sbuild (Debian sbuild) 0.62.6 (07 Dec 2011) on build00.raspbian.lan ╔══════════════════════════════════════════════════════════════════════════════╗ ║ t-coffee 9.02.r1228-2 (armhf) 22 May 2012 17:10 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: t-coffee Version: 9.02.r1228-2 Source Version: 9.02.r1228-2 Distribution: testing Architecture: armhf I: NOTICE: Log filtering will replace 'build/t-coffee-DTbwGl/t-coffee-9.02.r1228' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/t-coffee-DTbwGl' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/testing-armhf-sbuild-7e6c45d0-f2fe-4526-aab2-d287572c72a1' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Hit http://repo.raspbian.lan testing InRelease Hit http://repo.raspbian.lan testing/main Sources Hit http://repo.raspbian.lan testing/main armhf Packages Ign http://repo.raspbian.lan testing/main TranslationIndex Ign http://repo.raspbian.lan testing/main Translation-en Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 't-coffee' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/debian-med/trunk/packages/t-coffee/trunk/ Need to get 3373 kB of source archives. Get:1 http://repo.raspbian.lan/raspbian/ testing/main t-coffee 9.02.r1228-2 (dsc) [2241 B] Get:2 http://repo.raspbian.lan/raspbian/ testing/main t-coffee 9.02.r1228-2 (tar) [3364 kB] Get:3 http://repo.raspbian.lan/raspbian/ testing/main t-coffee 9.02.r1228-2 (diff) [7372 B] Fetched 3373 kB in 0s (9141 kB/s) Download complete and in download only mode Check arch ────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-xtdWzb/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 13 not upgraded. Need to get 0 B/704 B of archives. After this operation, 0 B of additional disk space will be used. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10670 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: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, gfortran Filtered Build-Depends: libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, gfortran dpkg-deb: building package `sbuild-build-depends-t-coffee-dummy' in `/«BUILDDIR»/resolver-cQ8oMd/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 gfortran gfortran-4.6 groff-base html2text intltool-debian libcroco3 libffi5 libgfortran3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt Suggested packages: wamerican wordlist whois vacation devscripts dh-make gettext-doc gfortran-doc gfortran-4.6-doc libgfortran3-dbg groff less www-browser libmail-box-perl procmail graphviz default-mta mail-transport-agent 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 gfortran gfortran-4.6 groff-base html2text intltool-debian libcroco3 libffi5 libgfortran3 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, 25 newly installed, 0 to remove and 13 not upgraded. Need to get 0 B/14.9 MB of archives. After this operation, 38.1 MB of additional disk space will be used. Selecting previously unselected package libpcre3:armhf. (Reading database ... 10670 files and directories currently installed.) Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.30-5_armhf.deb) ... Selecting previously unselected package libpipeline1:armhf. Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.1-1_armhf.deb) ... Selecting previously unselected package libmagic1:armhf. Unpacking libmagic1:armhf (from .../libmagic1_5.11-1_armhf.deb) ... Selecting previously unselected package libxml2:armhf. Unpacking libxml2:armhf (from .../libxml2_2.7.8.dfsg-9_armhf.deb) ... Selecting previously unselected package libffi5:armhf. Unpacking libffi5:armhf (from .../libffi5_3.0.10-3+b3_armhf.deb) ... Selecting previously unselected package libglib2.0-0:armhf. Unpacking libglib2.0-0:armhf (from .../libglib2.0-0_2.32.2-1_armhf.deb) ... Selecting previously unselected package libcroco3:armhf. Unpacking libcroco3:armhf (from .../libcroco3_0.6.5-1_armhf.deb) ... Selecting previously unselected package libgfortran3:armhf. Unpacking libgfortran3:armhf (from .../libgfortran3_4.7.0-1.1+rpi_armhf.deb) ... Selecting previously unselected package libunistring0:armhf. Unpacking libunistring0:armhf (from .../libunistring0_0.9.3-5_armhf.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_armhf.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-7_armhf.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.1-2_armhf.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.11-1_armhf.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-5+rpi1_armhf.deb) ... Selecting previously unselected package cdbs. Unpacking cdbs (from .../archives/cdbs_0.4.111_all.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_armhf.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-5+rpi1_armhf.deb) ... Selecting previously unselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously unselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ... Selecting previously unselected package debhelper. Unpacking debhelper (from .../debhelper_9.20120419_all.deb) ... Selecting previously unselected package diffstat. Unpacking diffstat (from .../diffstat_1.55-2_armhf.deb) ... Selecting previously unselected package gfortran-4.6. Unpacking gfortran-4.6 (from .../gfortran-4.6_4.6.3-1.1+rpi2_armhf.deb) ... Selecting previously unselected package gfortran. Unpacking gfortran (from .../gfortran_4%3a4.6.2-4_armhf.deb) ... Selecting previously unselected package quilt. Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ... Selecting previously unselected package sbuild-build-depends-t-coffee-dummy. Unpacking sbuild-build-depends-t-coffee-dummy (from .../sbuild-build-depends-t-coffee-dummy.deb) ... Setting up libpcre3:armhf (1:8.30-5) ... Setting up libpipeline1:armhf (1.2.1-1) ... Setting up libmagic1:armhf (5.11-1) ... Setting up libxml2:armhf (2.7.8.dfsg-9) ... Setting up libffi5:armhf (3.0.10-3+b3) ... Setting up libglib2.0-0:armhf (2.32.2-1) ... No schema files found: doing nothing. Setting up libcroco3:armhf (0.6.5-1) ... Setting up libgfortran3:armhf (4.7.0-1.1+rpi) ... Setting up libunistring0:armhf (0.9.3-5) ... Setting up bsdmainutils (9.0.1) ... 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 (1.21-7) ... Setting up man-db (2.6.1-2) ... Building database of manual pages ... Setting up file (5.11-1) ... Setting up gettext-base (0.18.1.1-5+rpi1) ... Setting up cdbs (0.4.111) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5+rpi1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120419) ... Setting up diffstat (1.55-2) ... Setting up gfortran-4.6 (4.6.3-1.1+rpi2) ... Setting up gfortran (4:4.6.2-4) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode. Setting up quilt (0.60-2) ... Setting up sbuild-build-depends-t-coffee-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.2.12-mx5 armhf (armv7l) Toolchain package versions: binutils_2.22-6 dpkg-dev_1.16.2 g++-4.6_4.6.3-1.1+rpi2 gcc-4.6_4.6.3-1.1+rpi2 libc6-dev_2.13-32 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 linux-libc-dev_3.2.12-1 Package versions: apt_0.8.15.10 base-files_6.7 base-passwd_3.5.24 bash_4.2-2 binutils_2.22-6 bsdmainutils_9.0.1 bsdutils_1:2.20.1-4 build-essential_11.5+b1 bzip2_1.0.6-1 cdbs_0.4.111 coreutils_8.13-3.1 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1.1+rpi2 dash_0.5.7-3 debconf_1.5.42 debfoster_2.7-1.1 debhelper_9.20120419 debian-archive-keyring_2010.08.28 debianutils_4.3 diffstat_1.55-2 diffutils_1:3.2-6 dpkg_1.16.2 dpkg-dev_1.16.2 e2fslibs_1.42.2-2 e2fsprogs_1.42.2-2 fakeroot_1.18.3-1 file_5.11-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.3-1.1+rpi2 gcc_4:4.6.2-4 gcc-4.4-base_4.4.7-1.1+rpi1 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.3-1.1+rpi2 gcc-4.6-base_4.6.3-1.1+rpi2 gcc-4.7-base_4.7.0-1.1+rpi gettext_0.18.1.1-5+rpi1 gettext-base_0.18.1.1-5+rpi1 gfortran_4:4.6.2-4 gfortran-4.6_4.6.3-1.1+rpi2 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.11-3 groff-base_1.21-7 gzip_1.4-5 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-22.1 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-4 libbz2-1.0_1.0.6-1 libc-bin_2.13-32 libc-dev-bin_2.13-32 libc6_2.13-32 libc6-dev_2.13-32 libclass-isa-perl_0.36-3 libcomerr2_1.42.2-2 libcroco3_0.6.5-1 libdb5.1_5.1.29-1 libdpkg-perl_1.16.2 libffi5_3.0.10-3+b3 libfile-fcntllock-perl_0.14-1 libgc1c2_1:7.1-8 libgcc1_1:4.7.0-1.1+rpi libgdbm3_1.8.3-10 libgfortran3_4.7.0-1.1+rpi libglib2.0-0_2.32.2-1 libgmp10_2:5.0.5+dfsg-1.1 libgomp1_4.7.0-1.1+rpi liblocale-gettext-perl_1.05-7 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.11-1 libmount1_2.20.1-4 libmpc2_0.9-4 libmpfr4_3.1.0-4 libncurses5_5.9-7 libncursesw5_5.9-7 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-2 libsemanage-common_2.1.6-2 libsemanage1_2.1.6-2 libsepol1_2.1.4-3 libslang2_2.2.4-10 libss2_1.42.2-2 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-7 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-2 libuuid1_2.20.1-4 libxml2_2.7.8.dfsg-9 linux-libc-dev_3.2.12-1 login_1:4.1.5-1 lsb-base_4.1+Debian2 make_3.81-8.2 man-db_2.6.1-2 mawk_1.3.3-17 mount_2.20.1-4 multiarch-support_2.13-32 ncurses-base_5.9-6 ncurses-bin_5.9-7 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-9 perl-base_5.14.2-9 perl-modules_5.14.2-9 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 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-22.1 sysvinit_2.88dsf-22.1 sysvinit-utils_2.88dsf-22.1 tar_1.26-4 tzdata_2012c-1 ucf_3.0025+nmu3 util-linux_2.20.1-4 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.7.dfsg-1 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Fri Mar 2 05:20:45 2012 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_9.02.r1228-2.dsc dpkg-source: info: extracting t-coffee in t-coffee-9.02.r1228 dpkg-source: info: unpacking t-coffee_9.02.r1228.orig.tar.gz dpkg-source: info: unpacking t-coffee_9.02.r1228-2.debian.tar.gz dpkg-source: info: applying probconsrna.patch Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=buildd PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/usr/games SCHROOT_CHROOT_NAME=testing-armhf-sbuild SCHROOT_COMMAND=env SCHROOT_GID=108 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=testing-armhf-sbuild-7e6c45d0-f2fe-4526-aab2-d287572c72a1 SCHROOT_UID=106 SCHROOT_USER=buildd SHELL=/bin/sh TERM=xterm USER=buildd dpkg-buildpackage ───────────────── dpkg-buildpackage: source package t-coffee dpkg-buildpackage: source version 9.02.r1228-2 dpkg-source --before-build t-coffee-9.02.r1228 dpkg-buildpackage: host architecture armhf 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean make[1]: Entering directory `/«PKGBUILDDIR»' make[1]: *** No rule to make target `clean'. make[1]: Leaving directory `/«PKGBUILDDIR»' make: [makefile-clean] Error 2 (ignored) /usr/bin/make -f debian/rules reverse-config make[1]: Entering directory `/«PKGBUILDDIR»' make[1]: Nothing to be done for `reverse-config'. make[1]: Leaving directory `/«PKGBUILDDIR»' if [ -d "." ]; then \ cd . && QUILT_PATCHES=/«PKGBUILDDIR»/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/* debian/rules build-arch 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 `/«PKGBUILDDIR»' make[1]: Nothing to be done for `reverse-config'. make[1]: Leaving directory `/«PKGBUILDDIR»' cd . && QUILT_PATCHES=/«PKGBUILDDIR»/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2 Applying patch probconsrna.patch patching file t_coffee_source/define_header.h Hunk #1 succeeded at 592 (offset 3 lines). Now at patch probconsrna.patch touch debian/stamp-patched /usr/bin/make -f debian/rules update-config make[1]: Entering directory `/«PKGBUILDDIR»' make[1]: Nothing to be done for `update-config'. make[1]: Leaving directory `/«PKGBUILDDIR»' /usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C t_coffee_source -i USER_BIN=../bin/ FCC="gfortran -g -O2" all make[1]: Entering directory `/«PKGBUILDDIR»/t_coffee_source' cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_constraints_list.o util_constraints_list.c util_constraints_list.c: In function 'fork_subset_produce_list': util_constraints_list.c:136:20: warning: unused variable 't' [-Wunused-variable] util_constraints_list.c:135:10: warning: unused variable 'fp' [-Wunused-variable] util_constraints_list.c:89:6: warning: unused variable 'n_aln' [-Wunused-variable] util_constraints_list.c:88:17: warning: unused variable 'nlines' [-Wunused-variable] util_constraints_list.c:88:12: warning: unused variable 'seq' [-Wunused-variable] util_constraints_list.c:88:6: warning: unused variable 'cseq' [-Wunused-variable] util_constraints_list.c:87:24: warning: unused variable 'submited' [-Wunused-variable] util_constraints_list.c:81:8: warning: unused variable 'b' [-Wunused-variable] util_constraints_list.c: In function 'fork_line_produce_list': util_constraints_list.c:193:8: warning: unused variable 'b' [-Wunused-variable] util_constraints_list.c: In function 'fork_cell_produce_list': util_constraints_list.c:331:11: warning: unused variable 'n' [-Wunused-variable] util_constraints_list.c:331:8: warning: unused variable 'b' [-Wunused-variable] util_constraints_list.c: In function 'nfork_produce_list': util_constraints_list.c:435:21: warning: unused variable 'n_new_elements' [-Wunused-variable] util_constraints_list.c:435:6: 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:513:14: warning: unused variable 'log' [-Wunused-variable] util_constraints_list.c:512:16: warning: unused variable 'log_output' [-Wunused-variable] util_constraints_list.c:501:16: 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:535:13: warning: unused variable 'log' [-Wunused-variable] util_constraints_list.c: In function 'submit_lib_job': util_constraints_list.c:584:13: warning: unused variable 'log' [-Wunused-variable] util_constraints_list.c:583:15: warning: unused variable 'l' [-Wunused-variable] util_constraints_list.c: In function 'method2job_list': util_constraints_list.c:801:12: warning: unused variable 'used' [-Wunused-variable] util_constraints_list.c:800:14: warning: unused variable 'y' [-Wunused-variable] util_constraints_list.c:643:7: 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:1034:6: warning: unused variable 'status' [-Wunused-variable] util_constraints_list.c:1033:6: warning: unused variable 'n' [-Wunused-variable] util_constraints_list.c: In function 'undump_constraint_list': util_constraints_list.c:1388:8: warning: unused variable 'nl' [-Wunused-variable] util_constraints_list.c:1376:16: warning: variable 'tot' set but not used [-Wunused-but-set-variable] util_constraints_list.c:1376:12: warning: variable 'c' set but not used [-Wunused-but-set-variable] util_constraints_list.c:1376:6: warning: unused variable 'a' [-Wunused-variable] util_constraints_list.c: In function 'safe_dump_constraint_list': util_constraints_list.c:1409:55: 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:1468:27: warning: variable 'n' set but not used [-Wunused-but-set-variable] util_constraints_list.c:1468:10: warning: unused variable 'l' [-Wunused-variable] util_constraints_list.c:1468:8: warning: unused variable 'c' [-Wunused-variable] util_constraints_list.c: In function 'evaluate_constraint_list_reference': util_constraints_list.c:1505:27: warning: unused variable 'r2' [-Wunused-variable] util_constraints_list.c:1505:19: warning: unused variable 's2' [-Wunused-variable] util_constraints_list.c:1505:12: warning: unused variable 'c' [-Wunused-variable] util_constraints_list.c:1504:21: warning: unused variable 'entry' [-Wunused-variable] util_constraints_list.c: In function 'extract_entry': util_constraints_list.c:1607:6: warning: unused variable 'v' [-Wunused-variable] util_constraints_list.c: In function 'get_entry_index': util_constraints_list.c:1860:8: warning: unused variable 'r' [-Wunused-variable] util_constraints_list.c: In function 'remove_entry': util_constraints_list.c:1962:14: warning: unused variable 'to' [-Wunused-variable] util_constraints_list.c:1962:7: warning: unused variable 'from' [-Wunused-variable] util_constraints_list.c: In function 'insert_entry': util_constraints_list.c:1982:17: warning: unused variable 'to' [-Wunused-variable] util_constraints_list.c:1982:10: warning: unused variable 'from' [-Wunused-variable] util_constraints_list.c:1982:6: warning: unused variable 'a' [-Wunused-variable] util_constraints_list.c: In function 'update_entry': util_constraints_list.c:2011:7: warning: unused variable 'r2' [-Wunused-variable] util_constraints_list.c:2009:7: warning: unused variable 's2' [-Wunused-variable] util_constraints_list.c: In function 'return_max_constraint_list': util_constraints_list.c:2065:2: warning: implicit declaration of function 'constraint_list2max' [-Wimplicit-function-declaration] util_constraints_list.c: In function 'invert_constraint_list': util_constraints_list.c:2086:13: warning: unused variable 'tp' [-Wunused-variable] util_constraints_list.c:2085:12: warning: unused variable 'c' [-Wunused-variable] util_constraints_list.c:2085:9: warning: unused variable 'b' [-Wunused-variable] util_constraints_list.c:2085:6: warning: unused variable 'a' [-Wunused-variable] util_constraints_list.c: In function 'sort_constraint_list': util_constraints_list.c:2096:22: warning: unused variable 'w2' [-Wunused-variable] util_constraints_list.c:2096:19: warning: unused variable 'r2' [-Wunused-variable] util_constraints_list.c:2096:16: warning: unused variable 's2' [-Wunused-variable] util_constraints_list.c:2096:8: warning: unused variable 'l' [-Wunused-variable] util_constraints_list.c:2096:6: warning: unused variable 'b' [-Wunused-variable] util_constraints_list.c:2094:6: warning: unused variable 'max' [-Wunused-variable] util_constraints_list.c: In function 'fork_read_n_constraint_list': util_constraints_list.c:2219:4: warning: too many arguments for format [-Wformat-extra-args] util_constraints_list.c: In function 'old_read_constraint_list_file': util_constraints_list.c:2707:6: warning: unused variable 'a' [-Wunused-variable] util_constraints_list.c: In function 'read_constraint_list_file': util_constraints_list.c:2841:5: warning: too many arguments for format [-Wformat-extra-args] util_constraints_list.c:2800:6: warning: unused variable 'a' [-Wunused-variable] util_constraints_list.c: In function 'read_seq_in_list': util_constraints_list.c:2930:14: warning: unused variable 'value' [-Wunused-variable] util_constraints_list.c: In function 'save_constraint_list_ascii': util_constraints_list.c:3255:35: warning: unused variable 'x2' [-Wunused-variable] util_constraints_list.c:3255:31: warning: unused variable 'x1' [-Wunused-variable] util_constraints_list.c:3255:28: warning: unused variable 'w2' [-Wunused-variable] util_constraints_list.c: In function 'extend_constraint_list': util_constraints_list.c:3386:14: warning: unused variable 'tr' [-Wunused-variable] util_constraints_list.c:3386:11: warning: unused variable 'ts' [-Wunused-variable] util_constraints_list.c: In function 'relax_constraint_list': util_constraints_list.c:3428:24: warning: left-hand operand of comma expression has no effect [-Wunused-value] util_constraints_list.c: In function 'fork_relax_constraint_list': util_constraints_list.c:3451:7: warning: unused variable 'np' [-Wunused-variable] util_constraints_list.c: In function 'expand_constraint_list_4gp': util_constraints_list.c:3566:6: warning: unused variable 'n' [-Wunused-variable] util_constraints_list.c:3565:6: warning: unused variable 'max' [-Wunused-variable] util_constraints_list.c:3564:6: warning: unused variable 'chunck' [-Wunused-variable] util_constraints_list.c:3563:7: warning: unused variable 'L' [-Wunused-variable] util_constraints_list.c: In function 'fork_relax_constraint_list_4gp': util_constraints_list.c:3636:6: warning: unused variable 'in' [-Wunused-variable] util_constraints_list.c:3635:8: warning: unused variable 'pid_list' [-Wunused-variable] util_constraints_list.c:3634:9: warning: unused variable 'pid_tmpfile' [-Wunused-variable] util_constraints_list.c:3633:8: warning: unused variable 'fp' [-Wunused-variable] util_constraints_list.c:3632:23: warning: unused variable 'pid' [-Wunused-variable] util_constraints_list.c:3632:19: warning: unused variable 'job' [-Wunused-variable] util_constraints_list.c:3632:13: warning: unused variable 'npid' [-Wunused-variable] util_constraints_list.c:3632:6: warning: unused variable 'chunk' [-Wunused-variable] util_constraints_list.c:3631:6: warning: unused variable 'thr' [-Wunused-variable] util_constraints_list.c:3630:6: warning: unused variable 'score' [-Wunused-variable] util_constraints_list.c:3629:24: warning: unused variable 'n' [-Wunused-variable] util_constraints_list.c:3629:21: warning: unused variable 'r2' [-Wunused-variable] util_constraints_list.c:3629:17: warning: unused variable 'r1' [-Wunused-variable] util_constraints_list.c:3629:13: warning: unused variable 's2' [-Wunused-variable] util_constraints_list.c:3629:9: warning: unused variable 's1' [-Wunused-variable] util_constraints_list.c:3629:6: warning: unused variable 'a' [-Wunused-variable] util_constraints_list.c: In function 'nfork_relax_constraint_list_4gp': util_constraints_list.c:3730:20: warning: unused variable 'l' [-Wunused-variable] util_constraints_list.c:3729:6: warning: unused variable 'thr' [-Wunused-variable] util_constraints_list.c: In function 'constraint_list2max': util_constraints_list.c:3784:19: warning: variable 'r2' set but not used [-Wunused-but-set-variable] util_constraints_list.c:3784:16: warning: variable 's2' set but not used [-Wunused-but-set-variable] util_constraints_list.c:3784:8: warning: unused variable 'l' [-Wunused-variable] util_constraints_list.c: In function 'constraint_list2ne': util_constraints_list.c:3804:22: warning: unused variable 'w2' [-Wunused-variable] util_constraints_list.c:3804:19: warning: unused variable 'r2' [-Wunused-variable] util_constraints_list.c:3804:16: warning: unused variable 's2' [-Wunused-variable] util_constraints_list.c:3804:8: warning: unused variable 'l' [-Wunused-variable] util_constraints_list.c:3804:6: warning: unused variable 'b' [-Wunused-variable] util_constraints_list.c: In function 'constraint_list2avg': util_constraints_list.c:3858:19: warning: variable 'r2' set but not used [-Wunused-but-set-variable] util_constraints_list.c:3858:16: warning: variable 's2' set but not used [-Wunused-but-set-variable] util_constraints_list.c:3858:8: warning: unused variable 'l' [-Wunused-variable] util_constraints_list.c: In function 'filter_constraint_list': util_constraints_list.c:3883:13: warning: unused variable 'bs' [-Wunused-variable] util_constraints_list.c:3882:14: warning: unused variable 'buf' [-Wunused-variable] util_constraints_list.c: In function 'aln2constraint_list_generic': util_constraints_list.c:4135:10: warning: unused variable 'lw' [-Wunused-variable] util_constraints_list.c:4058:12: warning: unused variable 's' [-Wunused-variable] util_constraints_list.c:4056:6: 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:4196:6: warning: unused variable 'max' [-Wunused-variable] util_constraints_list.c: In function 'seq2defined_residues': util_constraints_list.c:4289:22: warning: unused variable 'b' [-Wunused-variable] util_constraints_list.c:4289:18: warning: unused variable 'l' [-Wunused-variable] util_constraints_list.c:4289:15: warning: unused variable 'r2' [-Wunused-variable] util_constraints_list.c:4289:12: warning: unused variable 's2' [-Wunused-variable] util_constraints_list.c: In function 're_weight_constraint_list': util_constraints_list.c:4541:12: warning: unused variable 'b' [-Wunused-variable] util_constraints_list.c:4540:10: warning: unused variable 'sB' [-Wunused-variable] util_constraints_list.c:4540:6: warning: unused variable 'sA' [-Wunused-variable] util_constraints_list.c:4538:8: warning: unused variable 'w' [-Wunused-variable] util_constraints_list.c: In function 'cl2distance_matrix': util_constraints_list.c:4564:8: warning: unused variable 'a' [-Wunused-variable] util_constraints_list.c: In function 'rna_lib_extension': util_constraints_list.c:4942:23: warning: unused variable 'ne' [-Wunused-variable] util_constraints_list.c:4942:6: warning: unused variable 'a' [-Wunused-variable] util_constraints_list.c: In function 'cl2worst_seq': util_constraints_list.c:6502:24: warning: unused variable 'r2' [-Wunused-variable] util_constraints_list.c: At top level: io_lib_header.h:971:16: 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:1852:13: warning: 'sent' defined but not used [-Wunused-variable] util_constraints_list.c:1853:25: warning: 'sCL' defined but not used [-Wunused-variable] util_constraints_list.c: In function 'nfork_relax_constraint_list_4gp': util_constraints_list.c:3771:12: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util_constraints_list.c: In function 'read_seq_in_list': util_constraints_list.c:2900:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util_constraints_list.c:2905:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util_constraints_list.c:2936:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util_constraints_list.c:2961:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] util_constraints_list.c: In function 'read_cpu_in_list': util_constraints_list.c:2608:20: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util_constraints_list.c: In function 'unfreeze_constraint_list': util_constraints_list.c:1333:1: warning: control reaches end of non-void function [-Wreturn-type] util_constraints_list.c: In function 'method_file2TC_method': util_constraints_list.c:1219:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] util_constraints_list.c: In function 'method_file_tag2value': util_constraints_list.c:1177:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] util_constraints_list.c: In function 'submit_lib_job': util_constraints_list.c:608:12: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] util_constraints_list.c:611:12: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] util_constraints_list.c: In function 'read_seq_in_list': util_constraints_list.c:2911:16: warning: 'gn_co' may be used uninitialized in this function [-Wuninitialized] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -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:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_dps.o util_dps.c io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -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:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_analyse_constraints_list.o util_analyse_constraints_list.c io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -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:971:16: 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:6263:7: warning: 'i' may be used uninitialized in this function [-Wuninitialized] util_aln_analyze.c:6262:7: 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 'compound2regexp_motif': util_aln_analyze.c:6048:3: warning: 'i' may be used uninitialized in this function [-Wuninitialized] util_aln_analyze.c:6047:3: 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -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:1296:3: warning: 'return' with no value, in function returning non-void [-Wreturn-type] aln_convertion_util.c: In function 'gene2exons': aln_convertion_util.c:1398:13: warning: unused variable 'c' [-Wunused-variable] aln_convertion_util.c: In function 'fill_sequence_struc': aln_convertion_util.c:1754:16: warning: unused variable 'len' [-Wunused-variable] aln_convertion_util.c: In function 'unalign_aln_2': aln_convertion_util.c:2113:13: warning: unused variable 'S' [-Wunused-variable] aln_convertion_util.c:2112:18: warning: unused variable 'len' [-Wunused-variable] aln_convertion_util.c:2112:13: warning: unused variable 'pos' [-Wunused-variable] aln_convertion_util.c: In function 'unalign_aln_pos': aln_convertion_util.c:2247:7: warning: unused variable 'unalign' [-Wunused-variable] aln_convertion_util.c: In function 'search_best_combo_sar_aln': aln_convertion_util.c:3092:9: warning: variable 's' set but not used [-Wunused-but-set-variable] aln_convertion_util.c: In function 'seq_list2fasta_file': aln_convertion_util.c:4085:12: warning: unused variable 's' [-Wunused-variable] aln_convertion_util.c: In function 'seq2template_type': aln_convertion_util.c:5063:22: warning: variable 'F' set but not used [-Wunused-but-set-variable] aln_convertion_util.c:5058:7: warning: variable 's' set but not used [-Wunused-but-set-variable] aln_convertion_util.c: In function 'seq2template_seq': aln_convertion_util.c:5449:11: warning: unused variable 'z' [-Wunused-variable] aln_convertion_util.c:5558:11: warning: unused variable 'z' [-Wunused-variable] aln_convertion_util.c:5551:9: warning: unused variable 'x' [-Wunused-variable] aln_convertion_util.c: In function 'complement_string': aln_convertion_util.c:6511:16: warning: unused variable 'c' [-Wunused-variable] aln_convertion_util.c:6511:10: warning: unused variable 'a' [-Wunused-variable] aln_convertion_util.c:6510:9: warning: unused variable 'buf' [-Wunused-variable] aln_convertion_util.c: In function 'complement_aln': aln_convertion_util.c:6534:16: warning: unused variable 'c' [-Wunused-variable] aln_convertion_util.c:6534:13: warning: unused variable 'b' [-Wunused-variable] aln_convertion_util.c:6534:7: warning: unused variable 'l' [-Wunused-variable] aln_convertion_util.c:6533:9: warning: unused variable 'buf' [-Wunused-variable] aln_convertion_util.c: In function 'aln2sim_mat_km': aln_convertion_util.c:8459:16: warning: unused variable 'd' [-Wunused-variable] aln_convertion_util.c: In function 'remove_empty_sequence': aln_convertion_util.c:8718:10: warning: variable 'b' set but not used [-Wunused-but-set-variable] aln_convertion_util.c: In function 'sub_aln2nseq_prf': aln_convertion_util.c:8936:10: warning: variable 'c' set but not used [-Wunused-but-set-variable] aln_convertion_util.c: In function 'sim_filter': aln_convertion_util.c:9568:7: warning: unused variable 'coverage' [-Wunused-variable] aln_convertion_util.c:9567:7: warning: unused variable 'direction' [-Wunused-variable] aln_convertion_util.c:9566:7: warning: unused variable 'outlayers' [-Wunused-variable] aln_convertion_util.c:9563:16: warning: unused variable 'k' [-Wunused-variable] aln_convertion_util.c:9562:7: warning: unused variable 'new_nseq' [-Wunused-variable] aln_convertion_util.c:9561:28: warning: unused variable 'nc' [-Wunused-variable] aln_convertion_util.c:9561:16: warning: unused variable 'nseq_ratio' [-Wunused-variable] aln_convertion_util.c:9561:7: warning: unused variable 'maxnseq' [-Wunused-variable] aln_convertion_util.c: In function 'km2centroids': aln_convertion_util.c:9671:13: warning: variable 'S' set but not used [-Wunused-but-set-variable] aln_convertion_util.c:9669:9: warning: variable 'group' set but not used [-Wunused-but-set-variable] aln_convertion_util.c:9667:9: warning: unused variable 'b' [-Wunused-variable] aln_convertion_util.c: In function 'km_group2centroid': aln_convertion_util.c:9701:13: warning: unused variable 'gs' [-Wunused-variable] aln_convertion_util.c: In function 'seq2id_subset': aln_convertion_util.c:9855:12: warning: unused variable 'tmpfile' [-Wunused-variable] aln_convertion_util.c:9852:11: warning: unused variable 'n2' [-Wunused-variable] aln_convertion_util.c:9829:7: warning: unused variable 'count' [-Wunused-variable] aln_convertion_util.c:9827:16: warning: unused variable 'file2' [-Wunused-variable] aln_convertion_util.c: In function 'km_seq': aln_convertion_util.c:9901:9: warning: unused variable 'sd' [-Wunused-variable] aln_convertion_util.c:9900:9: warning: unused variable 'b' [-Wunused-variable] aln_convertion_util.c: In function 'simple_trimseq': aln_convertion_util.c:10178:11: warning: unused variable 'b' [-Wunused-variable] aln_convertion_util.c:10071:9: warning: unused variable 'b' [-Wunused-variable] aln_convertion_util.c: In function 'test_gene2prot': aln_convertion_util.c:11766:17: warning: unused variable 'entry' [-Wunused-variable] aln_convertion_util.c: In function 'pw_aln2clean_pw_aln_fsa2': aln_convertion_util.c:12465:11: warning: unused variable 'v' [-Wunused-variable] aln_convertion_util.c:12262:7: warning: unused variable 'model_type' [-Wunused-variable] aln_convertion_util.c:12259:7: warning: variable 'MID_EXON_FACTOR' set but not used [-Wunused-but-set-variable] aln_convertion_util.c:12257:39: warning: unused variable 'K' [-Wunused-variable] aln_convertion_util.c:12257:35: warning: unused variable 'G2' [-Wunused-variable] aln_convertion_util.c:12257:32: warning: unused variable 'G1' [-Wunused-variable] aln_convertion_util.c:12254:7: warning: unused variable 'T0' [-Wunused-variable] aln_convertion_util.c:12253:19: warning: unused variable 'e1' [-Wunused-variable] aln_convertion_util.c:12253:15: warning: unused variable 'e0' [-Wunused-variable] aln_convertion_util.c:12252:16: warning: unused variable 'd' [-Wunused-variable] aln_convertion_util.c: In function 'pw_aln2clean_pw_aln_fsa1': aln_convertion_util.c:12489:26: warning: unused variable 'K' [-Wunused-variable] aln_convertion_util.c:12486:7: warning: unused variable 'T0' [-Wunused-variable] aln_convertion_util.c:12485:19: warning: unused variable 'e1' [-Wunused-variable] aln_convertion_util.c:12485:15: warning: unused variable 'e0' [-Wunused-variable] aln_convertion_util.c:12484:16: warning: unused variable 'd' [-Wunused-variable] aln_convertion_util.c: In function 'aln2pred': aln_convertion_util.c:12766:9: warning: array subscript has type 'char' [-Wchar-subscripts] aln_convertion_util.c:12766:9: warning: array subscript has type 'char' [-Wchar-subscripts] aln_convertion_util.c:12682:7: warning: unused variable 'print' [-Wunused-variable] aln_convertion_util.c:12681:29: warning: unused variable 'result' [-Wunused-variable] aln_convertion_util.c:12678:10: warning: unused variable 'N' [-Wunused-variable] aln_convertion_util.c:12678:7: warning: unused variable 'T' [-Wunused-variable] aln_convertion_util.c: In function 'mark_exon_boundaries': aln_convertion_util.c:12840:4: warning: suggest parentheses around '&&' within '||' [-Wparentheses] aln_convertion_util.c: In function 'simple_trimseq2': aln_convertion_util.c:12872:12: warning: unused variable 'a' [-Wunused-variable] aln_convertion_util.c: At top level: io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] aln_convertion_util.c: In function 'aln2N_replicate': aln_convertion_util.c:6943:1: warning: control reaches end of non-void function [-Wreturn-type] aln_convertion_util.c: In function 'extract_aln3': aln_convertion_util.c:6705:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] aln_convertion_util.c:6724:31: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] aln_convertion_util.c:6728:13: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] aln_convertion_util.c: In function 'aln2conservation': aln_convertion_util.c:3962:1: warning: control reaches end of non-void function [-Wreturn-type] aln_convertion_util.c: In function 'filter_aln_convert': aln_convertion_util.c:2924:14: warning: 'c' may be used uninitialized in this function [-Wuninitialized] aln_convertion_util.c: In function 'aln_column2string': aln_convertion_util.c:4532:5: warning: 's' may be used uninitialized in this function [-Wuninitialized] aln_convertion_util.c: In function 'invert_aln': aln_convertion_util.c:6505:8: 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:8563:36: warning: 'min' may be used uninitialized in this function [-Wuninitialized] aln_convertion_util.c:8563:51: warning: 'max' may be used uninitialized in this function [-Wuninitialized] aln_convertion_util.c: In function 'km_group2centroid': aln_convertion_util.c:9701:16: warning: 'ba' may be used uninitialized in this function [-Wuninitialized] aln_convertion_util.c: In function 'sar_aln2motif': aln_convertion_util.c:2999:3: warning: 'i' may be used uninitialized in this function [-Wuninitialized] aln_convertion_util.c:2998:3: warning: 'o' may be used uninitialized in this function [-Wuninitialized] aln_convertion_util.c: In function 'make_group_aa_upgma': aln_convertion_util.c:11587:14: warning: 'ba' may be used uninitialized in this function [-Wuninitialized] aln_convertion_util.c: In function 'aln2conservation': aln_convertion_util.c:3940:18: warning: 'c1' may be used uninitialized in this function [-Wuninitialized] aln_convertion_util.c: In function 'seq2blast': aln_convertion_util.c:1335:3: 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:12451:22: 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:12616:22: warning: 'best' may be used uninitialized in this function [-Wuninitialized] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -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: In function 'duplicate_sequence': util_declare.c:685:18: warning: unused variable 'i' [-Wunused-variable] util_declare.c:682:18: warning: unused variable 'len' [-Wunused-variable] util_declare.c: At top level: io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o hsearch.o hsearch.c io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o random.o random.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_make_tree.o util_make_tree.c util_make_tree.c: In function 'redundate': util_make_tree.c:32:9: warning: unused variable 'fp' [-Wunused-variable] util_make_tree.c: In function 'aln2km_vector': util_make_tree.c:1311:11: warning: unused variable 'window' [-Wunused-variable] util_make_tree.c:1326:11: warning: unused variable 'window' [-Wunused-variable] util_make_tree.c: In function 'aln2km_tree': util_make_tree.c:1508:13: warning: variable 'S' set but not used [-Wunused-but-set-variable] util_make_tree.c: In function 'rec_km_tree': util_make_tree.c:1571:11: warning: unused variable 'd' [-Wunused-variable] util_make_tree.c:1529:14: warning: unused variable 'A' [-Wunused-variable] util_make_tree.c: In function 'expand_km_node': util_make_tree.c:1607:9: warning: unused variable 'b' [-Wunused-variable] util_make_tree.c: At top level: io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] util_make_tree.c:1252:12: warning: 'count' defined but not used [-Wunused-variable] util_make_tree.c: In function 'redundate': util_make_tree.c:40:1: warning: control reaches end of non-void function [-Wreturn-type] util_make_tree.c: In function 'upgma_merge_aln_rows': util_make_tree.c:1193:7: warning: 'best_b' may be used uninitialized in this function [-Wuninitialized] util_make_tree.c:1196:6: warning: 'best_a' may be used uninitialized in this function [-Wuninitialized] util_make_tree.c: In function 'aln2km_vector': util_make_tree.c:1367:21: warning: 'c' may be used uninitialized in this function [-Wuninitialized] util_make_tree.c: In function 'upgma_merge': util_make_tree.c:1723:9: warning: 'best_s' may be used uninitialized in this function [-Wuninitialized] util_make_tree.c:1693:24: warning: 'best_b' may be used uninitialized in this function [-Wuninitialized] util_make_tree.c:1693:16: warning: 'best_a' may be used uninitialized in this function [-Wuninitialized] util_make_tree.c: In function 'int_dist2upgma_tree': util_make_tree.c:1684:11: warning: 'T' may be used uninitialized in this function [-Wuninitialized] util_make_tree.c: In function 'split_upgma_merge': util_make_tree.c:1837:9: warning: 'best_s' may be used uninitialized in this function [-Wuninitialized] util_make_tree.c:1836:8: warning: 'best_b' may be used uninitialized in this function [-Wuninitialized] util_make_tree.c:1835:8: warning: 'best_a' may be used uninitialized in this function [-Wuninitialized] util_make_tree.c: In function 'split2upgma_tree': util_make_tree.c:1793:3: warning: 'T' may be used uninitialized in this function [-Wuninitialized] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util.o util.c util.c: In function 'cmp_list_int2': util.c:567:10: warning: unused variable 'd' [-Wunused-variable] util.c: In function 'cmp_list_int': util.c:699:6: warning: variable 'ret' set but not used [-Wunused-but-set-variable] util.c: In function 'fprintf_fork': util.c:3684:9: warning: unused variable 'flag' [-Wunused-variable] util.c: In function 'printf_system': util.c:3778:16: warning: unused variable 'cdir' [-Wunused-variable] util.c:3777:16: warning: unused variable 'tmpdir' [-Wunused-variable] util.c: In function 'vvfork': util.c:4215:7: warning: implicit declaration of function 'wait' [-Wimplicit-function-declaration] util.c: In function 'vwaitpid': util.c:4264:3: warning: implicit declaration of function 'waitpid' [-Wimplicit-function-declaration] util.c: In function 'get_lockdir_4_tcoffee': util.c:4709:12: warning: unused variable 'buf' [-Wunused-variable] util.c: In function 'my_rmdir': util.c:7392:9: warning: unused variable 'buf' [-Wunused-variable] util.c:7392:6: warning: unused variable 'a' [-Wunused-variable] util.c:7390:7: warning: unused variable 'dir_sep' [-Wunused-variable] util.c: In function 'clean_exit': util.c:8629:9: warning: unused variable 'tmp' [-Wunused-variable] util.c:8628:12: warning: variable 'b' set but not used [-Wunused-but-set-variable] util.c: In function 'bachup_env': util.c:8850:16: warning: variable 'buf' set but not used [-Wunused-but-set-variable] util.c: In function 'km_main': util.c:8892:7: warning: unused variable 'scan' [-Wunused-variable] util.c:8886:10: warning: unused variable 'b' [-Wunused-variable] util.c:8883:20: warning: unused variable 'sdata' [-Wunused-variable] util.c: In function 'km_file2dim': util.c:8971:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] util.c:8990:3: warning: statement with no effect [-Wunused-value] util.c:8954:14: warning: variable 's2' set but not used [-Wunused-but-set-variable] util.c:8947:12: warning: unused variable 'data' [-Wunused-variable] util.c: In function 'km_read_data': util.c:9017:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] util.c:9003:11: warning: unused variable 'c' [-Wunused-variable] util.c: In function 'km_kmeans_bs': util.c:9318:10: warning: unused variable 'cscore' [-Wunused-variable] util.c: At top level: io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] util.c:74:13: warning: 'exchange' defined but not used [-Wunused-function] util.c:4874:12: warning: 'n_warning' defined but not used [-Wunused-variable] util.c:4875:15: warning: 'warning_list' defined but not used [-Wunused-variable] util.c:7669:15: warning: 'EXP_UNDERFLOW_THRESHOLD' defined but not used [-Wunused-variable] util.c:7672:15: warning: 'LOG_ONE' defined but not used [-Wunused-variable] util.c: In function 'km_main': util.c:8930:1: warning: control reaches end of non-void function [-Wreturn-type] util.c: In function 'check_internet_connection': util.c:7123:1: warning: control reaches end of non-void function [-Wreturn-type] util.c: In function 'check_for_update': util.c:7035:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util.c: In function 'get_file_block_pattern': util.c:6918:11: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] util.c:6948:11: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] util.c: In function 'set_fp_id': util.c:6682:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util.c: In function 'get_parameter': util.c:6662:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] util.c: In function 'count_strings_in_file': util.c:4998:14: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util.c: In function 'kill_child_list': util.c:4333:1: warning: control reaches end of non-void function [-Wreturn-type] util.c: In function 'printf_system_direct_check': util.c:3759:1: warning: control reaches end of non-void function [-Wreturn-type] util.c: In function 'perl_strstr': util.c:1864:14: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util.c: In function 'get_pwd': util.c:1788:1: warning: control reaches end of non-void function [-Wreturn-type] util.c: In function 'input_array_int': util.c:1208:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util.c:1212:13: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util.c:1215:8: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util.c:1216:14: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util.c: In function 'quantile': util.c:821:14: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util.c: In function 'get_number_list_in_file': util.c:762:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] util.c: In function 'bsearch_file': util.c:341:13: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] util.c: In function 'hsort_file': util.c:202:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] util.c:207:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] util.c:210:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] util.c:227:15: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] util.c:232:11: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] util.c: In function 'festrstr': util.c:2074:6: warning: 'string' may be used uninitialized in this function [-Wuninitialized] util.c: In function 'r_generate_array_string_list': util.c:8317:10: warning: 'start' may be used uninitialized in this function [-Wuninitialized] util.c: In function 'lock': util.c:3967:9: warning: 'r' may be used uninitialized in this function [-Wuninitialized] util.c: In function 'km_kmeans': util.c:9219:7: warning: 'bestNewIndex' may be used uninitialized in this function [-Wuninitialized] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -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:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] reformat_struc.c: In function 'simple_read_ca_trace': reformat_struc.c:299:16: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat_struc.c:301:16: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat_struc.c:307:16: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat_struc.c:334:16: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat_struc.c:336:16: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat_struc.c:344:16: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat_struc.c: In function 'struclist2nb': reformat_struc.c:860:10: warning: 'R' may be used uninitialized in this function [-Wuninitialized] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o reformat.o reformat.c reformat.c: In function 'read_data_structure': reformat.c:877:12: warning: variable 'seq' set but not used [-Wunused-but-set-variable] reformat.c: In function 'identify_seq_format': reformat.c:1272:8: warning: implicit declaration of function 'is_stockholm_aln' [-Wimplicit-function-declaration] reformat.c:1275:5: warning: implicit declaration of function 'fast_format_determination' [-Wimplicit-function-declaration] reformat.c:1275:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses] reformat.c: In function 'is_pdb_struc': reformat.c:1531:11: warning: unused variable 'command' [-Wunused-variable] reformat.c: In function 'main_output': reformat.c:2416:23: warning: variable 'CL' set but not used [-Wunused-but-set-variable] reformat.c:2884:17: warning: variable 'A' set but not used [-Wunused-but-set-variable] reformat.c:3051:6: warning: implicit declaration of function 'output_header_mat' [-Wimplicit-function-declaration] reformat.c: In function 'get_fasta_sequence': reformat.c:4545:4: warning: array subscript has type 'char' [-Wchar-subscripts] reformat.c:4589:6: warning: array subscript has type 'char' [-Wchar-subscripts] reformat.c:4531:9: warning: unused variable 'name' [-Wunused-variable] reformat.c: In function 'output_generic_clustal_aln': reformat.c:7214:12: warning: unused variable 'nibit' [-Wunused-variable] reformat.c: In function 'unextend_seq': reformat.c:10271:12: warning: unused variable 'r2' [-Wunused-variable] reformat.c: In function 'modify_data': reformat.c:10515:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:10520:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:10687:23: warning: unused variable 'r2' [-Wunused-variable] reformat.c:10687:17: warning: unused variable 's2' [-Wunused-variable] reformat.c:10682:9: warning: unused variable 'l' [-Wunused-variable] reformat.c:10747:5: warning: implicit declaration of function 'redundate' [-Wimplicit-function-declaration] reformat.c:10753:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:10763:5: warning: implicit declaration of function 'tree2nnode_unresolved' [-Wimplicit-function-declaration] reformat.c:10852:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:10853:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:10860:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:10867:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:10957:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11062:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11596:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11596:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11603:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11604:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11605:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11606:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11607:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11608:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11575:10: warning: unused variable 'clean_mode' [-Wunused-variable] reformat.c:11572:22: warning: variable 't' set but not used [-Wunused-but-set-variable] reformat.c:11572:19: warning: variable 'f' set but not used [-Wunused-but-set-variable] reformat.c:11572:16: warning: unused variable 'p3' [-Wunused-variable] reformat.c:11572:13: warning: unused variable 'p2' [-Wunused-variable] reformat.c:11572:10: warning: unused variable 'p1' [-Wunused-variable] reformat.c:11631:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11755:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11756:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11760:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:11913:17: warning: variable 'A' set but not used [-Wunused-but-set-variable] reformat.c:12279:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:12280:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:12281:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:12282:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:12283:5: warning: null argument where non-null required (argument 1) [-Wnonnull] reformat.c:12273:10: warning: unused variable 'fname' [-Wunused-variable] reformat.c:12272:11: warning: unused variable 'fp' [-Wunused-variable] reformat.c:12270:33: warning: unused variable 'sp' [-Wunused-variable] reformat.c:12270:22: warning: unused variable 'sn' [-Wunused-variable] reformat.c: In function 'aln2mat': reformat.c:12523:3: warning: array subscript has type 'char' [-Wchar-subscripts] reformat.c: In function 'output_header_mat': reformat.c:12789:12: warning: variable 'l' set but not used [-Wunused-but-set-variable] reformat.c: At top level: io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] reformat.c: In function 'read_pavie_matrix': reformat.c:12886:12: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'output_header_mat': reformat.c:12814:1: warning: control reaches end of non-void function [-Wreturn-type] reformat.c: In function 'read_blast_matrix': reformat.c:12725:12: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] reformat.c:12735:13: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c:12748:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c:12775:12: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'output_suchard_aln': reformat.c:6801:1: warning: control reaches end of non-void function [-Wreturn-type] reformat.c: In function 'similarities_file2aln': reformat.c:5790:14: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'output_maln_pval': reformat.c:5625:12: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'read_gotoh_aln': reformat.c:5405:12: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] reformat.c:5427:12: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'get_amps_seq_name': reformat.c:5356:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'fscanf_seq_name': reformat.c:5003:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'get_swissprot_sequence': reformat.c:4965:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] reformat.c:4984:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'get_dialign_sequence': reformat.c:3804:12: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'get_sequence_dali': reformat.c:3729:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'get_struc_gor': reformat.c:3666:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c:3687:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c:3692:14: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'read_rna_struc_number': reformat.c:3466:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c:3469:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'get_amps_sd_scores': reformat.c:3158:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c:3165:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c:3174:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c:3180:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c:3182:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c:3193:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'fast_format_determination': reformat.c:1993:1: warning: control reaches end of non-void function [-Wreturn-type] reformat.c: In function 'format_is_msf': reformat.c:1890:12: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'get_pdb_id': reformat.c:1454:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'is_pdb_name': reformat.c:1416:14: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] reformat.c: In function 'fast_format_determination': reformat.c:1977:5: warning: 'last' may be used uninitialized in this function [-Wuninitialized] reformat.c: In function 'get_longest_frame': reformat.c:8626:3: warning: 'nf' may be used uninitialized in this function [-Wuninitialized] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o aln_compare.o aln_compare.c aln_compare.c: In function 'aln_compare': aln_compare.c:494:8: warning: suggest parentheses around assignment used as truth value [-Wparentheses] aln_compare.c:497:16: warning: unused variable 'c' [-Wunused-variable] aln_compare.c:496:9: warning: unused variable 'd' [-Wunused-variable] aln_compare.c:535:8: warning: suggest parentheses around assignment used as truth value [-Wparentheses] aln_compare.c:643:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses] aln_compare.c:737:5: 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:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] aln_compare.c: In function 'aln_compare': aln_compare.c:73:7: warning: 'correct_column' may be used uninitialized in this function [-Wuninitialized] aln_compare.c:604:16: warning: 'posA' may be used uninitialized in this function [-Wuninitialized] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o io_func.o io_func.c io_func.c: In function 'output_reliability_format_fasta': io_func.c:1041:23: warning: variable 'buf2' set but not used [-Wunused-but-set-variable] io_func.c:1038:17: warning: unused variable 'l' [-Wunused-variable] io_func.c: At top level: io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] io_func.c: In function 'get_rgb_values': io_func.c:625:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] io_func.c: In function 'read_matrice': io_func.c:428:16: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o pb_util_read_sequence.o pb_util_read_sequence.c io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] pb_util_read_sequence.c: In function 'get_clustal_seq': pb_util_read_sequence.c:118:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] pb_util_read_sequence.c:123:30: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] pb_util_read_sequence.c: In function 'get_msf_seq': pb_util_read_sequence.c:82:30: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] pb_util_read_sequence.c: In function 'get_seq': pb_util_read_sequence.c:157:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] pb_util_read_sequence.c:167:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] pb_util_read_sequence.c:187:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] pb_util_read_sequence.c:196:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] pb_util_read_sequence.c:223:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] pb_util_read_sequence.c:254:11: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o pb_util_read_seq_util.o pb_util_read_seq_util.c io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] pb_util_read_seq_util.c: In function 'do_system': pb_util_read_seq_util.c:302:9: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] pb_util_read_seq_util.c: In function 'getint': pb_util_read_seq_util.c:280:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] pb_util_read_seq_util.c: In function 'getreal': pb_util_read_seq_util.c:255:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] pb_util_read_seq_util.c: In function 'getstr': pb_util_read_seq_util.c:244:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o tree_util.o tree_util.c tree_util.c: In function 'tree_scan': tree_util.c:814:2: warning: too many arguments for format [-Wformat-extra-args] tree_util.c:842:32: warning: variable 'best_w2' set but not used [-Wunused-but-set-variable] tree_util.c: In function 'tree_cmp': tree_util.c:1080:7: warning: unused variable 'a' [-Wunused-variable] tree_util.c:1079:7: warning: unused variable 'n' [-Wunused-variable] tree_util.c: In function 'free_read_tree': tree_util.c:2497:10: warning: variable 's' set but not used [-Wunused-but-set-variable] tree_util.c: In function 'read_tree': tree_util.c:2523:8: warning: variable 'flag' set but not used [-Wunused-but-set-variable] tree_util.c: In function 'find_seq_chain': tree_util.c:3322:11: warning: variable 'delta_seq2' set but not used [-Wunused-but-set-variable] tree_util.c: In function 'treelist2leafgroup': tree_util.c:4170:11: warning: variable 'i' set but not used [-Wunused-but-set-variable] tree_util.c:4130:8: warning: variable 'used' set but not used [-Wunused-but-set-variable] tree_util.c: In function 'treelist2splits': tree_util.c:4592:8: warning: variable 'used' set but not used [-Wunused-but-set-variable] tree_util.c: In function 'treelist2splits_old': tree_util.c:4679:8: warning: variable 'used' set but not used [-Wunused-but-set-variable] tree_util.c: In function 'treelist2prune_treelist': tree_util.c:4761:13: warning: unused variable 'c' [-Wunused-variable] tree_util.c: In function 'treelist2frame': tree_util.c:4804:18: warning: unused variable 'd' [-Wunused-variable] tree_util.c:4804:16: warning: unused variable 'c' [-Wunused-variable] tree_util.c:4804:13: warning: unused variable 'b' [-Wunused-variable] tree_util.c: In function 'treelist2lti2': tree_util.c:4833:28: warning: unused variable 'i' [-Wunused-variable] tree_util.c:4833:22: warning: unused variable 'dist' [-Wunused-variable] tree_util.c:4833:15: warning: unused variable 'd' [-Wunused-variable] tree_util.c:4833:12: warning: unused variable 'c' [-Wunused-variable] tree_util.c:4832:12: warning: unused variable 'T' [-Wunused-variable] tree_util.c: In function 'treelist2lti': tree_util.c:4879:19: warning: unused variable 'score1' [-Wunused-variable] tree_util.c:4879:9: warning: unused variable 'score0' [-Wunused-variable] tree_util.c: In function 'treelist2groups': tree_util.c:5018:8: warning: unused variable 'cov' [-Wunused-variable] tree_util.c: In function 'simple_tree_cmp': tree_util.c:5088:18: warning: variable 'n' set but not used [-Wunused-but-set-variable] tree_util.c: In function 'treelist2bootstrap': tree_util.c:5205:9: warning: unused variable 'fp' [-Wunused-variable] tree_util.c: In function 'treelist2seq': tree_util.c:5228:13: warning: unused variable 'c' [-Wunused-variable] tree_util.c: In function 'treelist2sub_seq': tree_util.c:5266:20: warning: variable 'n' set but not used [-Wunused-but-set-variable] tree_util.c: In function 'treelist2frame': tree_util.c:4829:1: warning: control reaches end of non-void function [-Wreturn-type] tree_util.c: In function 'treelist2splits_old': tree_util.c:4756:1: warning: control reaches end of non-void function [-Wreturn-type] tree_util.c: In function 'treelist2splits': tree_util.c:4672:1: warning: control reaches end of non-void function [-Wreturn-type] tree_util.c: In function 'count_tree_groups': tree_util.c:4322:1: warning: control reaches end of non-void function [-Wreturn-type] tree_util.c: In function 'treelist2leafgroup': tree_util.c:4219:1: warning: control reaches end of non-void function [-Wreturn-type] tree_util.c: In function 'node_sort': tree_util.c:4003:1: warning: control reaches end of non-void function [-Wreturn-type] tree_util.c: In function 'create_tree': tree_util.c:2782:16: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] tree_util.c:2790:12: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] tree_util.c: In function 'compute_std_tree_2': tree_util.c:1543:8: warning: 'T' may be used uninitialized in this function [-Wuninitialized] tree_util.c: In function 'tree_scan_multiple_pos': tree_util.c:994:15: warning: 'n' may be used uninitialized in this function [-Wuninitialized] tree_util.c: In function 'count_splits': tree_util.c:4384:11: warning: 'OrderT' may be used uninitialized in this function [-Wuninitialized] tree_util.c: In function 'treelist2sub_seq': tree_util.c:5323:6: warning: 'tot' may be used uninitialized in this function [-Wuninitialized] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -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:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_dp_clean_maln.o util_dp_clean_maln.c io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_dp_ssec_pwaln.o util_dp_ssec_pwaln.c io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_dp_sim.o util_dp_sim.c io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -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:188:20: warning: variable 'ma' set but not used [-Wunused-but-set-variable] util_dp_mm_nw.c: At top level: io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -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:928:11: warning: unused variable 'fop2' [-Wunused-variable] util_dp_gotoh_nw.c:787:6: warning: unused variable 'ibit' [-Wunused-variable] util_dp_gotoh_nw.c: In function 'cl2list_borders': util_dp_gotoh_nw.c:1362:9: warning: unused variable 'pos' [-Wunused-variable] util_dp_gotoh_nw.c:1361:9: warning: unused variable 'list' [-Wunused-variable] util_dp_gotoh_nw.c:1360:10: warning: unused variable 'n' [-Wunused-variable] util_dp_gotoh_nw.c: In function 'cl2diag_cap': util_dp_gotoh_nw.c:1511:7: warning: unused variable 'nt' [-Wunused-variable] util_dp_gotoh_nw.c:1510:7: warning: unused variable 'ns' [-Wunused-variable] util_dp_gotoh_nw.c:1504:7: warning: unused variable 'k' [-Wunused-variable] util_dp_gotoh_nw.c:1502:7: warning: unused variable 'max_n' [-Wunused-variable] util_dp_gotoh_nw.c: In function 'fork_cl2pair_list_ext': util_dp_gotoh_nw.c:1671:44: warning: unused variable 'new' [-Wunused-variable] util_dp_gotoh_nw.c:1671:37: warning: unused variable 'avg' [-Wunused-variable] util_dp_gotoh_nw.c: In function 'linked_pair_wise': util_dp_gotoh_nw.c:1803:14: warning: unused variable 'a' [-Wunused-variable] util_dp_gotoh_nw.c: In function 'list2linked_pair_wise': util_dp_gotoh_nw.c:1934:44: warning: operation on '*(MJ + (unsigned int)((unsigned int)(a * 5 + b) * 4u))' may be undefined [-Wsequence-point] util_dp_gotoh_nw.c:1902:7: warning: unused variable 'nomatch' [-Wunused-variable] util_dp_gotoh_nw.c:1891:44: warning: variable 'prev_j' set but not used [-Wunused-but-set-variable] util_dp_gotoh_nw.c:1891:36: 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:2176:14: warning: unused variable 'a' [-Wunused-variable] util_dp_gotoh_nw.c: In function 'collapse_list': util_dp_gotoh_nw.c:2204:32: warning: unused variable 'cr2' [-Wunused-variable] util_dp_gotoh_nw.c: In function 'cl2pair_list_collapse': util_dp_gotoh_nw.c:2312:44: warning: unused variable 'new' [-Wunused-variable] util_dp_gotoh_nw.c:2312:37: warning: unused variable 'avg' [-Wunused-variable] util_dp_gotoh_nw.c:2306:7: warning: unused variable 'si' [-Wunused-variable] util_dp_gotoh_nw.c: In function 'aln2prf': util_dp_gotoh_nw.c:2594:4: warning: implicit declaration of function 'tolower' [-Wimplicit-function-declaration] util_dp_gotoh_nw.c: At top level: io_lib_header.h:971:16: 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:2071:7: warning: 'start_trace' may be used uninitialized in this function [-Wuninitialized] util_dp_gotoh_nw.c: In function 'add_sequence2prf': util_dp_gotoh_nw.c:2617:7: warning: 'li' may be used uninitialized in this function [-Wuninitialized] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -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:200:3: warning: implicit declaration of function 'idscore_pairseq' [-Wimplicit-function-declaration] util_dp_suboptimal_nw.c:133:34: warning: variable 'thres' set but not used [-Wunused-but-set-variable] util_dp_suboptimal_nw.c:133:26: 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:616:3: warning: implicit declaration of function 'proba_pair_wise' [-Wimplicit-function-declaration] util_dp_suboptimal_nw.c: In function 'get_tot_prob': util_dp_suboptimal_nw.c:896:14: warning: unused variable 'gtp' [-Wunused-variable] util_dp_suboptimal_nw.c: In function 'ProbaMatrix2CL': util_dp_suboptimal_nw.c:1112:7: warning: unused variable 'sim' [-Wunused-variable] util_dp_suboptimal_nw.c:1108:16: warning: unused variable 'k' [-Wunused-variable] util_dp_suboptimal_nw.c: In function 'backward_proba_pair_wise': util_dp_suboptimal_nw.c:1215:12: warning: variable 'c2' set but not used [-Wunused-but-set-variable] util_dp_suboptimal_nw.c:1215:8: 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:1309:17: warning: variable 'iter2' set but not used [-Wunused-but-set-variable] util_dp_suboptimal_nw.c:1309:9: 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:1668:15: warning: unused variable 'c' [-Wunused-variable] util_dp_suboptimal_nw.c: At top level: io_lib_header.h:971:16: 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_dp_cdna_fasta_nw.o util_dp_cdna_fasta_nw.c io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_dp_generic_fasta_nw.o util_dp_generic_fasta_nw.c io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -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:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_dp_fasta_sw.o util_dp_fasta_sw.c io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_dp_gotoh_sw.o util_dp_gotoh_sw.c io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] util_dp_gotoh_sw.c: In function 'gotoh_pair_wise_sw': util_dp_gotoh_sw.c:365:14: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_dp_est.o util_dp_est.c io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -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:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_dp_drivers.o util_dp_drivers.c util_dp_drivers.c: In function 'profile2list': util_dp_drivers.c:34:14: warning: variable 'M' set but not used [-Wunused-but-set-variable] util_dp_drivers.c:30:25: warning: unused variable 'RCL' [-Wunused-variable] util_dp_drivers.c:29:27: warning: unused variable 'w2' [-Wunused-variable] util_dp_drivers.c:29:24: warning: unused variable 'r2' [-Wunused-variable] util_dp_drivers.c:29:16: 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:318:17: warning: variable 'S' set but not used [-Wunused-but-set-variable] util_dp_drivers.c: In function 'hh_pair': util_dp_drivers.c:1001:25: warning: unused variable 'c' [-Wunused-variable] util_dp_drivers.c: In function 'thread_pair2': util_dp_drivers.c:1429:15: warning: variable 'STL' set but not used [-Wunused-but-set-variable] util_dp_drivers.c: In function 'sap_pair': util_dp_drivers.c:1647:7: warning: implicit declaration of function 'isalpha' [-Wimplicit-function-declaration] util_dp_drivers.c:1555:52: warning: unused variable 'string5' [-Wunused-variable] util_dp_drivers.c:1555:42: warning: unused variable 'string4' [-Wunused-variable] util_dp_drivers.c:1555:32: warning: unused variable 'string3' [-Wunused-variable] util_dp_drivers.c:1555:22: warning: unused variable 'string2' [-Wunused-variable] util_dp_drivers.c:1555:12: warning: unused variable 'string1' [-Wunused-variable] util_dp_drivers.c: In function 'best_pair4rna': util_dp_drivers.c:1794:13: warning: variable 'M' set but not used [-Wunused-but-set-variable] util_dp_drivers.c:1790:19: warning: variable 'PW_CL' set but not used [-Wunused-but-set-variable] util_dp_drivers.c:1789:13: warning: variable 'A' set but not used [-Wunused-but-set-variable] util_dp_drivers.c: In function 'best_pair4prot': util_dp_drivers.c:1877:14: warning: variable 'M' set but not used [-Wunused-but-set-variable] util_dp_drivers.c:1873:20: warning: variable 'PW_CL' set but not used [-Wunused-but-set-variable] util_dp_drivers.c:1872:14: warning: variable 'A' set but not used [-Wunused-but-set-variable] util_dp_drivers.c: In function 'fast_pair': util_dp_drivers.c:1965:10: warning: variable 'score' set but not used [-Wunused-but-set-variable] util_dp_drivers.c: In function 'realign_aln_best': util_dp_drivers.c:2553:9: warning: unused variable 'gc' [-Wunused-variable] util_dp_drivers.c:2552:14: warning: unused variable 'n' [-Wunused-variable] util_dp_drivers.c:2552:12: warning: unused variable 'p' [-Wunused-variable] util_dp_drivers.c: In function 'realign_aln_random_bipart': util_dp_drivers.c:2608:9: warning: unused variable 'gc' [-Wunused-variable] util_dp_drivers.c:2607:12: warning: unused variable 'n' [-Wunused-variable] util_dp_drivers.c: In function 'seq_aln': util_dp_drivers.c:2861:21: warning: variable 'n1' set but not used [-Wunused-but-set-variable] util_dp_drivers.c: In function 'sorted_aln_old': util_dp_drivers.c:3162:3: warning: implicit declaration of function 'sa_align_groups' [-Wimplicit-function-declaration] util_dp_drivers.c:3152:7: warning: unused variable 'a' [-Wunused-variable] util_dp_drivers.c: In function 'add_group2sorted_aln': util_dp_drivers.c:3174:10: warning: unused variable 'next' [-Wunused-variable] util_dp_drivers.c: In function 'sa2sc': util_dp_drivers.c:3225:7: warning: implicit declaration of function 'tolower' [-Wimplicit-function-declaration] util_dp_drivers.c: In function 'sa_get_next': util_dp_drivers.c:3248:15: warning: operation on 'CL->DM' may be undefined [-Wsequence-point] util_dp_drivers.c:3241:13: warning: unused variable 'c' [-Wunused-variable] util_dp_drivers.c: In function 'sorted_aln_new': util_dp_drivers.c:3274:9: warning: unused variable 'g' [-Wunused-variable] util_dp_drivers.c: In function 'sa_get_next_group': util_dp_drivers.c:3339:12: warning: type defaults to 'int' in declaration of 'sim2' [-Wimplicit-int] util_dp_drivers.c:3344:15: warning: operation on 'CL->DM' may be undefined [-Wsequence-point] util_dp_drivers.c:3339:12: warning: unused variable 'sim2' [-Wunused-variable] util_dp_drivers.c:3337:13: warning: unused variable 'c' [-Wunused-variable] util_dp_drivers.c: In function 'sorted_aln_seq': util_dp_drivers.c:3366:7: warning: variable 'old_seq' set but not used [-Wunused-but-set-variable] util_dp_drivers.c: In function 'tree_aln': util_dp_drivers.c:3597:7: warning: unused variable 'a' [-Wunused-variable] util_dp_drivers.c: In function 'tree_realn': util_dp_drivers.c:3979:25: warning: variable 'id2' set but not used [-Wunused-but-set-variable] util_dp_drivers.c:3979:20: warning: variable 'id1' set but not used [-Wunused-but-set-variable] util_dp_drivers.c: In function 'set_profile_master': util_dp_drivers.c:4681:7: warning: unused variable 'mode' [-Wunused-variable] util_dp_drivers.c: In function 'pair_wise_ms': util_dp_drivers.c:4783:17: warning: unused variable 'd' [-Wunused-variable] util_dp_drivers.c:4771:13: warning: unused variable 'a' [-Wunused-variable] util_dp_drivers.c: In function 'sorted_aln': util_dp_drivers.c:5511:11: warning: operation on 'CL->DM' may be undefined [-Wsequence-point] util_dp_drivers.c: In function 'tree_aln_N': util_dp_drivers.c:5726:7: warning: unused variable 'a' [-Wunused-variable] util_dp_drivers.c: In function 'rec_tree_aln_N': util_dp_drivers.c:5739:11: warning: 'return' with no value, in function returning non-void [-Wreturn-type] util_dp_drivers.c: At top level: io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] util_dp_drivers.c: In function 'rna_pair': util_dp_drivers.c:1735:6: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c: In function 'sap_pair': util_dp_drivers.c:1560:10: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c:1611:10: warning: ignoring return value of 'getcwd', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c:1612:9: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c:1621:9: warning: ignoring return value of 'chdir', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c: In function 'lsqman_pair': util_dp_drivers.c:1488:8: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c: In function 'thread_pair': util_dp_drivers.c:1413:8: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c: In function 'pdb_pair': util_dp_drivers.c:1274:8: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c: In function 'pdbid_pair': util_dp_drivers.c:1214:8: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c: In function 'profile_pair': util_dp_drivers.c:1119:8: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c: In function 'hh_pair': util_dp_drivers.c:1011:8: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c:1065:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c: In function 'align_pdb_pair': util_dp_drivers.c:970:10: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c: In function 'align_pdb_pair_2': util_dp_drivers.c:942:10: warning: ignoring return value of 'atoi', declared with attribute warn_unused_result [-Wunused-result] util_dp_drivers.c: In function 'sap_pair': util_dp_drivers.c:1703:14: warning: 'sap_lib' may be used uninitialized in this function [-Wuninitialized] util_dp_drivers.c: In function 'get_next_best': util_dp_drivers.c:3129:3: warning: 'bseq' may be used uninitialized in this function [-Wuninitialized] util_dp_drivers.c:3122:22: warning: 'bd' may be used uninitialized in this function [-Wuninitialized] util_dp_drivers.c: In function 'mpw_gap_padd': util_dp_drivers.c:4995:17: warning: 'p1' may be used uninitialized in this function [-Wuninitialized] util_dp_drivers.c: In function 'pair_wise_ms': util_dp_drivers.c:4889:14: warning: 'cpos' may be used uninitialized in this function [-Wuninitialized] util_dp_drivers.c:4860:10: warning: 'p' may be used uninitialized in this function [-Wuninitialized] util_dp_drivers.c: In function 'rec_local_tree_aln': util_dp_drivers.c:3765:16: warning: 'pid2' may be used uninitialized in this function [-Wuninitialized] util_dp_drivers.c: In function 'sa_align_groups': util_dp_drivers.c:3306:6: warning: 'g0' 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_domain_dp.o util_domain_dp.c io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o CUSTOM_evaluate_for_struc.o CUSTOM_evaluate_for_struc.c io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o evaluate_for_struc.o evaluate_for_struc.c evaluate_for_struc.c: In function 'apdb': evaluate_for_struc.c:91:8: warning: unused variable 'strike' [-Wunused-variable] 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:2348:19: warning: variable 'cont' set but not used [-Wunused-but-set-variable] evaluate_for_struc.c:2348:13: warning: unused variable 'tree' [-Wunused-variable] evaluate_for_struc.c:2237:7: warning: unused variable 'proceed' [-Wunused-variable] evaluate_for_struc.c:2223:16: warning: variable 'ntree2' set but not used [-Wunused-but-set-variable] evaluate_for_struc.c:2221:10: warning: variable 'pair_pos_list' set but not used [-Wunused-but-set-variable] evaluate_for_struc.c:2219:24: warning: variable 'PT' set but not used [-Wunused-but-set-variable] evaluate_for_struc.c:2219:20: warning: variable 'T2' set but not used [-Wunused-but-set-variable] evaluate_for_struc.c:2219:12: warning: unused variable 'T0' [-Wunused-variable] evaluate_for_struc.c:2217:17: warning: unused variable 'rapdb' [-Wunused-variable] evaluate_for_struc.c:2217:9: warning: unused variable 'nrapdb' [-Wunused-variable] evaluate_for_struc.c:2216:7: warning: unused variable 'print_rapdb' [-Wunused-variable] evaluate_for_struc.c:2210:7: warning: unused variable 'in_bubble' [-Wunused-variable] evaluate_for_struc.c:2209:12: warning: unused variable 'wd2' [-Wunused-variable] evaluate_for_struc.c:2209:7: warning: unused variable 'wd1' [-Wunused-variable] evaluate_for_struc.c:2207:24: warning: unused variable 'n' [-Wunused-variable] evaluate_for_struc.c:2207:13: warning: variable 'ncol' set but not used [-Wunused-but-set-variable] evaluate_for_struc.c:2205:14: warning: unused variable 'pdb_param' [-Wunused-variable] evaluate_for_struc.c:2196:14: warning: unused variable 'max' [-Wunused-variable] evaluate_for_struc.c:2196:9: warning: unused variable 'min' [-Wunused-variable] evaluate_for_struc.c:2192:13: warning: unused variable 'distances' [-Wunused-variable] evaluate_for_struc.c:2188:19: warning: unused variable 'c' [-Wunused-variable] evaluate_for_struc.c: In function 'aln_column_contains_gap': evaluate_for_struc.c:2563:10: warning: unused variable 'b' [-Wunused-variable] evaluate_for_struc.c: In function 'aln2ncol4trmsd': evaluate_for_struc.c:2577:26: warning: variable 'rs1' set but not used [-Wunused-but-set-variable] evaluate_for_struc.c: In function 'display_rna_ss': evaluate_for_struc.c:2831:14: warning: variable 'thread' set but not used [-Wunused-but-set-variable] evaluate_for_struc.c: At top level: io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] evaluate_for_struc.c: In function 'trmsdmat2tree': evaluate_for_struc.c:2507:45: warning: 'max' may be used uninitialized in this function [-Wuninitialized] evaluate_for_struc.c: In function 'msa2struc_dist': evaluate_for_struc.c:2356:37: warning: 'PP' may be used uninitialized in this function [-Wuninitialized] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o evaluate_for_domain.o evaluate_for_domain.c io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -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:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] evaluate_dirichlet.c: In function 'read_dirichlet': evaluate_dirichlet.c:291:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] evaluate_dirichlet.c:293:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] evaluate_dirichlet.c:297:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] evaluate_dirichlet.c:300:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -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:1992:30: warning: unused variable 'b2' [-Wunused-variable] evaluate.c: In function 'residue_pair_extended_list_quadruplet': evaluate.c:2162:8: warning: variable 'field' set but not used [-Wunused-but-set-variable] evaluate.c: In function 'residue_pair_extended_list_pc': evaluate.c:2540:8: warning: unused variable 'nclean' [-Wunused-variable] evaluate.c: In function 'id2_profile_get_dp_cost': evaluate.c:3452:5: warning: array subscript has type 'char' [-Wchar-subscripts] evaluate.c:3453:5: warning: array subscript has type 'char' [-Wchar-subscripts] evaluate.c:3453:5: warning: array subscript has type 'char' [-Wchar-subscripts] evaluate.c:3454:5: warning: array subscript has type 'char' [-Wchar-subscripts] evaluate.c:3454:5: warning: array subscript has type 'char' [-Wchar-subscripts] evaluate.c:3461:10: warning: unused variable 'r' [-Wunused-variable] evaluate.c:3433:14: warning: unused variable 'r' [-Wunused-variable] evaluate.c: In function 'consensus_get_dp_cost': evaluate.c:3507:30: warning: variable 'lenls2' set but not used [-Wunused-but-set-variable] evaluate.c:3507:22: warning: variable 'lenls1' set but not used [-Wunused-but-set-variable] evaluate.c: In function 'combine_two_matrices': evaluate.c:5025:20: warning: operation on '*(*(mat2 + (unsigned int)((unsigned int)Re1 * 4u)) + (unsigned int)((unsigned int)Re2 * 4u))' may be undefined [-Wsequence-point] evaluate.c: At top level: io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] evaluate.c: In function 'initialise_aa_physico_chemical_property_table': evaluate.c:4849:16: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] evaluate.c: In function 'fork_triplet_coffee_evaluate_output': evaluate.c:749:12: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] evaluate.c:754:12: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] evaluate.c:759:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] 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:2047:59: warning: 'RF' may be used uninitialized in this function [-Wuninitialized] evaluate.c: In function 'evaluate_tm_matrix_score': evaluate.c:2025:59: warning: 'RF' may be used uninitialized in this function [-Wuninitialized] evaluate.c: In function 'lat_sum_pair': evaluate.c:5067:13: warning: 'score' may be used uninitialized in this function [-Wuninitialized] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o showpair.o showpair.c io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -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:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o pavie_dp.o pavie_dp.c io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] pavie_dp.c: In function 'pavie_seq2pavie_msa': pavie_dp.c:1339:14: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] pavie_dp.c: In function 'output_pavie_mat_list': pavie_dp.c:1053:15: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] pavie_dp.c:1055:14: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] pavie_dp.c: In function 'pavie_seq2pavie_aln': pavie_dp.c:101:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -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:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o dev2.o dev2.c io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o dev3.o dev3.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o dev4.o dev4.c io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -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 + (unsigned int)((unsigned int)(a * 5 + b) * 4u))' 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:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] fastal.c: In function 'edit2alignment': fastal.c:3567:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:3569:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:3571:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:3573:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:3635:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c: In function 'edit_seq2aligned_seq': fastal.c:3494:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c: In function 'profile_file2profile': fastal.c:3315:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:3318:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:3321:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:3323:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:3325:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:3344:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c: In function 'file_pos2profile': fastal.c:3193:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c: In function 'seq_pair2blastz_diagonal': fastal.c:2251:8: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] fastal.c: In function 'seq_pair2blat_diagonal': fastal.c:2104:8: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] fastal.c: In function 'seq_pair2blast_diagonal': fastal.c:1913:8: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] fastal.c:1918:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:1919:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:1920:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:1965:9: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] fastal.c:1969:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:1970:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fastal.c:1971:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -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:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] parttree.c: In function 'euclidean_dist_half': parttree.c:925:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] parttree.c:936:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] parttree.c: In function 'euclidean_dist': parttree.c:865:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] parttree.c:877:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] parttree.c:880:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] parttree.c:886:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] parttree.c: In function 'get_table': parttree.c:822:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] parttree.c:833:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] parttree.c: In function 'make_distance_matrix_sim': parttree.c:669:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] parttree.c:675:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o tree.o tree.c io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -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:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] diagonal.c: In function 'seq_pair2blast_diagonal2': diagonal.c:408:8: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] diagonal.c:413:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] diagonal.c:414:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] diagonal.c:415:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -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:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] scoring.c: In function 'agreement_score': scoring.c:560:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] scoring.c:561:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] scoring.c:562:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] scoring.c: In function 'make_ref_alignment': scoring.c:464:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] scoring.c:478:8: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] scoring.c: In function 'compute_ref_alignments': scoring.c:359:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] scoring.c:373:9: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] scoring.c: In function 'calculate_sum_of_pairs_score_affine': scoring.c:50:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] scoring.c:52:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] scoring.c:56:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -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:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] iteration.c: In function 'edit2seq_pattern': iteration.c:533:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] iteration.c:535:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] iteration.c:537:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] iteration.c:539:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] iteration.c: In function 'write_iterated_aln': iteration.c:471:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] iteration.c:474:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] iteration.c:505:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] iteration.c: In function 'iterate': iteration.c:280:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] iteration.c:405:8: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] iteration.c: In function 'split_set': iteration.c:155:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o t_coffee.o t_coffee.c t_coffee.c: In function 'batch_main': t_coffee.c:4184:14: warning: unused variable 'j' [-Wunused-variable] t_coffee.c:391:10: warning: variable 'n_overaln_param' set but not used [-Wunused-but-set-variable] t_coffee.c:386:8: warning: unused variable 'tmp_4_tcoffee' [-Wunused-variable] t_coffee.c:152:6: warning: variable 'n_setenv' set but not used [-Wunused-but-set-variable] t_coffee.c: In function 'run_other_pg': t_coffee.c:5343:3: warning: implicit declaration of function 'fastal_main' [-Wimplicit-function-declaration] t_coffee.c: In function 'prepare_master': t_coffee.c:5470:15: warning: variable 'sim' set but not used [-Wunused-but-set-variable] t_coffee.c:5416:8: warning: unused variable 'trim_mode' [-Wunused-variable] t_coffee.c:5415:10: warning: unused variable 'fp' [-Wunused-variable] t_coffee.c:5414:19: warning: unused variable 'i' [-Wunused-variable] t_coffee.c:5414:16: warning: unused variable 'n' [-Wunused-variable] t_coffee.c:5414:12: warning: unused variable 's1' [-Wunused-variable] t_coffee.c: At top level: t_coffee.c:5608:8: warning: type defaults to 'int' in declaration of 'max_nseq' [-Wimplicit-int] t_coffee.c:5609:8: warning: type defaults to 'int' in declaration of 'cur_nseq' [-Wimplicit-int] t_coffee.c: In function 'km_coffee': t_coffee.c:5632:8: warning: variable 'tm' set but not used [-Wunused-but-set-variable] t_coffee.c: In function 'km_refine_msa': t_coffee.c:6021:8: warning: unused variable 'buf' [-Wunused-variable] t_coffee.c: At top level: io_lib_header.h:971:16: warning: 'compute_std_tree' declared 'static' but never defined [-Wunused-function] t_coffee.c:5301:6: warning: 'test' defined but not used [-Wunused-function] t_coffee.c:32:14: warning: 'get_rmcoffee_defaults_old' declared 'static' but never defined [-Wunused-function] t_coffee.c:33:14: warning: 'get_rcoffee_defaults_old' declared 'static' but never defined [-Wunused-function] t_coffee.c:5082:7: warning: 'get_cdna_defaults' defined but not used [-Wunused-function] t_coffee.c:5610:12: warning: 'kmk' defined but not used [-Wunused-variable] t_coffee.c: In function 'km_align_seq_slow': t_coffee.c:5904:1: warning: control reaches end of non-void function [-Wreturn-type] t_coffee.c: In function 'km_coffee': t_coffee.c:5695:1: warning: control reaches end of non-void function [-Wreturn-type] t_coffee.c: In function 'main': t_coffee.c:92:1: warning: control reaches end of non-void function [-Wreturn-type] t_coffee.c: In function 'km_coffee': t_coffee.c:5679:16: warning: 'A' is used uninitialized in this function [-Wuninitialized] t_coffee.c:5682:7: warning: 'S' may be used uninitialized in this function [-Wuninitialized] t_coffee.c: In function 'main': t_coffee.c:91:10: warning: 'r' may be used uninitialized in this function [-Wuninitialized] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -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 gfortran -g -O2 TMalign.f -o TMalign make[1]: Leaving directory `/«PKGBUILDDIR»/t_coffee_source' touch debian/stamp-makefile-build DEB_MAKE_CHECK_TARGET unset, not running checks fakeroot debian/rules binary-arch 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_CHECK_TARGET unset, not running checks DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target Adding cdbs dependencies to debian/t-coffee.substvars dh_installdirs -pt-coffee dh_installdocs -pt-coffee 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_9.02.r1228-2_armhf.deb'. dpkg-genchanges -B -mbuildd >../t-coffee_9.02.r1228-2_armhf.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build t-coffee-9.02.r1228 dpkg-buildpackage: binary only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120522-1723 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ t-coffee_9.02.r1228-2_armhf.changes: ──────────────────────────────────── Format: 1.8 Date: Fri, 02 Mar 2012 14:04:20 +0900 Source: t-coffee Binary: t-coffee t-coffee-examples t-coffee-doc Architecture: armhf Version: 9.02.r1228-2 Distribution: testing Urgency: low Maintainer: buildd Changed-By: Charles Plessy 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 Closes: 661516 Changes: t-coffee (9.02.r1228-2) unstable; urgency=low . * Recommend tm-align instead of distributing local copy (debian/control, debian/t-coffee.install, Closes: #661516). Checksums-Sha1: 27bb51c19d0d3754fefdfc1d303e48a133b6c7da 769796 t-coffee_9.02.r1228-2_armhf.deb Checksums-Sha256: b662a6072a3f6f26bc3cbf56f83dcdd2728f7f79757a04364de704d763d91b73 769796 t-coffee_9.02.r1228-2_armhf.deb Files: 7303ec582240329d765502c3a222d560 769796 science optional t-coffee_9.02.r1228-2_armhf.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ t-coffee_9.02.r1228-2_armhf.deb ─────────────────────────────── new debian package, version 2.0. size 769796 bytes: control archive= 1212 bytes. 1535 bytes, 29 lines control 333 bytes, 5 lines md5sums Package: t-coffee Version: 9.02.r1228-2 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 1702 Depends: libc6 (>= 2.13-28) Recommends: libsoap-lite-perl, libxml-simple-perl, tm-align 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. drwxr-xr-x root/root 0 2012-05-22 17:22 ./ drwxr-xr-x root/root 0 2012-05-22 17:23 ./usr/ drwxr-xr-x root/root 0 2012-05-22 17:22 ./usr/share/ drwxr-xr-x root/root 0 2012-05-22 17:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-05-22 17:23 ./usr/share/doc/t-coffee/ -rw-r--r-- root/root 2015 2012-03-01 21:05 ./usr/share/doc/t-coffee/changelog.Debian.gz -rw-r--r-- root/root 1744 2008-04-09 06:24 ./usr/share/doc/t-coffee/README.Debian -rw-r--r-- root/root 1630 2012-02-26 20:00 ./usr/share/doc/t-coffee/copyright drwxr-xr-x root/root 0 2012-05-22 17:22 ./usr/share/man/ drwxr-xr-x root/root 0 2012-05-22 17:23 ./usr/share/man/man1/ -rw-r--r-- root/root 1463 2012-05-22 17:22 ./usr/share/man/man1/t_coffee.1.gz drwxr-xr-x root/root 0 2012-05-22 17:23 ./usr/bin/ -rwxr-xr-x root/root 1698468 2012-05-22 17:23 ./usr/bin/t_coffee ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded. Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bsdmainutils* cdbs* debhelper* diffstat* file* gettext* gettext-base* gfortran* gfortran-4.6* groff-base* html2text* intltool-debian* libcroco3* libffi5* libgfortran3* 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, 26 to remove and 13 not upgraded. After this operation, 38.1 MB disk space will be freed. (Reading database ... 12216 files and directories currently installed.) Removing sbuild-build-depends-t-coffee-dummy ... Removing quilt ... Purging configuration files for quilt ... Removing debhelper ... Removing man-db ... Purging configuration files for man-db ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing cdbs ... Removing diffstat ... Removing file ... Removing po-debconf ... Removing intltool-debian ... Removing gettext ... Removing gettext-base ... Removing gfortran ... Removing gfortran-4.6 ... Removing groff-base ... Purging configuration files for groff-base ... Removing html2text ... Purging configuration files for html2text ... Removing libcroco3:armhf ... Purging configuration files for libcroco3:armhf ... Removing libglib2.0-0:armhf ... Purging configuration files for libglib2.0-0:armhf ... Removing libffi5:armhf ... Purging configuration files for libffi5:armhf ... Removing libgfortran3:armhf ... Purging configuration files for libgfortran3:armhf ... Removing libmagic1:armhf ... Purging configuration files for libmagic1:armhf ... Removing libpcre3:armhf ... Purging configuration files for libpcre3:armhf ... Removing libpipeline1:armhf ... Purging configuration files for libpipeline1:armhf ... Removing libunistring0:armhf ... Purging configuration files for libunistring0:armhf ... Removing libxml2:armhf ... Purging configuration files for libxml2:armhf ... Removing sbuild-build-depends-core-dummy ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: armhf Build-Space: 27368 Build-Time: 709 Distribution: testing Install-Time: 67 Job: t-coffee_9.02.r1228-2 Package: t-coffee Package-Time: 796 Source-Version: 9.02.r1228-2 Space: 27368 Status: successful Version: 9.02.r1228-2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120522-1723 Build needed 00:13:16, 27368k disc space