DC-Build-Header: t-coffee 11.00.8cbe486-5 / 2017-07-06 20:16:43 +0000 DC-Task: type:rebuild-binarch-only source:t-coffee version:11.00.8cbe486-5 chroot:unstable esttime:315 logfile:/tmp/t-coffee_11.00.8cbe486-5_unstable_clang3.9.log modes:clang:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --chroot-setup-commands=/tmp/clang t-coffee_11.00.8cbe486-5' sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on ip-172-31-37-135.eu-central-1.compute.internal +==============================================================================+ | t-coffee 11.00.8cbe486-5 (amd64) Thu, 06 Jul 2017 20:16:44 +0000 | +==============================================================================+ Package: t-coffee Version: 11.00.8cbe486-5 Source Version: 11.00.8cbe486-5 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-6f349815-61cc-43b4-8c0a-c6c21b098c56' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang ---------- + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=3.9 + echo 'Install of clang-3.9' Install of clang-3.9 + apt-get update Hit:1 http://127.0.0.1:9999/debian unstable InRelease Get:2 http://127.0.0.1:9999/debian unstable/main Translation-en [5730 kB] Fetched 5730 kB in 1s (3765 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-3.9 Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libbsd0 libclang-common-3.9-dev libclang1-3.9 libedit2 libjsoncpp1 libllvm3.9 libncurses5 libobjc-6-dev libobjc4 Suggested packages: gnustep gnustep-devel clang-3.9-doc Recommended packages: llvm-3.9-dev python libgpm2 The following NEW packages will be installed: clang-3.9 libbsd0 libclang-common-3.9-dev libclang1-3.9 libedit2 libjsoncpp1 libllvm3.9 libncurses5 libobjc-6-dev libobjc4 0 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. Need to get 57.7 MB of archives. After this operation, 251 MB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian unstable/main amd64 libbsd0 amd64 0.8.5-1 [89.6 kB] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 libncurses5 amd64 6.0+20161126-1 [93.4 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 libedit2 amd64 3.1-20170329-1 [85.2 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libllvm3.9 amd64 1:3.9.1-10 [11.3 MB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 libclang1-3.9 amd64 1:3.9.1-10 [5875 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libjsoncpp1 amd64 1.7.4-3 [75.6 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libobjc4 amd64 7.1.0-9 [51.0 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libobjc-6-dev amd64 6.4.0-1 [197 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 libclang-common-3.9-dev amd64 1:3.9.1-10 [2573 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 clang-3.9 amd64 1:3.9.1-10 [37.4 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 57.7 MB in 0s (97.4 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9711 files and directories currently installed.) Preparing to unpack .../0-libbsd0_0.8.5-1_amd64.deb ... Unpacking libbsd0:amd64 (0.8.5-1) ... Selecting previously unselected package libncurses5:amd64. Preparing to unpack .../1-libncurses5_6.0+20161126-1_amd64.deb ... Unpacking libncurses5:amd64 (6.0+20161126-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../2-libedit2_3.1-20170329-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20170329-1) ... Selecting previously unselected package libllvm3.9:amd64. Preparing to unpack .../3-libllvm3.9_1%3a3.9.1-10_amd64.deb ... Unpacking libllvm3.9:amd64 (1:3.9.1-10) ... Selecting previously unselected package libclang1-3.9:amd64. Preparing to unpack .../4-libclang1-3.9_1%3a3.9.1-10_amd64.deb ... Unpacking libclang1-3.9:amd64 (1:3.9.1-10) ... Selecting previously unselected package libjsoncpp1:amd64. Preparing to unpack .../5-libjsoncpp1_1.7.4-3_amd64.deb ... Unpacking libjsoncpp1:amd64 (1.7.4-3) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../6-libobjc4_7.1.0-9_amd64.deb ... Unpacking libobjc4:amd64 (7.1.0-9) ... Selecting previously unselected package libobjc-6-dev:amd64. Preparing to unpack .../7-libobjc-6-dev_6.4.0-1_amd64.deb ... Unpacking libobjc-6-dev:amd64 (6.4.0-1) ... Selecting previously unselected package libclang-common-3.9-dev. Preparing to unpack .../8-libclang-common-3.9-dev_1%3a3.9.1-10_amd64.deb ... Unpacking libclang-common-3.9-dev (1:3.9.1-10) ... Selecting previously unselected package clang-3.9. Preparing to unpack .../9-clang-3.9_1%3a3.9.1-10_amd64.deb ... Unpacking clang-3.9 (1:3.9.1-10) ... Setting up libncurses5:amd64 (6.0+20161126-1) ... Setting up libobjc4:amd64 (7.1.0-9) ... Setting up libbsd0:amd64 (0.8.5-1) ... Processing triggers for libc-bin (2.24-12) ... Setting up libobjc-6-dev:amd64 (6.4.0-1) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up libedit2:amd64 (3.1-20170329-1) ... Setting up libllvm3.9:amd64 (1:3.9.1-10) ... Setting up libclang-common-3.9-dev (1:3.9.1-10) ... Setting up libclang1-3.9:amd64 (1:3.9.1-10) ... Setting up clang-3.9 (1:3.9.1-10) ... Processing triggers for libc-bin (2.24-12) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5 6 7' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-3.9 g++-4.6 + ln -s clang-3.9 gcc-4.6 + ln -s clang-3.9 cpp-4.6 + ln -s clang-3.9 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-3.9 g++-4.7 + ln -s clang-3.9 gcc-4.7 + ln -s clang-3.9 cpp-4.7 + ln -s clang-3.9 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-3.9 g++-4.8 + ln -s clang-3.9 gcc-4.8 + ln -s clang-3.9 cpp-4.8 + ln -s clang-3.9 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-3.9 g++-4.9 + ln -s clang-3.9 gcc-4.9 + ln -s clang-3.9 cpp-4.9 + ln -s clang-3.9 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-5 gcc-5 cpp-5 gcc + ln -s clang++-3.9 g++-5 + ln -s clang-3.9 gcc-5 + ln -s clang-3.9 cpp-5 + ln -s clang-3.9 gcc + echo 'gcc-5 hold' + dpkg --set-selections + echo 'g++-5 hold' + dpkg --set-selections + for VERSION in $VERSIONS + rm -f g++-6 gcc-6 cpp-6 gcc + ln -s clang++-3.9 g++-6 + ln -s clang-3.9 gcc-6 + ln -s clang-3.9 cpp-6 + ln -s clang-3.9 gcc + echo 'gcc-6 hold' + dpkg --set-selections + echo 'g++-6 hold' + dpkg --set-selections + for VERSION in $VERSIONS + rm -f g++-7 gcc-7 cpp-7 gcc + ln -s clang++-3.9 g++-7 + ln -s clang-3.9 gcc-7 + ln -s clang-3.9 cpp-7 + ln -s clang-3.9 gcc + echo 'gcc-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + cd - /build/t-coffee-hpja4W + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version + grep clang I: Finished running '/tmp/clang'. Finished processing commands. -------------------------------------------------------------------------------- +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:9999/debian unstable InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 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... NOTICE: 't-coffee' packaging is maintained in the 'Git' version control system at: https://anonscm.debian.org/git/debian-med/t-coffee.git Please use: git clone https://anonscm.debian.org/git/debian-med/t-coffee.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3544 kB of source archives. Get:1 http://127.0.0.1:9999/debian unstable/main t-coffee 11.00.8cbe486-5 (dsc) [2177 B] Get:2 http://127.0.0.1:9999/debian unstable/main t-coffee 11.00.8cbe486-5 (tar) [3526 kB] Get:3 http://127.0.0.1:9999/debian unstable/main t-coffee 11.00.8cbe486-5 (diff) [15.6 kB] Fetched 3544 kB in 0s (12.6 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/t-coffee-hpja4W/t-coffee-11.00.8cbe486' with '<>' I: NOTICE: Log filtering will replace 'build/t-coffee-hpja4W' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-Vh5frn/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-Vh5frn/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Vh5frn/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-Vh5frn/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Vh5frn/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-Vh5frn/apt_archive ./ Packages [433 B] Fetched 1739 B in 0s (0 B/s) Reading package lists... 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 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 782 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-Vh5frn/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [782 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 782 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10178 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 10) Filtered Build-Depends: debhelper (>= 10) dpkg-deb: building package 'sbuild-build-depends-t-coffee-dummy' in '/<>/resolver-Vh5frn/apt_archive/sbuild-build-depends-t-coffee-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-t-coffee-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-Vh5frn/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Vh5frn/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-Vh5frn/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Vh5frn/apt_archive ./ Sources [486 B] Get:5 copy:/<>/resolver-Vh5frn/apt_archive ./ Packages [567 B] Fetched 2016 B in 0s (0 B/s) Reading package lists... 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 additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libicu57 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl Recommended packages: curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev xml-core libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libicu57 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf sbuild-build-depends-t-coffee-dummy 0 upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 19.3 MB of archives. After this operation, 65.7 MB of additional disk space will be used. Get:1 copy:/<>/resolver-Vh5frn/apt_archive ./ sbuild-build-depends-t-coffee-dummy 0.invalid.0 [780 B] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 groff-base amd64 1.22.3-9 [1160 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 bsdmainutils amd64 9.0.12+nmu1 [186 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libpipeline1 amd64 1.4.1-2 [27.6 kB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 man-db amd64 2.7.6.1-2 [1044 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libmagic-mgc amd64 1:5.30-1 [222 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libmagic1 amd64 1:5.30-1 [111 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 file amd64 1:5.30-1 [63.9 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 gettext-base amd64 0.19.8.1-2+b1 [122 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 libicu57 amd64 57.1-6 [7701 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-3 [715 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 libsigsegv2 amd64 2.11-1 [29.9 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 m4 amd64 1.4.18-1 [202 kB] Get:14 http://127.0.0.1:9999/debian unstable/main amd64 autoconf all 2.69-10 [338 kB] Get:15 http://127.0.0.1:9999/debian unstable/main amd64 autotools-dev all 20161112.1 [73.4 kB] Get:16 http://127.0.0.1:9999/debian unstable/main amd64 automake all 1:1.15.1-2 [736 kB] Get:17 http://127.0.0.1:9999/debian unstable/main amd64 autopoint all 0.19.8.1-2 [433 kB] Get:18 http://127.0.0.1:9999/debian unstable/main amd64 libtool all 2.4.6-2 [545 kB] Get:19 http://127.0.0.1:9999/debian unstable/main amd64 dh-autoreconf all 14 [15.9 kB] Get:20 http://127.0.0.1:9999/debian unstable/main amd64 libarchive-zip-perl all 1.59-1 [95.5 kB] Get:21 http://127.0.0.1:9999/debian unstable/main amd64 libfile-stripnondeterminism-perl all 0.035-2 [17.0 kB] Get:22 http://127.0.0.1:9999/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:23 http://127.0.0.1:9999/debian unstable/main amd64 dh-strip-nondeterminism all 0.035-2 [10.7 kB] Get:24 http://127.0.0.1:9999/debian unstable/main amd64 libglib2.0-0 amd64 2.52.3-1 [2742 kB] Get:25 http://127.0.0.1:9999/debian unstable/main amd64 libcroco3 amd64 0.6.12-1 [144 kB] Get:26 http://127.0.0.1:9999/debian unstable/main amd64 gettext amd64 0.19.8.1-2+b1 [1301 kB] Get:27 http://127.0.0.1:9999/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB] Get:28 http://127.0.0.1:9999/debian unstable/main amd64 po-debconf all 1.0.20 [247 kB] Get:29 http://127.0.0.1:9999/debian unstable/main amd64 debhelper all 10.6.2 [968 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.3 MB in 0s (96.3 MB/s) Selecting previously unselected package groff-base. (Reading database ... 10178 files and directories currently installed.) Preparing to unpack .../00-groff-base_1.22.3-9_amd64.deb ... Unpacking groff-base (1.22.3-9) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_9.0.12+nmu1_amd64.deb ... Unpacking bsdmainutils (9.0.12+nmu1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../02-libpipeline1_1.4.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.4.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../03-man-db_2.7.6.1-2_amd64.deb ... Unpacking man-db (2.7.6.1-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.30-1_amd64.deb ... Unpacking libmagic-mgc (1:5.30-1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../05-libmagic1_1%3a5.30-1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.30-1) ... Selecting previously unselected package file. 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Setting up sbuild-build-depends-t-coffee-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-2-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.28-6 dpkg-dev_1.18.24 g++-6_6.4.0-1 gcc-6_6.4.0-1 libc6-dev_2.24-12 libstdc++-6-dev_6.4.0-1 libstdc++6_7.1.0-9 linux-libc-dev_4.11.6-1 Package versions: adduser_3.115 apt_1.5~beta1 autoconf_2.69-10 automake_1:1.15.1-2 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_10 base-passwd_3.5.43 bash_4.4-5 binutils_2.28-6 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-1 build-essential_12.3 bzip2_1.0.6-8.1 clang-3.9_1:3.9.1-10 coreutils_8.26-3 cpp_4:6.3.0-4d1 cpp-6_6.4.0-1 dash_0.5.8-2.4 debconf_1.5.62 debfoster_2.7-2.1+b1 debhelper_10.6.2 debian-archive-keyring_2017.5 debianutils_4.8.1.1 dh-autoreconf_14 dh-strip-nondeterminism_0.035-2 diffutils_1:3.5-3 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 eatmydata_105-5 fakeroot_1.21-3.1 file_1:5.30-1 findutils_4.6.0+git+20170606-2 g++_4:6.3.0-4d1 g++-6_6.4.0-1 gcc_4:6.3.0-4d1 gcc-6_6.4.0-1 gcc-6-base_6.4.0-1 gcc-7-base_7.1.0-9 gettext_0.19.8.1-2+b1 gettext-base_0.19.8.1-2+b1 gpgv_2.1.18-8 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-5+b1 hostname_3.18+b1 init-system-helpers_1.48 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3+b1 libapt-pkg5.0_1.5~beta1 libarchive-zip-perl_1.59-1 libasan3_6.4.0-1 libatomic1_7.1.0-9 libattr1_1:2.4.47-2+b2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1+b1 libblkid1_2.29.2-1 libbsd0_0.8.5-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-12 libc-dev-bin_2.24-12 libc6_2.24-12 libc6-dev_2.24-12 libcap-ng0_0.7.7-3+b1 libcc1-0_7.1.0-9 libcilkrts5_7.1.0-9 libclang-common-3.9-dev_1:3.9.1-10 libclang1-3.9_1:3.9.1-10 libcomerr2_1.43.4-2 libcroco3_0.6.12-1 libdb5.3_5.3.28-12+b1 libdebconfclient0_0.229 libdpkg-perl_1.18.24 libeatmydata1_105-5 libedit2_3.1-20170329-1 libfakeroot_1.21-3.1 libfdisk1_2.29.2-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.035-2 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.4.0-1 libgcc1_1:7.1.0-9 libgcrypt20_1.7.8-1 libgdbm3_1.8.3-14 libglib2.0-0_2.52.3-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.13-2 libgomp1_7.1.0-9 libgpg-error0_1.27-3 libhogweed4_3.3-1+b1 libicu57_57.1-6 libidn2-0_0.16-1+b1 libisl15_0.18-1 libitm1_7.1.0-9 libjsoncpp1_1.7.4-3 libllvm3.9_1:3.9.1-10 liblsan0_7.1.0-9 liblz4-1_0.0~r131-2+b1 liblzma5_5.2.2-1.2+b1 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmount1_2.29.2-1 libmpc3_1.0.3-1+b2 libmpfr4_3.1.5-1 libmpx2_7.1.0-9 libncurses5_6.0+20161126-1 libncursesw5_6.0+20161126-1 libnettle6_3.3-1+b1 libobjc-6-dev_6.4.0-1 libobjc4_7.1.0-9 libp11-kit0_0.23.7-2 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-3 libperl5.24_5.24.1-6 libpipeline1_1.4.1-2 libquadmath0_7.1.0-9 libselinux1_2.6-3+b2 libsemanage-common_2.6-2 libsemanage1_2.6-2+b1 libsepol1_2.6-2 libsigsegv2_2.11-1 libsmartcols1_2.29.2-1 libss2_1.43.4-2 libstdc++-6-dev_6.4.0-1 libstdc++6_7.1.0-9 libsystemd0_233-10 libtasn1-6_4.12-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20161126-1 libtool_2.4.6-2 libtsan0_7.1.0-9 libubsan0_7.1.0-9 libudev1_233-10 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-1 libxml2_2.9.4+dfsg1-3 linux-libc-dev_4.11.6-1 login_1:4.4-4.1 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-2 mawk_1.3.3-17+b3 mount_2.29.2-1 multiarch-support_2.24-12 ncurses-base_6.0+20161126-1 ncurses-bin_6.0+20161126-1 passwd_1:4.4-4.1 patch_2.7.5-1+b2 perl_5.24.1-6 perl-base_5.24.1-6 perl-modules-5.24_5.24.1-6 po-debconf_1.0.20 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-t-coffee-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 sysvinit-utils_2.88dsf-59.9 tar_1.29b-1.1 util-linux_2.29.2-1 xz-utils_5.2.2-1.2+b1 zlib1g_1:1.2.8.dfsg-5 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sat Dec 17 17:46:19 2016 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./t-coffee_11.00.8cbe486-5.dsc dpkg-source: info: extracting t-coffee in /<> dpkg-source: info: unpacking t-coffee_11.00.8cbe486.orig.tar.gz dpkg-source: info: unpacking t-coffee_11.00.8cbe486-5.debian.tar.xz dpkg-source: info: applying probconsrna.patch dpkg-source: info: applying ncbi-blast++_has_dropped_pl_extension.patch dpkg-source: info: applying use_debian_packaged_TMalign.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying set_proper_dir_permissions.patch dpkg-source: info: applying mayhem.patch dpkg-source: info: applying stable-linking-inputs.patch dpkg-source: info: applying clustalw2.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=POSIX LOGNAME=user42 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1001 SCHROOT_GROUP=user42 SCHROOT_SESSION_ID=unstable-amd64-sbuild-6f349815-61cc-43b4-8c0a-c6c21b098c56 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package t-coffee dpkg-buildpackage: info: source version 11.00.8cbe486-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build t-coffee-11.00.8cbe486 dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --sourcedirectory=t_coffee_source dh_testdir -O--sourcedirectory=t_coffee_source debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -rf t_coffee_source/*.o t_coffee_source/t_coffee bin/t_coffee example/t_coffee.log bin/t_coffee rm -rf t_coffee_source/TMalign find . -name "*.o" -delete find . -name "*.deps" -delete chmod 644 example/* make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--sourcedirectory=t_coffee_source dh_clean -O--sourcedirectory=t_coffee_source debian/rules build-arch dh build-arch --sourcedirectory=t_coffee_source dh_testdir -a -O--sourcedirectory=t_coffee_source dh_update_autotools_config -a -O--sourcedirectory=t_coffee_source dh_autoreconf -a -O--sourcedirectory=t_coffee_source dh_auto_configure -a -O--sourcedirectory=t_coffee_source debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- -i USER_BIN=../bin/ FCC="gfortran -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong" all make -j16 -i USER_BIN=../bin/ "FCC=gfortran -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong" all make[2]: Entering directory '/<>/t_coffee_source' CC dev_lib/dev1.c CC dp_lib/CUSTOM_evaluate_for_struc.c CC dp_lib/evaluate.c CC dp_lib/evaluate_dirichlet.c CC dp_lib/evaluate_for_domain.c CC dp_lib/evaluate_for_struc.c CC dp_lib/fsa_dp.c CC dp_lib/pavie_dp.c CC dp_lib/showpair.c CC dp_lib/util_dp_clean_maln.c CC dp_lib/util_domain_dp.c CC dp_lib/util_dp_cdna_fasta_nw.c CC dp_lib/util_dp_drivers.c CC dp_lib/util_domain_dp_drivers.c CC dp_lib/util_dp_fasta_nw.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated clang CC dp_lib/util_dp_est.c : warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated In file included from dp_lib/fsa_dp.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ In file included from dev_lib/dev1.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ In file included from dp_lib/evaluate.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ In file included from dp_lib/evaluate_for_domain.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ In file included from dp_lib/util_domain_dp.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ In file included from dp_lib/evaluate_dirichlet.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ In file included from dp_lib/CUSTOM_evaluate_for_struc.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ In file included from dp_lib/pavie_dp.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ In file included from dp_lib/showpair.c:33: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ In file included from dp_lib/util_dp_fasta_nw.c:35: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ dev_lib/dev1.c:89:42: warning: data argument not used by format string [-Wformat-extra-args] fprintf (stdout, "Process positions\n", i); ~~~~~~~~~~~~~~~~~~~~~ ^ In file included from dp_lib/util_dp_cdna_fasta_nw.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ In file included from dp_lib/evaluate_for_struc.c:35: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ In file included from dp_lib/util_dp_clean_maln.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ In file included from dp_lib/util_dp_est.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ In file included from dp_lib/util_dp_drivers.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ In file included from dp_lib/util_domain_dp_drivers.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ dp_lib/pavie_dp.c:127:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf (fp, "%s\n",mat_list[nch++]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:323:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(fp, "%f", &f); ^~~~~~ ~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:317:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(fp, "%f\n", &f); ^~~~~~ ~~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:319:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(fp, "%f", &f); ^~~~~~ ~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:326:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(fp, "\n"); ^~~~~~ ~~~~~~~~ dp_lib/evaluate.c:808:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf (fp, "%d ", &res); ^~~~~~ ~~~~~~~~~~~~~~~ dp_lib/evaluate.c:813:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf (fp, "%f %f", &sseq, &mseq); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate.c:818:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf (fp, "%f %f", &sseq, &mseq); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:543:8: error: 'lgamma_r' is missing exception specification 'throw()' double lgamma_r(double x, int *signgamp) ^ throw() ./dp_lib/evaluate_dirichlet.h:57:8: note: previous declaration is here double lgamma_r(double x, int *signgamp); ^ dp_lib/util_dp_cdna_fasta_nw.c:288:132: 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; ~~~~~~~~~~~~~~~~~~~^ dp_lib/util_dp_cdna_fasta_nw.c:288:132: 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; ^ ( ) dp_lib/util_dp_cdna_fasta_nw.c:288:132: 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; ^ ( ) dp_lib/util_dp_cdna_fasta_nw.c:290:132: 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; ~~~~~~~~~~~~~~~~~~~^ dp_lib/util_dp_cdna_fasta_nw.c:290:132: 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; ^ ( ) dp_lib/util_dp_cdna_fasta_nw.c:290:132: 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; ^ ( ) 5 warnings and 1 error generated. makefile:11: recipe for target 'dp_lib/evaluate_dirichlet.o' failed make[2]: [dp_lib/evaluate_dirichlet.o] Error 1 (ignored) CC dp_lib/util_dp_fasta_sw.c dp_lib/evaluate_for_struc.c:1035:21: warning: comparison of array 'S->T[i]->P->template_file' not equal to a null pointer is always true [-Wtautological-pointer-compare] if (S->T[i]->P->template_file != NULL) ~~~~~~~~~~~~^~~~~~~~~~~~~ ~~~~ dp_lib/pavie_dp.c:1079:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system (command); ^~~~~~ ~~~~~~~ dp_lib/pavie_dp.c:1081:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system (command); ^~~~~~ ~~~~~~~ 1 warning generated. dp_lib/pavie_dp.c:1144:58: 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); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ dp_lib/pavie_dp.c:1144:58: 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); ^ ( ) dp_lib/pavie_dp.c:1144:58: 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); ^ ( ) dp_lib/pavie_dp.c:1145:58: 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); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ dp_lib/pavie_dp.c:1145:58: 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); ^ ( ) dp_lib/pavie_dp.c:1145:58: 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); ^ ( ) 2 warnings generated. CC dp_lib/util_dp_gotoh_nw.c dp_lib/pavie_dp.c:1365:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] CC dp_lib/util_dp_generic_fasta_nw.c fscanf (fp, "%s", mat); ^~~~~~ ~~~~~~~~~~~~~ clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated 1 warning generated. CC dp_lib/util_dp_gotoh_sw.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated dp_lib/util_domain_dp_drivers.c:590:16: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] while (entry=extract_entry (CL)) ~~~~~^~~~~~~~~~~~~~~~~~~ dp_lib/util_domain_dp_drivers.c:590:16: note: place parentheses around the assignment to silence this warning while (entry=extract_entry (CL)) ^ ( ) dp_lib/util_domain_dp_drivers.c:590:16: note: use '==' to turn this assignment into an equality comparison while (entry=extract_entry (CL)) ^ == dp_lib/evaluate.c:1946:13: warning: if statement has empty body [-Wempty-body] if (w);free_int (w, -1); ^ dp_lib/evaluate.c:1946:13: note: put the semicolon on a separate line to silence this warning dp_lib/util_dp_drivers.c:968:6: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:996:6: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated dp_lib/util_dp_drivers.c:1037:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1048:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] dp_lib/evaluate.c tmpnam(aln1); ^~~~~~ ~~~~ dp_lib/util_dp_drivers.c:1049:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] tmpnam(aln2); ^~~~~~ ~~~~ dp_lib/util_dp_drivers.c:1052:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] tmpnam(hhfile); ^~~~~~ ~~~~~~ dp_lib/util_dp_drivers.c:1099:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets (buf2, 10000, fp); ^~~~~ ~~~~~~~~~~~~~~~ :2093:13: warning: if statement has empty body [-Wempty-body] if (w);free_int (w, -1); ^ dp_lib/evaluate.c:2093:13: note: put the semicolon on a separate line to silence this warning clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated dp_lib/util_dp_drivers.c:1300:10: warning: address of array 'M->param' will always evaluate to 'true' [-Wpointer-bool-conversion] if ( M->param) ~~ ~~~^~~~~ dp_lib/util_dp_drivers.c:1253:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1388:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ 1 warning generated. dp_lib/util_dp_drivers.c:1445:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_mm_nw.c dp_lib/util_dp_drivers.c:1577:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1652:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1792:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] getcwd (cdir, sizeof(char)*1000); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1793:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] chdir (get_cache_dir()); ^~~~~ ~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1813:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] chdir (cdir); ^~~~~ ~~~~ dp_lib/util_dp_drivers.c:1744:6: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated dp_lib/util_dp_drivers.c:1927:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2463:19: warning: address of array 'CL->tree_mode' will always evaluate to 'true' [-Wpointer-bool-conversion] if ( !CL || !CL->tree_mode || !CL->tree_mode[0]) ~~~~~^~~~~~~~~ In file included from dp_lib/util_dp_fasta_sw.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:541:1: warning: '/*' within block comment [-Wcomment] /* */ warning generated. ^ CC dp_lib/util_dp_sim.c In file included from dp_lib/util_dp_generic_fasta_nw.c:35: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated In file included from dp_lib/util_dp_gotoh_nw.c:35: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ In file included from dp_lib/util_dp_gotoh_sw.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ dp_lib/util_dp_drivers.c:3810:22: warning: address of array 'CL->dp_mode' will always evaluate to 'true' [-Wpointer-bool-conversion] if ( CL && CL->dp_mode && strstr (CL->dp_mode, "collapse"))dump_constraint_list (CL, tmp, "w"); ~~ ~~~~^~~~~~~ dp_lib/util_dp_drivers.c:3813:22: warning: address of array 'CL->dp_mode' will always evaluate to 'true' [-Wpointer-bool-conversion] if ( CL && CL->dp_mode && strstr (CL->dp_mode, "collapse")) ~~ ~~~~^~~~~~~ dp_lib/evaluate.c:5644:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf (fp, "%f %c %*s",&v1, &c1 ); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~ 1 warning generated. In file included from dp_lib/util_dp_mm_nw.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ CC dp_lib/util_dp_ssec_pwaln.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated dp_lib/util_dp_gotoh_sw.c:391:8: 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 dp_lib/util_dp_sim.c:33: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ dp_lib/util_dp_sim.c:248:20: warning: empty parentheses interpreted as a function declaration [-Wvexing-parse] vertexptr findmax(); /* return the largest score node */ ^~ dp_lib/util_dp_sim.c:248:20: note: replace parentheses with an initializer to declare a variable vertexptr findmax(); /* return the largest score node */ ^~ = NULL 1 warning generated. 2 warnings generated. CC dp_lib/util_dp_suboptimal_nw.c CC dp_lib/util_graph_maln.c In file included from dp_lib/util_dp_ssec_pwaln.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ dp_lib/util_dp_sim.c:572:16: warning: empty parentheses interpreted as a function declaration [-Wvexing-parse] int addnode(); /* function for inserting a node */ ^~ dp_lib/util_dp_sim.c:572:16: note: replace parentheses with an initializer to declare a variable int addnode(); /* function for inserting a node */ ^~ = 0 clangclang: : warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecatedwarning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated 1 warning generated. CC fastal/diagonal.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated 1 warning generated. CC fastal/fastal.c In file included from dp_lib/util_graph_maln.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ In file included from dp_lib/util_dp_suboptimal_nw.c^:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated In file included from fastal/diagonal.c:32: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ 1 warning generated. CC fastal/fastal_opt_parsing.c 2 warnings generated. clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated CC fastal/iteration.c fastal/diagonal.c:434:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system(blast_command); ^~~~~~ ~~~~~~~~~~~~~ fastal/diagonal.c:439:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 300, diag_f); ^~~~~ ~~~~~~~~~~~~~~~~~ fastal/diagonal.c:440:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 300, diag_f); ^~~~~ ~~~~~~~~~~~~~~~~~ fastal/diagonal.c:441:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 300, diag_f); ^~~~~ ~~~~~~~~~~~~~~~~~ clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated fastal/fastal_opt_parsing.c:39:29: warning: result of comparison against a string literal is unspecified (use strncmp instead) [-Wstring-compare] if (arguments->tree_method == "parttree") ^ ~~~~~~~~~~ In file included from fastal/fastal.c:35: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ 3 warnings generated. CC fastal/parttree.c 1 warning generated. CC fastal/scoring.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated In file included from fastal/iteration.c:35: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated 1 warning generated. CC fastal/tree.c fastal/fastal.c:1976:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system(blast_command); ^~~~~~ ~~~~~~~~~~~~~ fastal/fastal.c:1980:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 300, diag_f); ^~~~~ ~~~~~~~~~~~~~~~~~ fastal/fastal.c:1981:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 300, diag_f); ^~~~~ ~~~~~~~~~~~~~~~~~ fastal/fastal.c:1982:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 300, diag_f); ^~~~~ ~~~~~~~~~~~~~~~~~ fastal/fastal.c:1924:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system(blast_command); ^~~~~~ ~~~~~~~~~~~~~ fastal/fastal.c:1929:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 300, diag_f); ^~~~~ ~~~~~~~~~~~~~~~~~ fastal/fastal.c:1930:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 300, diag_f); ^~~~~ ~~~~~~~~~~~~~~~~~ fastal/fastal.c:1931:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 300, diag_f); ^~~~~ ~~~~~~~~~~~~~~~~~ clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated fastal/fastal.c:2115:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system(blast_command); ^~~~~~ ~~~~~~~~~~~~~ fastal/iteration.c:185:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH , alignment_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:2262:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system(blast_command); ^~~~~~ ~~~~~~~~~~~~~ fastal/iteration.c:310:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH , alignment_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:435:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system(command); ^~~~~~ ~~~~~~~ fastal/iteration.c:535:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(alnline, ALNLINE_LENGTH, old_aln_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:501:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(alnline, ALNLINE_LENGTH , old_aln_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:504:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(alnline, ALNLINE_LENGTH , old_aln_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:563:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:565:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:567:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:569:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5 warnings generated. fastal/fastal.c:3201:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] CC io_lib/io_func.c fgets (line, LINE_LENGTH , seq_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3352:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH , profile_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/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/fastal.c:3326:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3329:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3331:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3333:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3502:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets (line, LINE_LENGTH , sequence_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3575:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3577:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3579:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3581:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3643:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(aligned_sequence, alignment_length+3, edit_seq_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated In file included from fastal/scoring.c:38: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ In file included from fastal/parttree.c:37: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ 1 warning generated. CC io_lib/pb_util_read_seq_util.c fastal/scoring.c:76:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH, alignment_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:82:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH, alignment_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:78:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH, alignment_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated fastal/scoring.c:384:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH, seq_file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:398:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system(aln_command); ^~~~~~ ~~~~~~~~~~~ fastal/scoring.c:488:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH, seq_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:502:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system(command); ^~~~~~ ~~~~~~~ fastal/scoring.c:583:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH, result); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:584:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH, result); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:585:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH, result); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from fastal/tree.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ fastal/parttree.c:701:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 500, aln_f); ^~~~~ ~~~~~~~~~~~~~~~~ fastal/parttree.c:695:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 500, aln_f); ^~~~~ ~~~~~~~~~~~~~~~~ In file included from io_lib/io_func.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ fastal/parttree.c:859:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH, tables_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:848:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH, tables_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:903:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:912:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:891:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:906:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:962:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:951:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from io_lib/pb_util_read_seq_util.c:35: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ io_lib/io_func.c:511:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "\n"); ^~~~~~ ~~~~~~~~ 11 warnings generated. CC io_lib/pb_util_read_sequence.c io_lib/io_func.c:747:7: warning: '/*' within block comment [-Wcomment] /* ^ io_lib/io_func.c:749:7: warning: '/*' within block comment [-Wcomment] /*3*/ ^ io_lib/io_func.c:971:8: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf (fp, "%s %f %f %f", html_code[classC], &ps_code[classC][0], &ps_code[classC][1],&ps_code[classC][2]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_seq_util.c:224:31: warning: if statement has empty body [-Wempty-body] else if (isspace(str[i])); ^ io_lib/pb_util_read_seq_util.c:224:31: note: put the semicolon on a separate line to silence this warning io_lib/pb_util_read_seq_util.c:269:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(outstr, 100, stdin); ^~~~~ ~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_seq_util.c:280:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, MAXLINE, stdin); ^~~~~ ~~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_seq_util.c:305:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, MAXLINE, stdin); ^~~~~ ~~~~~~~~~~~~~~~~~~~~ clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated io_lib/pb_util_read_seq_util.c:327:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system(line); ^~~~~~ ~~~~ io_lib/io_func.c:1235:17: warning: implicit conversion of NULL constant to 'int' [-Wnull-conversion] if (!A)return NULL; ~~~~~~ ^~~~ 0 io_lib/io_func.c:2076:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 7 warnings generated. CC io_lib/tree_util.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated In file included from io_lib/pb_util_read_sequence.c:36: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ 6 warnings generated. CC km_coffee/Stack.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated 1 warning generated. io_lib/pb_util_read_sequence.c:108:25: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] for(i=1;itemplate_file' will always evaluate to 'true' [-Wpointer-bool-conversion] else if ( T && T->template_file && T->template_file[0]) ~~ ~~~^~~~~~~~~~~~~ :12: warning: if statement has empty body [-Wempty-body] if (!name); ^ util_lib/reformat.c:1692:12: note: put the semicolon on a separate line to silence this warning In file included from util_lib/reformat_struc.c:35: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ util_lib/reformat.c:2092:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf (fp , "%s", buf); ^~~~~~ ~~~~~~~~~~~~~~ util_lib/reformat.c:2196:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ util_lib/reformat.c:2890:16: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (p=strstr (out_format, "filter")){action=0;p+=strlen ("filter");} ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:2890:16: note: place parentheses around the assignment to silence this warning if (p=strstr (out_format, "filter")){action=0;p+=strlen ("filter");} ^ ( ) util_lib/reformat.c:2890:16: note: use '==' to turn this assignment into an equality comparison if (p=strstr (out_format, "filter")){action=0;p+=strlen ("filter");} ^ == util_lib/reformat.c:2891:16: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] else if (p=strstr (out_format, "lower")){action=1;p+=strlen("lower");} ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:2891:16: note: place parentheses around the assignment to silence this warning else if (p=strstr (out_format, "lower")){action=1;p+=strlen("lower");} ^ ( ) util_lib/reformat.c:2891:16: note: use '==' to turn this assignment into an equality comparison else if (p=strstr (out_format, "lower")){action=1;p+=strlen("lower");} ^ == util_lib/reformat.c:2892:16: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] else if (p=strstr (out_format, "weighted")){action=2; p=NULL;} ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:2892:16: note: place parentheses around the assignment to silence this warning else if (p=strstr (out_format, "weighted")){action=2; p=NULL;} ^ ( ) util_lib/reformat.c:2892:16: note: use '==' to turn this assignment into an equality comparison else if (p=strstr (out_format, "weighted")){action=2; p=NULL;} ^ == util_lib/reformat.c:2893:16: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] else if (p=strstr (out_format, "replicate")){action=3; p+=strlen ("replicate");} ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:2893:16: note: place parentheses around the assignment to silence this warning else if (p=strstr (out_format, "replicate")){action=3; p+=strlen ("replicate");} ^ ( ) util_lib/reformat.c:2893:16: note: use '==' to turn this assignment into an equality comparison else if (p=strstr (out_format, "replicate")){action=3; p+=strlen ("replicate");} ^ == util_lib/aln_convertion_util.c:5516:25: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion] S->seq_comment[a]='\0'; ^~~~ 7 warnings generated. CC util_lib/util_analyse_constraints_list.c util_lib/reformat_struc.c:334:9: 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); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat_struc.c:372:9: 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); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat_struc.c:326:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "%*s" ); ^~~~~~ ~~~~~~~~~ util_lib/reformat_struc.c:328:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "%*s" ); ^~~~~~ ~~~~~~~~~ util_lib/reformat_struc.c:361:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "%*s" ); ^~~~~~ ~~~~~~~~~ util_lib/reformat_struc.c:363:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "%*s" ); ^~~~~~ ~~~~~~~~~ clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated In file included from util_lib/util_aln_analyze.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ util_lib/reformat.c:3597:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "%s", buf2); ^~~~~~ ~~~~~~~~~~~~~~ util_lib/reformat.c:3612:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "%s",W->seq_name[a]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:3614:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "%s", buf2); ^~~~~~ ~~~~~~~~~~~~~~ util_lib/reformat.c:3625:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "\n"); ^~~~~~ ~~~~~~~~ util_lib/reformat.c:3590:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "%s", buf2); ^~~~~~ ~~~~~~~~~~~~~~ util_lib/reformat.c:3606:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "%s", buf2); ^~~~~~ ~~~~~~~~~~~~~~ In file included from util_lib/util.c:53: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ util_lib/reformat.c:3901:3: 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); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:3898:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "%c\n%d\n",&x, &(ST)->tot_list); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4098:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "%s %d", name, &len); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4124:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, " %*c %c %*f %*f %*f\n",&(S->seq[S->nseq][a])); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4119:3: 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])); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4161:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf (fp, "%s",name); ^~~~~~ ~~~~~~~~~~~~~ util_lib/reformat.c:4236:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] {fscanf (fp, "%s",name); ^~~~~~ ~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7269:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets ( line, VERY_LONG_STRING,fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7292:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets ( line, VERY_LONG_STRING,fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7288:25: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] if ( c=='#' || c=='!')fgets ( line, VERY_LONG_STRING,fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7507:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ In file included from util_lib/util.c:55: ./perl_header_lib.h:8837:11: warning: illegal character encoding in string literal [-Winvalid-source-encoding] $id=~s/[|_]//g;\n return $id;\n }\nsub set_b\ ^~~~ util_lib/reformat.c:5281:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets (buf, LONG_STRING, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:5300:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets (buf, LONG_STRING, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:5319:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf (fp, "%s", name); ^~~~~~ ~~~~~~~~~~~~~~ util_lib/util.c:97:1: warning: '/*' within block comment [-Wcomment] /* */ ^ util_lib/reformat.c:5474:25: warning: if statement has empty body [-Wempty-body] if ( !isblanc (buf)); ^ util_lib/reformat.c:5474:25: note: put the semicolon on a separate line to silence this warning util_lib/reformat.c:5495:38: warning: while loop has empty body [-Wempty-body] while ( isgraph ((c=fgetc(fp)))); ^ util_lib/reformat.c:5495:38: util_lib/util.c:281:6: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread( rra, size, len,fp); /*rra=ra[--l]*/ note: put the semicolon on a separate line to silence this warning ^~~~~ ~~~~~~~~~~~~~~~~~ util_lib/util.c:286:6: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread( rra, size, len,fp); /*rra=ra[ir]*/ ^~~~~ ~~~~~~~~~~~~~~~~~ util_lib/util.c:289:6: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread( rrb, size, len,fp); /*rrb=ra[0]*/ ^~~~~ ~~~~~~~~~~~~~~~~~ util_lib/util.c:311:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread (ra_j_1, size, len, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:306:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread (ra_j, size, len, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~ util_lib/util_aln_analyze.c:713:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ util_lib/util.c:420:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread ( key2, el_size, entry_len,fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:5672:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] {fscanf (fp, "%*d >%s", name[nseq++]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:5721:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(buf, VERY_LONG_STRING, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:5743:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(buf, VERY_LONG_STRING, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:5941:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "%s",string); ^~~~~~ ~~~~~~~~~~~~~~~ util_lib/reformat.c:6106:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf (fp, "%s %d", name,&i); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:847:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "%d",&list[n[0]++]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:906:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "%s %s\n", s1, s2); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~ 1 warning generated. CC util_lib/util_constraints_list.c In file included from util_lib/util_analyse_constraints_list.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ util_lib/util.c:1269:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(fp, "%d ", &array[a][b]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:1266:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(fp, "%d ", &len2); ^~~~~~ ~~~~~~~~~~~~~~~~ util_lib/util.c:1270:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf (fp, "\n"); ^~~~~~ ~~~~~~~~ util_lib/util.c:1262:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf (fp, "%d\n", &len); ^~~~~~ ~~~~~~~~~~~~~~~~ clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated util_lib/reformat.c:7124:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 1 warning generated. CC util_lib/util_declare.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated util_lib/util.c:1849:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ util_lib/util.c:1925:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf (fp, "%d", &r); ^~~~~~ ~~~~~~~~~~~~ util_lib/util_aln_analyze.c:4480:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ In file included from util_lib/util_constraints_list.c:38: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ 1 warning generated. CC util_lib/util_domain_constraints_list.c util_lib/util_aln_analyze.c:4914:36: warning: operator '?:' has lower precedence than '-'; '-' will be evaluated first [-Wparentheses] valP=matP[p][res]-(sar=='I')?1:0; ~~~~~~~~~~~~~~~~~~~~~~~^ util_lib/util_aln_analyze.c:4914:36: note: place parentheses around the '-' expression to silence this warning valP=matP[p][res]-(sar=='I')?1:0; ^ ( ) util_lib/util_aln_analyze.c:4914:36: note: place parentheses around the '?:' expression to evaluate it first valP=matP[p][res]-(sar=='I')?1:0; ^ ( ) util_lib/util_aln_analyze.c:4917:36: warning: operator '?:' has lower precedence than '-'; '-' will be evaluated first [-Wparentheses] valN=matN[p][res]-(sar=='O')?1:0; ~~~~~~~~~~~~~~~~~~~~~~~^ util_lib/util_aln_analyze.c:4917:36: note: place parentheses around the '-' expression to silence this warning valN=matN[p][res]-(sar=='O')?1:0; ^ ( ) util_lib/util_aln_analyze.c:4917:36: note: place parentheses around the '?:' expression to evaluate it first valN=matN[p][res]-(sar=='O')?1:0; ^ ( ) util_lib/aln_convertion_util.c:12740:16: warning: address of array 'F->mode' will always evaluate to 'true' [-Wpointer-bool-conversion] if (!F->mode || strm (F->mode, "number")) ~~~~^~~~ util_lib/aln_convertion_util.c:12742:21: warning: address of array 'F->mode' will always evaluate to 'true' [-Wpointer-bool-conversion] else if ( F->mode && (strm (F->mode, "unalign") ||strm (F->mode, "unalign2"))) ~~~^~~~ ~~ util_lib/aln_convertion_util.c:12744:21: warning: address of array 'F->mode' will always evaluate to 'true' [-Wpointer-bool-conversion] else if ( F->mode && strm (F->mode, "lower") ) ~~~^~~~ ~~ util_lib/aln_convertion_util.c:12753:10: warning: address of array 'F->mode' will always evaluate to 'true' [-Wpointer-bool-conversion] if (F->mode && strm (F->mode, "unalign")) ~~~^~~~ ~~ util_lib/aln_convertion_util.c:12759:15: warning: address of array 'F->mode' will always evaluate to 'true' [-Wpointer-bool-conversion] else if (F->mode && strm (F->mode, "unalign2")) ~~~^~~~ ~~ clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated util_lib/aln_convertion_util.c:13406:35: warning: '&&' within '||' [-Wlogical-op-parentheses] if (buf[b]=='b' || buf[b]=='o' && c>=1)buf2[c-1]=tolower(buf2[c-1]); ~~ ~~~~~~~~~~~~^~~~~~~ util_lib/aln_convertion_util.c:13406:35: 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]); ^ ( ) util_lib/util.c:3827:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ In file included from util_lib/util_declare.c:38: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ util_lib/util_constraints_list.c:577:6: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] chdir (tdir); ^~~~~ ~~~~ util_lib/util_constraints_list.c:580:6: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] chdir (cdir); ^~~~~ ~~~~ util_lib/util_constraints_list.c:844:119: warning: address of array 'method->executable2' will always evaluate to 'true' [-Wpointer-bool-conversion] add_information(stderr, "Method %s cannot be applied to [%s vs %s], proba_pair will be used instead",(method->executable2)?method->executable2:method->executable, (CL->S)->name[x], (CL->S)->name [y]); ~~~~~~~~^~~~~~~~~~~ ~ util_lib/util_constraints_list.c:1140:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets ( line,LONG_STRING, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:1182:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets ( line,LONG_STRING, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:1246:9: warning: address of array 'm->seq_type' will always evaluate to 'true' [-Wpointer-bool-conversion] if (m->seq_type)fprintf (fp, "SEQ_TYPE %s\n", m->seq_type); ~~ ~~~^~~~~~~~ util_lib/util.c:5090:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf (fp, "%s\n",list[n]); ^~~~~~ ~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:1294:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ util_lib/util.c:5304:26: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion] else val_array[a]='\0'; ^~~~ util_lib/util.c:5453:41: warning: if statement has empty body [-Wempty-body] else if ((proxy=getenv ("ALL_PROXY")));//id ^ util_lib/util.c:5453:41: note: put the semicolon on a separate line to silence this warning 1 warning generated. CC util_lib/util_dps.c In file included from util_lib/util_domain_constraints_list.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ util_lib/util.c:5801:23: warning: if statement has empty body [-Wempty-body] else if ( mode==GET); ^ util_lib/util.c:5801:23: note: put the semicolon on a separate line to silence this warning util_lib/util_constraints_list.c:2163:79: warning: data argument not used by format string [-Wformat-extra-args] fprintf ( local_stderr, "\n\t--- Process Method/Library/Aln %s", fname[a], ns); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated util_lib/util_constraints_list.c:2525:14: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] if ( c=='C')fscanf( fp, "PU %d\n", &cpu); ^~~~~~ ~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2775:71: 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_lib/util.c:6461:11: warning: '/*' within block comment [-Wcomment] * /*argc* / argc , ^ util_lib/util.c:6462:17: warning: '/*' within block comment [-Wcomment] * /*argv* / argv ,\ ^ util_lib/util.c:6463:17: warning: '/*' within block comment [-Wcomment] * /*output* / &le ,\ ^ util_lib/util.c:6464:17: warning: '/*' within block comment [-Wcomment] * /*Name* / "-extend_mode" ,\ util_lib/util_constraints_list.cutil_lib/util_domain_constraints_list.c:2838:3: warning: ^ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] util_lib/util.c:6465:17: warning: '/*' within block comment [-Wcomment] fscanf (fp, "%*s %d %*s\n", &l); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~ * /*Flag* / &garbage ,\ ^ util_lib/util.c:52:11: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] while (e=extract_entry (CL)) ~^~~~~~~~~~~~~~~~~~~ :6466:17: warning: '/*' within block comment [-Wcomment] util_lib/util_domain_constraints_list.c * /*TYPE* / "S" ,\ ^ util_lib/util.c:6467:17: warning: '/*' within block comment [-Wcomment] :52:11: note: place parentheses around the assignment to silence this warning while (e=extract_entry (CL)) * /*OPTIONAL?* / OPTIONAL ,\ ^ ( ) util_lib/util_domain_constraints_list.c:52:11: note: use '==' to turn this assignment into an equality comparison while (e=extract_entry (CL)) ^ == ^ util_lib/util.c:6468:17: warning: '/*' within block comment [-Wcomment] * /*MAX Nval* / 1 ,\ ^ util_lib/util.c:6469:17: warning: '/*' within block comment [-Wcomment] * /*DOC* / "Library extension mode" ,\ ^ util_lib/util.cutil_lib/util_constraints_list.c:2895:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets (line , 200 , fp); :6470:17: warning: '/*' within block comment [-Wcomment] * /*Parameter* / &extend_mode ,\ ^ util_lib/util.c:6471:17: warning: ^~~~~ ~~~~~~~~~~~~~~~'/*' within block comment [-Wcomment] * /*Def 1* / "very_fast_triplet" ,\ ^ util_lib/util.c:6472: util_lib/util_constraints_list.c17: warning: '/*' within block comment [-Wcomment] * /*Def 2* / "" ,\ ^ util_lib/util.c:6473:17: warning: '/*' within block comment [-Wcomment] * /*Min_value* / "any" ,\ ^ util_lib/util.c:6474:17: warning: '/*' within block comment [-Wcomment] * /*Max Value* / "any" \: ^ 2870:3: 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_lib/util_constraints_list.c:2833:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf (fp, "%d\n", &max_nseq); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:6571:16: warning: second argument to 'va_start' is not the last named parameter [-Wvarargs] va_start (ap, usage); ^ 2 warnings generated. util_lib/util.c:6838:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets ( line, VERY_LONG_STRING,fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:6858:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "%s", string); ^~~~~~ ~~~~~~~~~~~~~~~~ CC util_lib/util_job_handling.c util_lib/util.c:7022:10: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] if ( (c==EOF)){return NULL;} ~^~~~~ util_lib/util.c:7022:10: note: remove extraneous parentheses around the comparison to silence this warning if ( (c==EOF)){return NULL;} ~ ^ ~ util_lib/util.c:7022:10: note: use '=' to turn this equality comparison into an assignment if ( (c==EOF)){return NULL;} ^~ = util_lib/util.c:7214:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets ( line, lline,fp); ^~~~~ ~~~~~~~~~~~~~~ util_lib/util.c:7244:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets ( line, lline,fp); ^~~~~ ~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:3903:5: 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_lib/util.c:7331:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "Version_%f", &new_version); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:7424:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated util_lib/util.c:7849:62: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses] else if ( check_file_exists (to) && !vremove (to) && !rename ( from, to)==0 ); ^ ~~ util_lib/util.c:7849:62: note: add parentheses after the '!' to evaluate the comparison first else if ( check_file_exists (to) && !vremove (to) && !rename ( from, to)==0 ); ^ ( ) util_lib/util.c:7849:62: note: add parentheses around left hand side expression to silence this warning else if ( check_file_exists (to) && !vremove (to) && !rename ( from, to)==0 ); ^ ( ) util_lib/util_constraints_list.c:4956:175: warning: address of array 'NCL->dp_mode' will always evaluate to 'true' [-Wpointer-bool-conversion] if (CL->local_stderr && print>0)fprintf ( (CL->local_stderr), "\nCOMPUTE PAIRWISE SIMILARITY [dp_mode: %s] [distance_matrix_mode: %s][Similarity Measure: %s] \n", (NCL->dp_mode)?NCL->dp_mode:"NO_DP",mode, sim_mode); ~~~~~^~~~~~~ ~ util_lib/reformat.c:13570:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "%d ", &value); ^~~~~~ ~~~~~~~~~~~~~~~~~ util_lib/reformat.c:13557:6: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "%s ", buf); ^~~~~~ ~~~~~~~~~~~~~~ util_lib/reformat.c:13595:6: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(fp, "\n"); ^~~~~~ ~~~~~~~~ In file included from util_lib/util_dps.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ util_lib/reformat.c:13620:6: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets ( sbuf, VERY_LONG_STRING, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:13650:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "%d ", &value); ^~~~~~ ~~~~~~~~~~~~~~~~~ util_lib/reformat.c:13637:6: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "%s ", buf); ^~~~~~ ~~~~~~~~~~~~~~ util_lib/reformat.c:13677:6: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(fp, "\n"); ^~~~~~ ~~~~~~~~ util_lib/reformat.c:13716:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ util_lib/reformat.c:13789:48: warning: if statement has empty body [-Wempty-body] if ( sscanf (sbuf, "ALPHABET=%s", alp)==1); ^ util_lib/reformat.c:13789:48: note: put the semicolon on a separate line to silence this warning util_lib/reformat.c:13788:6: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets ( sbuf, VERY_LONG_STRING, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:9257:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ util_lib/util.c:9317:6: warning: expression result unused [-Wunused-value] n[0]; ~ ~^ 1 warning generated. CC util_lib/util_make_tree.c In file included from util_lib/util_job_handling.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated In file included from util_lib/util_make_tree.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ util_lib/util_make_tree.c:66:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 7 warnings generated. 1 warning generated. 22 warnings generated. 1 warning generated. 24 warnings generated. 7 warnings generated. 2 warnings generated. 6 warnings generated. 1 warning generated. 11 warnings generated. 17 warnings generated. 5 warnings generated. 45 warnings generated. 47 warnings generated. 14 warnings generated. Linking... clang: error: no such file or directory: 'dp_lib/evaluate_dirichlet.o' makefile:8: recipe for target 't_coffee' failed make[2]: [t_coffee] Error 1 (ignored) make[2]: Leaving directory '/<>/t_coffee_source' make[1]: Leaving directory '/<>' dh_auto_test -a -O--sourcedirectory=t_coffee_source create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --sourcedirectory=t_coffee_source dh_testroot -a -O--sourcedirectory=t_coffee_source dh_prep -a -O--sourcedirectory=t_coffee_source dh_auto_install -a -O--sourcedirectory=t_coffee_source dh_install -a -O--sourcedirectory=t_coffee_source dh_install: Cannot find (any matches for) "t_coffee_source/t_coffee" (tried in ., debian/tmp) dh_install: t-coffee missing files: t_coffee_source/t_coffee dh_install: missing files, aborting debian/rules:13: recipe for target 'binary-arch' failed make: *** [binary-arch] Error 25 dpkg-buildpackage: error: fakeroot debian/rules binary-arch gave error exit status 2 -------------------------------------------------------------------------------- Build finished at 2017-07-06T20:17:14Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 26044 Build-Time: 9 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 5 Job: t-coffee_11.00.8cbe486-5 Machine Architecture: amd64 Package: t-coffee Package-Time: 30 Source-Version: 11.00.8cbe486-5 Space: 26044 Status: attempted Version: 11.00.8cbe486-5 -------------------------------------------------------------------------------- Finished at 2017-07-06T20:17:14Z Build needed 00:00:30, 26044k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 31.036950802s DC-Time-Estimation: 31.036950802 versus expected 315 (r/m: 9.149192876888591 ; m: 31.036950802)