[Debian-med-packaging] t-coffee_8.99-1_amd64.changes ACCEPTED into unstable
Charles Plessy
plessy at debian.org
Tue Jun 21 07:23:37 UTC 2011
Le Tue, Jun 21, 2011 at 06:32:15AM +0000, Debian FTP Masters a écrit :
>
> Accepted:
> t-coffee-doc_8.99-1_all.deb
> to main/t/t-coffee/t-coffee-doc_8.99-1_all.deb
> t-coffee-examples_8.99-1_all.deb
> to main/t/t-coffee/t-coffee-examples_8.99-1_all.deb
> t-coffee_8.99-1.debian.tar.gz
> to main/t/t-coffee/t-coffee_8.99-1.debian.tar.gz
> t-coffee_8.99-1.dsc
> to main/t/t-coffee/t-coffee_8.99-1.dsc
> t-coffee_8.99-1_amd64.deb
> to main/t/t-coffee/t-coffee_8.99-1_amd64.deb
> t-coffee_8.99.orig.tar.gz
> to main/t/t-coffee/t-coffee_8.99.orig.tar.gz
Build logs…
-------------- next part --------------
sbuild (Debian sbuild) 0.62.2 (05 Apr 2011) on anx191
╔══════════════════════════════════════════════════════════════════════════════╗
║ t-coffee 8.99-1 (amd64) 21 Jun 2011 15:20 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: t-coffee
Version: 8.99-1
Source Version: 8.99-1
Distribution: unstable
Architecture: amd64
I: NOTICE: Log filtering will replace 'build/t-coffee-6Lvb7g' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-a94581e3-d03d-4191-8337-0444f9ac8f63' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Hit http://ftp.jp.debian.org sid InRelease
Hit http://ftp.jp.debian.org sid/main amd64 Packages/DiffIndex
Hit http://ftp.jp.debian.org sid/main TranslationIndex
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
─────────────
t-coffee_8.99-1.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-i4jIoP/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/704 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 ... 10816 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), cdbs, quilt
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), cdbs, quilt
dpkg-deb: building package `sbuild-build-depends-t-coffee-dummy' in `/«BUILDDIR»/resolver-bQrrqZ/apt_archive/sbuild-build-depends-t-coffee-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install t-coffee build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
www-browser libmail-box-perl procmail graphviz
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
sbuild-build-depends-t-coffee-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 21 newly installed, 0 to remove and 0 not upgraded.
Need to get 0 B/9666 kB of archives.
After this operation, 28.3 MB of additional disk space will be used.
Selecting previously deselected package libpipeline1.
(Reading database ... 10816 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 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_8.1.6_all.deb) ...
Selecting previously deselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_amd64.deb) ...
Selecting previously deselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected package sbuild-build-depends-t-coffee-dummy.
Unpacking sbuild-build-depends-t-coffee-dummy (from .../sbuild-build-depends-t-coffee-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 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 (8.1.6) ...
Setting up cdbs (0.4.94) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-7) ...
Setting up sbuild-build-depends-t-coffee-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 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 cdbs_0.4.94 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_1.5.39 debconf-i18n_1.5.39 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 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_2.2.49-5 libattr1_1:2.4.44-3 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_1.41.12-4 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 libelfg0_0.8.13-2 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 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_1.1.3-1 libpam-runtime_1.1.3-1 libpam0g_1.1.3-1 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+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-4 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 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 quilt_0.48-7 readline-common_6.2-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-t-coffee-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
─────────────
gpgv: keyblock resource `/var/lib/sbuild/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Tue Jun 21 05:27:29 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./t-coffee_8.99-1.dsc
dpkg-source: info: extracting t-coffee in t-coffee-8.99
dpkg-source: info: unpacking t-coffee_8.99.orig.tar.gz
dpkg-source: info: unpacking t-coffee_8.99-1.debian.tar.gz
dpkg-source: info: applying probconsrna.patch
Check disc space
────────────────
Sufficient free space for build
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 t-coffee
dpkg-buildpackage: source version 8.99-1
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
dpkg-source --before-build t-coffee-8.99
dpkg-buildpackage: host architecture amd64
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
make[1]: *** No rule to make target `clean'.make[1]: Entering directory `/«BUILDDIR»/t-coffee-8.99'
make[1]: Leaving directory `/«BUILDDIR»/t-coffee-8.99'
make: [makefile-clean] Error 2 (ignored)
rm -f debian/stamp-makefile-check
/usr/bin/make -f debian/rules reverse-config
make[1]: Entering directory `/«BUILDDIR»/t-coffee-8.99'
make[1]: Nothing to be done for `reverse-config'.
make[1]: Leaving directory `/«BUILDDIR»/t-coffee-8.99'
if [ -d "." ]; then \
cd . && QUILT_PATCHES=/«BUILDDIR»/t-coffee-8.99/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch probconsrna.patch
Restoring t_coffee_source/define_header.h
No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
dh_clean
dh_clean t_coffee_source/*.o t_coffee_source/t_coffee bin/t_coffee example/t_coffee.log bin/t_coffee
chmod 644 example/*
dpkg-source -b t-coffee-8.99
dpkg-source: info: using source format `3.0 (quilt)'
dpkg-source: warning: patches have not been applied, applying them now (use --no-preparation to override)
dpkg-source: info: applying probconsrna.patch
dpkg-source: info: building t-coffee using existing ./t-coffee_8.99.orig.tar.gz
dpkg-source: warning: ignoring deletion of file example/t_coffee.log
dpkg-source: info: building t-coffee in t-coffee_8.99-1.debian.tar.gz
dpkg-source: info: building t-coffee in t-coffee_8.99-1.dsc
debian/rules build
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
make[1]: Entering directory `/«BUILDDIR»/t-coffee-8.99'
make[1]: Nothing to be done for `reverse-config'.
make[1]: Leaving directory `/«BUILDDIR»/t-coffee-8.99'
cd . && QUILT_PATCHES=/«BUILDDIR»/t-coffee-8.99/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
File series fully applied, ends at patch probconsrna.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
make[1]: Entering directory `/«BUILDDIR»/t-coffee-8.99'
make[1]: Nothing to be done for `update-config'.
make[1]: Leaving directory `/«BUILDDIR»/t-coffee-8.99'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C t_coffee_source -i USER_BIN=../bin/ all
make[1]: Entering directory `/«BUILDDIR»/t-coffee-8.99/t_coffee_source'
cc -g -O2 -g -O2 -Wall -c -o util_constraints_list.o util_constraints_list.c
util_constraints_list.c: In function 'fork_subset_produce_list':
util_constraints_list.c:135:20: warning: unused variable 't' [-Wunused-variable]
util_constraints_list.c:134:10: warning: unused variable 'fp' [-Wunused-variable]
util_constraints_list.c:88:6: warning: unused variable 'n_aln' [-Wunused-variable]
util_constraints_list.c:87:17: warning: unused variable 'nlines' [-Wunused-variable]
util_constraints_list.c:87:12: warning: unused variable 'seq' [-Wunused-variable]
util_constraints_list.c:87:6: warning: unused variable 'cseq' [-Wunused-variable]
util_constraints_list.c:86:24: warning: unused variable 'submited' [-Wunused-variable]
util_constraints_list.c:80:8: warning: unused variable 'b' [-Wunused-variable]
util_constraints_list.c: In function 'fork_line_produce_list':
util_constraints_list.c:192:8: warning: unused variable 'b' [-Wunused-variable]
util_constraints_list.c: In function 'fork_cell_produce_list':
util_constraints_list.c:330:11: warning: unused variable 'n' [-Wunused-variable]
util_constraints_list.c:330:8: warning: unused variable 'b' [-Wunused-variable]
util_constraints_list.c: In function 'nfork_produce_list':
util_constraints_list.c:434:21: warning: unused variable 'n_new_elements' [-Wunused-variable]
util_constraints_list.c:434:6: warning: variable 'n_elements_in' set but not used [-Wunused-but-set-variable]
util_constraints_list.c: In function 'retrieve_lib_job':
util_constraints_list.c:512:14: warning: unused variable 'log' [-Wunused-variable]
util_constraints_list.c:511:16: warning: unused variable 'log_output' [-Wunused-variable]
util_constraints_list.c:500:16: warning: variable 'p' set but not used [-Wunused-but-set-variable]
util_constraints_list.c: In function 'add_method_output2method_log':
util_constraints_list.c:534:13: warning: unused variable 'log' [-Wunused-variable]
util_constraints_list.c: In function 'submit_lib_job':
util_constraints_list.c:577:13: warning: unused variable 'log' [-Wunused-variable]
util_constraints_list.c:576:15: warning: unused variable 'l' [-Wunused-variable]
util_constraints_list.c: In function 'method2job_list':
util_constraints_list.c:780:11: warning: unused variable 'used' [-Wunused-variable]
util_constraints_list.c:779:13: warning: unused variable 'y' [-Wunused-variable]
util_constraints_list.c:623:6: warning: variable 'preset_method' set but not used [-Wunused-but-set-variable]
util_constraints_list.c: In function 'display_method_names':
util_constraints_list.c:1032:6: warning: unused variable 'status' [-Wunused-variable]
util_constraints_list.c:1031:6: warning: unused variable 'n' [-Wunused-variable]
util_constraints_list.c: In function 'undump_constraint_list':
util_constraints_list.c:1386:8: warning: unused variable 'nl' [-Wunused-variable]
util_constraints_list.c:1374:16: warning: variable 'tot' set but not used [-Wunused-but-set-variable]
util_constraints_list.c:1374:12: warning: variable 'c' set but not used [-Wunused-but-set-variable]
util_constraints_list.c:1374:6: warning: unused variable 'a' [-Wunused-variable]
util_constraints_list.c: In function 'safe_dump_constraint_list':
util_constraints_list.c:1407:55: warning: 'return' with no value, in function returning non-void [-Wreturn-type]
util_constraints_list.c: In function 'display_constraint_list':
util_constraints_list.c:1466:27: warning: variable 'n' set but not used [-Wunused-but-set-variable]
util_constraints_list.c:1466:10: warning: unused variable 'l' [-Wunused-variable]
util_constraints_list.c:1466:8: warning: unused variable 'c' [-Wunused-variable]
util_constraints_list.c: In function 'evaluate_constraint_list_reference':
util_constraints_list.c:1506:27: warning: unused variable 'r2' [-Wunused-variable]
util_constraints_list.c:1506:19: warning: unused variable 's2' [-Wunused-variable]
util_constraints_list.c:1505:21: warning: unused variable 'entry' [-Wunused-variable]
util_constraints_list.c: In function 'extract_entry':
util_constraints_list.c:1621:6: warning: unused variable 'v' [-Wunused-variable]
util_constraints_list.c: In function 'add_entry2list2':
util_constraints_list.c:1838:7: warning: unused variable 'r2' [-Wunused-variable]
util_constraints_list.c:1837:7: warning: unused variable 's2' [-Wunused-variable]
util_constraints_list.c: In function 'get_entry_index':
util_constraints_list.c:1861:8: warning: unused variable 'r' [-Wunused-variable]
util_constraints_list.c: In function 'remove_entry':
util_constraints_list.c:1963:14: warning: unused variable 'to' [-Wunused-variable]
util_constraints_list.c:1963:7: warning: unused variable 'from' [-Wunused-variable]
util_constraints_list.c: In function 'insert_entry':
util_constraints_list.c:1983:17: warning: unused variable 'to' [-Wunused-variable]
util_constraints_list.c:1983:10: warning: unused variable 'from' [-Wunused-variable]
util_constraints_list.c:1983:6: warning: unused variable 'a' [-Wunused-variable]
util_constraints_list.c: In function 'update_entry':
util_constraints_list.c:2012:7: warning: unused variable 'r2' [-Wunused-variable]
util_constraints_list.c:2010:7: warning: unused variable 's2' [-Wunused-variable]
util_constraints_list.c: In function 'return_max_constraint_list':
util_constraints_list.c:2066:2: warning: implicit declaration of function 'constraint_list2max' [-Wimplicit-function-declaration]
util_constraints_list.c: In function 'invert_constraint_list':
util_constraints_list.c:2087:13: warning: unused variable 'tp' [-Wunused-variable]
util_constraints_list.c:2086:12: warning: unused variable 'c' [-Wunused-variable]
util_constraints_list.c:2086:9: warning: unused variable 'b' [-Wunused-variable]
util_constraints_list.c:2086:6: warning: unused variable 'a' [-Wunused-variable]
util_constraints_list.c: In function 'sort_constraint_list':
util_constraints_list.c:2097:22: warning: unused variable 'w2' [-Wunused-variable]
util_constraints_list.c:2097:19: warning: unused variable 'r2' [-Wunused-variable]
util_constraints_list.c:2097:16: warning: unused variable 's2' [-Wunused-variable]
util_constraints_list.c:2097:8: warning: unused variable 'l' [-Wunused-variable]
util_constraints_list.c:2097:6: warning: unused variable 'b' [-Wunused-variable]
util_constraints_list.c:2095:6: warning: unused variable 'max' [-Wunused-variable]
util_constraints_list.c: In function 'fork_read_n_constraint_list':
util_constraints_list.c:2215:4: warning: too many arguments for format [-Wformat-extra-args]
util_constraints_list.c: In function 'save_constraint_list_ascii':
util_constraints_list.c:2993:35: warning: unused variable 'x2' [-Wunused-variable]
util_constraints_list.c:2993:31: warning: unused variable 'x1' [-Wunused-variable]
util_constraints_list.c:2993:28: warning: unused variable 'w2' [-Wunused-variable]
util_constraints_list.c: In function 'extend_constraint_list':
util_constraints_list.c:3124:14: warning: unused variable 'tr' [-Wunused-variable]
util_constraints_list.c:3124:11: warning: unused variable 'ts' [-Wunused-variable]
util_constraints_list.c: In function 'fork_relax_constraint_list':
util_constraints_list.c:3189:7: warning: unused variable 'np' [-Wunused-variable]
util_constraints_list.c: In function 'nfork_relax_constraint_list':
util_constraints_list.c:3301:6: warning: variable 'nne' set but not used [-Wunused-but-set-variable]
util_constraints_list.c: In function 'expand_constraint_list_4gp':
util_constraints_list.c:3399:6: warning: unused variable 'n' [-Wunused-variable]
util_constraints_list.c:3398:6: warning: unused variable 'max' [-Wunused-variable]
util_constraints_list.c:3397:6: warning: unused variable 'chunck' [-Wunused-variable]
util_constraints_list.c:3396:7: warning: unused variable 'L' [-Wunused-variable]
util_constraints_list.c: In function 'fork_relax_constraint_list_4gp':
util_constraints_list.c:3469:6: warning: unused variable 'in' [-Wunused-variable]
util_constraints_list.c:3468:8: warning: unused variable 'pid_list' [-Wunused-variable]
util_constraints_list.c:3467:9: warning: unused variable 'pid_tmpfile' [-Wunused-variable]
util_constraints_list.c:3466:8: warning: unused variable 'fp' [-Wunused-variable]
util_constraints_list.c:3465:23: warning: unused variable 'pid' [-Wunused-variable]
util_constraints_list.c:3465:19: warning: unused variable 'job' [-Wunused-variable]
util_constraints_list.c:3465:13: warning: unused variable 'npid' [-Wunused-variable]
util_constraints_list.c:3465:6: warning: unused variable 'chunk' [-Wunused-variable]
util_constraints_list.c:3464:6: warning: unused variable 'thr' [-Wunused-variable]
util_constraints_list.c:3463:6: warning: unused variable 'score' [-Wunused-variable]
util_constraints_list.c:3462:24: warning: unused variable 'n' [-Wunused-variable]
util_constraints_list.c:3462:21: warning: unused variable 'r2' [-Wunused-variable]
util_constraints_list.c:3462:17: warning: unused variable 'r1' [-Wunused-variable]
util_constraints_list.c:3462:13: warning: unused variable 's2' [-Wunused-variable]
util_constraints_list.c:3462:9: warning: unused variable 's1' [-Wunused-variable]
util_constraints_list.c:3462:6: warning: unused variable 'a' [-Wunused-variable]
util_constraints_list.c: In function 'nfork_relax_constraint_list_4gp':
util_constraints_list.c:3563:20: warning: unused variable 'l' [-Wunused-variable]
util_constraints_list.c:3562:6: warning: unused variable 'thr' [-Wunused-variable]
util_constraints_list.c: In function 'constraint_list2max':
util_constraints_list.c:3617:19: warning: variable 'r2' set but not used [-Wunused-but-set-variable]
util_constraints_list.c:3617:16: warning: variable 's2' set but not used [-Wunused-but-set-variable]
util_constraints_list.c:3617:8: warning: unused variable 'l' [-Wunused-variable]
util_constraints_list.c: In function 'constraint_list2ne':
util_constraints_list.c:3637:22: warning: unused variable 'w2' [-Wunused-variable]
util_constraints_list.c:3637:19: warning: unused variable 'r2' [-Wunused-variable]
util_constraints_list.c:3637:16: warning: unused variable 's2' [-Wunused-variable]
util_constraints_list.c:3637:8: warning: unused variable 'l' [-Wunused-variable]
util_constraints_list.c:3637:6: warning: unused variable 'b' [-Wunused-variable]
util_constraints_list.c: In function 'constraint_list2avg':
util_constraints_list.c:3685:19: warning: variable 'r2' set but not used [-Wunused-but-set-variable]
util_constraints_list.c:3685:16: warning: variable 's2' set but not used [-Wunused-but-set-variable]
util_constraints_list.c:3685:8: warning: unused variable 'l' [-Wunused-variable]
util_constraints_list.c: In function 'filter_constraint_list':
util_constraints_list.c:3709:13: warning: unused variable 'bs' [-Wunused-variable]
util_constraints_list.c:3708:14: warning: unused variable 'buf' [-Wunused-variable]
util_constraints_list.c: In function 'aln2constraint_list':
util_constraints_list.c:3876:12: warning: unused variable 's' [-Wunused-variable]
util_constraints_list.c:3874:6: warning: variable 'set_misc' set but not used [-Wunused-but-set-variable]
util_constraints_list.c: In function 'list2residue_total_weight':
util_constraints_list.c:4012:6: warning: unused variable 'max' [-Wunused-variable]
util_constraints_list.c: In function 'seq2defined_residues':
util_constraints_list.c:4105:22: warning: unused variable 'b' [-Wunused-variable]
util_constraints_list.c:4105:18: warning: unused variable 'l' [-Wunused-variable]
util_constraints_list.c:4105:15: warning: unused variable 'r2' [-Wunused-variable]
util_constraints_list.c:4105:12: warning: unused variable 's2' [-Wunused-variable]
util_constraints_list.c: In function 're_weight_constraint_list':
util_constraints_list.c:4358:12: warning: unused variable 'b' [-Wunused-variable]
util_constraints_list.c:4357:10: warning: unused variable 'sB' [-Wunused-variable]
util_constraints_list.c:4357:6: warning: unused variable 'sA' [-Wunused-variable]
util_constraints_list.c:4355:8: warning: unused variable 'w' [-Wunused-variable]
util_constraints_list.c: In function 'rna_lib_extension':
util_constraints_list.c:4760:23: warning: unused variable 'ne' [-Wunused-variable]
util_constraints_list.c:4760:6: warning: unused variable 'a' [-Wunused-variable]
util_constraints_list.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
util_constraints_list.c:15:12: warning: 'entry_len' defined but not used [-Wunused-variable]
util_constraints_list.c:1853:13: warning: 'sent' defined but not used [-Wunused-variable]
util_constraints_list.c:1854:25: warning: 'sCL' defined but not used [-Wunused-variable]
util_constraints_list.c: In function 'unfreeze_constraint_list':
util_constraints_list.c:1331:1: warning: control reaches end of non-void function [-Wreturn-type]
cc -g -O2 -g -O2 -Wall -c -o util_job_handling.o util_job_handling.c
util_job_handling.c: In function 'split_job_list':
util_job_handling.c:217:11: warning: variable 'ljob' set but not used [-Wunused-but-set-variable]
util_job_handling.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o util_dps.o util_dps.c
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o util_domain_constraints_list.o util_domain_constraints_list.c
util_domain_constraints_list.c: In function 'get_undefined_list':
util_domain_constraints_list.c:26:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
util_domain_constraints_list.c:20:7: warning: unused variable 'a' [-Wunused-variable]
util_domain_constraints_list.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o util_analyse_constraints_list.o util_analyse_constraints_list.c
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o util_aln_analyze.o util_aln_analyze.c
util_aln_analyze.c: In function 'filter_aln4sar1':
util_aln_analyze.c:149:24: warning: variable 'n1' set but not used [-Wunused-but-set-variable]
util_aln_analyze.c: In function 'sar_analyze':
util_aln_analyze.c:522:10: warning: variable 'tot2' set but not used [-Wunused-but-set-variable]
util_aln_analyze.c: In function 'cache2pred1':
util_aln_analyze.c:972:8: warning: variable 'max1' set but not used [-Wunused-but-set-variable]
util_aln_analyze.c:949:26: warning: variable 'm' set but not used [-Wunused-but-set-variable]
util_aln_analyze.c:949:22: warning: variable 'id' set but not used [-Wunused-but-set-variable]
util_aln_analyze.c: In function 'cache2pred3':
util_aln_analyze.c:1123:8: warning: variable 'used' set but not used [-Wunused-but-set-variable]
util_aln_analyze.c:1096:39: warning: variable 'pred' set but not used [-Wunused-but-set-variable]
util_aln_analyze.c: In function 'sar2cache_proba_old':
util_aln_analyze.c:1815:67: warning: variable 't' set but not used [-Wunused-but-set-variable]
util_aln_analyze.c:1815:39: warning: variable 'res1' set but not used [-Wunused-but-set-variable]
util_aln_analyze.c: In function 'sar2cache_proba_new':
util_aln_analyze.c:2319:67: warning: variable 't' set but not used [-Wunused-but-set-variable]
util_aln_analyze.c:2319:45: warning: variable 'n' set but not used [-Wunused-but-set-variable]
util_aln_analyze.c: In function 'sar2cache_adriana':
util_aln_analyze.c:2465:53: warning: variable 't' set but not used [-Wunused-but-set-variable]
util_aln_analyze.c:2465:44: warning: variable 'res1' set but not used [-Wunused-but-set-variable]
util_aln_analyze.c: In function 'sar2cache_proba2':
util_aln_analyze.c:2521:47: warning: variable 't' set but not used [-Wunused-but-set-variable]
util_aln_analyze.c: In function 'display_simple_sar_analyze_col':
util_aln_analyze.c:2900:8: warning: variable 'activity' set but not used [-Wunused-but-set-variable]
util_aln_analyze.c: In function 'simple_sar_analyze_col':
util_aln_analyze.c:3086:7: warning: variable 'best_pos' set but not used [-Wunused-but-set-variable]
util_aln_analyze.c: In function 'compare_sar_sequence':
util_aln_analyze.c:3518:7: warning: unused variable 'score' [-Wunused-variable]
util_aln_analyze.c:3516:7: warning: unused variable 'max' [-Wunused-variable]
util_aln_analyze.c:3515:52: warning: unused variable 'n5' [-Wunused-variable]
util_aln_analyze.c:3515:47: warning: unused variable 'n4' [-Wunused-variable]
util_aln_analyze.c:3515:42: warning: unused variable 'n3' [-Wunused-variable]
util_aln_analyze.c:3515:37: warning: unused variable 'n2' [-Wunused-variable]
util_aln_analyze.c:3515:32: warning: unused variable 'n1' [-Wunused-variable]
util_aln_analyze.c:3515:27: warning: unused variable 's5' [-Wunused-variable]
util_aln_analyze.c:3515:23: warning: unused variable 's4' [-Wunused-variable]
util_aln_analyze.c:3515:19: warning: unused variable 's3' [-Wunused-variable]
util_aln_analyze.c:3515:14: warning: unused variable 's2' [-Wunused-variable]
util_aln_analyze.c:3515:9: warning: unused variable 's1' [-Wunused-variable]
util_aln_analyze.c:3514:22: warning: unused variable 'f' [-Wunused-variable]
util_aln_analyze.c: In function 'sar_aln2ev':
util_aln_analyze.c:3626:13: warning: unused variable 'c' [-Wunused-variable]
util_aln_analyze.c:3625:13: warning: unused variable 'n11' [-Wunused-variable]
util_aln_analyze.c:3625:9: warning: unused variable 'n1' [-Wunused-variable]
util_aln_analyze.c: In function 'evaluate_sar_score1':
util_aln_analyze.c:3679:12: warning: variable 'n01' set but not used [-Wunused-but-set-variable]
util_aln_analyze.c:3679:7: warning: variable 'n10' set but not used [-Wunused-but-set-variable]
util_aln_analyze.c: In function 'or_scan':
util_aln_analyze.c:4245:15: warning: unused variable 'cx' [-Wunused-variable]
util_aln_analyze.c: In function 'display_or_summary':
util_aln_analyze.c:4624:14: warning: variable 'A' set but not used [-Wunused-but-set-variable]
util_aln_analyze.c: In function 'or_self_predict':
util_aln_analyze.c:5319:14: warning: variable 'P' set but not used [-Wunused-but-set-variable]
util_aln_analyze.c: In function 'new_evaluate_prediction':
util_aln_analyze.c:5441:10: warning: variable 'recall' set but not used [-Wunused-but-set-variable]
util_aln_analyze.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
util_aln_analyze.c: In function 'or_scan':
util_aln_analyze.c:4454:1: warning: control reaches end of non-void function [-Wreturn-type]
util_aln_analyze.c: In function 'sar_analyze':
util_aln_analyze.c:687:1: warning: control reaches end of non-void function [-Wreturn-type]
util_aln_analyze.c:669:33: warning: 'real' may be used uninitialized in this function [-Wuninitialized]
util_aln_analyze.c: In function 'sarseq_pair2ev':
util_aln_analyze.c:3667:12: warning: 'n2' may be used uninitialized in this function [-Wuninitialized]
util_aln_analyze.c:3667:10: warning: 'n1' may be used uninitialized in this function [-Wuninitialized]
util_aln_analyze.c: In function 'sar_aln2delta':
util_aln_analyze.c:6227:8: warning: 'i' may be used uninitialized in this function [-Wuninitialized]
util_aln_analyze.c:6227:8: warning: 'o' may be used uninitialized in this function [-Wuninitialized]
util_aln_analyze.c: In function 'aln2predictive_positions_scan':
util_aln_analyze.c:5936:28: warning: 'best_score' may be used uninitialized in this function [-Wuninitialized]
util_aln_analyze.c:5908:14: warning: 'score' may be used uninitialized in this function [-Wuninitialized]
util_aln_analyze.c: In function 'or_jack':
util_aln_analyze.c:5244:15: warning: 'S' may be used uninitialized in this function [-Wuninitialized]
util_aln_analyze.c:5244:15: warning: 'A' may be used uninitialized in this function [-Wuninitialized]
util_aln_analyze.c: In function 'or_comp_pos':
util_aln_analyze.c:4977:15: warning: 'p' may be used uninitialized in this function [-Wuninitialized]
util_aln_analyze.c: In function 'compound2regexp_motif':
util_aln_analyze.c:5996:9: warning: 'i' may be used uninitialized in this function [-Wuninitialized]
util_aln_analyze.c:5996:9: warning: 'o' may be used uninitialized in this function [-Wuninitialized]
util_aln_analyze.c: In function 'or_comp_loo':
util_aln_analyze.c:5068:20: warning: 'A' may be used uninitialized in this function [-Wuninitialized]
util_aln_analyze.c: In function 'or_sar':
util_aln_analyze.c:4490:17: warning: 'c' may be used uninitialized in this function [-Wuninitialized]
util_aln_analyze.c: In function 'or_scan':
util_aln_analyze.c:4416:8: warning: 'count' may be used uninitialized in this function [-Wuninitialized]
util_aln_analyze.c:4373:9: warning: 'nbest' may be used uninitialized in this function [-Wuninitialized]
cc -g -O2 -g -O2 -Wall -c -o aln_convertion_util.o aln_convertion_util.c
aln_convertion_util.c: In function 'add_alifold2aln':
aln_convertion_util.c:203:20: warning: variable 'tmp2' set but not used [-Wunused-but-set-variable]
aln_convertion_util.c:203:13: warning: variable 'tmp1' set but not used [-Wunused-but-set-variable]
aln_convertion_util.c:198:15: warning: unused variable 'fold_l' [-Wunused-variable]
aln_convertion_util.c:197:16: warning: unused variable 'nwatson' [-Wunused-variable]
aln_convertion_util.c:197:7: warning: unused variable 'ncomp' [-Wunused-variable]
aln_convertion_util.c:196:9: warning: unused variable 'list' [-Wunused-variable]
aln_convertion_util.c:195:7: warning: unused variable 'minseq' [-Wunused-variable]
aln_convertion_util.c:194:14: warning: unused variable 'k' [-Wunused-variable]
aln_convertion_util.c:194:12: warning: unused variable 'p' [-Wunused-variable]
aln_convertion_util.c:194:7: warning: unused variable 'max' [-Wunused-variable]
aln_convertion_util.c:193:9: warning: unused variable 'compmat' [-Wunused-variable]
aln_convertion_util.c:192:20: warning: unused variable 'tot' [-Wunused-variable]
aln_convertion_util.c:192:15: warning: unused variable 'comp' [-Wunused-variable]
aln_convertion_util.c:192:7: warning: unused variable 'watson' [-Wunused-variable]
aln_convertion_util.c:191:20: warning: unused variable 'rr2' [-Wunused-variable]
aln_convertion_util.c:191:16: warning: unused variable 'r2' [-Wunused-variable]
aln_convertion_util.c:191:11: warning: unused variable 'rr1' [-Wunused-variable]
aln_convertion_util.c:191:7: warning: unused variable 'r1' [-Wunused-variable]
aln_convertion_util.c:190:18: warning: unused variable 'p2' [-Wunused-variable]
aln_convertion_util.c:190:15: warning: unused variable 'p1' [-Wunused-variable]
aln_convertion_util.c:190:13: warning: unused variable 'd' [-Wunused-variable]
aln_convertion_util.c:190:11: warning: unused variable 'c' [-Wunused-variable]
aln_convertion_util.c: In function 'alifold_list2cov_list':
aln_convertion_util.c:297:15: warning: unused variable 'fold_l' [-Wunused-variable]
aln_convertion_util.c:297:7: warning: unused variable 'cons_l' [-Wunused-variable]
aln_convertion_util.c:296:39: warning: unused variable 'ncomp_wc' [-Wunused-variable]
aln_convertion_util.c:296:27: warning: unused variable 'nneutral' [-Wunused-variable]
aln_convertion_util.c:296:16: warning: unused variable 'nwatson' [-Wunused-variable]
aln_convertion_util.c:296:7: warning: unused variable 'ncomp' [-Wunused-variable]
aln_convertion_util.c:294:7: warning: unused variable 'minseq' [-Wunused-variable]
aln_convertion_util.c:293:14: warning: unused variable 'k' [-Wunused-variable]
aln_convertion_util.c:293:12: warning: unused variable 'p' [-Wunused-variable]
aln_convertion_util.c:292:9: warning: unused variable 'compmat' [-Wunused-variable]
aln_convertion_util.c:291:28: warning: variable 'tot' set but not used [-Wunused-but-set-variable]
aln_convertion_util.c:289:22: warning: unused variable 's' [-Wunused-variable]
aln_convertion_util.c:289:10: warning: unused variable 'b' [-Wunused-variable]
aln_convertion_util.c: In function 'aln2sample':
aln_convertion_util.c:501:13: warning: unused variable 'p' [-Wunused-variable]
aln_convertion_util.c: In function 'aln2gap_cache':
aln_convertion_util.c:659:13: warning: unused variable 'c' [-Wunused-variable]
aln_convertion_util.c: In function 'index_seq_res':
aln_convertion_util.c:815:12: warning: variable 'len1' set but not used [-Wunused-but-set-variable]
aln_convertion_util.c: In function 'set_blast_default_values':
aln_convertion_util.c:1182:3: warning: 'return' with no value, in function returning non-void [-Wreturn-type]
aln_convertion_util.c: In function 'gene2exons':
aln_convertion_util.c:1284:13: warning: unused variable 'c' [-Wunused-variable]
aln_convertion_util.c: In function 'unalign_aln_2':
aln_convertion_util.c:1971:13: warning: unused variable 'S' [-Wunused-variable]
aln_convertion_util.c:1970:18: warning: unused variable 'len' [-Wunused-variable]
aln_convertion_util.c:1970:13: warning: unused variable 'pos' [-Wunused-variable]
aln_convertion_util.c: In function 'unalign_aln_pos':
aln_convertion_util.c:2105:7: warning: unused variable 'unalign' [-Wunused-variable]
aln_convertion_util.c: In function 'search_best_combo_sar_aln':
aln_convertion_util.c:2950:9: warning: variable 's' set but not used [-Wunused-but-set-variable]
aln_convertion_util.c: In function 'seq_list2fasta_file':
aln_convertion_util.c:3943:12: warning: unused variable 's' [-Wunused-variable]
aln_convertion_util.c: In function 'seq2template_type':
aln_convertion_util.c:4886:22: warning: variable 'F' set but not used [-Wunused-but-set-variable]
aln_convertion_util.c:4881:7: warning: variable 's' set but not used [-Wunused-but-set-variable]
aln_convertion_util.c: In function 'seq2template_seq':
aln_convertion_util.c:5251:11: warning: unused variable 'z' [-Wunused-variable]
aln_convertion_util.c:5359:11: warning: unused variable 'z' [-Wunused-variable]
aln_convertion_util.c:5352:9: warning: unused variable 'x' [-Wunused-variable]
aln_convertion_util.c: In function 'complement_string':
aln_convertion_util.c:6289:16: warning: unused variable 'c' [-Wunused-variable]
aln_convertion_util.c:6289:10: warning: unused variable 'a' [-Wunused-variable]
aln_convertion_util.c:6288:9: warning: unused variable 'buf' [-Wunused-variable]
aln_convertion_util.c: In function 'complement_aln':
aln_convertion_util.c:6312:16: warning: unused variable 'c' [-Wunused-variable]
aln_convertion_util.c:6312:13: warning: unused variable 'b' [-Wunused-variable]
aln_convertion_util.c:6312:7: warning: unused variable 'l' [-Wunused-variable]
aln_convertion_util.c:6311:9: warning: unused variable 'buf' [-Wunused-variable]
aln_convertion_util.c: In function 'remove_empty_sequence':
aln_convertion_util.c:8382:10: warning: variable 'b' set but not used [-Wunused-but-set-variable]
aln_convertion_util.c: In function 'sub_aln2nseq_prf':
aln_convertion_util.c:8600:10: warning: variable 'c' set but not used [-Wunused-but-set-variable]
aln_convertion_util.c: In function 'sim_filter':
aln_convertion_util.c:9221:7: warning: unused variable 'coverage' [-Wunused-variable]
aln_convertion_util.c:9220:7: warning: unused variable 'direction' [-Wunused-variable]
aln_convertion_util.c:9219:7: warning: unused variable 'outlayers' [-Wunused-variable]
aln_convertion_util.c:9216:16: warning: unused variable 'k' [-Wunused-variable]
aln_convertion_util.c:9215:7: warning: unused variable 'new_nseq' [-Wunused-variable]
aln_convertion_util.c:9214:28: warning: unused variable 'nc' [-Wunused-variable]
aln_convertion_util.c:9214:16: warning: unused variable 'nseq_ratio' [-Wunused-variable]
aln_convertion_util.c:9214:7: warning: unused variable 'maxnseq' [-Wunused-variable]
aln_convertion_util.c: In function 'simple_trimseq':
aln_convertion_util.c:9427:11: warning: unused variable 'b' [-Wunused-variable]
aln_convertion_util.c:9324:9: warning: unused variable 'b' [-Wunused-variable]
aln_convertion_util.c: In function 'test_gene2prot':
aln_convertion_util.c:11004:17: warning: unused variable 'entry' [-Wunused-variable]
aln_convertion_util.c: In function 'pw_aln2clean_pw_aln_fsa2':
aln_convertion_util.c:11705:11: warning: unused variable 'v' [-Wunused-variable]
aln_convertion_util.c:11502:7: warning: unused variable 'model_type' [-Wunused-variable]
aln_convertion_util.c:11499:7: warning: variable 'MID_EXON_FACTOR' set but not used [-Wunused-but-set-variable]
aln_convertion_util.c:11497:39: warning: unused variable 'K' [-Wunused-variable]
aln_convertion_util.c:11497:35: warning: unused variable 'G2' [-Wunused-variable]
aln_convertion_util.c:11497:32: warning: unused variable 'G1' [-Wunused-variable]
aln_convertion_util.c:11494:7: warning: unused variable 'T0' [-Wunused-variable]
aln_convertion_util.c:11493:19: warning: unused variable 'e1' [-Wunused-variable]
aln_convertion_util.c:11493:15: warning: unused variable 'e0' [-Wunused-variable]
aln_convertion_util.c:11492:16: warning: unused variable 'd' [-Wunused-variable]
aln_convertion_util.c: In function 'pw_aln2clean_pw_aln_fsa1':
aln_convertion_util.c:11729:26: warning: unused variable 'K' [-Wunused-variable]
aln_convertion_util.c:11726:7: warning: unused variable 'T0' [-Wunused-variable]
aln_convertion_util.c:11725:19: warning: unused variable 'e1' [-Wunused-variable]
aln_convertion_util.c:11725:15: warning: unused variable 'e0' [-Wunused-variable]
aln_convertion_util.c:11724:16: warning: unused variable 'd' [-Wunused-variable]
aln_convertion_util.c: In function 'aln2pred':
aln_convertion_util.c:12006:9: warning: array subscript has type 'char' [-Wchar-subscripts]
aln_convertion_util.c:12006:9: warning: array subscript has type 'char' [-Wchar-subscripts]
aln_convertion_util.c:11922:7: warning: unused variable 'print' [-Wunused-variable]
aln_convertion_util.c:11921:29: warning: unused variable 'result' [-Wunused-variable]
aln_convertion_util.c:11918:10: warning: unused variable 'N' [-Wunused-variable]
aln_convertion_util.c:11918:7: warning: unused variable 'T' [-Wunused-variable]
aln_convertion_util.c: In function 'mark_exon_boundaries':
aln_convertion_util.c:12080:4: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
aln_convertion_util.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
aln_convertion_util.c: In function 'aln2N_replicate':
aln_convertion_util.c:6721:1: warning: control reaches end of non-void function [-Wreturn-type]
aln_convertion_util.c: In function 'aln2conservation':
aln_convertion_util.c:3820:1: warning: control reaches end of non-void function [-Wreturn-type]
aln_convertion_util.c: In function 'filter_aln_convert':
aln_convertion_util.c:2782:14: warning: 'c' may be used uninitialized in this function [-Wuninitialized]
aln_convertion_util.c: In function 'aln_column2string':
aln_convertion_util.c:4383:5: warning: 's' may be used uninitialized in this function [-Wuninitialized]
aln_convertion_util.c: In function 'invert_aln':
aln_convertion_util.c:6283:8: warning: 'buf' may be used uninitialized in this function [-Wuninitialized]
aln_convertion_util.c: In function 'get_raw_sim_aln_array':
aln_convertion_util.c:8227:36: warning: 'min' may be used uninitialized in this function [-Wuninitialized]
aln_convertion_util.c:8227:51: warning: 'max' may be used uninitialized in this function [-Wuninitialized]
aln_convertion_util.c: In function 'sar_aln2motif':
aln_convertion_util.c:2809:9: warning: 'i' may be used uninitialized in this function [-Wuninitialized]
aln_convertion_util.c:2809:9: warning: 'o' may be used uninitialized in this function [-Wuninitialized]
aln_convertion_util.c: In function 'make_group_aa_upgma':
aln_convertion_util.c:10830:14: warning: 'ba' may be used uninitialized in this function [-Wuninitialized]
aln_convertion_util.c: In function 'aln2conservation':
aln_convertion_util.c:3798:18: warning: 'c1' may be used uninitialized in this function [-Wuninitialized]
aln_convertion_util.c: In function 'seq2blast':
aln_convertion_util.c:1221:3: warning: 'A' may be used uninitialized in this function [-Wuninitialized]
aln_convertion_util.c: In function 'pw_aln2clean_pw_aln_fsa2':
aln_convertion_util.c:11691:22: warning: 'best' may be used uninitialized in this function [-Wuninitialized]
aln_convertion_util.c: In function 'pw_aln2clean_pw_aln_fsa1':
aln_convertion_util.c:11856:22: warning: 'best' may be used uninitialized in this function [-Wuninitialized]
cc -g -O2 -g -O2 -Wall -c -o util_declare.o util_declare.c
util_declare.c: In function 'declare_residue_index':
util_declare.c:52:11: warning: unused variable 'c' [-Wunused-variable]
util_declare.c: In function 'copy_constraint_list':
util_declare.c:154:12: warning: unused variable 'b' [-Wunused-variable]
util_declare.c: In function 'free_constraint_list':
util_declare.c:365:12: warning: unused variable 'b' [-Wunused-variable]
util_declare.c:365:9: warning: unused variable 'a' [-Wunused-variable]
util_declare.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o hsearch.o hsearch.c
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o random.o random.c
cc -g -O2 -g -O2 -Wall -c -o util_make_tree.o util_make_tree.c
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
util_make_tree.c: In function 'upgma_merge_aln_rows':
util_make_tree.c:1147:7: warning: 'best_b' may be used uninitialized in this function [-Wuninitialized]
util_make_tree.c:1150:6: warning: 'best_a' may be used uninitialized in this function [-Wuninitialized]
util_make_tree.c: In function 'upgma_merge':
util_make_tree.c:1276:9: warning: 'best_s' may be used uninitialized in this function [-Wuninitialized]
util_make_tree.c:1246:24: warning: 'best_b' may be used uninitialized in this function [-Wuninitialized]
util_make_tree.c:1246:16: warning: 'best_a' may be used uninitialized in this function [-Wuninitialized]
util_make_tree.c: In function 'int_dist2upgma_tree':
util_make_tree.c:1237:11: warning: 'T' may be used uninitialized in this function [-Wuninitialized]
util_make_tree.c: In function 'split_upgma_merge':
util_make_tree.c:1390:9: warning: 'best_s' may be used uninitialized in this function [-Wuninitialized]
util_make_tree.c:1389:8: warning: 'best_b' may be used uninitialized in this function [-Wuninitialized]
util_make_tree.c:1388:8: warning: 'best_a' may be used uninitialized in this function [-Wuninitialized]
util_make_tree.c: In function 'split2upgma_tree':
util_make_tree.c:1346:3: warning: 'T' may be used uninitialized in this function [-Wuninitialized]
cc -g -O2 -g -O2 -Wall -c -o util.o util.c
util.c: In function 'cmp_list_int2':
util.c:540:10: warning: unused variable 'd' [-Wunused-variable]
util.c: In function 'cmp_list_int':
util.c:613:6: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
util.c: In function 'fprintf_fork':
util.c:3536:9: warning: unused variable 'flag' [-Wunused-variable]
util.c: In function 'vvfork':
util.c:4018:7: warning: implicit declaration of function 'wait' [-Wimplicit-function-declaration]
util.c: In function 'vwaitpid':
util.c:4067:3: warning: implicit declaration of function 'waitpid' [-Wimplicit-function-declaration]
util.c: In function 'get_lockdir_4_tcoffee':
util.c:4490:12: warning: unused variable 'buf' [-Wunused-variable]
util.c: In function 'my_rmdir':
util.c:7079:14: warning: 'return' with no value, in function returning non-void [-Wreturn-type]
util.c:7067:9: warning: unused variable 'buf' [-Wunused-variable]
util.c:7067:6: warning: unused variable 'a' [-Wunused-variable]
util.c:7065:7: warning: unused variable 'dir_sep' [-Wunused-variable]
util.c: In function 'clean_exit':
util.c:8298:9: warning: unused variable 'tmp' [-Wunused-variable]
util.c:8297:12: warning: variable 'b' set but not used [-Wunused-but-set-variable]
util.c: In function 'bachup_env':
util.c:8519:16: warning: variable 'buf' set but not used [-Wunused-but-set-variable]
util.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
util.c:73:13: warning: 'exchange' defined but not used [-Wunused-function]
util.c:4657:12: warning: 'n_warning' defined but not used [-Wunused-variable]
util.c:4658:15: warning: 'warning_list' defined but not used [-Wunused-variable]
util.c:7341:15: warning: 'EXP_UNDERFLOW_THRESHOLD' defined but not used [-Wunused-variable]
util.c:7344:15: warning: 'LOG_ONE' defined but not used [-Wunused-variable]
util.c: In function 'check_internet_connection':
util.c:6806:1: warning: control reaches end of non-void function [-Wreturn-type]
util.c: In function 'kill_child_list':
util.c:4135:1: warning: control reaches end of non-void function [-Wreturn-type]
util.c: In function 'festrstr':
util.c:1991:6: warning: 'string' may be used uninitialized in this function [-Wuninitialized]
util.c: In function 'r_generate_array_string_list':
util.c:7989:10: warning: 'start' may be used uninitialized in this function [-Wuninitialized]
util.c: In function 'lock':
util.c:3779:9: warning: 'r' may be used uninitialized in this function [-Wuninitialized]
cc -g -O2 -g -O2 -Wall -c -o reformat_struc.o reformat_struc.c
reformat_struc.c: In function 'struclist2nb':
reformat_struc.c:858:9: warning: variable 'list' set but not used [-Wunused-but-set-variable]
reformat_struc.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
reformat_struc.c: In function 'struclist2nb':
reformat_struc.c:880:6: warning: 'R' may be used uninitialized in this function [-Wuninitialized]
cc -g -O2 -g -O2 -Wall -c -o reformat.o reformat.c
reformat.c: In function 'read_data_structure':
reformat.c:873:12: warning: variable 'seq' set but not used [-Wunused-but-set-variable]
reformat.c: In function 'identify_seq_format':
reformat.c:1268:8: warning: implicit declaration of function 'is_stockholm_aln' [-Wimplicit-function-declaration]
reformat.c: In function 'is_pdb_struc':
reformat.c:1513:11: warning: unused variable 'command' [-Wunused-variable]
reformat.c: In function 'main_output':
reformat.c:2304:23: warning: variable 'CL' set but not used [-Wunused-but-set-variable]
reformat.c:2766:17: warning: variable 'A' set but not used [-Wunused-but-set-variable]
reformat.c:2933:6: warning: implicit declaration of function 'output_header_mat' [-Wimplicit-function-declaration]
reformat.c: In function 'output_generic_clustal_aln':
reformat.c:6818:12: warning: unused variable 'nibit' [-Wunused-variable]
reformat.c: In function 'unextend_seq':
reformat.c:9866:12: warning: unused variable 'r2' [-Wunused-variable]
reformat.c: In function 'modify_data':
reformat.c:10107:5: warning: null argument where non-null required (argument 1) [-Wnonnull]
reformat.c:10112:5: warning: null argument where non-null required (argument 1) [-Wnonnull]
reformat.c:10279:23: warning: unused variable 'r2' [-Wunused-variable]
reformat.c:10279:17: warning: unused variable 's2' [-Wunused-variable]
reformat.c:10274:9: warning: unused variable 'l' [-Wunused-variable]
reformat.c:10332:5: warning: null argument where non-null required (argument 1) [-Wnonnull]
reformat.c:10342:5: warning: implicit declaration of function 'tree2nnode_unresolved' [-Wimplicit-function-declaration]
reformat.c:10431:5: warning: null argument where non-null required (argument 1) [-Wnonnull]
reformat.c:10432:5: warning: null argument where non-null required (argument 1) [-Wnonnull]
reformat.c:10439:5: warning: null argument where non-null required (argument 1) [-Wnonnull]
reformat.c:10446:5: warning: null argument where non-null required (argument 1) [-Wnonnull]
reformat.c:10620:5: warning: null argument where non-null required (argument 1) [-Wnonnull]
reformat.c:11154:5: warning: null argument where non-null required (argument 1) [-Wnonnull]
reformat.c:11154:5: warning: null argument where non-null required (argument 1) [-Wnonnull]
reformat.c:11161:5: warning: null argument where non-null required (argument 1) [-Wnonnull]
reformat.c:11162:5: warning: null argument where non-null required (argument 1) [-Wnonnull]
reformat.c:11163:5: warning: null argument where non-null required (argument 1) [-Wnonnull]
reformat.c:11164:5: warning: null argument where non-null required (argument 1) [-Wnonnull]
reformat.c:11165:5: warning: null argument where non-null required (argument 1) [-Wnonnull]
reformat.c:11166:5: warning: null argument where non-null required (argument 1) [-Wnonnull]
reformat.c:11133:10: warning: unused variable 'clean_mode' [-Wunused-variable]
reformat.c:11130:22: warning: variable 't' set but not used [-Wunused-but-set-variable]
reformat.c:11130:19: warning: variable 'f' set but not used [-Wunused-but-set-variable]
reformat.c:11130:16: warning: unused variable 'p3' [-Wunused-variable]
reformat.c:11130:13: warning: unused variable 'p2' [-Wunused-variable]
reformat.c:11130:10: warning: unused variable 'p1' [-Wunused-variable]
reformat.c:11189:5: warning: null argument where non-null required (argument 1) [-Wnonnull]
reformat.c:11458:17: warning: variable 'A' set but not used [-Wunused-but-set-variable]
reformat.c:11824:5: warning: null argument where non-null required (argument 1) [-Wnonnull]
reformat.c:11825:5: warning: null argument where non-null required (argument 1) [-Wnonnull]
reformat.c:11826:5: warning: null argument where non-null required (argument 1) [-Wnonnull]
reformat.c:11827:5: warning: null argument where non-null required (argument 1) [-Wnonnull]
reformat.c:11828:5: warning: null argument where non-null required (argument 1) [-Wnonnull]
reformat.c:11818:10: warning: unused variable 'fname' [-Wunused-variable]
reformat.c:11817:11: warning: unused variable 'fp' [-Wunused-variable]
reformat.c:11815:33: warning: unused variable 'sp' [-Wunused-variable]
reformat.c:11815:22: warning: unused variable 'sn' [-Wunused-variable]
reformat.c: In function 'aln2mat':
reformat.c:12068:3: warning: array subscript has type 'char' [-Wchar-subscripts]
reformat.c: In function 'output_header_mat':
reformat.c:12334:12: warning: variable 'l' set but not used [-Wunused-but-set-variable]
reformat.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
reformat.c: In function 'output_header_mat':
reformat.c:12359:1: warning: control reaches end of non-void function [-Wreturn-type]
reformat.c: In function 'output_suchard_aln':
reformat.c:6451:1: warning: control reaches end of non-void function [-Wreturn-type]
reformat.c: In function 'get_longest_frame':
reformat.c:8220:3: warning: 'nf' may be used uninitialized in this function [-Wuninitialized]
cc -g -O2 -g -O2 -Wall -c -o aln_compare.o aln_compare.c
aln_compare.c: In function 'aln_compare':
aln_compare.c:488:8: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
aln_compare.c:526:8: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
aln_compare.c:634:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
aln_compare.c:722:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
aln_compare.c:18:6: warning: unused variable 'ik' [-Wunused-variable]
aln_compare.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
aln_compare.c: In function 'aln_compare':
aln_compare.c:605:22: warning: 'correct_column' may be used uninitialized in this function [-Wuninitialized]
aln_compare.c:595:15: warning: 'posA' may be used uninitialized in this function [-Wuninitialized]
cc -g -O2 -g -O2 -Wall -c -o io_func.o io_func.c
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o pb_util_read_sequence.o pb_util_read_sequence.c
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o pb_util_read_seq_util.o pb_util_read_seq_util.c
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o tree_util.o tree_util.c
tree_util.c: In function 'tree_scan':
tree_util.c:772:2: warning: too many arguments for format [-Wformat-extra-args]
tree_util.c:800:32: warning: variable 'best_w2' set but not used [-Wunused-but-set-variable]
tree_util.c: In function 'tree_cmp':
tree_util.c:1038:7: warning: unused variable 'a' [-Wunused-variable]
tree_util.c:1037:7: warning: unused variable 'n' [-Wunused-variable]
tree_util.c: In function 'free_read_tree':
tree_util.c:2429:10: warning: variable 's' set but not used [-Wunused-but-set-variable]
tree_util.c: In function 'read_tree':
tree_util.c:2455:8: warning: variable 'flag' set but not used [-Wunused-but-set-variable]
tree_util.c: In function 'find_seq_chain':
tree_util.c:3254:11: warning: variable 'delta_seq2' set but not used [-Wunused-but-set-variable]
tree_util.c: In function 'treelist2leafgroup':
tree_util.c:4103:11: warning: variable 'i' set but not used [-Wunused-but-set-variable]
tree_util.c:4063:8: warning: variable 'used' set but not used [-Wunused-but-set-variable]
tree_util.c: In function 'treelist2splits':
tree_util.c:4525:8: warning: variable 'used' set but not used [-Wunused-but-set-variable]
tree_util.c: In function 'treelist2splits_old':
tree_util.c:4612:8: warning: variable 'used' set but not used [-Wunused-but-set-variable]
tree_util.c: In function 'treelist2prune_treelist':
tree_util.c:4694:13: warning: unused variable 'c' [-Wunused-variable]
tree_util.c: In function 'treelist2frame':
tree_util.c:4737:18: warning: unused variable 'd' [-Wunused-variable]
tree_util.c:4737:16: warning: unused variable 'c' [-Wunused-variable]
tree_util.c:4737:13: warning: unused variable 'b' [-Wunused-variable]
tree_util.c: In function 'treelist2lti2':
tree_util.c:4766:28: warning: unused variable 'i' [-Wunused-variable]
tree_util.c:4766:22: warning: unused variable 'dist' [-Wunused-variable]
tree_util.c:4766:15: warning: unused variable 'd' [-Wunused-variable]
tree_util.c:4766:12: warning: unused variable 'c' [-Wunused-variable]
tree_util.c:4765:12: warning: unused variable 'T' [-Wunused-variable]
tree_util.c: In function 'treelist2lti':
tree_util.c:4812:19: warning: unused variable 'score1' [-Wunused-variable]
tree_util.c:4812:9: warning: unused variable 'score0' [-Wunused-variable]
tree_util.c: In function 'treelist2groups':
tree_util.c:4951:8: warning: unused variable 'cov' [-Wunused-variable]
tree_util.c: In function 'simple_tree_cmp':
tree_util.c:5021:18: warning: variable 'n' set but not used [-Wunused-but-set-variable]
tree_util.c: In function 'treelist2bootstrap':
tree_util.c:5138:9: warning: unused variable 'fp' [-Wunused-variable]
tree_util.c: In function 'treelist2seq':
tree_util.c:5161:13: warning: unused variable 'c' [-Wunused-variable]
tree_util.c: In function 'treelist2sub_seq':
tree_util.c:5199:20: warning: variable 'n' set but not used [-Wunused-but-set-variable]
tree_util.c: In function 'treelist2frame':
tree_util.c:4762:1: warning: control reaches end of non-void function [-Wreturn-type]
tree_util.c: In function 'treelist2splits_old':
tree_util.c:4689:1: warning: control reaches end of non-void function [-Wreturn-type]
tree_util.c: In function 'treelist2splits':
tree_util.c:4605:1: warning: control reaches end of non-void function [-Wreturn-type]
tree_util.c: In function 'count_tree_groups':
tree_util.c:4255:1: warning: control reaches end of non-void function [-Wreturn-type]
tree_util.c: In function 'treelist2leafgroup':
tree_util.c:4152:1: warning: control reaches end of non-void function [-Wreturn-type]
tree_util.c: In function 'node_sort':
tree_util.c:3936:1: warning: control reaches end of non-void function [-Wreturn-type]
tree_util.c: In function 'compute_std_tree_2':
tree_util.c:1499:8: warning: 'T' may be used uninitialized in this function [-Wuninitialized]
tree_util.c: In function 'tree_scan_multiple_pos':
tree_util.c:952:15: warning: 'n' may be used uninitialized in this function [-Wuninitialized]
tree_util.c: In function 'count_splits':
tree_util.c:4317:11: warning: 'OrderT' may be used uninitialized in this function [-Wuninitialized]
tree_util.c: In function 'treelist2sub_seq':
tree_util.c:5256:6: warning: 'tot' may be used uninitialized in this function [-Wuninitialized]
cc -g -O2 -g -O2 -Wall -c -o util_graph_maln.o util_graph_maln.c
util_graph_maln.c: In function 'graph_aln':
util_graph_maln.c:37:20: warning: unused variable 'CL' [-Wunused-variable]
util_graph_maln.c:36:15: warning: unused variable 'entry' [-Wunused-variable]
util_graph_maln.c:35:9: warning: unused variable 'start' [-Wunused-variable]
util_graph_maln.c:35:7: warning: unused variable 'a' [-Wunused-variable]
util_graph_maln.c:34:14: warning: unused variable 'G' [-Wunused-variable]
util_graph_maln.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o util_dp_clean_maln.o util_dp_clean_maln.c
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o util_dp_ssec_pwaln.o util_dp_ssec_pwaln.c
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o util_dp_sim.o util_dp_sim.c
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o util_dp_mm_nw.o util_dp_mm_nw.c
util_dp_mm_nw.c: In function 'diff':
util_dp_mm_nw.c:184:20: warning: variable 'ma' set but not used [-Wunused-but-set-variable]
util_dp_mm_nw.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o util_dp_gotoh_nw.o util_dp_gotoh_nw.c
util_dp_gotoh_nw.c: In function 'gotoh_pair_wise':
util_dp_gotoh_nw.c:918:11: warning: unused variable 'fop2' [-Wunused-variable]
util_dp_gotoh_nw.c:777:6: warning: unused variable 'ibit' [-Wunused-variable]
util_dp_gotoh_nw.c: In function 'cl2list_borders':
util_dp_gotoh_nw.c:1352:9: warning: unused variable 'pos' [-Wunused-variable]
util_dp_gotoh_nw.c:1351:9: warning: unused variable 'list' [-Wunused-variable]
util_dp_gotoh_nw.c:1350:10: warning: unused variable 'n' [-Wunused-variable]
util_dp_gotoh_nw.c: In function 'cl2diag_cap':
util_dp_gotoh_nw.c:1397:7: warning: unused variable 'nt' [-Wunused-variable]
util_dp_gotoh_nw.c:1396:7: warning: unused variable 'ns' [-Wunused-variable]
util_dp_gotoh_nw.c:1390:7: warning: unused variable 'k' [-Wunused-variable]
util_dp_gotoh_nw.c:1388:7: warning: unused variable 'max_n' [-Wunused-variable]
util_dp_gotoh_nw.c: In function 'fork_cl2pair_list_ecl_pc':
util_dp_gotoh_nw.c:1533:44: warning: unused variable 'new' [-Wunused-variable]
util_dp_gotoh_nw.c:1533:37: warning: unused variable 'avg' [-Wunused-variable]
util_dp_gotoh_nw.c: In function 'nfork_cl2pair_list_ecl_pc':
util_dp_gotoh_nw.c:1673:44: warning: unused variable 'new' [-Wunused-variable]
util_dp_gotoh_nw.c:1673:37: warning: unused variable 'avg' [-Wunused-variable]
util_dp_gotoh_nw.c: In function 'linked_pair_wise':
util_dp_gotoh_nw.c:1777:14: warning: unused variable 'a' [-Wunused-variable]
util_dp_gotoh_nw.c: In function 'list2linked_pair_wise':
util_dp_gotoh_nw.c:1906:44: warning: operation on '*(MJ + (long unsigned int)((long unsigned int)(a * 5 + b) * 8ul))' may be undefined [-Wsequence-point]
util_dp_gotoh_nw.c:1876:7: warning: unused variable 'nomatch' [-Wunused-variable]
util_dp_gotoh_nw.c:1865:44: warning: variable 'prev_j' set but not used [-Wunused-but-set-variable]
util_dp_gotoh_nw.c:1865:36: warning: variable 'prev_i' set but not used [-Wunused-but-set-variable]
util_dp_gotoh_nw.c: In function 'linked_pair_wise_collapse':
util_dp_gotoh_nw.c:2148:14: warning: unused variable 'a' [-Wunused-variable]
util_dp_gotoh_nw.c: In function 'collapse_list':
util_dp_gotoh_nw.c:2176:32: warning: unused variable 'cr2' [-Wunused-variable]
util_dp_gotoh_nw.c: In function 'cl2pair_list_collapse':
util_dp_gotoh_nw.c:2284:44: warning: unused variable 'new' [-Wunused-variable]
util_dp_gotoh_nw.c:2284:37: warning: unused variable 'avg' [-Wunused-variable]
util_dp_gotoh_nw.c:2278:7: warning: unused variable 'si' [-Wunused-variable]
util_dp_gotoh_nw.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
util_dp_gotoh_nw.c: In function 'list2linked_pair_wise':
util_dp_gotoh_nw.c:2043:7: warning: 'start_trace' may be used uninitialized in this function [-Wuninitialized]
cc -g -O2 -g -O2 -Wall -c -o util_dp_suboptimal_nw.o util_dp_suboptimal_nw.c
util_dp_suboptimal_nw.c: In function 'suboptimal_pair_wise':
util_dp_suboptimal_nw.c:195:3: warning: implicit declaration of function 'idscore_pairseq' [-Wimplicit-function-declaration]
util_dp_suboptimal_nw.c:128:34: warning: variable 'thres' set but not used [-Wunused-but-set-variable]
util_dp_suboptimal_nw.c:128:26: warning: variable 'nscore' set but not used [-Wunused-but-set-variable]
util_dp_suboptimal_nw.c: In function 'free_proba_pair_wise':
util_dp_suboptimal_nw.c:611:3: warning: implicit declaration of function 'proba_pair_wise' [-Wimplicit-function-declaration]
util_dp_suboptimal_nw.c: In function 'ProbaMatrix2CL':
util_dp_suboptimal_nw.c:1101:7: warning: unused variable 'sim' [-Wunused-variable]
util_dp_suboptimal_nw.c:1097:16: warning: unused variable 'k' [-Wunused-variable]
util_dp_suboptimal_nw.c: In function 'backward_proba_pair_wise':
util_dp_suboptimal_nw.c:1204:12: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
util_dp_suboptimal_nw.c:1204:8: warning: variable 'c1' set but not used [-Wunused-but-set-variable]
util_dp_suboptimal_nw.c: In function 'forward_proba_pair_wise':
util_dp_suboptimal_nw.c:1298:17: warning: variable 'iter2' set but not used [-Wunused-but-set-variable]
util_dp_suboptimal_nw.c:1298:9: warning: variable 'iter1' set but not used [-Wunused-but-set-variable]
util_dp_suboptimal_nw.c: In function 'get_emitPairs':
util_dp_suboptimal_nw.c:1656:15: warning: unused variable 'c' [-Wunused-variable]
util_dp_suboptimal_nw.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
util_dp_suboptimal_nw.c:15:14: warning: 'EXP_UNDERFLOW_THRESHOLD' defined but not used [-Wunused-variable]
util_dp_suboptimal_nw.c:16:14: warning: 'LOG_UNDERFLOW_THRESHOLD' defined but not used [-Wunused-variable]
util_dp_suboptimal_nw.c:21:14: warning: 'DNAinitDistrib2Default' defined but not used [-Wunused-variable]
util_dp_suboptimal_nw.c:28:14: warning: 'DNAemitPairsDefault' defined but not used [-Wunused-variable]
util_dp_suboptimal_nw.c:38:14: warning: 'RNAinitDistrib2Default' defined but not used [-Wunused-variable]
cc -g -O2 -g -O2 -Wall -c -o util_dp_cdna_fasta_nw.o util_dp_cdna_fasta_nw.c
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o util_dp_generic_fasta_nw.o util_dp_generic_fasta_nw.c
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o util_dp_fasta_nw.o util_dp_fasta_nw.c
util_dp_fasta_nw.c: In function 'evaluate_diagonals_with_clist':
util_dp_fasta_nw.c:471:18: warning: unused variable 'd' [-Wunused-variable]
util_dp_fasta_nw.c:471:15: warning: unused variable 'c' [-Wunused-variable]
util_dp_fasta_nw.c: In function 'seq2hasch':
util_dp_fasta_nw.c:1779:4: warning: array subscript has type 'char' [-Wchar-subscripts]
util_dp_fasta_nw.c:1779:4: warning: array subscript has type 'char' [-Wchar-subscripts]
util_dp_fasta_nw.c:1780:4: warning: array subscript has type 'char' [-Wchar-subscripts]
util_dp_fasta_nw.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o util_dp_fasta_sw.o util_dp_fasta_sw.c
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o util_dp_gotoh_sw.o util_dp_gotoh_sw.c
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o util_dp_est.o util_dp_est.c
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o util_domain_dp_drivers.o util_domain_dp_drivers.c
util_domain_dp_drivers.c: In function 'get_starting_point':
util_domain_dp_drivers.c:564:4: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
util_domain_dp_drivers.c:545:7: warning: unused variable 'a' [-Wunused-variable]
util_domain_dp_drivers.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o util_dp_drivers.o util_dp_drivers.c
util_dp_drivers.c: In function 'profile2list':
util_dp_drivers.c:33:14: warning: variable 'M' set but not used [-Wunused-but-set-variable]
util_dp_drivers.c:29:25: warning: unused variable 'RCL' [-Wunused-variable]
util_dp_drivers.c:28:27: warning: unused variable 'w2' [-Wunused-variable]
util_dp_drivers.c:28:24: warning: unused variable 'r2' [-Wunused-variable]
util_dp_drivers.c:28:16: warning: unused variable 's2' [-Wunused-variable]
util_dp_drivers.c: In function 'seq2list':
util_dp_drivers.c:138:21: warning: variable 'STL' set but not used [-Wunused-but-set-variable]
util_dp_drivers.c:138:17: warning: variable 'S' set but not used [-Wunused-but-set-variable]
util_dp_drivers.c:134:11: warning: variable 'full_prf' set but not used [-Wunused-but-set-variable]
util_dp_drivers.c:131:24: warning: variable 'PW_CL' set but not used [-Wunused-but-set-variable]
util_dp_drivers.c: In function 'method2pw_cl':
util_dp_drivers.c:314:17: warning: variable 'S' set but not used [-Wunused-but-set-variable]
util_dp_drivers.c: In function 'thread_pair2':
util_dp_drivers.c:1315:15: warning: variable 'STL' set but not used [-Wunused-but-set-variable]
util_dp_drivers.c: In function 'best_pair4rna':
util_dp_drivers.c:1690:13: warning: variable 'M' set but not used [-Wunused-but-set-variable]
util_dp_drivers.c:1686:19: warning: variable 'PW_CL' set but not used [-Wunused-but-set-variable]
util_dp_drivers.c:1685:13: warning: variable 'A' set but not used [-Wunused-but-set-variable]
util_dp_drivers.c: In function 'best_pair4prot':
util_dp_drivers.c:1773:14: warning: variable 'M' set but not used [-Wunused-but-set-variable]
util_dp_drivers.c:1769:20: warning: variable 'PW_CL' set but not used [-Wunused-but-set-variable]
util_dp_drivers.c:1768:14: warning: variable 'A' set but not used [-Wunused-but-set-variable]
util_dp_drivers.c: In function 'fast_pair':
util_dp_drivers.c:1861:10: warning: variable 'score' set but not used [-Wunused-but-set-variable]
util_dp_drivers.c: In function 'seq_aln':
util_dp_drivers.c:2632:21: warning: variable 'n1' set but not used [-Wunused-but-set-variable]
util_dp_drivers.c: In function 'sorted_aln_seq':
util_dp_drivers.c:2901:7: warning: variable 'old_seq' set but not used [-Wunused-but-set-variable]
util_dp_drivers.c: In function 'tree_aln':
util_dp_drivers.c:3132:7: warning: unused variable 'a' [-Wunused-variable]
util_dp_drivers.c: In function 'tree_realn':
util_dp_drivers.c:3487:25: warning: variable 'id2' set but not used [-Wunused-but-set-variable]
util_dp_drivers.c:3487:20: warning: variable 'id1' set but not used [-Wunused-but-set-variable]
util_dp_drivers.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
util_dp_drivers.c: In function 'get_next_best':
util_dp_drivers.c:2877:3: warning: 'bseq' may be used uninitialized in this function [-Wuninitialized]
util_dp_drivers.c:2870:22: warning: 'bd' may be used uninitialized in this function [-Wuninitialized]
util_dp_drivers.c: In function 'rec_local_tree_aln':
util_dp_drivers.c:3298:16: warning: 'pid2' may be used uninitialized in this function [-Wuninitialized]
util_dp_drivers.c: In function 'iterate_aln':
util_dp_drivers.c:2857:11: warning: 'delta' may be used uninitialized in this function [-Wuninitialized]
util_dp_drivers.c: In function 'seq2list':
util_dp_drivers.c:182:7: warning: 'nprf' may be used uninitialized in this function [-Wuninitialized]
cc -g -O2 -g -O2 -Wall -c -o util_domain_dp.o util_domain_dp.c
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o CUSTOM_evaluate_for_struc.o CUSTOM_evaluate_for_struc.c
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o evaluate_for_struc.o evaluate_for_struc.c
evaluate_for_struc.c: In function 'apdb':
evaluate_for_struc.c:43:6: warning: variable 'n_struc_to_use' set but not used [-Wunused-but-set-variable]
evaluate_for_struc.c: In function 'msa2struc_dist':
evaluate_for_struc.c:2323:19: warning: variable 'cont' set but not used [-Wunused-but-set-variable]
evaluate_for_struc.c:2323:13: warning: unused variable 'tree' [-Wunused-variable]
evaluate_for_struc.c:2212:7: warning: unused variable 'proceed' [-Wunused-variable]
evaluate_for_struc.c:2198:16: warning: variable 'ntree2' set but not used [-Wunused-but-set-variable]
evaluate_for_struc.c:2196:10: warning: variable 'pair_pos_list' set but not used [-Wunused-but-set-variable]
evaluate_for_struc.c:2194:24: warning: variable 'PT' set but not used [-Wunused-but-set-variable]
evaluate_for_struc.c:2194:20: warning: variable 'T2' set but not used [-Wunused-but-set-variable]
evaluate_for_struc.c:2194:12: warning: unused variable 'T0' [-Wunused-variable]
evaluate_for_struc.c:2192:17: warning: unused variable 'rapdb' [-Wunused-variable]
evaluate_for_struc.c:2192:9: warning: unused variable 'nrapdb' [-Wunused-variable]
evaluate_for_struc.c:2191:7: warning: unused variable 'print_rapdb' [-Wunused-variable]
evaluate_for_struc.c:2185:7: warning: unused variable 'in_bubble' [-Wunused-variable]
evaluate_for_struc.c:2184:12: warning: unused variable 'wd2' [-Wunused-variable]
evaluate_for_struc.c:2184:7: warning: unused variable 'wd1' [-Wunused-variable]
evaluate_for_struc.c:2182:24: warning: unused variable 'n' [-Wunused-variable]
evaluate_for_struc.c:2182:13: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
evaluate_for_struc.c:2180:14: warning: unused variable 'pdb_param' [-Wunused-variable]
evaluate_for_struc.c:2171:14: warning: unused variable 'max' [-Wunused-variable]
evaluate_for_struc.c:2171:9: warning: unused variable 'min' [-Wunused-variable]
evaluate_for_struc.c:2167:13: warning: unused variable 'distances' [-Wunused-variable]
evaluate_for_struc.c:2163:19: warning: unused variable 'c' [-Wunused-variable]
evaluate_for_struc.c: In function 'aln_column_contains_gap':
evaluate_for_struc.c:2538:10: warning: unused variable 'b' [-Wunused-variable]
evaluate_for_struc.c: In function 'aln2ncol4trmsd':
evaluate_for_struc.c:2552:26: warning: variable 'rs1' set but not used [-Wunused-but-set-variable]
evaluate_for_struc.c: In function 'display_rna_ss':
evaluate_for_struc.c:2806:14: warning: variable 'thread' set but not used [-Wunused-but-set-variable]
evaluate_for_struc.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
evaluate_for_struc.c: In function 'trmsdmat2tree':
evaluate_for_struc.c:2482:45: warning: 'max' may be used uninitialized in this function [-Wuninitialized]
evaluate_for_struc.c: In function 'msa2struc_dist':
evaluate_for_struc.c:2331:37: warning: 'PP' may be used uninitialized in this function [-Wuninitialized]
cc -g -O2 -g -O2 -Wall -c -o evaluate_for_domain.o evaluate_for_domain.c
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o evaluate_dirichlet.o evaluate_dirichlet.c
evaluate_dirichlet.c: In function 'sin_pi':
evaluate_dirichlet.c:433:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
evaluate_dirichlet.c:453:25: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
evaluate_dirichlet.c: In function 'lgamma_r':
evaluate_dirichlet.c:482:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
evaluate_dirichlet.c:483:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
evaluate_dirichlet.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o evaluate.o evaluate.c
evaluate.c: In function 'overlay_alignment_evaluation':
evaluate.c:166:8: warning: variable 'buf' set but not used [-Wunused-but-set-variable]
evaluate.c:165:19: warning: unused variable 'i' [-Wunused-variable]
evaluate.c:165:13: warning: unused variable 'c' [-Wunused-variable]
evaluate.c: In function 'categories_evaluate_output':
evaluate.c:527:18: warning: variable 'nseq2' set but not used [-Wunused-but-set-variable]
evaluate.c: In function 'categories_evaluate_output_old':
evaluate.c:570:18: warning: variable 'nseq2' set but not used [-Wunused-but-set-variable]
evaluate.c: In function 'coffee_seq_evaluate_output':
evaluate.c:1126:10: warning: unused variable 'count' [-Wunused-variable]
evaluate.c:1125:14: warning: unused variable 'A' [-Wunused-variable]
evaluate.c:1123:32: warning: unused variable 'acc' [-Wunused-variable]
evaluate.c:1120:9: warning: unused variable 'fp' [-Wunused-variable]
evaluate.c:1118:12: warning: unused variable 'min_avg' [-Wunused-variable]
evaluate.c:1118:7: warning: unused variable 'avg' [-Wunused-variable]
evaluate.c:1117:20: warning: unused variable 'i' [-Wunused-variable]
evaluate.c:1117:18: warning: unused variable 'l' [-Wunused-variable]
evaluate.c:1117:16: warning: unused variable 'c' [-Wunused-variable]
evaluate.c:1117:14: warning: unused variable 'b' [-Wunused-variable]
evaluate.c: In function 'genepred2sd':
evaluate.c:1214:10: warning: unused variable 'b' [-Wunused-variable]
evaluate.c: In function 'genepred2avg':
evaluate.c:1230:10: warning: unused variable 'b' [-Wunused-variable]
evaluate.c: In function 'genepred2zsum2':
evaluate.c:1242:10: warning: unused variable 'b' [-Wunused-variable]
evaluate.c:1241:17: warning: unused variable 'sum2' [-Wunused-variable]
evaluate.c:1241:10: warning: unused variable 'sum' [-Wunused-variable]
evaluate.c: In function 'coffee_seq_evaluate_output_old2':
evaluate.c:1284:11: warning: unused variable 't' [-Wunused-variable]
evaluate.c:1272:27: warning: unused variable 'fp' [-Wunused-variable]
evaluate.c:1270:20: warning: unused variable 'i' [-Wunused-variable]
evaluate.c:1270:18: warning: unused variable 'l' [-Wunused-variable]
evaluate.c: In function 'get_curvature':
evaluate.c:1969:30: warning: unused variable 'b2' [-Wunused-variable]
evaluate.c: In function 'residue_pair_extended_list_quadruplet':
evaluate.c:2139:8: warning: variable 'field' set but not used [-Wunused-but-set-variable]
evaluate.c: In function 'residue_pair_extended_list_pc':
evaluate.c:2517:8: warning: unused variable 'nclean' [-Wunused-variable]
evaluate.c: In function 'consensus_get_dp_cost':
evaluate.c:3515:30: warning: variable 'lenls2' set but not used [-Wunused-but-set-variable]
evaluate.c:3515:22: warning: variable 'lenls1' set but not used [-Wunused-but-set-variable]
evaluate.c: In function 'combine_two_matrices':
evaluate.c:5032:20: warning: operation on '*(*(mat2 + (long unsigned int)((long unsigned int)Re1 * 8ul)) + (long unsigned int)((long unsigned int)Re2 * 4ul))' may be undefined [-Wsequence-point]
evaluate.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
evaluate.c: In function 'coffee_seq_evaluate_output':
evaluate.c:1150:24: warning: 'best_score' may be used uninitialized in this function [-Wuninitialized]
evaluate.c:1160:11: warning: 'best_cycle' may be used uninitialized in this function [-Wuninitialized]
evaluate.c: In function 'coffee_seq_evaluate_output_old2':
evaluate.c:1305:34: warning: 'best_cycle' may be used uninitialized in this function [-Wuninitialized]
evaluate.c: In function 'evaluate_ssp_matrix_score':
evaluate.c:2024:59: warning: 'RF' may be used uninitialized in this function [-Wuninitialized]
evaluate.c: In function 'evaluate_tm_matrix_score':
evaluate.c:2002:59: warning: 'RF' may be used uninitialized in this function [-Wuninitialized]
evaluate.c: In function 'lat_sum_pair':
evaluate.c:5074:13: warning: 'score' may be used uninitialized in this function [-Wuninitialized]
cc -g -O2 -g -O2 -Wall -c -o showpair.o showpair.c
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o fsa_dp.o fsa_dp.c
fsa_dp.c: In function 'analyze_sequence':
fsa_dp.c:247:8: warning: variable 'path' set but not used [-Wunused-but-set-variable]
fsa_dp.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o pavie_dp.o pavie_dp.c
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o dev1.o dev1.c
dev1.c: In function 'aln2hitMat':
dev1.c:63:2: warning: too many arguments for format [-Wformat-extra-args]
dev1.c:76:6: warning: implicit declaration of function 'tolower' [-Wimplicit-function-declaration]
dev1.c:29:6: warning: unused variable 'itmpScore' [-Wunused-variable]
dev1.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o dev2.o dev2.c
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o dev3.o dev3.c
cc -g -O2 -g -O2 -Wall -c -o dev4.o dev4.c
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o fastal.o fastal.c
fastal.c: In function 'diagonals2int':
fastal.c:264:6: warning: variable 'dig_num' set but not used [-Wunused-but-set-variable]
fastal.c: In function 'diagonals2int_gap_test':
fastal.c:475:6: warning: variable 'dig_num' set but not used [-Wunused-but-set-variable]
fastal.c: In function 'diagonals2int_euclidf':
fastal.c:718:6: warning: variable 'dig_num' set but not used [-Wunused-but-set-variable]
fastal.c: In function 'diagonals2int_dot':
fastal.c:944:6: warning: variable 'dig_num' set but not used [-Wunused-but-set-variable]
fastal.c: In function 'list2linked_pair_wise_fastal':
fastal.c:1227:28: warning: operation on '*(MJ + (long unsigned int)((long unsigned int)(a * 5 + b) * 8ul))' may be undefined [-Wsequence-point]
fastal.c:1200:7: warning: variable 'score' set but not used [-Wunused-but-set-variable]
fastal.c:1191:43: warning: variable 'prev_j' set but not used [-Wunused-but-set-variable]
fastal.c:1191:35: warning: variable 'prev_i' set but not used [-Wunused-but-set-variable]
fastal.c: In function 'prf_gotoh':
fastal.c:3042:8: warning: unused variable 'num' [-Wunused-variable]
fastal.c: In function 'fastal_main':
fastal.c:3786:3: warning: implicit declaration of function 'complete_agreement_score' [-Wimplicit-function-declaration]
fastal.c:3793:3: warning: implicit declaration of function 'compute_ref_alignments' [-Wimplicit-function-declaration]
fastal.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o parttree.o parttree.c
parttree.c: In function 'make_pos_len_index_of_file':
parttree.c:1016:7: warning: variable 'c_seq' set but not used [-Wunused-but-set-variable]
parttree.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
parttree.c: In function 'int_dist2upgma_tree_fastal':
parttree.c:211:10: warning: 'T' may be used uninitialized in this function [-Wuninitialized]
cc -g -O2 -g -O2 -Wall -c -o tree.o tree.c
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o diagonal.o diagonal.c
diagonal.c: In function 'segments2int':
diagonal.c:284:5: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration]
diagonal.c:228:6: warning: variable 'dig_num' set but not used [-Wunused-but-set-variable]
diagonal.c:218:6: warning: unused variable 'tmpy_value' [-Wunused-variable]
diagonal.c:217:6: warning: unused variable 'tmpy_pos' [-Wunused-variable]
diagonal.c: In function 'seq_pair2blast_diagonal2':
diagonal.c:398:7: warning: unused variable 'blast_command2' [-Wunused-variable]
diagonal.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o fastal_opt_parsing.o fastal_opt_parsing.c
fastal_opt_parsing.c: In function 'tree_parse':
fastal_opt_parsing.c:13:29: warning: comparison with string literal results in unspecified behavior [-Waddress]
cc -g -O2 -g -O2 -Wall -c -o scoring.o scoring.c
scoring.c: In function 'calculate_sum_of_pairs_score_affine':
scoring.c:177:6: warning: unused variable 'chunk' [-Wunused-variable]
scoring.c: In function 'compute_ref_alignments':
scoring.c:326:9: warning: unused variable 'j' [-Wunused-variable]
scoring.c: At top level:
scoring.c:578:1: warning: return type defaults to 'int' [-Wreturn-type]
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o iteration.o iteration.c
iteration.c: In function 'seq2profile2':
iteration.c:28:4: warning: array subscript has type 'char' [-Wchar-subscripts]
iteration.c: In function 'split_set':
iteration.c:150:8: warning: unused variable 'j' [-Wunused-variable]
iteration.c:150:6: warning: unused variable 'i' [-Wunused-variable]
iteration.c: In function 'iterate':
iteration.c:387:3: warning: implicit declaration of function 'gotoh_dyn' [-Wimplicit-function-declaration]
iteration.c:411:2: warning: implicit declaration of function 'strcmp' [-Wimplicit-function-declaration]
iteration.c:417:3: warning: implicit declaration of function 'free_nw' [-Wimplicit-function-declaration]
iteration.c:329:10: warning: unused variable 'p' [-Wunused-variable]
iteration.c:328:10: warning: unused variable 'last' [-Wunused-variable]
iteration.c:327:10: warning: unused variable 'entrop' [-Wunused-variable]
iteration.c:325:10: warning: unused variable 'max_entrop' [-Wunused-variable]
iteration.c:261:6: warning: unused variable 'it_counter' [-Wunused-variable]
iteration.c: In function 'write_iterated_aln':
iteration.c:431:6: warning: unused variable 'i' [-Wunused-variable]
iteration.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
cc -g -O2 -g -O2 -Wall -c -o t_coffee.o t_coffee.c
t_coffee.c: In function 'batch_main':
t_coffee.c:4138:14: warning: unused variable 'j' [-Wunused-variable]
t_coffee.c:380:10: warning: variable 'n_overaln_param' set but not used [-Wunused-but-set-variable]
t_coffee.c:143:6: warning: variable 'n_setenv' set but not used [-Wunused-but-set-variable]
t_coffee.c: In function 'run_other_pg':
t_coffee.c:5268:3: warning: implicit declaration of function 'fastal_main' [-Wimplicit-function-declaration]
t_coffee.c: In function 'prepare_master':
t_coffee.c:5385:15: warning: variable 'sim' set but not used [-Wunused-but-set-variable]
t_coffee.c:5340:10: warning: unused variable 'fp' [-Wunused-variable]
t_coffee.c:5339:19: warning: unused variable 'i' [-Wunused-variable]
t_coffee.c:5339:16: warning: unused variable 'n' [-Wunused-variable]
t_coffee.c:5339:12: warning: unused variable 's1' [-Wunused-variable]
t_coffee.c: At top level:
io_lib_header.h:950:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function]
t_coffee.c:5226:6: warning: 'test' defined but not used [-Wunused-function]
t_coffee.c:27:14: warning: 'get_rmcoffee_defaults_old' declared 'static' but never defined [-Wunused-function]
t_coffee.c:28:14: warning: 'get_rcoffee_defaults_old' declared 'static' but never defined [-Wunused-function]
t_coffee.c:5021:7: warning: 'get_cdna_defaults' defined but not used [-Wunused-function]
t_coffee.c: In function 'main':
t_coffee.c:83:1: warning: control reaches end of non-void function [-Wreturn-type]
t_coffee.c:82:10: warning: 'r' may be used uninitialized in this function [-Wuninitialized]
cc -g -O2 -g -O2 -Wall -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o t_coffee.o -lm
TMalign.f -o TMalign
make[1]: TMalign.f: Command not found
make[1]: [TMalign] Error 127 (ignored)
make[1]: Leaving directory `/«BUILDDIR»/t-coffee-8.99/t_coffee_source'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -f debian/rules check
make[1]: Entering directory `/«BUILDDIR»/t-coffee-8.99'
cd bin && ln -sf ../t_coffee_source/t_coffee
./bin/test.pl
PROGRAM: T-COFFEE (Version_8.99)
-full_log S [0]
-genepred_score S [0] nsd
-run_name S [0]
-mem_mode S [0] mem
-extend D [1] 1
-extend_mode S [0] very_fast_triplet
-max_n_pair D [0] 10
-seq_name_for_quadruplet S [0] all
-compact S [0] default
-clean S [0] no
-do_self FL [0] 0
-do_normalise D [0] 1000
-template_file S [0]
-setenv S [0] 0
-template_mode S [0]
-remove_template_file D [0] 0
-profile_template_file S [0]
-in S [0]
-seq S [1] test.pep
-aln S [0]
-method_limits S [0]
-method S [1] fast_pair
-lib S [0]
-profile S [0]
-profile1 S [0]
-profile2 S [0]
-pdb S [0]
-relax_lib D [0] 1
-filter_lib D [0] 0
-shrink_lib D [0] 0
-out_lib W_F [0] no
-out_lib_mode S [0] primary
-lib_only D [0] 0
-outseqweight W_F [0] no
-dpa FL [0] 0
-seq_source S [0] ANY
-cosmetic_penalty D [0] 0
-gapopen D [0] 0
-gapext D [0] 0
-fgapopen D [0] 0
-fgapext D [0] 0
-nomatch D [0] 0
-newtree W_F [0] default
-tree W_F [0] NO
-usetree R_F [0]
-tree_mode S [0] nj
-distance_matrix_mode S [0] ktup
-distance_matrix_sim_mode S [0] idmat_sim1
-quicktree FL [0] 0
-outfile W_F [1] new_reference_test.aln
-maximise FL [1] 1
-output S [0] aln html
-infile R_F [0]
-matrix S [0] default
-tg_mode D [0] 1
-profile_mode S [0] cw_profile_profile
-profile_comparison S [0] profile
-dp_mode S [0] linked_pair_wise
-ktuple D [0] 1
-ndiag D [0] 0
-diag_threshold D [0] 0
-diag_mode D [0] 0
-sim_matrix S [0] vasiliky
-transform S [0]
-extend_seq FL [0] 0
-outorder S [1] input
-inorder S [0] aligned
-seqnos S [0] off
-case S [0] keep
-cpu D [0] 0
-maxnseq D [0] 1000
-maxlen D [0] -1
-sample_dp D [0] 0
-weight S [0] default
-seq_weight S [0] t_coffee
-align FL [1] 1
-mocca FL [0] 0
-domain FL [0] 0
-start D [0] 0
-len D [0] 0
-scale D [0] 0
-mocca_interactive FL [0] 0
-method_evaluate_mode S [0] default
-evaluate_mode S [0] triplet
-get_type FL [0] 0
-clean_aln D [0] 0
-clean_threshold D [1] 1
-clean_iteration D [1] 1
-clean_evaluate_mode S [0] t_coffee_fast
-extend_matrix FL [0] 0
-prot_min_sim D [40] 40
-prot_max_sim D [90] 90
-prot_min_cov D [40] 40
-pdb_type S [0] d
-pdb_min_sim D [35] 35
-pdb_max_sim D [100] 100
-pdb_min_cov D [50] 50
-pdb_blast_server W_F [0] EBI
-blast W_F [0]
-blast_server W_F [0] EBI
-pdb_db W_F [0] pdb
-protein_db W_F [0] uniprot
-method_log W_F [0] no
-struc_to_use S [0]
-cache W_F [0] use
-align_pdb_param_file W_F [0] no
-align_pdb_hasch_mode W_F [0] hasch_ca_trace_bubble
-external_aligner S [0] NO
-msa_mode S [0] tree
-master S [0] no
-blast_nseq D [0] 0
-lalign_n_top D [0] 10
-iterate D [0] 0
-trim D [0] 0
-split D [0] 0
-trimfile S [0] default
-split D [0] 0
-split_nseq_thres D [0] 0
-split_score_thres D [0] 0
-check_pdb_status D [0] 0
-clean_seq_name D [0] 0
-seq_to_keep S [0]
-dpa_master_aln S [0]
-dpa_maxnseq D [0] 0
-dpa_min_score1 D [0]
-dpa_min_score2 D [0]
-dpa_keep_tmpfile FL [0] 0
-dpa_debug D [0] 0
-multi_core S [0] templates_jobs_relax_msa_evaluate
-n_core D [0] 0
-lib_list S [0]
-prune_lib_mode S [0] 5
-tip S [0] none
-rna_lib S [0]
-no_warning D [0] 0
-run_local_script D [0] 0
-plugins S [0] default
-proxy S [0] unset
-email S [0]
-clean_overaln D [0] 0
-overaln_param S [0]
-overaln_mode S [0]
-overaln_model S [0]
-overaln_threshold D [0] 0
-overaln_target D [0] 0
-overaln_P1 D [0] 0
-overaln_P2 D [0] 0
-overaln_P3 D [0] 0
-overaln_P4 D [0] 0
-exon_boundaries S [0]
-dump S [0] no
INPUT FILES
Input File (S) test.pep Format fasta_seq
Input File (M) fast_pair
COMPUTE PAIRWISE SIMILARITY [dp_mode: ] [distance_matrix_mode: ktup][Similarity Measure: idmat_sim1]
Seq: 1aboA
Seq: 1ihvA
Seq: 1pht
Seq: 1vie
Seq: 1ycsB
INPUT SEQUENCES: 5 SEQUENCES [PROTEIN]
Input File test.pep Seq 1aboA Length 57 type PROTEIN Struct Unchecked
Input File test.pep Seq 1ihvA Length 49 type PROTEIN Struct Unchecked
Input File test.pep Seq 1pht Length 80 type PROTEIN Struct Unchecked
Input File test.pep Seq 1vie Length 51 type PROTEIN Struct Unchecked
Input File test.pep Seq 1ycsB Length 60 type PROTEIN Struct Unchecked
READ/MAKE LIBRARIES:[2]
fast_pair [method]
Multi Core Mode: 8 processors [subset]
[Submit Job][TOT= 2][ 0 %][ELAPSED TIME: 0 sec.]
[Submit Job][TOT= 2][100 %][ELAPSED TIME: 0 sec.]
MANUAL PENALTIES: gapopen=0 gapext=0
Library Total Size: [962]
Library Relaxation: Multi_proc [8]
Relaxation Summary: [962]--->[962]
WEIGHTED MODE:t_coffee
1aboA 1.00
1ihvA 1.00
1pht 1.00
1vie 1.00
1ycsB 1.00
MAKE GUIDE TREE
[MODE=nj][DONE]
PROGRESSIVE_ALIGNMENT [Tree Based]
Group 1: 1aboA
Group 2: 1ihvA
Group 3: 1pht
Group 4: 1vie
Group 5: 1ycsB
Group 6: [Group 2 ( 1 seq)] with [Group 1 ( 1 seq)]-->[Len= 76][PID:25541]
Group 7: [Group 3 ( 1 seq)] with [Group 6 ( 2 seq)]-->[Len= 100][PID:25541]
Group 8: [Group 5 ( 1 seq)] with [Group 7 ( 3 seq)]-->[Len= 100][PID:25541]
Group 9: [Group 4 ( 1 seq)] with [Group 8 ( 4 seq)]-->[Len= 100][PID:25541]
[Final Evaluation][TOT= 12][ 0 %][ELAPSED TIME: 0 sec.]
[Final Evaluation][TOT= 12][ 16 %][ELAPSED TIME: 0 sec.]
[Final Evaluation][TOT= 12][ 25 %][ELAPSED TIME: 0 sec.]
[Final Evaluation][TOT= 12][ 33 %][ELAPSED TIME: 0 sec.]
[Final Evaluation][TOT= 12][ 41 %][ELAPSED TIME: 0 sec.]
[Final Evaluation][TOT= 12][ 50 %][ELAPSED TIME: 0 sec.]
[Final Evaluation][TOT= 12][ 58 %][ELAPSED TIME: 0 sec.]
[Final Evaluation][TOT= 12][ 66 %][ELAPSED TIME: 0 sec.]
[Final Evaluation][TOT= 12][ 75 %][ELAPSED TIME: 0 sec.]
[Final Evaluation][TOT= 12][ 83 %][ELAPSED TIME: 0 sec.]
[Final Evaluation][TOT= 12][ 91 %][ELAPSED TIME: 0 sec.]
[Final Evaluation][TOT= 12][100 %][ELAPSED TIME: 0 sec.]
OUTPUT RESULTS
#### File Type= GUIDE_TREE Format= newick Name= test.dnd
#### File Type= MSA Format= aln Name= new_reference_test.aln
#### File Type= MSA Format= html Name= new_reference_test.aln.html
# Command Line: ../bin/t_coffee test.pep -method fast_pair -outfile new_reference_test.aln -outorder input [PROGRAM:T-COFFEE]
# Results Produced with T-COFFEE (Version_8.99)
# T-COFFEE is available from http://www.tcoffee.org
# Register on: https://groups.google.com/group/tcoffee/
Installation of t_coffee Successful
make[1]: Leaving directory `/«BUILDDIR»/t-coffee-8.99'
touch debian/stamp-makefile-check
fakeroot debian/rules binary
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/t-coffee-examples.substvars
dh_installdirs -pt-coffee-examples
Adding cdbs dependencies to debian/t-coffee-doc.substvars
dh_installdirs -pt-coffee-doc
dh_installdocs -pt-coffee-examples ./README
dh_installexamples -pt-coffee-examples
dh_installman -pt-coffee-examples
dh_installinfo -pt-coffee-examples
dh_installmenu -pt-coffee-examples
dh_installcron -pt-coffee-examples
dh_installinit -pt-coffee-examples
dh_installdebconf -pt-coffee-examples
dh_installemacsen -pt-coffee-examples
dh_installcatalogs -pt-coffee-examples
dh_installpam -pt-coffee-examples
dh_installlogrotate -pt-coffee-examples
dh_installlogcheck -pt-coffee-examples
dh_installchangelogs -pt-coffee-examples
dh_installudev -pt-coffee-examples
dh_lintian -pt-coffee-examples
dh_bugfiles -pt-coffee-examples
dh_install -pt-coffee-examples
dh_link -pt-coffee-examples
dh_installmime -pt-coffee-examples
dh_installgsettings -pt-coffee-examples
dh_installdocs -pt-coffee-doc ./README
dh_installexamples -pt-coffee-doc
dh_installman -pt-coffee-doc
dh_installinfo -pt-coffee-doc
dh_installmenu -pt-coffee-doc
dh_installcron -pt-coffee-doc
dh_installinit -pt-coffee-doc
dh_installdebconf -pt-coffee-doc
dh_installemacsen -pt-coffee-doc
dh_installcatalogs -pt-coffee-doc
dh_installpam -pt-coffee-doc
dh_installlogrotate -pt-coffee-doc
dh_installlogcheck -pt-coffee-doc
dh_installchangelogs -pt-coffee-doc
dh_installudev -pt-coffee-doc
dh_lintian -pt-coffee-doc
dh_bugfiles -pt-coffee-doc
dh_install -pt-coffee-doc
dh_link -pt-coffee-doc
dh_installmime -pt-coffee-doc
dh_installgsettings -pt-coffee-doc
dh_strip -pt-coffee-examples
dh_compress -pt-coffee-examples -X .doc
dh_fixperms -pt-coffee-examples
dh_makeshlibs -pt-coffee-examples
dh_strip -pt-coffee-doc
dh_compress -pt-coffee-doc -X .doc
dh_fixperms -pt-coffee-doc
dh_makeshlibs -pt-coffee-doc
dh_installdeb -pt-coffee-examples
dh_perl -pt-coffee-examples
dh_shlibdeps -pt-coffee-examples
dh_installdeb -pt-coffee-doc
dh_perl -pt-coffee-doc
dh_shlibdeps -pt-coffee-doc
dh_gencontrol -pt-coffee-examples
dh_md5sums -pt-coffee-examples
dh_builddeb -pt-coffee-examples
dpkg-deb: building package `t-coffee-examples' in `../t-coffee-examples_8.99-1_all.deb'.
dh_gencontrol -pt-coffee-doc
dh_md5sums -pt-coffee-doc
dh_builddeb -pt-coffee-doc
dpkg-deb: building package `t-coffee-doc' in `../t-coffee-doc_8.99-1_all.deb'.
Adding cdbs dependencies to debian/t-coffee.substvars
dh_installdirs -pt-coffee
dh_installdocs -pt-coffee ./README
dh_installexamples -pt-coffee
dh_installman -pt-coffee
dh_installinfo -pt-coffee
dh_installmenu -pt-coffee
dh_installcron -pt-coffee
dh_installinit -pt-coffee
dh_installdebconf -pt-coffee
dh_installemacsen -pt-coffee
dh_installcatalogs -pt-coffee
dh_installpam -pt-coffee
dh_installlogrotate -pt-coffee
dh_installlogcheck -pt-coffee
dh_installchangelogs -pt-coffee
dh_installudev -pt-coffee
dh_lintian -pt-coffee
dh_bugfiles -pt-coffee
dh_install -pt-coffee
dh_link -pt-coffee
dh_installmime -pt-coffee
dh_installgsettings -pt-coffee
dh_strip -pt-coffee
dh_compress -pt-coffee -X .doc
dh_fixperms -pt-coffee
dh_makeshlibs -pt-coffee
dh_installdeb -pt-coffee
dh_perl -pt-coffee
dh_shlibdeps -pt-coffee
dh_gencontrol -pt-coffee
dh_md5sums -pt-coffee
dh_builddeb -pt-coffee
dpkg-deb: building package `t-coffee' in `../t-coffee_8.99-1_amd64.deb'.
dpkg-genchanges -sa >../t-coffee_8.99-1_amd64.changes
dpkg-genchanges: including full source code in upload
dpkg-source --after-build t-coffee-8.99
dpkg-buildpackage: full upload (original source is included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20110621-1521
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
t-coffee_8.99-1_amd64.changes:
──────────────────────────────
Format: 1.8
Date: Tue, 21 Jun 2011 14:14:10 +0900
Source: t-coffee
Binary: t-coffee t-coffee-examples t-coffee-doc
Architecture: source all amd64
Version: 8.99-1
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:
t-coffee - Multiple Sequence Alignment
t-coffee-doc - PDF and HTML accompaning documents to T-Coffee
t-coffee-examples - annotated examples for the use of T-Coffee
Changes:
t-coffee (8.99-1) unstable; urgency=low
.
* New upstream release in Debian.
* Converted and validated debian/copyright to DEP 5 machine-readable format.
* Using debhelper 8 (debian/control, debian/compat).
* Incremented Standards-Version to reflect conformance with Policy 3.9.2.
(debian/control, no change needed).
* Corrected VCS URLs in debian/control.
* Run upstream tests at build time (debian/rules, debian/README.test).
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
t-coffee-examples_8.99-1_all.deb
────────────────────────────────
new debian package, version 2.0.
size 1017104 bytes: control archive= 5431 bytes.
514 bytes, 14 lines control
16120 bytes, 190 lines md5sums
Package: t-coffee-examples
Source: t-coffee
Version: 8.99-1
Architecture: all
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 1508
Recommends: t-coffee
Section: science
Priority: optional
Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
Description: annotated examples for the use of T-Coffee
To help increasing the proficiency in the use of T-Coffee, this
package provides examples for input sequences and their proper
alignment.
drwxr-xr-x root/root 0 2011-06-21 15:21 ./
drwxr-xr-x root/root 0 2011-06-21 15:21 ./usr/
drwxr-xr-x root/root 0 2011-06-21 15:21 ./usr/share/
drwxr-xr-x root/root 0 2011-06-21 15:21 ./usr/share/doc/
drwxr-xr-x root/root 0 2011-06-21 15:21 ./usr/share/doc/t-coffee-examples/
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-rw-r--r-- root/root 557 2011-02-18 16:29 ./usr/share/doc/t-coffee-examples/3d.fasta
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-rw-r--r-- root/root 79 2011-02-18 16:29 ./usr/share/doc/t-coffee-examples/sample_tree2.dnd
-rw-r--r-- root/root 1889 2011-02-18 16:29 ./usr/share/doc/t-coffee-examples/sample_rnaseq2.fasta
-rw-r--r-- root/root 1196 2011-02-18 16:29 ./usr/share/doc/t-coffee-examples/command_line.txt.gz
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-rw-r--r-- root/root 13 2011-02-18 16:29 ./usr/share/doc/t-coffee-examples/sample_seq8.seq
-rw-r--r-- root/root 95 2011-02-18 16:29 ./usr/share/doc/t-coffee-examples/sample_tree.dnd
-rw-r--r-- root/root 2056 2011-02-18 16:29 ./usr/share/doc/t-coffee-examples/test.lib.gz
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t-coffee-doc_8.99-1_all.deb
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size 745658 bytes: control archive= 958 bytes.
530 bytes, 14 lines control
1110 bytes, 14 lines md5sums
Package: t-coffee-doc
Source: t-coffee
Version: 8.99-1
Architecture: all
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 3296
Recommends: t-coffee
Suggests: t-coffee-examples
Section: doc
Priority: optional
Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
Description: PDF and HTML accompaning documents to T-Coffee
The tool for multiple sequence alignment, T-Coffee, is explained
both from the users' perspective and for its technical background.
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t-coffee_8.99-1_amd64.deb
─────────────────────────
new debian package, version 2.0.
size 809966 bytes: control archive= 1229 bytes.
1515 bytes, 29 lines control
397 bytes, 6 lines md5sums
Package: t-coffee
Version: 8.99-1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 1864
Depends: libc6 (>= 2.7)
Recommends: libsoap-lite-perl, libxml-simple-perl
Suggests: boxshade, seaview, t-coffee-doc, t-coffee-examples, dialign-tx, kalign, mafft, muscle, poa, probcons, clustalw, amap-align, proda
Section: science
Priority: optional
Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
Description: Multiple Sequence Alignment
T-Coffee is a multiple sequence alignment package. Given a set of
sequences (Proteins or DNA), T-Coffee generates a multiple sequence
alignment. Version 2.00 and higher can mix sequences and structures.
.
T-Coffee allows the combination of a collection of multiple/pairwise,
global or local alignments into a single model. It also allows to
estimate the level of consistency of each position within the new
alignment with the rest of the alignments. See the pre-print for more
information
.
T-Coffee has a special called M-Coffee that makes it possible to combine the
output of many multiple sequence alignment packages. In its published version,
it uses MUSCLE, PROBCONS, POA, DiAlign-TS, MAFFT, Clustal W, PCMA and
T-Coffee. A special version has been made for Debian, DM-Coffee, that uses
only free software by replacing Clustal W by Kalign. Using the 8 Methods of
M-Coffee can sometimes be a bit heavy. You can use a subset of your favorite
methods if you prefer.
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-rw-r--r-- root/root 1602 2011-06-21 13:43 ./usr/share/doc/t-coffee/copyright
-rw-r--r-- root/root 2559 2011-02-18 16:29 ./usr/share/doc/t-coffee/README
-rw-r--r-- root/root 1793 2011-06-21 14:14 ./usr/share/doc/t-coffee/changelog.Debian.gz
-rw-r--r-- root/root 1744 2008-04-09 22:24 ./usr/share/doc/t-coffee/README.Debian
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
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Purging /«CHROOT»/«BUILDDIR»
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The following packages will be REMOVED:
bsdmainutils* cdbs* debhelper* diffstat* file* gettext* gettext-base*
groff-base* html2text* intltool-debian* libcroco3* libglib2.0-0* libmagic1*
libpcre3* libpipeline1* libunistring0* libxml2* man-db* po-debconf* quilt*
sbuild-build-depends-core-dummy* sbuild-build-depends-t-coffee-dummy*
0 upgraded, 0 newly installed, 22 to remove and 0 not upgraded.
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: amd64
Build-Space: 44268
Build-Time: 44
Distribution: unstable
Install-Time: 27
Job: t-coffee_8.99-1.dsc
Package: t-coffee
Package-Time: 78
Source-Version: 8.99-1
Space: 44268
Status: successful
Version: 8.99-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20110621-1521
Build needed 00:01:18, 44268k disc space
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