755 1089 science optional phyml_20110526-1.dsc
 04e707ee6e0bda6259e75ab82a87e818 2746094 science optional phyml_20110526.orig.tar.gz
 c8f2d9882e4e1c3c9dcfd977a6385403 9449 science optional phyml_20110526-1.debian.tar.gz
 9c0ef67cbf419afb5411d8cce2b79a2a 1011470 science optional phyml_20110526-1_amd64.deb

┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents                                                             │
└──────────────────────────────────────────────────────────────────────────────┘

phyml_20110526-1_amd64.deb
──────────────────────────

 new debian package, version 2.0.
 size 1011470 bytes: control archive= 1346 bytes.
    1658 bytes,    32 lines      control              
     500 bytes,     8 lines      md5sums              
 Package: phyml
 Version: 2:20110526-1
 Architecture: amd64
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Installed-Size: 1716
 Depends: libc6 (>= 2.7)
 Enhances: bioperl-run
 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 2011-06-26 13:20 ./
drwxr-xr-x root/root         0 2011-06-26 13:20 ./usr/
drwxr-xr-x root/root         0 2011-06-26 13:20 ./usr/share/
drwxr-xr-x root/root         0 2011-06-26 13:20 ./usr/share/doc/
drwxr-xr-x root/root         0 2011-06-26 13:20 ./usr/share/doc/phyml/
-rw-r--r-- root/root    390987 2011-05-26 05:15 ./usr/share/doc/phyml/phyml_manual.pdf.gz
-rw-r--r-- root/root      8590 2011-06-26 10:25 ./usr/share/doc/phyml/copyright
-rw-r--r-- root/root      5458 2010-01-09 10:12 ./usr/share/doc/phyml/changelog.gz
-rw-r--r-- root/root      1085 2011-06-26 12:15 ./usr/share/doc/phyml/changelog.Debian.gz
drwxr-xr-x root/root         0 2011-06-26 13:20 ./usr/share/doc-base/
-rw-r--r-- root/root       205 2009-03-12 14:41 ./usr/share/doc-base/phyml
drwxr-xr-x root/root         0 2011-06-26 13:20 ./usr/share/man/
drwxr-xr-x root/root         0 2011-06-26 13:20 ./usr/share/man/man1/
-rw-r--r-- root/root      2898 2011-06-26 13:20 ./usr/share/man/man1/phyml.1.gz
drwxr-xr-x root/root         0 2011-06-26 13:20 ./usr/bin/
-rwxr-xr-x root/root    638320 2011-06-26 13:20 ./usr/bin/phyml
-rwxr-xr-x root/root    638160 2011-06-26 13:20 ./usr/bin/phytime

┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build                                                                   │
└──────────────────────────────────────────────────────────────────────────────┘

lintian
───────

P: phyml source: source-contains-svn-control-dir doc/.svn
P: phyml source: source-contains-svn-control-dir examples/.svn
P: phyml source: source-contains-svn-control-dir bin/.svn
I: phyml: spelling-error-in-binary usr/bin/phyml ouput output
I: phyml: spelling-error-in-binary usr/bin/phytime ouput output
E: phyml: helper-templates-in-copyright
W: phyml: binary-without-manpage usr/bin/phytime

E: Lintian run failed (policy violation)

┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘

Purging /«BUILDDIR»
Reading package lists...
Building dependency tree...
Reading state information...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
  autoconf* automake* autotools-dev* bsdmainutils* debhelper* file* gettext*
  gettext-base* groff-base* html2text* intltool-debian* libcroco3*
  libglib2.0-0* libmagic1* libpcre3* libpipeline1* libunistring0* libxml2* m4*
  man-db* po-debconf* sbuild-build-depends-core-dummy*
  sbuild-build-depends-phyml-dummy*
0 upgraded, 0 newly installed, 23 to remove and 0 not upgraded.
After this operation, 32.0 MB disk space will be freed.
(Reading database ... 12426 files and directories currently installed.)
Removing sbuild-build-depends-phyml-dummy ...
Removing automake ...
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Purging configuration files for autoconf ...
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Removing libglib2.0-0 ...
Purging configuration files for libglib2.0-0 ...
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Removing libxml2 ...
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Removing m4 ...
Removing sbuild-build-depends-core-dummy ...

┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘

Architecture: amd64
Build-Space: 18748
Build-Time: 67
Distribution: unstable
Install-Time: 8
Job: phyml_20110526-1.dsc
Lintian: fail
Package: phyml
Package-Time: 79
Source-Version: 2:20110526-1
Space: 18748
Status: successful
Version: 2:20110526-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20110626-1320
Build needed 00:01:19, 18748k disc space