DC-Build-Header: t-coffee 9.02.r1228-2 / Sat Jun 23 16:18:15 +0000 2012 DC-Task: logfile:/tmp/t-coffee_9.02.r1228-2_unstable_clang.log version:9.02.r1228-2 chroot:unstable modes:binary-only:clang source:t-coffee architecture:any esttime:326 DC-Sbuild-call: su user -c 'sbuild -n --apt-update -d unstable -v --chroot-setup-commands=/tmp/switch-to-clang t-coffee_9.02.r1228-2' sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on ip-10-28-33-247.ec2.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ t-coffee 9.02.r1228-2 (amd64) 23 Jun 2012 16:18 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: t-coffee Version: 9.02.r1228-2 Source Version: 9.02.r1228-2 Distribution: unstable Architecture: amd64 I: NOTICE: Log filtering will replace 'build/t-coffee-NgIcNA/t-coffee-9.02.r1228' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/t-coffee-NgIcNA' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-adff8047-9ddb-43b7-9776-55d09f27e099' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost unstable InRelease Get:1 http://localhost unstable Release.gpg [836 B] Get:2 http://localhost unstable Release [233 kB] Get:3 http://localhost unstable/main Sources/DiffIndex [7876 B] Get:4 http://localhost unstable/main amd64 Packages/DiffIndex [7876 B] Get:5 http://localhost unstable/main Translation-en/DiffIndex [7876 B] Get:6 http://localhost unstable/main 2012-06-23-0814.36.pdiff [8967 B] Get:7 http://localhost unstable/main 2012-06-23-0814.36.pdiff [8967 B] Get:8 http://localhost unstable/main amd64 2012-06-23-0814.36.pdiff [6101 B] Get:9 http://localhost unstable/main 2012-06-23-0814.36.pdiff [1297 B] Get:10 http://localhost unstable/main amd64 2012-06-23-0814.36.pdiff [6101 B] Get:11 http://localhost unstable/main 2012-06-23-0814.36.pdiff [1297 B] Fetched 274 kB in 4s (60.5 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ 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://localhost/debian/ unstable/main t-coffee 9.02.r1228-2 (dsc) [2241 B] Get:2 http://localhost/debian/ unstable/main t-coffee 9.02.r1228-2 (tar) [3364 kB] Get:3 http://localhost/debian/ unstable/main t-coffee 9.02.r1228-2 (diff) [7372 B] Fetched 3373 kB in 0s (7664 kB/s) Download complete and in download only mode Check arch ────────── ┌──────────────────────────────────────────────────────────────────────────────┐ │ Chroot Setup Commands │ └──────────────────────────────────────────────────────────────────────────────┘ /tmp/switch-to-clang ──────────────────── + echo 'Entering customization script...' Entering customization script... + apt-get update Ign http://localhost unstable InRelease Hit http://localhost unstable Release.gpg Hit http://localhost unstable Release Hit http://localhost unstable/main Sources/DiffIndex Hit http://localhost unstable/main amd64 Packages/DiffIndex Hit http://localhost unstable/main Translation-en/DiffIndex Reading package lists... + echo 'Install of clang' Install of clang + apt-get update Ign http://localhost unstable InRelease Hit http://localhost unstable Release.gpg Hit http://localhost unstable Release Hit http://localhost unstable/main Sources/DiffIndex Hit http://localhost unstable/main amd64 Packages/DiffIndex Hit http://localhost unstable/main Translation-en/DiffIndex Reading package lists... + apt-get install --yes --no-install-recommends clang -t unstable Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libclang-common-dev libffi5 libllvm3.1 Recommended packages: llvm-3.1-dev python The following NEW packages will be installed: clang libclang-common-dev libffi5 libllvm3.1 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 13.1 MB of archives. After this operation, 35.6 MB of additional disk space will be used. Get:1 http://localhost/debian/ unstable/main libffi5 amd64 3.0.10-3 [24.8 kB] Get:2 http://localhost/debian/ unstable/main libllvm3.1 amd64 3.1-1 [7276 kB] Get:3 http://localhost/debian/ unstable/main libclang-common-dev amd64 3.1-6 [84.0 kB] Get:4 http://localhost/debian/ unstable/main clang amd64 3.1-6 [5755 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 13.1 MB in 0s (30.2 MB/s) Selecting previously unselected package libffi5:amd64. (Reading database ... 11730 files and directories currently installed.) Unpacking libffi5:amd64 (from .../libffi5_3.0.10-3_amd64.deb) ... Selecting previously unselected package libllvm3.1:amd64. Unpacking libllvm3.1:amd64 (from .../libllvm3.1_3.1-1_amd64.deb) ... Selecting previously unselected package libclang-common-dev. Unpacking libclang-common-dev (from .../libclang-common-dev_3.1-6_amd64.deb) ... Selecting previously unselected package clang. Unpacking clang (from .../archives/clang_3.1-6_amd64.deb) ... Setting up libffi5:amd64 (3.0.10-3) ... Setting up libllvm3.1:amd64 (3.1-1) ... Setting up libclang-common-dev (3.1-6) ... Setting up clang (3.1-6) ... + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSION=4.7 + cd /usr/bin + rm g++-4.7 gcc-4.7 cpp-4.7 + ln -s clang++ g++-4.7 + ln -s clang gcc-4.7 + ln -s clang cpp-4.7 + cd - /«BUILDDIR» + echo 'Block the installation of new gcc version' Block the installation of new gcc version + dpkg --set-selections + echo 'gcc-4.6 hold' + dpkg --set-selections + echo 'cpp-4.6 hold' + dpkg --set-selections + echo 'g++-4.6 hold' + dpkg --set-selections + echo 'gcc-4.7 hold' + dpkg --set-selections + echo 'cpp-4.7 hold' + dpkg --set-selections + echo 'g++-4.7 hold' + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + grep clang + gcc --version I: Finished running '/tmp/switch-to-clang'. Finished processing commands. ──────────────────────────────────────────────────────────────────────────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-ioZ7oO/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/706 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 ... 11810 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, gfortran Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, gfortran dpkg-deb: building package `sbuild-build-depends-t-coffee-dummy' in `/«BUILDDIR»/resolver-HK_A_z/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-4.7 groff-base html2text intltool-debian libasprintf0c2 libcroco3 libgettextpo0 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-multilib gfortran-doc gfortran-4.7-multilib gfortran-4.7-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-4.7 groff-base html2text intltool-debian libasprintf0c2 libcroco3 libgettextpo0 libgfortran3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt sbuild-build-depends-t-coffee-dummy 0 upgraded, 26 newly installed, 0 to remove and 0 not upgraded. Need to get 16.9 MB/17.0 MB of archives. After this operation, 44.4 MB of additional disk space will be used. Get:1 http://localhost/debian/ unstable/main libpipeline1 amd64 1.2.1-1 [39.2 kB] Get:2 http://localhost/debian/ unstable/main libasprintf0c2 amd64 0.18.1.1-9 [26.8 kB] Get:3 http://localhost/debian/ unstable/main libmagic1 amd64 5.11-1 [250 kB] Get:4 http://localhost/debian/ unstable/main libpcre3 amd64 1:8.30-5 [242 kB] Get:5 http://localhost/debian/ unstable/main libxml2 amd64 2.8.0+dfsg1-4 [903 kB] Get:6 http://localhost/debian/ unstable/main libglib2.0-0 amd64 2.32.3-1 [2081 kB] Get:7 http://localhost/debian/ unstable/main libcroco3 amd64 0.6.5-1 [151 kB] Get:8 http://localhost/debian/ unstable/main libunistring0 amd64 0.9.3-5 [434 kB] Get:9 http://localhost/debian/ unstable/main libgettextpo0 amd64 0.18.1.1-9 [145 kB] Get:10 http://localhost/debian/ unstable/main libgfortran3 amd64 4.7.1-1 [352 kB] Get:11 http://localhost/debian/ unstable/main bsdmainutils amd64 9.0.3 [209 kB] Get:12 http://localhost/debian/ unstable/main groff-base amd64 1.21-8 [1152 kB] Get:13 http://localhost/debian/ unstable/main man-db amd64 2.6.2-1 [1061 kB] Get:14 http://localhost/debian/ unstable/main file amd64 5.11-1 [53.2 kB] Get:15 http://localhost/debian/ unstable/main gettext-base amd64 0.18.1.1-9 [154 kB] Get:16 http://localhost/debian/ unstable/main cdbs all 0.4.115 [80.2 kB] Get:17 http://localhost/debian/ unstable/main html2text amd64 1.3.2a-15 [103 kB] Get:18 http://localhost/debian/ unstable/main gettext amd64 0.18.1.1-9 [1975 kB] Get:19 http://localhost/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:20 http://localhost/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB] Get:21 http://localhost/debian/ unstable/main debhelper all 9.20120608 [700 kB] Get:22 http://localhost/debian/ unstable/main diffstat amd64 1.55-3 [30.0 kB] Get:23 http://localhost/debian/ unstable/main gfortran-4.7 amd64 4.7.1-1 [6176 kB] Get:24 http://localhost/debian/ unstable/main gfortran amd64 4:4.7.0-6 [1138 B] Get:25 http://localhost/debian/ unstable/main quilt all 0.60-2 [377 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 16.9 MB in 0s (26.3 MB/s) Selecting previously unselected package libpipeline1:amd64. (Reading database ... 11810 files and directories currently installed.) Unpacking libpipeline1:amd64 (from .../libpipeline1_1.2.1-1_amd64.deb) ... Selecting previously unselected package libasprintf0c2:amd64. Unpacking libasprintf0c2:amd64 (from .../libasprintf0c2_0.18.1.1-9_amd64.deb) ... Selecting previously unselected package libmagic1:amd64. Unpacking libmagic1:amd64 (from .../libmagic1_5.11-1_amd64.deb) ... Selecting previously unselected package libpcre3:amd64. Unpacking libpcre3:amd64 (from .../libpcre3_1%3a8.30-5_amd64.deb) ... Selecting previously unselected package libxml2:amd64. Unpacking libxml2:amd64 (from .../libxml2_2.8.0+dfsg1-4_amd64.deb) ... Selecting previously unselected package libglib2.0-0:amd64. Unpacking libglib2.0-0:amd64 (from .../libglib2.0-0_2.32.3-1_amd64.deb) ... Selecting previously unselected package libcroco3:amd64. Unpacking libcroco3:amd64 (from .../libcroco3_0.6.5-1_amd64.deb) ... Selecting previously unselected package libunistring0:amd64. Unpacking libunistring0:amd64 (from .../libunistring0_0.9.3-5_amd64.deb) ... Selecting previously unselected package libgettextpo0:amd64. Unpacking libgettextpo0:amd64 (from .../libgettextpo0_0.18.1.1-9_amd64.deb) ... Selecting previously unselected package libgfortran3:amd64. Unpacking libgfortran3:amd64 (from .../libgfortran3_4.7.1-1_amd64.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_amd64.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-8_amd64.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.2-1_amd64.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.11-1_amd64.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_amd64.deb) ... Selecting previously unselected package cdbs. Unpacking cdbs (from .../archives/cdbs_0.4.115_all.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-9_amd64.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_9.20120608_all.deb) ... Selecting previously unselected package diffstat. Unpacking diffstat (from .../diffstat_1.55-3_amd64.deb) ... Selecting previously unselected package gfortran-4.7. Unpacking gfortran-4.7 (from .../gfortran-4.7_4.7.1-1_amd64.deb) ... Selecting previously unselected package gfortran. Unpacking gfortran (from .../gfortran_4%3a4.7.0-6_amd64.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 libpipeline1:amd64 (1.2.1-1) ... Setting up libasprintf0c2:amd64 (0.18.1.1-9) ... Setting up libmagic1:amd64 (5.11-1) ... Setting up libpcre3:amd64 (1:8.30-5) ... Setting up libxml2:amd64 (2.8.0+dfsg1-4) ... Setting up libglib2.0-0:amd64 (2.32.3-1) ... No schema files found: doing nothing. Setting up libcroco3:amd64 (0.6.5-1) ... Setting up libunistring0:amd64 (0.9.3-5) ... Setting up libgettextpo0:amd64 (0.18.1.1-9) ... Setting up libgfortran3:amd64 (4.7.1-1) ... Setting up bsdmainutils (9.0.3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode. update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode. Setting up groff-base (1.21-8) ... Setting up man-db (2.6.2-1) ... Building database of manual pages ... Setting up file (5.11-1) ... Setting up gettext-base (0.18.1.1-9) ... Setting up cdbs (0.4.115) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-9) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120608) ... Setting up diffstat (1.55-3) ... Setting up gfortran-4.7 (4.7.1-1) ... Setting up gfortran (4:4.7.0-6) ... 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 2.6.32-5-xen-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.22-6.1 dpkg-dev_1.16.4.3 g++-4.6_4.6.3-7 g++-4.7_4.7.1-1 gcc-4.6_4.6.3-7 gcc-4.7_4.7.1-1 libc6-dev_2.13-33 libstdc++6_4.7.1-1 libstdc++6-4.6-dev_4.6.3-7 libstdc++6-4.7-dev_4.7.1-1 linux-libc-dev_3.2.20-1 Package versions: apt_0.9.7 base-files_6.11 base-passwd_3.5.25 bash_4.2-2 binutils_2.22-6.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5 build-essential_11.5 bzip2_1.0.6-3 cdbs_0.4.115 clang_3.1-6 coreutils_8.13-3.2 cpp_4:4.7.0-6 cpp-4.6_4.6.3-7 cpp-4.7_4.7.1-1 dash_0.5.7-3 debconf_1.5.44 debconf-i18n_1.5.44 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.1 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.4.3 dpkg-dev_1.16.4.3 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-1 findutils_4.4.2-4 g++_4:4.7.0-6 g++-4.6_4.6.3-7 g++-4.7_4.7.1-1 gcc_4:4.7.0-6 gcc-4.4-base_4.4.7-1 gcc-4.5-base_4.5.3-12 gcc-4.6_4.6.3-7 gcc-4.6-base_4.6.3-7 gcc-4.7_4.7.1-1 gcc-4.7-base_4.7.1-1 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gfortran_4:4.7.0-6 gfortran-4.7_4.7.1-1 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.12-2 groff-base_1.21-8 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-27 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5 libbz2-1.0_1.0.6-3 libc-bin_2.13-33 libc-dev-bin_2.13-33 libc6_2.13-33 libc6-dev_2.13-33 libclang-common-dev_3.1-6 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-4 libdpkg-perl_1.16.4.3 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-8 libgcc1_1:4.7.1-1 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libgfortran3_4.7.1-1 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-1 libitm1_4.7.1-1 libllvm3.1_3.1-1 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-1 libmount1_2.20.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-9 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libquadmath0_4.7.1-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-13 libss2_1.42.4-3 libstdc++6_4.7.1-1 libstdc++6-4.6-dev_4.6.3-7 libstdc++6-4.7-dev_4.7.1-1 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-9 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5 libxml2_2.8.0+dfsg1-4 linux-libc-dev_3.2.20-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5 multiarch-support_2.13-33 ncurses-base_5.9-9 ncurses-bin_5.9-9 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 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_4.2.1-10 sensible-utils_0.0.7 sysv-rc_2.88dsf-27 sysvinit_2.88dsf-27 sysvinit-utils_2.88dsf-27 tar_1.26-4 tzdata_2012c-1 ucf_3.0025+nmu3 util-linux_2.20.1-5 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 ┌──────────────────────────────────────────────────────────────────────────────┐ │ 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=root PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/bin/X11 SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=0 SCHROOT_GROUP=root SCHROOT_SESSION_ID=unstable-amd64-sbuild-adff8047-9ddb-43b7-9776-55d09f27e099 SCHROOT_UID=0 SCHROOT_USER=root SHELL=/bin/sh USER=root dpkg-buildpackage ───────────────── dpkg-buildpackage: warning: using a gain-root-command while being root dpkg-buildpackage: source package t-coffee dpkg-buildpackage: source version 9.02.r1228-2 dpkg-buildpackage: source changed by Charles Plessy dpkg-source --before-build t-coffee-9.02.r1228 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean test -x debian/rules dh_testroot rm -f debian/stamp-makefile-build debian/stamp-makefile-install /usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -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 -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -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 -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_constraints_list.o util_constraints_list.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' util_constraints_list.c:135:10: warning: unused variable 'fp' [-Wunused-variable] FILE *fp; ^ util_constraints_list.c:136:20: warning: unused variable 't' [-Wunused-variable] int done, todo, t; ^ util_constraints_list.c:89:6: warning: unused variable 'n_aln' [-Wunused-variable] int n_aln; ^ util_constraints_list.c:88:12: warning: unused variable 'seq' [-Wunused-variable] int cseq, seq, nlines; ^ util_constraints_list.c:81:8: warning: unused variable 'b' [-Wunused-variable] int a,b; ^ util_constraints_list.c:88:17: warning: unused variable 'nlines' [-Wunused-variable] int cseq, seq, nlines; ^ util_constraints_list.c:87:24: warning: unused variable 'submited' [-Wunused-variable] int nproc, max_nproc, submited; ^ util_constraints_list.c:88:6: warning: unused variable 'cseq' [-Wunused-variable] int cseq, seq, nlines; ^ util_constraints_list.c:193:8: warning: unused variable 'b' [-Wunused-variable] int a,b; ^ util_constraints_list.c:331:8: warning: unused variable 'b' [-Wunused-variable] int a,b, n; ^ util_constraints_list.c:331:11: warning: unused variable 'n' [-Wunused-variable] int a,b, n; ^ util_constraints_list.c:435:21: warning: unused variable 'n_new_elements' [-Wunused-variable] int n_elements_in, n_new_elements; ^ util_constraints_list.c:512:16: warning: unused variable 'log_output' [-Wunused-variable] static char *log_output; ^ util_constraints_list.c:513:14: warning: unused variable 'log' [-Wunused-variable] static int log; ^ util_constraints_list.c:535:13: warning: unused variable 'log' [-Wunused-variable] static int log; ^ util_constraints_list.c:608:6: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] chdir (tdir); ^~~~~ ~~~~ util_constraints_list.c:611:6: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] chdir (cdir); ^~~~~ ~~~~ util_constraints_list.c:584:13: warning: unused variable 'log' [-Wunused-variable] static int log; ^ util_constraints_list.c:583:15: warning: unused variable 'l' [-Wunused-variable] static char *l; ^ util_constraints_list.c:800:14: warning: unused variable 'y' [-Wunused-variable] int x, y, n; ^ util_constraints_list.c:801:12: warning: unused variable 'used' [-Wunused-variable] int *used; ^ util_constraints_list.c:1033:6: warning: unused variable 'n' [-Wunused-variable] int n=0, a, ml1=0, ml2=0, ml3=0; ^ util_constraints_list.c:1034:6: warning: unused variable 'status' [-Wunused-variable] int status; ^ util_constraints_list.c:1177:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets ( line,LONG_STRING, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~ util_constraints_list.c:1219:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets ( line,LONG_STRING, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~ util_constraints_list.c:1333:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ util_constraints_list.c:1388:8: warning: unused variable 'nl' [-Wunused-variable] int nl; ^ util_constraints_list.c:1376:6: warning: unused variable 'a' [-Wunused-variable] int a, b, c,e,tot; ^ util_constraints_list.c:1409:55: error: non-void function 'safe_dump_constraint_list' should return a value [-Wreturn-type] if (!CL || !CL->S || !CL->residue_index || CL->ne==0)return; ^ util_constraints_list.c:1468:8: warning: unused variable 'c' [-Wunused-variable] int b,c,l,s1,r1,s2,r2,w2,n; ^ util_constraints_list.c:1468:10: warning: unused variable 'l' [-Wunused-variable] int b,c,l,s1,r1,s2,r2,w2,n; ^ util_constraints_list.c:1504:21: warning: unused variable 'entry' [-Wunused-variable] static CLIST_TYPE *entry; ^ util_constraints_list.c:1505:12: warning: unused variable 'c' [-Wunused-variable] int a, b, c, s1, s2, r1, r2; ^ util_constraints_list.c:1505:19: warning: unused variable 's2' [-Wunused-variable] int a, b, c, s1, s2, r1, r2; ^ util_constraints_list.c:1505:27: warning: unused variable 'r2' [-Wunused-variable] int a, b, c, s1, s2, r1, r2; ^ util_constraints_list.c:1607:6: warning: unused variable 'v' [-Wunused-variable] int v; ^ util_constraints_list.c:1860:8: warning: unused variable 'r' [-Wunused-variable] int *r= CL->residue_index[s1][r1]; ^ util_constraints_list.c:1962:7: warning: unused variable 'from' [-Wunused-variable] int *from, *to; ^ util_constraints_list.c:1962:14: warning: unused variable 'to' [-Wunused-variable] int *from, *to; ^ util_constraints_list.c:1982:6: warning: unused variable 'a' [-Wunused-variable] int a, *from, *to; ^ util_constraints_list.c:1982:10: warning: unused variable 'from' [-Wunused-variable] int a, *from, *to; ^ util_constraints_list.c:1982:17: warning: unused variable 'to' [-Wunused-variable] int a, *from, *to; ^ util_constraints_list.c:2009:7: warning: unused variable 's2' [-Wunused-variable] int s2=entry[SEQ2]; ^ util_constraints_list.c:2011:7: warning: unused variable 'r2' [-Wunused-variable] int r2=entry[R2]; ^ util_constraints_list.c:2065:9: warning: implicit declaration of function 'constraint_list2max' is invalid in C99 [-Wimplicit-function-declaration] return constraint_list2max (CL); ^ util_constraints_list.c:2085:6: warning: unused variable 'a' [-Wunused-variable] int a, b, c; ^ util_constraints_list.c:2085:9: warning: unused variable 'b' [-Wunused-variable] int a, b, c; ^ util_constraints_list.c:2085:12: warning: unused variable 'c' [-Wunused-variable] int a, b, c; ^ util_constraints_list.c:2086:13: warning: unused variable 'tp' [-Wunused-variable] CLIST_TYPE tp; ^ util_constraints_list.c:2094:6: warning: unused variable 'max' [-Wunused-variable] int max=0; ^ util_constraints_list.c:2096:6: warning: unused variable 'b' [-Wunused-variable] int b,l,s1,r1,s2,r2,w2; ^ util_constraints_list.c:2096:8: warning: unused variable 'l' [-Wunused-variable] int b,l,s1,r1,s2,r2,w2; ^ util_constraints_list.c:2096:16: warning: unused variable 's2' [-Wunused-variable] int b,l,s1,r1,s2,r2,w2; ^ util_constraints_list.c:2096:19: warning: unused variable 'r2' [-Wunused-variable] int b,l,s1,r1,s2,r2,w2; ^ util_constraints_list.c:2096:22: warning: unused variable 'w2' [-Wunused-variable] int b,l,s1,r1,s2,r2,w2; ^ util_constraints_list.c:2608:14: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] if ( c=='C')fscanf( fp, "PU %d\n", &cpu); ^~~~~~ ~~~~~~~~~~~~~~~~~~~ util_constraints_list.c:2707:6: warning: unused variable 'a' [-Wunused-variable] int a; ^ util_constraints_list.c:2841:72: warning: data argument not used by format string [-Wformat-extra-args] x=sscanf (buf, "%s %d %d %d %d %d",arg, &length, &r1,&r2,&we,&cons,&misc); ~~~~~~~~~~~~~~~~~~~ ^ util_constraints_list.c:2800:6: warning: unused variable 'a' [-Wunused-variable] int a; ^ util_constraints_list.c:2905:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf (fp, "%*s %d %*s\n", &l); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~ util_constraints_list.c:2961:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets (line , 200 , fp); ^~~~~ ~~~~~~~~~~~~~~~ util_constraints_list.c:2936:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf ( fp, "%s %d %s\n", name, &seq_len, sequence); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_constraints_list.c:2900:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf (fp, "%d\n", &max_nseq); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~ util_constraints_list.c:2930:14: warning: unused variable 'value' [-Wunused-variable] char *tag, *value; ^ util_constraints_list.c:3255:28: warning: unused variable 'w2' [-Wunused-variable] int a, b, s1, s2, r1, r2, w2,x1, x2; ^ util_constraints_list.c:3255:31: warning: unused variable 'x1' [-Wunused-variable] int a, b, s1, s2, r1, r2, w2,x1, x2; ^ util_constraints_list.c:3255:35: warning: unused variable 'x2' [-Wunused-variable] int a, b, s1, s2, r1, r2, w2,x1, x2; ^ util_constraints_list.c:3386:11: warning: unused variable 'ts' [-Wunused-variable] int ts,tr; ^ util_constraints_list.c:3386:14: warning: unused variable 'tr' [-Wunused-variable] int ts,tr; ^ util_constraints_list.c:3428:7: warning: expression result unused [-Wunused-value] if (!CL->multi_thread, "relax")njobs=1; ^~~~~~~~~~~~~~~~~ util_constraints_list.c:3451:7: warning: unused variable 'np' [-Wunused-variable] int np; ^ util_constraints_list.c:3563:7: warning: unused variable 'L' [-Wunused-variable] int *L; ^ util_constraints_list.c:3564:6: warning: unused variable 'chunck' [-Wunused-variable] int chunck=500; ^ util_constraints_list.c:3565:6: warning: unused variable 'max' [-Wunused-variable] int max=500; ^ util_constraints_list.c:3566:6: warning: unused variable 'n' [-Wunused-variable] int n=0; ^ util_constraints_list.c:3629:6: warning: unused variable 'a' [-Wunused-variable] int a, s1, s2, r1, r2,n; ^ util_constraints_list.c:3629:9: warning: unused variable 's1' [-Wunused-variable] int a, s1, s2, r1, r2,n; ^ util_constraints_list.c:3629:13: warning: unused variable 's2' [-Wunused-variable] int a, s1, s2, r1, r2,n; ^ util_constraints_list.c:3629:17: warning: unused variable 'r1' [-Wunused-variable] int a, s1, s2, r1, r2,n; ^ util_constraints_list.c:3629:21: warning: unused variable 'r2' [-Wunused-variable] int a, s1, s2, r1, r2,n; ^ util_constraints_list.c:3629:24: warning: unused variable 'n' [-Wunused-variable] int a, s1, s2, r1, r2,n; ^ util_constraints_list.c:3630:6: warning: unused variable 'score' [-Wunused-variable] int score; ^ util_constraints_list.c:3631:6: warning: unused variable 'thr' [-Wunused-variable] int thr; ^ util_constraints_list.c:3632:6: warning: unused variable 'chunk' [-Wunused-variable] int chunk, npid, job,pid; ^ util_constraints_list.c:3632:13: warning: unused variable 'npid' [-Wunused-variable] int chunk, npid, job,pid; ^ util_constraints_list.c:3632:19: warning: unused variable 'job' [-Wunused-variable] int chunk, npid, job,pid; ^ util_constraints_list.c:3632:23: warning: unused variable 'pid' [-Wunused-variable] int chunk, npid, job,pid; ^ util_constraints_list.c:3633:8: warning: unused variable 'fp' [-Wunused-variable] FILE *fp; ^ util_constraints_list.c:3634:9: warning: unused variable 'pid_tmpfile' [-Wunused-variable] char **pid_tmpfile; ^ util_constraints_list.c:3635:8: warning: unused variable 'pid_list' [-Wunused-variable] int * pid_list; ^ util_constraints_list.c:3636:6: warning: unused variable 'in' [-Wunused-variable] int in; ^ util_constraints_list.c:3771:5: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf (fp, "%d ", &CL->residue_index[s][r][a+WE]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_constraints_list.c:3729:6: warning: unused variable 'thr' [-Wunused-variable] int thr=10; ^ util_constraints_list.c:3730:20: warning: unused variable 'l' [-Wunused-variable] int s,r,a,t_s,t_r,l; ^ util_constraints_list.c:3784:8: warning: unused variable 'l' [-Wunused-variable] int b,l,s1,r1,s2,r2,w2; ^ util_constraints_list.c:3804:6: warning: unused variable 'b' [-Wunused-variable] int b,l,s1,r1,s2,r2,w2; ^ util_constraints_list.c:3804:8: warning: unused variable 'l' [-Wunused-variable] int b,l,s1,r1,s2,r2,w2; ^ util_constraints_list.c:3804:16: warning: unused variable 's2' [-Wunused-variable] int b,l,s1,r1,s2,r2,w2; ^ util_constraints_list.c:3804:19: warning: unused variable 'r2' [-Wunused-variable] int b,l,s1,r1,s2,r2,w2; ^ util_constraints_list.c:3804:22: warning: unused variable 'w2' [-Wunused-variable] int b,l,s1,r1,s2,r2,w2; ^ util_constraints_list.c:3858:8: warning: unused variable 'l' [-Wunused-variable] int b,l,s1,r1,s2,r2,w2; ^ util_constraints_list.c:3882:14: warning: unused variable 'buf' [-Wunused-variable] static int *buf; ^ util_constraints_list.c:3883:13: warning: unused variable 'bs' [-Wunused-variable] static int bs; ^ util_constraints_list.c:4135:10: warning: unused variable 'lw' [-Wunused-variable] float lw; ^ util_constraints_list.c:4058:12: warning: unused variable 's' [-Wunused-variable] char *p, *s; ^ util_constraints_list.c:4196:6: warning: unused variable 'max' [-Wunused-variable] int max=0; ^ util_constraints_list.c:4289:12: warning: unused variable 's2' [-Wunused-variable] int s1,r1,s2,r2,l,a,b; ^ util_constraints_list.c:4289:15: warning: unused variable 'r2' [-Wunused-variable] int s1,r1,s2,r2,l,a,b; ^ util_constraints_list.c:4289:18: warning: unused variable 'l' [-Wunused-variable] int s1,r1,s2,r2,l,a,b; ^ util_constraints_list.c:4289:22: warning: unused variable 'b' [-Wunused-variable] int s1,r1,s2,r2,l,a,b; ^ util_constraints_list.c:4538:8: warning: unused variable 'w' [-Wunused-variable] float w; ^ util_constraints_list.c:4540:6: warning: unused variable 'sA' [-Wunused-variable] int sA, sB; ^ util_constraints_list.c:4540:10: warning: unused variable 'sB' [-Wunused-variable] int sA, sB; ^ util_constraints_list.c:4541:12: warning: unused variable 'b' [-Wunused-variable] int s,r,a,b; ^ util_constraints_list.c:4564:8: warning: unused variable 'a' [-Wunused-variable] int *a; ^ util_constraints_list.c:4942:6: warning: unused variable 'a' [-Wunused-variable] int a,b,c,d,e,n1,n2, ne,s1,r1,s2,r2,w2; ^ util_constraints_list.c:4942:23: warning: unused variable 'ne' [-Wunused-variable] int a,b,c,d,e,n1,n2, ne,s1,r1,s2,r2,w2; ^ util_constraints_list.c:6502:24: warning: unused variable 'r2' [-Wunused-variable] int bs,a,b,s1,s2,r1,r2; ^ 117 warnings and 1 error generated. make[1]: [util_constraints_list.o] Error 1 (ignored) cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_job_handling.o util_job_handling.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' In file included from util_job_handling.c:7: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 1 warning generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_dps.o util_dps.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' In file included from util_dps.c:7: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 1 warning generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_domain_constraints_list.o util_domain_constraints_list.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' util_domain_constraints_list.c:26:11: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] while (e=extract_entry (CL)) ~^~~~~~~~~~~~~~~~~~~ util_domain_constraints_list.c:26:11: note: place parentheses around the assignment to silence this warning while (e=extract_entry (CL)) ^ ( ) util_domain_constraints_list.c:26:11: note: use '==' to turn this assignment into an equality comparison while (e=extract_entry (CL)) ^ == util_domain_constraints_list.c:20:7: warning: unused variable 'a' [-Wunused-variable] int a; ^ In file included from util_domain_constraints_list.c:7: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 3 warnings generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_analyse_constraints_list.o util_analyse_constraints_list.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' In file included from util_analyse_constraints_list.c:7: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 1 warning generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_aln_analyze.o util_aln_analyze.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' util_aln_analyze.c:687:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ util_aln_analyze.c:3514:22: warning: unused variable 'f' [-Wunused-variable] int a, b, c, d, e, f; ^ util_aln_analyze.c:3515:9: warning: unused variable 's1' [-Wunused-variable] char *s1, *s2, *s3,*s4,*s5, *n1, *n2, *n3, *n4, *n5; ^ util_aln_analyze.c:3515:14: warning: unused variable 's2' [-Wunused-variable] char *s1, *s2, *s3,*s4,*s5, *n1, *n2, *n3, *n4, *n5; ^ util_aln_analyze.c:3515:19: warning: unused variable 's3' [-Wunused-variable] char *s1, *s2, *s3,*s4,*s5, *n1, *n2, *n3, *n4, *n5; ^ util_aln_analyze.c:3515:23: warning: unused variable 's4' [-Wunused-variable] char *s1, *s2, *s3,*s4,*s5, *n1, *n2, *n3, *n4, *n5; ^ util_aln_analyze.c:3515:27: warning: unused variable 's5' [-Wunused-variable] char *s1, *s2, *s3,*s4,*s5, *n1, *n2, *n3, *n4, *n5; ^ util_aln_analyze.c:3515:32: warning: unused variable 'n1' [-Wunused-variable] char *s1, *s2, *s3,*s4,*s5, *n1, *n2, *n3, *n4, *n5; ^ util_aln_analyze.c:3515:37: warning: unused variable 'n2' [-Wunused-variable] char *s1, *s2, *s3,*s4,*s5, *n1, *n2, *n3, *n4, *n5; ^ util_aln_analyze.c:3515:42: warning: unused variable 'n3' [-Wunused-variable] char *s1, *s2, *s3,*s4,*s5, *n1, *n2, *n3, *n4, *n5; ^ util_aln_analyze.c:3515:47: warning: unused variable 'n4' [-Wunused-variable] char *s1, *s2, *s3,*s4,*s5, *n1, *n2, *n3, *n4, *n5; ^ util_aln_analyze.c:3515:52: warning: unused variable 'n5' [-Wunused-variable] char *s1, *s2, *s3,*s4,*s5, *n1, *n2, *n3, *n4, *n5; ^ util_aln_analyze.c:3516:7: warning: unused variable 'max' [-Wunused-variable] int max=0;; ^ util_aln_analyze.c:3518:7: warning: unused variable 'score' [-Wunused-variable] int score; ^ util_aln_analyze.c:3625:9: warning: unused variable 'n1' [-Wunused-variable] float n1, n11; ^ util_aln_analyze.c:3625:13: warning: unused variable 'n11' [-Wunused-variable] float n1, n11; ^ util_aln_analyze.c:3626:13: warning: unused variable 'c' [-Wunused-variable] int a, b, c, tot=0, n=0; ^ util_aln_analyze.c:4168:4: warning: variable 't' is uninitialized when used here [-Wuninitialized] t++; ^ util_aln_analyze.c:4057:61: note: initialize the variable 't' to silence this warning float n11, n10, n01, n00, n, sn2, prediction,sp, n1, n0, t, entropy, Delta; ^ = 0.0 util_aln_analyze.c:4245:15: warning: unused variable 'cx' [-Wunused-variable] int l, a,ax,cx, b; ^ util_aln_analyze.c:4454:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ util_aln_analyze.c:4888:36: warning: operator '?:' has lower precedence than '-'; '-' will be evaluated first [-Wparentheses] valP=matP[p][res]-(sar=='I')?1:0; ~~~~~~~~~~~~~~~~~~~~~~~^ util_aln_analyze.c:4888:36: note: place parentheses around the '-' expression to silence this warning valP=matP[p][res]-(sar=='I')?1:0; ^ ( ) util_aln_analyze.c:4888:36: note: place parentheses around the '?:' expression to evaluate it first valP=matP[p][res]-(sar=='I')?1:0; ^ ( ) util_aln_analyze.c:4891:36: warning: operator '?:' has lower precedence than '-'; '-' will be evaluated first [-Wparentheses] valN=matN[p][res]-(sar=='O')?1:0; ~~~~~~~~~~~~~~~~~~~~~~~^ util_aln_analyze.c:4891:36: note: place parentheses around the '-' expression to silence this warning valN=matN[p][res]-(sar=='O')?1:0; ^ ( ) util_aln_analyze.c:4891:36: note: place parentheses around the '?:' expression to evaluate it first valN=matN[p][res]-(sar=='O')?1:0; ^ ( ) In file included from util_aln_analyze.c:7: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 23 warnings generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o aln_convertion_util.o aln_convertion_util.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' aln_convertion_util.c:193:9: warning: unused variable 'compmat' [-Wunused-variable] int **compmat; ^ aln_convertion_util.c:194:7: warning: unused variable 'max' [-Wunused-variable] int max, p,k; ^ aln_convertion_util.c:192:15: warning: unused variable 'comp' [-Wunused-variable] int watson, comp,tot; ^ aln_convertion_util.c:192:20: warning: unused variable 'tot' [-Wunused-variable] int watson, comp,tot; ^ aln_convertion_util.c:195:7: warning: unused variable 'minseq' [-Wunused-variable] int minseq=3; ^ aln_convertion_util.c:190:11: warning: unused variable 'c' [-Wunused-variable] int a,b,c,d,p1,p2; ^ aln_convertion_util.c:194:12: warning: unused variable 'p' [-Wunused-variable] int max, p,k; ^ aln_convertion_util.c:194:14: warning: unused variable 'k' [-Wunused-variable] int max, p,k; ^ aln_convertion_util.c:190:18: warning: unused variable 'p2' [-Wunused-variable] int a,b,c,d,p1,p2; ^ aln_convertion_util.c:197:16: warning: unused variable 'nwatson' [-Wunused-variable] int ncomp=0, nwatson=0; ^ aln_convertion_util.c:191:7: warning: unused variable 'r1' [-Wunused-variable] int r1, rr1, r2, rr2; ^ aln_convertion_util.c:190:13: warning: unused variable 'd' [-Wunused-variable] int a,b,c,d,p1,p2; ^ aln_convertion_util.c:196:9: warning: unused variable 'list' [-Wunused-variable] int **list; ^ aln_convertion_util.c:190:15: warning: unused variable 'p1' [-Wunused-variable] int a,b,c,d,p1,p2; ^ aln_convertion_util.c:197:7: warning: unused variable 'ncomp' [-Wunused-variable] int ncomp=0, nwatson=0; ^ aln_convertion_util.c:191:20: warning: unused variable 'rr2' [-Wunused-variable] int r1, rr1, r2, rr2; ^ aln_convertion_util.c:192:7: warning: unused variable 'watson' [-Wunused-variable] int watson, comp,tot; ^ aln_convertion_util.c:198:15: warning: unused variable 'fold_l' [-Wunused-variable] int cons_l, fold_l; ^ aln_convertion_util.c:191:11: warning: unused variable 'rr1' [-Wunused-variable] int r1, rr1, r2, rr2; ^ aln_convertion_util.c:191:16: warning: unused variable 'r2' [-Wunused-variable] int r1, rr1, r2, rr2; ^ aln_convertion_util.c:293:12: warning: unused variable 'p' [-Wunused-variable] int max, p,k; ^ aln_convertion_util.c:289:10: warning: unused variable 'b' [-Wunused-variable] int a,b,c,d,p1,p2,s; ^ aln_convertion_util.c:292:9: warning: unused variable 'compmat' [-Wunused-variable] int **compmat; ^ aln_convertion_util.c:296:7: warning: unused variable 'ncomp' [-Wunused-variable] int ncomp=0, nwatson=0, nneutral=0, ncomp_wc=0; ^ aln_convertion_util.c:289:22: warning: unused variable 's' [-Wunused-variable] int a,b,c,d,p1,p2,s; ^ aln_convertion_util.c:294:7: warning: unused variable 'minseq' [-Wunused-variable] int minseq=3; ^ aln_convertion_util.c:293:14: warning: unused variable 'k' [-Wunused-variable] int max, p,k; ^ aln_convertion_util.c:296:39: warning: unused variable 'ncomp_wc' [-Wunused-variable] int ncomp=0, nwatson=0, nneutral=0, ncomp_wc=0; ^ aln_convertion_util.c:296:27: warning: unused variable 'nneutral' [-Wunused-variable] int ncomp=0, nwatson=0, nneutral=0, ncomp_wc=0; ^ aln_convertion_util.c:296:16: warning: unused variable 'nwatson' [-Wunused-variable] int ncomp=0, nwatson=0, nneutral=0, ncomp_wc=0; ^ aln_convertion_util.c:297:15: warning: unused variable 'fold_l' [-Wunused-variable] int cons_l, fold_l; ^ aln_convertion_util.c:297:7: warning: unused variable 'cons_l' [-Wunused-variable] int cons_l, fold_l; ^ aln_convertion_util.c:501:13: warning: unused variable 'p' [-Wunused-variable] int a, b, p; ^ aln_convertion_util.c:659:13: warning: unused variable 'c' [-Wunused-variable] int a, b, c, nr; ^ aln_convertion_util.c:1296:3: error: non-void function 'set_blast_default_values' should return a value [-Wreturn-type] return; ^ aln_convertion_util.c:1398:13: warning: unused variable 'c' [-Wunused-variable] int a, b, c,r; ^ aln_convertion_util.c:1754:16: warning: unused variable 'len' [-Wunused-variable] unsigned int len; ^ aln_convertion_util.c:2112:13: warning: unused variable 'pos' [-Wunused-variable] int a, b, pos, len; ^ aln_convertion_util.c:2112:18: warning: unused variable 'len' [-Wunused-variable] int a, b, pos, len; ^ aln_convertion_util.c:2113:13: warning: unused variable 'S' [-Wunused-variable] Sequence *S; ^ aln_convertion_util.c:2247:7: warning: unused variable 'unalign' [-Wunused-variable] int unalign=0; ^ aln_convertion_util.c:4085:12: warning: unused variable 's' [-Wunused-variable] int n, a, s; ^ aln_convertion_util.c:5449:11: warning: unused variable 'z' [-Wunused-variable] int z, i; ^ aln_convertion_util.c:5551:9: warning: unused variable 'x' [-Wunused-variable] char x[299]; ^ aln_convertion_util.c:5558:11: warning: unused variable 'z' [-Wunused-variable] int z; ^ aln_convertion_util.c:6510:9: warning: unused variable 'buf' [-Wunused-variable] char *buf; ^ aln_convertion_util.c:6511:10: warning: unused variable 'a' [-Wunused-variable] int l, a, b, c; ^ aln_convertion_util.c:6511:16: warning: unused variable 'c' [-Wunused-variable] int l, a, b, c; ^ aln_convertion_util.c:6533:9: warning: unused variable 'buf' [-Wunused-variable] char *buf; ^ aln_convertion_util.c:6534:7: warning: unused variable 'l' [-Wunused-variable] int l, a, b, c; ^ aln_convertion_util.c:6534:13: warning: unused variable 'b' [-Wunused-variable] int l, a, b, c; ^ aln_convertion_util.c:6534:16: warning: unused variable 'c' [-Wunused-variable] int l, a, b, c; ^ aln_convertion_util.c:6705:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets ( line, VERY_LONG_STRING,fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ aln_convertion_util.c:6728:7: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets ( line, VERY_LONG_STRING,fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ aln_convertion_util.c:6724:25: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] if ( c=='#' || c=='!')fgets ( line, VERY_LONG_STRING,fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ aln_convertion_util.c:8459:16: warning: unused variable 'd' [-Wunused-variable] int a, b, c, d, dim; ^ aln_convertion_util.c:9561:7: warning: unused variable 'maxnseq' [-Wunused-variable] int maxnseq, nseq_ratio, nc; ^ aln_convertion_util.c:9561:16: warning: unused variable 'nseq_ratio' [-Wunused-variable] int maxnseq, nseq_ratio, nc; ^ aln_convertion_util.c:9561:28: warning: unused variable 'nc' [-Wunused-variable] int maxnseq, nseq_ratio, nc; ^ aln_convertion_util.c:9562:7: warning: unused variable 'new_nseq' [-Wunused-variable] int new_nseq; ^ aln_convertion_util.c:9563:16: warning: unused variable 'k' [-Wunused-variable] int a, s, n, k; ^ aln_convertion_util.c:9566:7: warning: unused variable 'outlayers' [-Wunused-variable] int outlayers; ^ aln_convertion_util.c:9567:7: warning: unused variable 'direction' [-Wunused-variable] int direction=1;//remove the higher than ^ aln_convertion_util.c:9568:7: warning: unused variable 'coverage' [-Wunused-variable] int coverage=0; //remove based on coverage ^ aln_convertion_util.c:9667:9: warning: unused variable 'b' [-Wunused-variable] int a,b; ^ aln_convertion_util.c:9701:13: warning: unused variable 'gs' [-Wunused-variable] int a, b, gs,ba; ^ aln_convertion_util.c:9852:11: warning: unused variable 'n2' [-Wunused-variable] int n2=0; ^ aln_convertion_util.c:9855:12: warning: unused variable 'tmpfile' [-Wunused-variable] char tmpfile[100]; ^ aln_convertion_util.c:9827:16: warning: unused variable 'file2' [-Wunused-variable] static char *file2; ^ aln_convertion_util.c:9829:7: warning: unused variable 'count' [-Wunused-variable] int count=0; ^ aln_convertion_util.c:9900:9: warning: unused variable 'b' [-Wunused-variable] int a,b, *gs; ^ aln_convertion_util.c:9901:9: warning: unused variable 'sd' [-Wunused-variable] int **sd; ^ aln_convertion_util.c:10178:11: warning: unused variable 'b' [-Wunused-variable] int b; ^ aln_convertion_util.c:10071:9: warning: unused variable 'b' [-Wunused-variable] int a,b, s, n, k; ^ aln_convertion_util.c:11766:17: warning: unused variable 'entry' [-Wunused-variable] static int *entry; ^ aln_convertion_util.c:12465:11: warning: unused variable 'v' [-Wunused-variable] int v; ^ aln_convertion_util.c:12253:15: warning: unused variable 'e0' [-Wunused-variable] int c1, c2, e0, e1,tb, obs; ^ aln_convertion_util.c:12253:19: warning: unused variable 'e1' [-Wunused-variable] int c1, c2, e0, e1,tb, obs; ^ aln_convertion_util.c:12262:7: warning: unused variable 'model_type' [-Wunused-variable] int model_type=1; ^ aln_convertion_util.c:12252:16: warning: unused variable 'd' [-Wunused-variable] int a, b, c, d, l, id; ^ aln_convertion_util.c:12257:39: warning: unused variable 'K' [-Wunused-variable] int S, M1, M2, m1, m2,B1, B2,G1,G2, K; ^ aln_convertion_util.c:12257:32: warning: unused variable 'G1' [-Wunused-variable] int S, M1, M2, m1, m2,B1, B2,G1,G2, K; ^ aln_convertion_util.c:12257:35: warning: unused variable 'G2' [-Wunused-variable] int S, M1, M2, m1, m2,B1, B2,G1,G2, K; ^ aln_convertion_util.c:12254:7: warning: unused variable 'T0' [-Wunused-variable] int T0, T1,T2; ^ aln_convertion_util.c:12485:15: warning: unused variable 'e0' [-Wunused-variable] int c1, c2, e0, e1,tb, obs; ^ aln_convertion_util.c:12485:19: warning: unused variable 'e1' [-Wunused-variable] int c1, c2, e0, e1,tb, obs; ^ aln_convertion_util.c:12489:26: warning: unused variable 'K' [-Wunused-variable] int S, M1, M2, m1, m2, K; ^ aln_convertion_util.c:12486:7: warning: unused variable 'T0' [-Wunused-variable] int T0, T1,T2; ^ aln_convertion_util.c:12484:16: warning: unused variable 'd' [-Wunused-variable] int a, b, c, d, l, id; ^ aln_convertion_util.c:12766:13: warning: array subscript is of type 'char' [-Wchar-subscripts] r[n][alp[c1]][alp[c2]]++; ^~~~~~~~ aln_convertion_util.c:12766:22: warning: array subscript is of type 'char' [-Wchar-subscripts] r[n][alp[c1]][alp[c2]]++; ^~~~~~~~ aln_convertion_util.c:12682:7: warning: unused variable 'print' [-Wunused-variable] int print=1; ^ aln_convertion_util.c:12678:7: warning: unused variable 'T' [-Wunused-variable] int T, N; ^ aln_convertion_util.c:12678:10: warning: unused variable 'N' [-Wunused-variable] int T, N; ^ aln_convertion_util.c:12681:29: warning: unused variable 'result' [-Wunused-variable] float sp, sn, sen2, best, result; ^ aln_convertion_util.c:12840:35: warning: '&&' within '||' [-Wlogical-op-parentheses] if (buf[b]=='b' || buf[b]=='o' && c>=1)buf2[c-1]=tolower(buf2[c-1]); ~~ ~~~~~~~~~~~~^~~~~~~ aln_convertion_util.c:12840:35: note: place parentheses around the '&&' expression to silence this warning if (buf[b]=='b' || buf[b]=='o' && c>=1)buf2[c-1]=tolower(buf2[c-1]); ^ ( ) aln_convertion_util.c:12872:12: warning: unused variable 'a' [-Wunused-variable] int tot, a, b,c, s1,s2, ng, g; ^ 96 warnings and 1 error generated. make[1]: [aln_convertion_util.o] Error 1 (ignored) cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_declare.o util_declare.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' util_declare.c:52:11: warning: unused variable 'c' [-Wunused-variable] int a,b,c; ^ util_declare.c:154:12: warning: unused variable 'b' [-Wunused-variable] int a, b; ^ util_declare.c:365:9: warning: unused variable 'a' [-Wunused-variable] int a, b; ^ util_declare.c:365:12: warning: unused variable 'b' [-Wunused-variable] int a, b; ^ util_declare.c:682:18: warning: unused variable 'len' [-Wunused-variable] unsigned int len; ^ util_declare.c:685:18: warning: unused variable 'i' [-Wunused-variable] unsigned int i; ^ In file included from util_declare.c:11: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 7 warnings generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o hsearch.o hsearch.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' In file included from hsearch.c:8: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 1 warning generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o random.o random.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_make_tree.o util_make_tree.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' util_make_tree.c:32:9: warning: unused variable 'fp' [-Wunused-variable] FILE *fp; ^ util_make_tree.c:40:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ util_make_tree.c:1311:11: warning: unused variable 'window' [-Wunused-variable] int window=10; ^ util_make_tree.c:1326:11: warning: unused variable 'window' [-Wunused-variable] int window=10; ^ util_make_tree.c:1571:11: warning: unused variable 'd' [-Wunused-variable] int d; ^ util_make_tree.c:1529:14: warning: unused variable 'A' [-Wunused-variable] Alignment *A; ^ util_make_tree.c:1607:9: warning: unused variable 'b' [-Wunused-variable] int a,b; ^ In file included from util_make_tree.c:7: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ util_make_tree.c:1252:12: warning: unused variable 'count' [-Wunused-variable] static int count; ^ 9 warnings generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util.o util.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' In file included from util.c:22: ./perl_header_lib.h:8397:41: warning: illegal character encoding in string literal [-Winvalid-source-encoding] n} #m\n\nexit;\n\n\n\n\n\n\n\n\n\n\n\n","use Env;\\ ^ util.c:202:6: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread( rra, size, len,fp); /*rra=ra[--l]*/ ^~~~~ ~~~~~~~~~~~~~~~~~ util.c:207:6: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread( rra, size, len,fp); /*rra=ra[ir]*/ ^~~~~ ~~~~~~~~~~~~~~~~~ util.c:210:6: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread( rrb, size, len,fp); /*rrb=ra[0]*/ ^~~~~ ~~~~~~~~~~~~~~~~~ util.c:232:5: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread (ra_j_1, size, len, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~ util.c:227:9: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread (ra_j, size, len, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~ util.c:341:7: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread ( key2, el_size, entry_len,fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ util.c:567:10: warning: unused variable 'd' [-Wunused-variable] int c,d; ^ util.c:762:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf ( fp, "%d",&list[n[0]++]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~ util.c:821:7: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf ( fp, "%s %s\n", s1, s2); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~ util.c:1215:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf(fp, "%d ", &array[a][b]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ util.c:1212:7: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf(fp, "%d ", &len2); ^~~~~~ ~~~~~~~~~~~~~~~~ util.c:1216:7: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf (fp, "\n"); ^~~~~~ ~~~~~~~~ util.c:1208:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf (fp, "%d\n", &len); ^~~~~~ ~~~~~~~~~~~~~~~~ util.c:1788:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ util.c:1864:7: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf (fp, "%d", &r); ^~~~~~ ~~~~~~~~~~~~ util.c:2074:27: warning: variable 'string' is uninitialized when used here [-Wuninitialized] if ((string=file2string(string))) ^~~~~~ util.c:2069:15: note: initialize the variable 'string' to silence this warning char *string; ^ = NULL util.c:3684:9: warning: unused variable 'flag' [-Wunused-variable] FILE *flag; ^ util.c:3759:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ util.c:3777:16: warning: unused variable 'tmpdir' [-Wunused-variable] char static *tmpdir; ^ util.c:3778:16: warning: unused variable 'cdir' [-Wunused-variable] char static *cdir; ^ util.c:4215:7: warning: implicit declaration of function 'wait' is invalid in C99 [-Wimplicit-function-declaration] wait((pid_t*)-1); ^ util.c:4264:5: warning: implicit declaration of function 'waitpid' is invalid in C99 [-Wimplicit-function-declaration] p=waitpid (p, status, options); ^ util.c:4333:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ util.c:4396:8: warning: variable 'n' is uninitialized when used here [-Wuninitialized] n++; ^ util.c:4372:8: note: initialize the variable 'n' to silence this warning int n; ^ = 0 util.c:4709:12: warning: unused variable 'buf' [-Wunused-variable] char buf[1000]; ^ util.c:4998:7: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf (fp, "%s\n",list[n]); ^~~~~~ ~~~~~~~~~~~~~~~~~~ util.c:5346:41: warning: if statement has empty body [-Wempty-body] else if ((proxy=getenv ("ALL_PROXY")));//id ^ util.c:5346:41: note: put the semicolon on a separate line to silence this warning [-Wempty-body] util.c:6662:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets ( line, VERY_LONG_STRING,fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ util.c:6682:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf ( fp, "%s", string); ^~~~~~ ~~~~~~~~~~~~~~~~ util.c:6918:5: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets ( line, lline,fp); ^~~~~ ~~~~~~~~~~~~~~ util.c:6948:5: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets ( line, lline,fp); ^~~~~ ~~~~~~~~~~~~~~ util.c:7035:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf ( fp, "Version_%f", &new_version); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util.c:7123:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ util.c:7390:7: warning: unused variable 'dir_sep' [-Wunused-variable] int dir_sep='/'; ^ util.c:7392:6: warning: unused variable 'a' [-Wunused-variable] int a, buf; ^ util.c:7392:9: warning: unused variable 'buf' [-Wunused-variable] int a, buf; ^ util.c:8629:9: warning: unused variable 'tmp' [-Wunused-variable] char *tmp; ^ util.c:8883:20: warning: unused variable 'sdata' [-Wunused-variable] double **data, **sdata; ^ util.c:8886:10: warning: unused variable 'b' [-Wunused-variable] int a, b; ^ util.c:8892:7: warning: unused variable 'scan' [-Wunused-variable] int scan=0; ^ util.c:8930:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ util.c:8971:18: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if ( buf[0]='#') ~~~~~~^~~~ util.c:8971:18: note: place parentheses around the assignment to silence this warning if ( buf[0]='#') ^ ( ) util.c:8971:18: note: use '==' to turn this assignment into an equality comparison if ( buf[0]='#') ^ == util.c:8990:6: warning: expression result unused [-Wunused-value] n[0]; ~ ~^ util.c:8947:12: warning: unused variable 'data' [-Wunused-variable] double **data; ^ util.c:9017:18: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if ( buf[0]='#') ~~~~~~^~~~ util.c:9017:18: note: place parentheses around the assignment to silence this warning if ( buf[0]='#') ^ ( ) util.c:9017:18: note: use '==' to turn this assignment into an equality comparison if ( buf[0]='#') ^ == util.c:9003:11: warning: unused variable 'c' [-Wunused-variable] int a,b,c,p; ^ util.c:9318:10: warning: unused variable 'cscore' [-Wunused-variable] double cscore=0; ^ In file included from util.c:19: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ util.c:74:13: warning: unused function 'exchange' [-Wunused-function] static void exchange(void *a, void *b, size_t size) { ^ util.c:4874:12: warning: unused variable 'n_warning' [-Wunused-variable] static int n_warning; ^ util.c:4875:15: warning: unused variable 'warning_list' [-Wunused-variable] static char **warning_list; ^ util.c:7669:15: warning: unused variable 'EXP_UNDERFLOW_THRESHOLD' [-Wunused-variable] static double EXP_UNDERFLOW_THRESHOLD = -4.60f; ^ util.c:7672:15: warning: unused variable 'LOG_ONE' [-Wunused-variable] static double LOG_ONE = 0.0f; ^ 54 warnings generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o reformat_struc.o reformat_struc.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' reformat_struc.c:307:9: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf (fp, "%*s %*s %c %*c %d %*f %*f %*f\n",&res,&res_num); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ reformat_struc.c:344:9: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf (fp, "%*s %s %s %*c %d %f %f %f\n",A->type, A->res,&A->res_num, &A->x, &A->y, &A->z); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ reformat_struc.c:299:9: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf ( fp, "%*s" ); ^~~~~~ ~~~~~~~~~ reformat_struc.c:301:9: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf ( fp, "%*s" ); ^~~~~~ ~~~~~~~~~ reformat_struc.c:334:9: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf ( fp, "%*s" ); ^~~~~~ ~~~~~~~~~ reformat_struc.c:336:9: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf ( fp, "%*s" ); ^~~~~~ ~~~~~~~~~ In file included from reformat_struc.c:8: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 7 warnings generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o reformat.o reformat.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' reformat.c:1272:13: warning: implicit declaration of function 'is_stockholm_aln' is invalid in C99 [-Wimplicit-function-declaration] if ( is_stockholm_aln (file))sprintf (format, "stockholm_aln"); ^ reformat.c:1275:27: warning: implicit declaration of function 'fast_format_determination' is invalid in C99 [-Wimplicit-function-declaration] else if (format_val = fast_format_determination(file)) ^ reformat.c:1275:25: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] else if (format_val = fast_format_determination(file)) ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ reformat.c:1275:25: note: place parentheses around the assignment to silence this warning else if (format_val = fast_format_determination(file)) ^ ( ) reformat.c:1275:25: note: use '==' to turn this assignment into an equality comparison else if (format_val = fast_format_determination(file)) ^ == reformat.c:1416:7: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf ( fp, "%d", &result); ^~~~~~ ~~~~~~~~~~~~~~~~~ reformat.c:1454:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf ( fp, "\n%s\n", buf); ^~~~~~ ~~~~~~~~~~~~~~~~~ reformat.c:1531:11: warning: unused variable 'command' [-Wunused-variable] char command[1000]; ^ reformat.c:1606:12: warning: if statement has empty body [-Wempty-body] if (!name); ^ reformat.c:1606:12: note: put the semicolon on a separate line to silence this warning [-Wempty-body] reformat.c:1890:5: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf (fp , "%s", buf); ^~~~~~ ~~~~~~~~~~~~~~ reformat.c:1993:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ reformat.c:3051:6: warning: implicit declaration of function 'output_header_mat' is invalid in C99 [-Wimplicit-function-declaration] output_header_mat(D1->M, out_file); ^ reformat.c:3165:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf ( fp, "%s", buf2); ^~~~~~ ~~~~~~~~~~~~~~ reformat.c:3180:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf ( fp, "%s",W->seq_name[a]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ reformat.c:3182:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf ( fp, "%s", buf2); ^~~~~~ ~~~~~~~~~~~~~~ reformat.c:3193:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf ( fp, "\n"); ^~~~~~ ~~~~~~~~ reformat.c:3158:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf ( fp, "%s", buf2); ^~~~~~ ~~~~~~~~~~~~~~ reformat.c:3174:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf ( fp, "%s", buf2); ^~~~~~ ~~~~~~~~~~~~~~ reformat.c:3469:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf ( fp, "%d %d %d %c %c %f\n", &(ST)->list[a][0],&(ST)->list[a][1],&(ST)->list[a][2], &x, &y, &f); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ reformat.c:3466:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf ( fp, "%c\n%d\n",&x, &(ST)->tot_list); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ reformat.c:3525:30: warning: variable 'b' is uninitialized when used here [-Wuninitialized] for ( n[0]=0,a=1; aseq[S->nseq][a])); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ reformat.c:3687:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf ( fp, "%s %d\n",S->name[S->nseq], &(S->len[S->nseq])); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ reformat.c:3729:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf (fp, "%s",name); ^~~~~~ ~~~~~~~~~~~~~ reformat.c:3804:5: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] {fscanf (fp, "%s",name); ^~~~~~ ~~~~~~~~~~~~~ reformat.c:4545:11: warning: array subscript is of type 'char' [-Wchar-subscripts] al_test[allowed[i]] = 1; ^~~~~~~~~~~ reformat.c:4589:17: warning: array subscript is of type 'char' [-Wchar-subscripts] if (al_test[*tmp]) ^~~~~ reformat.c:4531:9: warning: unused variable 'name' [-Wunused-variable] char *name; ^ reformat.c:4965:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets (buf, LONG_STRING, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~ reformat.c:4984:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets (buf, LONG_STRING, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~ reformat.c:5003:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf (fp, "%s", name); ^~~~~~ ~~~~~~~~~~~~~~ reformat.c:5158:25: warning: if statement has empty body [-Wempty-body] if ( !isblanc (buf)); ^ reformat.c:5158:25: note: put the semicolon on a separate line to silence this warning [-Wempty-body] reformat.c:5356:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] {fscanf (fp, "%*d >%s", name[nseq++]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ reformat.c:5405:7: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(buf, VERY_LONG_STRING, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ reformat.c:5427:7: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(buf, VERY_LONG_STRING, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ reformat.c:5625:5: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf ( fp, "%s",string); ^~~~~~ ~~~~~~~~~~~~~~~ reformat.c:5790:7: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf (fp, "%s %d", name,&i); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~ reformat.c:6801:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ reformat.c:7214:12: warning: unused variable 'nibit' [-Wunused-variable] float nibit=(float)log(ibit/(B->len_aln*B->nseq)); ^ reformat.c:10271:12: warning: unused variable 'r2' [-Wunused-variable] char r1, r2; ^ reformat.c:10687:17: warning: unused variable 's2' [-Wunused-variable] int s1, s2,r1,r2; ^ reformat.c:10687:23: warning: unused variable 'r2' [-Wunused-variable] int s1, s2,r1,r2; ^ reformat.c:10682:9: warning: unused variable 'l' [-Wunused-variable] int l; ^ reformat.c:10747:5: warning: implicit declaration of function 'redundate' is invalid in C99 [-Wimplicit-function-declaration] redundate (D1->S, D2->T,seq, tree); ^ reformat.c:10763:5: warning: implicit declaration of function 'tree2nnode_unresolved' is invalid in C99 [-Wimplicit-function-declaration] tree2nnode_unresolved (D1->T, l); ^ reformat.c:11572:10: warning: unused variable 'p1' [-Wunused-variable] int p1,p2,p3,f, t; ^ reformat.c:11572:13: warning: unused variable 'p2' [-Wunused-variable] int p1,p2,p3,f, t; ^ reformat.c:11572:16: warning: unused variable 'p3' [-Wunused-variable] int p1,p2,p3,f, t; ^ reformat.c:11575:10: warning: unused variable 'clean_mode' [-Wunused-variable] char clean_mode[100]; ^ reformat.c:12270:22: warning: unused variable 'sn' [-Wunused-variable] float *re, tre=0,sn, tsn=0, sp, tsp=0; ^ reformat.c:12270:33: warning: unused variable 'sp' [-Wunused-variable] float *re, tre=0,sn, tsn=0, sp, tsp=0; ^ reformat.c:12272:11: warning: unused variable 'fp' [-Wunused-variable] FILE *fp; ^ reformat.c:12273:10: warning: unused variable 'fname' [-Wunused-variable] char fname [100]; ^ reformat.c:12523:51: warning: array subscript is of type 'char' [-Wchar-subscripts] for (a=0; aseq[li[a]][i-1]==S->seq[li[a]][i-1])t++; ^ util_dp_gotoh_nw.c:1286:14: note: initialize the variable 'S' to silence this warning Sequence *S; ^ = NULL util_dp_gotoh_nw.c:1360:10: warning: unused variable 'n' [-Wunused-variable] int a,n, p1, p2, l1, l2; ^ util_dp_gotoh_nw.c:1362:9: warning: unused variable 'pos' [-Wunused-variable] int **pos; ^ util_dp_gotoh_nw.c:1361:9: warning: unused variable 'list' [-Wunused-variable] int **list; ^ util_dp_gotoh_nw.c:1511:7: warning: unused variable 'nt' [-Wunused-variable] int nt=0; ^ util_dp_gotoh_nw.c:1510:7: warning: unused variable 'ns' [-Wunused-variable] int ns=0; ^ util_dp_gotoh_nw.c:1504:7: warning: unused variable 'k' [-Wunused-variable] int k=0; ^ util_dp_gotoh_nw.c:1502:7: warning: unused variable 'max_n' [-Wunused-variable] int max_n; ^ util_dp_gotoh_nw.c:1671:37: warning: unused variable 'avg' [-Wunused-variable] float nscore, score, tot, filter, avg=0, new=0; ^ util_dp_gotoh_nw.c:1671:44: warning: unused variable 'new' [-Wunused-variable] float nscore, score, tot, filter, avg=0, new=0; ^ util_dp_gotoh_nw.c:1803:14: warning: unused variable 'a' [-Wunused-variable] int score, a; ^ util_dp_gotoh_nw.c:1902:7: warning: unused variable 'nomatch' [-Wunused-variable] int nomatch; ^ util_dp_gotoh_nw.c:2176:14: warning: unused variable 'a' [-Wunused-variable] int score, a; ^ util_dp_gotoh_nw.c:2204:32: warning: unused variable 'cr2' [-Wunused-variable] int s1, s2,s, cs1, cs2, cr1, cr2,l,ll; ^ util_dp_gotoh_nw.c:2306:7: warning: unused variable 'si' [-Wunused-variable] int si, r1,r2,t_s, t_r,t_w, t_s2, t_r2, t_w2, s1, s2; ^ util_dp_gotoh_nw.c:2312:37: warning: unused variable 'avg' [-Wunused-variable] float nscore, score, tot, filter, avg=0, new=0; ^ util_dp_gotoh_nw.c:2312:44: warning: unused variable 'new' [-Wunused-variable] float nscore, score, tot, filter, avg=0, new=0; ^ util_dp_gotoh_nw.c:2594:6: warning: implicit declaration of function 'tolower' is invalid in C99 [-Wimplicit-function-declaration] r=tolower(A->seq_al[b][a]); ^ In file included from util_dp_gotoh_nw.c:8: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 21 warnings generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_dp_suboptimal_nw.o util_dp_suboptimal_nw.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' util_dp_suboptimal_nw.c:200:6: warning: implicit declaration of function 'idscore_pairseq' is invalid in C99 [-Wimplicit-function-declaration] id=idscore_pairseq(seqI,seqJ,-12, -1, CL->M, "idmat"); ^ util_dp_suboptimal_nw.c:616:3: warning: implicit declaration of function 'proba_pair_wise' is invalid in C99 [-Wimplicit-function-declaration] proba_pair_wise (NULL, NULL, NULL, NULL); ^ util_dp_suboptimal_nw.c:896:14: warning: unused variable 'gtp' [-Wunused-variable] static int gtp=0; ^ util_dp_suboptimal_nw.c:1108:16: warning: unused variable 'k' [-Wunused-variable] int ij, i, j,k, I, J, s1, s2; ^ util_dp_suboptimal_nw.c:1112:7: warning: unused variable 'sim' [-Wunused-variable] int sim; ^ util_dp_suboptimal_nw.c:1668:15: warning: unused variable 'c' [-Wunused-variable] int a, b, c, l; ^ In file included from util_dp_suboptimal_nw.c:7: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ util_dp_suboptimal_nw.c:15:14: warning: unused variable 'EXP_UNDERFLOW_THRESHOLD' [-Wunused-variable] static float EXP_UNDERFLOW_THRESHOLD = -4.60f; ^ util_dp_suboptimal_nw.c:16:14: warning: unused variable 'LOG_UNDERFLOW_THRESHOLD' [-Wunused-variable] static float LOG_UNDERFLOW_THRESHOLD = 7.50f; ^ util_dp_suboptimal_nw.c:21:14: warning: unused variable 'DNAinitDistrib2Default' [-Wunused-variable] static float DNAinitDistrib2Default[] ={ 0.9588437676f, 0.0205782652f, 0.0205782652f }; ^ util_dp_suboptimal_nw.c:28:14: warning: unused variable 'DNAemitPairsDefault' [-Wunused-variable] static float DNAemitPairsDefault[6][6] = { ^ util_dp_suboptimal_nw.c:38:14: warning: unused variable 'RNAinitDistrib2Default' [-Wunused-variable] static float RNAinitDistrib2Default[] = { 0.9615409374f, 0.0000004538f, 0.0000004538f, 0.0192291681f, 0.0192291681f }; ^ 12 warnings generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_dp_cdna_fasta_nw.o util_dp_cdna_fasta_nw.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' util_dp_cdna_fasta_nw.c:262:132: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] else if ( type==M->INSERTION && deltatype==1)M->model[a][M->END]=M->model[M->START][a]=(M->TG_MODE==0)?M->gop:0+(M->F_TG_MODE==0)?M->f_gop:0; ~~~~~~~~~~~~~~~~~~~^ util_dp_cdna_fasta_nw.c:262:132: note: place parentheses around the '+' expression to silence this warning else if ( type==M->INSERTION && deltatype==1)M->model[a][M->END]=M->model[M->START][a]=(M->TG_MODE==0)?M->gop:0+(M->F_TG_MODE==0)?M->f_gop:0; ^ ( ) util_dp_cdna_fasta_nw.c:262:132: note: place parentheses around the '?:' expression to evaluate it first else if ( type==M->INSERTION && deltatype==1)M->model[a][M->END]=M->model[M->START][a]=(M->TG_MODE==0)?M->gop:0+(M->F_TG_MODE==0)?M->f_gop:0; ^ ( ) util_dp_cdna_fasta_nw.c:264:132: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] else if ( type==M->DELETION && deltatype==1)M->model[a][M->END]=M->model[M->START][a]=(M->TG_MODE==0)?M->gop:0+(M->F_TG_MODE==0)?M->f_gop:0; ~~~~~~~~~~~~~~~~~~~^ util_dp_cdna_fasta_nw.c:264:132: note: place parentheses around the '+' expression to silence this warning else if ( type==M->DELETION && deltatype==1)M->model[a][M->END]=M->model[M->START][a]=(M->TG_MODE==0)?M->gop:0+(M->F_TG_MODE==0)?M->f_gop:0; ^ ( ) util_dp_cdna_fasta_nw.c:264:132: note: place parentheses around the '?:' expression to evaluate it first else if ( type==M->DELETION && deltatype==1)M->model[a][M->END]=M->model[M->START][a]=(M->TG_MODE==0)?M->gop:0+(M->F_TG_MODE==0)?M->f_gop:0; ^ ( ) In file included from util_dp_cdna_fasta_nw.c:7: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 3 warnings generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_dp_generic_fasta_nw.o util_dp_generic_fasta_nw.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' In file included from util_dp_generic_fasta_nw.c:8: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 1 warning generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_dp_fasta_nw.o util_dp_fasta_nw.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' util_dp_fasta_nw.c:471:15: warning: unused variable 'c' [-Wunused-variable] int a, b, c, d; ^ util_dp_fasta_nw.c:471:18: warning: unused variable 'd' [-Wunused-variable] int a, b, c, d; ^ util_dp_fasta_nw.c:1779:14: warning: array subscript is of type 'char' [-Wchar-subscripts] if (!h->hl[r]) h->hl[r]=vcalloc (1, sizeof (hseq)); ^~ util_dp_fasta_nw.c:1779:25: warning: array subscript is of type 'char' [-Wchar-subscripts] if (!h->hl[r]) h->hl[r]=vcalloc (1, sizeof (hseq)); ^~ util_dp_fasta_nw.c:1780:11: warning: array subscript is of type 'char' [-Wchar-subscripts] h=h->hl[r]; ^~ In file included from util_dp_fasta_nw.c:8: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 6 warnings generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_dp_fasta_sw.o util_dp_fasta_sw.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' In file included from util_dp_fasta_sw.c:7: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 1 warning generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_dp_gotoh_sw.o util_dp_gotoh_sw.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' util_dp_gotoh_sw.c:365:8: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread ( &k, sizeof (TRACE_TYPE), 1, long_trace); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from util_dp_gotoh_sw.c:7: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 2 warnings generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_dp_est.o util_dp_est.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' In file included from util_dp_est.c:7: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 1 warning generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_domain_dp_drivers.o util_domain_dp_drivers.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' util_domain_dp_drivers.c:564:16: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] while (entry=extract_entry (CL)) ~~~~~^~~~~~~~~~~~~~~~~~~ util_domain_dp_drivers.c:564:16: note: place parentheses around the assignment to silence this warning while (entry=extract_entry (CL)) ^ ( ) util_domain_dp_drivers.c:564:16: note: use '==' to turn this assignment into an equality comparison while (entry=extract_entry (CL)) ^ == util_domain_dp_drivers.c:545:7: warning: unused variable 'a' [-Wunused-variable] int a; ^ In file included from util_domain_dp_drivers.c:7: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 3 warnings generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_dp_drivers.o util_dp_drivers.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' util_dp_drivers.c:29:16: warning: unused variable 's2' [-Wunused-variable] int a,b, s1, s2, r1, r2,w2; ^ util_dp_drivers.c:30:25: warning: unused variable 'RCL' [-Wunused-variable] Constraint_list *CL, *RCL; ^ util_dp_drivers.c:29:24: warning: unused variable 'r2' [-Wunused-variable] int a,b, s1, s2, r1, r2,w2; ^ util_dp_drivers.c:29:27: warning: unused variable 'w2' [-Wunused-variable] int a,b, s1, s2, r1, r2,w2; ^ util_dp_drivers.c:942:6: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ util_dp_drivers.c:970:6: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ util_dp_drivers.c:1011:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ util_dp_drivers.c:1065:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets (buf2, 10000, fp); ^~~~~ ~~~~~~~~~~~~~~~ util_dp_drivers.c:1001:25: warning: unused variable 'c' [-Wunused-variable] int r1, r2, s1, s2,a,c; ^ util_dp_drivers.c:1119:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ util_dp_drivers.c:1214:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ util_dp_drivers.c:1274:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ util_dp_drivers.c:1413:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ util_dp_drivers.c:1488:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ util_dp_drivers.c:1611:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] getcwd (cdir, sizeof(char)*1000); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ util_dp_drivers.c:1612:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] chdir (get_cache_dir()); ^~~~~ ~~~~~~~~~~~~~~~ util_dp_drivers.c:1621:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] chdir (cdir); ^~~~~ ~~~~ util_dp_drivers.c:1647:12: warning: implicit declaration of function 'isalpha' is invalid in C99 [-Wimplicit-function-declaration] if (!isalpha(r1) || !isalpha(r2))continue; ^ util_dp_drivers.c:1560:6: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ util_dp_drivers.c:1555:12: warning: unused variable 'string1' [-Wunused-variable] char *string1, *string2, *string3, *string4, *string5; ^ util_dp_drivers.c:1555:22: warning: unused variable 'string2' [-Wunused-variable] char *string1, *string2, *string3, *string4, *string5; ^ util_dp_drivers.c:1555:32: warning: unused variable 'string3' [-Wunused-variable] char *string1, *string2, *string3, *string4, *string5; ^ util_dp_drivers.c:1555:42: warning: unused variable 'string4' [-Wunused-variable] char *string1, *string2, *string3, *string4, *string5; ^ util_dp_drivers.c:1555:52: warning: unused variable 'string5' [-Wunused-variable] char *string1, *string2, *string3, *string4, *string5; ^ util_dp_drivers.c:1735:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ util_dp_drivers.c:2552:12: warning: unused variable 'p' [-Wunused-variable] int a,b,p,n,g; ^ util_dp_drivers.c:2552:14: warning: unused variable 'n' [-Wunused-variable] int a,b,p,n,g; ^ util_dp_drivers.c:2553:9: warning: unused variable 'gc' [-Wunused-variable] int **gc; ^ util_dp_drivers.c:2607:12: warning: unused variable 'n' [-Wunused-variable] int a,p,n,g; ^ util_dp_drivers.c:2608:9: warning: unused variable 'gc' [-Wunused-variable] int **gc; ^ util_dp_drivers.c:3162:10: warning: implicit declaration of function 'sa_align_groups' is invalid in C99 [-Wimplicit-function-declaration] while (sa_align_groups (A,CL,used,0,50)!=-1); ^ util_dp_drivers.c:3152:7: warning: unused variable 'a' [-Wunused-variable] int a,g=0; ^ util_dp_drivers.c:3174:10: warning: unused variable 'next' [-Wunused-variable] int a, next, id, cov; ^ util_dp_drivers.c:3225:14: warning: implicit declaration of function 'tolower' is invalid in C99 [-Wimplicit-function-declaration] int r1=tolower(s1[a]); ^ util_dp_drivers.c:3241:13: warning: unused variable 'c' [-Wunused-variable] int a, b, c,n; ^ util_dp_drivers.c:3274:9: warning: unused variable 'g' [-Wunused-variable] int a,g=0; ^ util_dp_drivers.c:3306:7: warning: variable 'g0' is uninitialized when used here [-Wuninitialized] if (g0==-1) return -1; ^~ util_dp_drivers.c:3293:15: note: initialize the variable 'g0' to silence this warning int s0,s1,g0, g1,a,id,cov; ^ = 0 util_dp_drivers.c:3339:12: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] static **sim2; ~~~~~~ ^ util_dp_drivers.c:3337:13: warning: unused variable 'c' [-Wunused-variable] int a, b, c, bsim; ^ util_dp_drivers.c:3339:12: warning: unused variable 'sim2' [-Wunused-variable] static **sim2; ^ util_dp_drivers.c:3597:7: warning: unused variable 'a' [-Wunused-variable] int a; ^ util_dp_drivers.c:4681:7: warning: unused variable 'mode' [-Wunused-variable] int mode=1; ^ util_dp_drivers.c:4783:17: warning: unused variable 'd' [-Wunused-variable] int a,b,c,d,s,ss,g,p,l,ml; ^ util_dp_drivers.c:4771:13: warning: unused variable 'a' [-Wunused-variable] int score,a; ^ util_dp_drivers.c:5726:7: warning: unused variable 'a' [-Wunused-variable] int a; ^ util_dp_drivers.c:5739:11: error: non-void function 'rec_tree_aln_N' should return a value [-Wreturn-type] if (!P) return; ^ 45 warnings and 1 error generated. make[1]: [util_dp_drivers.o] Error 1 (ignored) cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o util_domain_dp.o util_domain_dp.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' In file included from util_domain_dp.c:7: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 1 warning generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o CUSTOM_evaluate_for_struc.o CUSTOM_evaluate_for_struc.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' In file included from CUSTOM_evaluate_for_struc.c:7: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 1 warning generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o evaluate_for_struc.o evaluate_for_struc.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' evaluate_for_struc.c:91:8: warning: unused variable 'strike' [-Wunused-variable] char *strike; ^ evaluate_for_struc.c:2348:13: warning: unused variable 'tree' [-Wunused-variable] int w,tree, cont; ^ evaluate_for_struc.c:2209:7: warning: unused variable 'wd1' [-Wunused-variable] int wd1, wd2; ^ evaluate_for_struc.c:2192:13: warning: unused variable 'distances' [-Wunused-variable] float ****distances; ^ evaluate_for_struc.c:2207:24: warning: unused variable 'n' [-Wunused-variable] int a, b, ncol, npos,n; ^ evaluate_for_struc.c:2237:7: warning: unused variable 'proceed' [-Wunused-variable] int proceed=1; ^ evaluate_for_struc.c:2216:7: warning: unused variable 'print_rapdb' [-Wunused-variable] int print_rapdb; ^ evaluate_for_struc.c:2205:14: warning: unused variable 'pdb_param' [-Wunused-variable] Pdb_param *pdb_param; ^ evaluate_for_struc.c:2217:9: warning: unused variable 'nrapdb' [-Wunused-variable] float nrapdb, rapdb; ^ evaluate_for_struc.c:2196:14: warning: unused variable 'max' [-Wunused-variable] float min, max; ^ evaluate_for_struc.c:2217:17: warning: unused variable 'rapdb' [-Wunused-variable] float nrapdb, rapdb; ^ evaluate_for_struc.c:2196:9: warning: unused variable 'min' [-Wunused-variable] float min, max; ^ evaluate_for_struc.c:2188:19: warning: unused variable 'c' [-Wunused-variable] int **pos, c; ^ evaluate_for_struc.c:2210:7: warning: unused variable 'in_bubble' [-Wunused-variable] int in_bubble=0; ^ evaluate_for_struc.c:2219:12: warning: unused variable 'T0' [-Wunused-variable] NT_node *T0,*T1,*T2,*PT, *POS; ^ evaluate_for_struc.c:2209:12: warning: unused variable 'wd2' [-Wunused-variable] int wd1, wd2; ^ evaluate_for_struc.c:2563:10: warning: unused variable 'b' [-Wunused-variable] int a, b; ^ In file included from evaluate_for_struc.c:8: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 18 warnings generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o evaluate_for_domain.o evaluate_for_domain.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' In file included from evaluate_for_domain.c:7: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 1 warning generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o evaluate_dirichlet.o evaluate_dirichlet.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' evaluate_dirichlet.c:297:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf(fp, "%f", &f); ^~~~~~ ~~~~~~~~~~~~ evaluate_dirichlet.c:291:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf(fp, "%f\n", &f); ^~~~~~ ~~~~~~~~~~~~~~ evaluate_dirichlet.c:293:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf(fp, "%f", &f); ^~~~~~ ~~~~~~~~~~~~ evaluate_dirichlet.c:300:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf(fp, "\n"); ^~~~~~ ~~~~~~~~ In file included from evaluate_dirichlet.c:7: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 5 warnings generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o evaluate.o evaluate.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' evaluate.c:165:19: warning: unused variable 'i' [-Wunused-variable] int a, b, c, r, i; ^ evaluate.c:165:13: warning: unused variable 'c' [-Wunused-variable] int a, b, c, r, i; ^ evaluate.c:749:5: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf (fp, "%d ", &res); ^~~~~~ ~~~~~~~~~~~~~~~ evaluate.c:754:5: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf (fp, "%f %f", &sseq, &mseq); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ evaluate.c:759:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf (fp, "%f %f", &sseq, &mseq); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ evaluate.c:1135:13: warning: if statement has empty body [-Wempty-body] if (w);free_int (w, -1); ^ evaluate.c:1135:13: note: put the semicolon on a separate line to silence this warning [-Wempty-body] evaluate.c:1117:20: warning: unused variable 'i' [-Wunused-variable] int **w, a,b,c,l,i; ^ evaluate.c:1126:10: warning: unused variable 'count' [-Wunused-variable] float *count; ^ evaluate.c:1125:14: warning: unused variable 'A' [-Wunused-variable] Alignment *A; ^ evaluate.c:1117:18: warning: unused variable 'l' [-Wunused-variable] int **w, a,b,c,l,i; ^ evaluate.c:1117:16: warning: unused variable 'c' [-Wunused-variable] int **w, a,b,c,l,i; ^ evaluate.c:1120:9: warning: unused variable 'fp' [-Wunused-variable] FILE *fp; ^ evaluate.c:1118:12: warning: unused variable 'min_avg' [-Wunused-variable] int avg, min_avg, best_cycle; ^ evaluate.c:1117:14: warning: unused variable 'b' [-Wunused-variable] int **w, a,b,c,l,i; ^ evaluate.c:1118:7: warning: unused variable 'avg' [-Wunused-variable] int avg, min_avg, best_cycle; ^ evaluate.c:1123:32: warning: unused variable 'acc' [-Wunused-variable] float nsd, best_score,score, acc; ^ evaluate.c:1214:10: warning: unused variable 'b' [-Wunused-variable] int a, b; ^ evaluate.c:1230:10: warning: unused variable 'b' [-Wunused-variable] int a, b; ^ evaluate.c:1242:10: warning: unused variable 'b' [-Wunused-variable] int a, b; ^ evaluate.c:1241:10: warning: unused variable 'sum' [-Wunused-variable] double sum=0, sum2=0, zscore=0, zsum2=0; ^ evaluate.c:1241:17: warning: unused variable 'sum2' [-Wunused-variable] double sum=0, sum2=0, zscore=0, zsum2=0; ^ evaluate.c:1285:13: warning: if statement has empty body [-Wempty-body] if (w);free_int (w, -1); ^ evaluate.c:1285:13: note: put the semicolon on a separate line to silence this warning [-Wempty-body] evaluate.c:1284:11: warning: unused variable 't' [-Wunused-variable] int t; ^ evaluate.c:1272:27: warning: unused variable 'fp' [-Wunused-variable] char **pred_list; FILE *fp; ^ evaluate.c:1270:18: warning: unused variable 'l' [-Wunused-variable] int **w, a,b,c,l,i; ^ evaluate.c:1270:20: warning: unused variable 'i' [-Wunused-variable] int **w, a,b,c,l,i; ^ evaluate.c:1992:30: warning: unused variable 'b2' [-Wunused-variable] char name [1000], b1[100], b2[100]; ^ evaluate.c:2540:8: warning: unused variable 'nclean' [-Wunused-variable] int nclean; ^ evaluate.c:3452:7: warning: array subscript is of type 'char' [-Wchar-subscripts] aa[r]+=pr[a][b+1]; ^~ evaluate.c:3453:17: warning: array subscript is of type 'char' [-Wchar-subscripts] if (a==2){aa[r]*=aa[r];} ^~ evaluate.c:3453:24: warning: array subscript is of type 'char' [-Wchar-subscripts] if (a==2){aa[r]*=aa[r];} ^~ evaluate.c:3454:11: warning: array subscript is of type 'char' [-Wchar-subscripts] if (aa[r]>score)score=aa[r]; ^~ evaluate.c:3454:29: warning: array subscript is of type 'char' [-Wchar-subscripts] if (aa[r]>score)score=aa[r]; ^~ evaluate.c:3461:10: warning: unused variable 'r' [-Wunused-variable] char r=tolower (pr[a][b]); ^ evaluate.c:3433:14: warning: unused variable 'r' [-Wunused-variable] int a, b, r; ^ evaluate.c:4849:9: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf (fp, "%f %c %*s",&v1, &c1 ); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~ In file included from evaluate.c:7: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 37 warnings generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o showpair.o showpair.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' In file included from showpair.c:6: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 1 warning generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o fsa_dp.o fsa_dp.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' In file included from fsa_dp.c:7: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 1 warning generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o pavie_dp.o pavie_dp.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' pavie_dp.c:101:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf (fp, "%s\n",mat_list[nch++]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ pavie_dp.c:1053:7: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] system (command); ^~~~~~ ~~~~~~~ pavie_dp.c:1055:7: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] system (command); ^~~~~~ ~~~~~~~ pavie_dp.c:1118:58: warning: operator '?:' has lower precedence than '*'; '*' will be evaluated first [-Wparentheses] gap_inY= F[i-1][j] + (CL->M[x[i-1]-'A'][gap]*(j==YL)?factor:1); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ pavie_dp.c:1118:58: note: place parentheses around the '*' expression to silence this warning gap_inY= F[i-1][j] + (CL->M[x[i-1]-'A'][gap]*(j==YL)?factor:1); ^ ( ) pavie_dp.c:1118:58: note: place parentheses around the '?:' expression to evaluate it first gap_inY= F[i-1][j] + (CL->M[x[i-1]-'A'][gap]*(j==YL)?factor:1); ^ ( ) pavie_dp.c:1119:58: warning: operator '?:' has lower precedence than '*'; '*' will be evaluated first [-Wparentheses] gap_inX= F[i][j-1] + (CL->M[y[j-1]-'A'][gap]*(i==XL)?factor:1); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ pavie_dp.c:1119:58: note: place parentheses around the '*' expression to silence this warning gap_inX= F[i][j-1] + (CL->M[y[j-1]-'A'][gap]*(i==XL)?factor:1); ^ ( ) pavie_dp.c:1119:58: note: place parentheses around the '?:' expression to evaluate it first gap_inX= F[i][j-1] + (CL->M[y[j-1]-'A'][gap]*(i==XL)?factor:1); ^ ( ) pavie_dp.c:1339:7: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf (fp, "%s", mat); ^~~~~~ ~~~~~~~~~~~~~ In file included from pavie_dp.c:7: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 7 warnings generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o dev1.o dev1.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' dev1.c:76:9: warning: implicit declaration of function 'tolower' is invalid in C99 [-Wimplicit-function-declaration] r1=tolower(A->seq_al[k][i]); ^ dev1.c:29:6: warning: unused variable 'itmpScore' [-Wunused-variable] int itmpScore; ^ In file included from dev1.c:7: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 3 warnings generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o dev2.o dev2.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' In file included from dev2.c:7: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 1 warning generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o dev3.o dev3.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o dev4.o dev4.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' In file included from dev4.c:7: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 1 warning generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o fastal.o fastal.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' fastal.c:1965:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] system(blast_command); ^~~~~~ ~~~~~~~~~~~~~ fastal.c:1969:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, 300, diag_f); ^~~~~ ~~~~~~~~~~~~~~~~~ fastal.c:1970:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, 300, diag_f); ^~~~~ ~~~~~~~~~~~~~~~~~ fastal.c:1971:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, 300, diag_f); ^~~~~ ~~~~~~~~~~~~~~~~~ fastal.c:1913:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] system(blast_command); ^~~~~~ ~~~~~~~~~~~~~ fastal.c:1918:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, 300, diag_f); ^~~~~ ~~~~~~~~~~~~~~~~~ fastal.c:1919:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, 300, diag_f); ^~~~~ ~~~~~~~~~~~~~~~~~ fastal.c:1920:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, 300, diag_f); ^~~~~ ~~~~~~~~~~~~~~~~~ fastal.c:2104:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] system(blast_command); ^~~~~~ ~~~~~~~~~~~~~ fastal.c:2251:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] system(blast_command); ^~~~~~ ~~~~~~~~~~~~~ fastal.c:3042:8: warning: unused variable 'num' [-Wunused-variable] int num = 0; ^ fastal.c:3193:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets (line, LINE_LENGTH , seq_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal.c:3344:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH , profile_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal.c:3315:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal.c:3318:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal.c:3321:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal.c:3323:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal.c:3325:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal.c:3494:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets (line, LINE_LENGTH , sequence_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal.c:3567:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal.c:3569:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal.c:3571:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal.c:3573:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal.c:3635:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(aligned_sequence, alignment_length+3, edit_seq_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal.c:3786:3: warning: implicit declaration of function 'complete_agreement_score' is invalid in C99 [-Wimplicit-function-declaration] complete_agreement_score(arguments.aln2test, arguments.aln_ref); ^ fastal.c:3793:3: warning: implicit declaration of function 'compute_ref_alignments' is invalid in C99 [-Wimplicit-function-declaration] compute_ref_alignments(arguments.sequence_file, arguments.aln_ref, arguments.num_ref_aln, arguments.num_seq_in_ref); ^ In file included from fastal.c:8: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 27 warnings generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o parttree.o parttree.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' parttree.c:675:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, 500, aln_f); ^~~~~ ~~~~~~~~~~~~~~~~ parttree.c:669:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, 500, aln_f); ^~~~~ ~~~~~~~~~~~~~~~~ parttree.c:833:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH, tables_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ parttree.c:822:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH, tables_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ parttree.c:877:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ parttree.c:886:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ parttree.c:865:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ parttree.c:880:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ parttree.c:936:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ parttree.c:925:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from parttree.c:10: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 11 warnings generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o tree.o tree.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' In file included from tree.c:7: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 1 warning generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o diagonal.o diagonal.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' diagonal.c:284:27: warning: implicit declaration of function 'toupper' is invalid in C99 [-Wimplicit-function-declaration] list[list_pos][2] = M[toupper(seq1[tmpx-1])-'A'][toupper(seq2[tmpy-1])-'A']; ^ diagonal.c:217:6: warning: unused variable 'tmpy_pos' [-Wunused-variable] int tmpy_pos; ^ diagonal.c:218:6: warning: unused variable 'tmpy_value' [-Wunused-variable] int tmpy_value; ^ diagonal.c:408:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] system(blast_command); ^~~~~~ ~~~~~~~~~~~~~ diagonal.c:413:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, 300, diag_f); ^~~~~ ~~~~~~~~~~~~~~~~~ diagonal.c:414:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, 300, diag_f); ^~~~~ ~~~~~~~~~~~~~~~~~ diagonal.c:415:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, 300, diag_f); ^~~~~ ~~~~~~~~~~~~~~~~~ diagonal.c:398:7: warning: unused variable 'blast_command2' [-Wunused-variable] char blast_command2[200]; ^ In file included from diagonal.c:5: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 9 warnings generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o fastal_opt_parsing.o fastal_opt_parsing.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' fastal_opt_parsing.c:13:29: warning: result of comparison against a string literal is unspecified (use strncmp instead) [-Wstring-compare] if (arguments->tree_method == "parttree") ^ ~~~~~~~~~~ 1 warning generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o scoring.o scoring.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' scoring.c:50:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH, alignment_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scoring.c:56:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH, alignment_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scoring.c:52:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH, alignment_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scoring.c:177:6: warning: unused variable 'chunk' [-Wunused-variable] int chunk = 500; ^ scoring.c:359:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH, seq_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ scoring.c:373:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] system(aln_command); ^~~~~~ ~~~~~~~~~~~ scoring.c:326:9: warning: unused variable 'j' [-Wunused-variable] int i, j, k, tmp, already, num_already; ^ scoring.c:464:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH, seq_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~ scoring.c:478:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] system(command); ^~~~~~ ~~~~~~~ scoring.c:560:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH, result); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ scoring.c:561:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH, result); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ scoring.c:562:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH, result); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ scoring.c:578:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] complete_agreement_score(char *aln_file_name, const char *ref_directory) ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from scoring.c:11: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 14 warnings generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o iteration.o iteration.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' iteration.c:28:22: warning: array subscript is of type 'char' [-Wchar-subscripts] ++(prf_in[char2pos[*seq]][++i]); ^~~~~ iteration.c:155:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH , alignment_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iteration.c:150:8: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ iteration.c:150:6: warning: unused variable 'i' [-Wunused-variable] int i,j; ^ iteration.c:387:22: warning: implicit declaration of function 'gotoh_dyn' is invalid in C99 [-Wimplicit-function-declaration] alignment_length = gotoh_dyn(profiles, param, method_arguments_p, 0, edit_file, profile_file, 0); ^ iteration.c:411:7: warning: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)' if (!strcmp(param->method, "fast")) ^ iteration.c:411:7: note: please include the header or explicitly provide a declaration for 'strcmp' iteration.c:417:3: warning: implicit declaration of function 'free_nw' is invalid in C99 [-Wimplicit-function-declaration] free_nw((Nw_param*)method_arguments_p, alphabet_size); ^ iteration.c:280:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH , alignment_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iteration.c:405:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] system(command); ^~~~~~ ~~~~~~~ iteration.c:325:10: warning: unused variable 'max_entrop' [-Wunused-variable] double max_entrop = 0; ^ iteration.c:329:10: warning: unused variable 'p' [-Wunused-variable] double p; ^ iteration.c:327:10: warning: unused variable 'entrop' [-Wunused-variable] double entrop = 0; ^ iteration.c:328:10: warning: unused variable 'last' [-Wunused-variable] double last = 0; ^ iteration.c:261:6: warning: unused variable 'it_counter' [-Wunused-variable] int it_counter = 0; ^ iteration.c:505:5: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(alnline, ALNLINE_LENGTH, old_aln_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iteration.c:471:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(alnline, ALNLINE_LENGTH , old_aln_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iteration.c:474:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(alnline, ALNLINE_LENGTH , old_aln_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iteration.c:431:6: warning: unused variable 'i' [-Wunused-variable] int i; ^ iteration.c:533:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iteration.c:535:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iteration.c:537:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iteration.c:539:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iteration.c:8: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ 23 warnings generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -D_FORTIFY_SOURCE=2 -c -o t_coffee.o t_coffee.c clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' t_coffee.c:4184:14: warning: unused variable 'j' [-Wunused-variable] int j; ^ t_coffee.c:386:8: warning: unused variable 'tmp_4_tcoffee' [-Wunused-variable] char *tmp_4_tcoffee; ^ t_coffee.c:5343:10: warning: implicit declaration of function 'fastal_main' is invalid in C99 [-Wimplicit-function-declaration] return fastal_main(argc, argv); ^ t_coffee.c:5414:12: warning: unused variable 's1' [-Wunused-variable] int a,b,s1, n, i; ^ t_coffee.c:5414:16: warning: unused variable 'n' [-Wunused-variable] int a,b,s1, n, i; ^ t_coffee.c:5414:19: warning: unused variable 'i' [-Wunused-variable] int a,b,s1, n, i; ^ t_coffee.c:5415:10: warning: unused variable 'fp' [-Wunused-variable] FILE *fp; ^ t_coffee.c:5416:8: warning: unused variable 'trim_mode' [-Wunused-variable] int trim_mode=2; ^ t_coffee.c:5608:8: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] static max_nseq; ~~~~~~ ^ t_coffee.c:5609:8: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] static cur_nseq; ~~~~~~ ^ t_coffee.c:5695:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ t_coffee.c:5679:15: warning: variable 'A' is uninitialized when used here [-Wuninitialized] max_kmcoffee=A->nseq; ^ t_coffee.c:5631:14: note: initialize the variable 'A' to silence this warning Alignment *A; ^ = NULL t_coffee.c:5904:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ t_coffee.c:6021:8: warning: unused variable 'buf' [-Wunused-variable] char buf [10000]; ^ In file included from t_coffee.c:9: ./io_lib_header.h:971:16: warning: unused function 'compute_std_tree' [-Wunused-function] static NT_node compute_std_tree (Alignment *A, int n, char **arg_list); ^ t_coffee.c:5301:6: warning: unused function 'test' [-Wunused-function] void test () ^ t_coffee.c:32:14: warning: unused function 'get_rmcoffee_defaults_old' [-Wunused-function] static char *get_rmcoffee_defaults_old(char *buf, char *type);//Original R-Coffee Paper ^ t_coffee.c:33:14: warning: unused function 'get_rcoffee_defaults_old' [-Wunused-function] static char *get_rcoffee_defaults_old(char *buf, char *type);//Original R-Coffee Paper ^ t_coffee.c:5082:7: warning: unused function 'get_cdna_defaults' [-Wunused-function] char *get_cdna_defaults(char *buf, char *type) ^ t_coffee.c:5610:12: warning: unused variable 'kmk' [-Wunused-variable] static int kmk; ^ 20 warnings generated. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -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 clang: error: no such file or directory: 'util_constraints_list.o' clang: error: no such file or directory: 'aln_convertion_util.o' clang: error: no such file or directory: 'util_dp_drivers.o' make[1]: [t_coffee] Error 1 (ignored) 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 cp: cannot stat `debian/tmp/t_coffee_source/t_coffee': No such file or directory dh_install: cp -a debian/tmp/t_coffee_source/t_coffee debian/t-coffee//usr/bin/ returned exit code 1 make: *** [binary-install/t-coffee] Error 2 dpkg-buildpackage: error: fakeroot debian/rules binary-arch gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120623-1619 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 22848 Build-Time: 41 Distribution: unstable Fail-Stage: build Install-Time: 7 Job: t-coffee_9.02.r1228-2 Package: t-coffee Package-Time: 72 Source-Version: 9.02.r1228-2 Space: 22848 Status: attempted Version: 9.02.r1228-2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120623-1619 Build needed 00:01:12, 22848k disc space DC-Status: Failed 73.247897s DC-Time-Estimation: 73.247897 versus expected 326 (r/m: 3.45063972280324 ; m: 73.247897)