DC-Build-Header: t-coffee 11.00.8cbe486-6 / 2018-05-02 13:28:10 +0000 DC-Task: type:rebuild-binarch-only source:t-coffee version:11.00.8cbe486-6 chroot:unstable esttime:39 logfile:/tmp/t-coffee_11.00.8cbe486-6_unstable_clang60.log modes:clang60:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --chroot-setup-commands=/tmp/clang60 t-coffee_11.00.8cbe486-6' sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on ip-172-31-9-42.eu-central-1.compute.internal +==============================================================================+ | t-coffee 11.00.8cbe486-6 (amd64) Wed, 02 May 2018 13:28:11 +0000 | +==============================================================================+ Package: t-coffee Version: 11.00.8cbe486-6 Source Version: 11.00.8cbe486-6 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-91556204-385a-498b-a1ed-cdaf0a56abfb' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang60 ------------ + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=6.0 + echo 'Install of clang-6.0' Install of clang-6.0 + apt-get update Get:1 http://127.0.0.1:9999/debian unstable InRelease [242 kB] Get:2 http://127.0.0.1:9999/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://127.0.0.1:9999/debian unstable/main Sources 2018-05-02-0830.09.pdiff [16.2 kB] Get:4 http://127.0.0.1:9999/debian unstable/main Sources 2018-05-02-0830.09.pdiff [16.2 kB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 Packages 2018-05-02-0830.09.pdiff [1781 B] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 Packages 2018-05-02-0830.09.pdiff [1781 B] Get:6 http://127.0.0.1:9999/debian unstable/main Translation-en [6016 kB] Fetched 6332 kB in 2s (2842 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-6.0 Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-6.0-dev libclang1-6.0 libedit2 libjsoncpp1 libllvm6.0 libncurses5 libobjc-7-dev libobjc4 Suggested packages: gnustep gnustep-devel clang-6.0-doc Recommended packages: llvm-6.0-dev python libomp-dev libgpm2 The following NEW packages will be installed: clang-6.0 lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-6.0-dev libclang1-6.0 libedit2 libjsoncpp1 libllvm6.0 libncurses5 libobjc-7-dev libobjc4 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. Need to get 37.7 MB of archives. After this operation, 187 MB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian unstable/main amd64 libjsoncpp1 amd64 1.7.4-3 [75.6 kB] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 libbsd0 amd64 0.8.7-1 [92.1 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 libncurses5 amd64 6.1+20180210-2 [95.7 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libedit2 amd64 3.1-20170329-1 [85.2 kB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 libllvm6.0 amd64 1:6.0-3 [14.5 MB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libobjc4 amd64 8-20180425-1 [52.4 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libobjc-7-dev amd64 7.3.0-17 [204 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libc6-i386 amd64 2.27-3 [2855 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 lib32gcc1 amd64 1:8-20180425-1 [47.8 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 lib32stdc++6 amd64 8-20180425-1 [406 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 libclang-common-6.0-dev amd64 1:6.0-3 [3102 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 libclang1-6.0 amd64 1:6.0-3 [6995 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 clang-6.0 amd64 1:6.0-3 [9175 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 37.7 MB in 0s (95.8 MB/s) Selecting previously unselected package libjsoncpp1: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 ... 10022 files and directories currently installed.) Preparing to unpack .../00-libjsoncpp1_1.7.4-3_amd64.deb ... Unpacking libjsoncpp1:amd64 (1.7.4-3) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../01-libbsd0_0.8.7-1_amd64.deb ... Unpacking libbsd0:amd64 (0.8.7-1) ... Selecting previously unselected package libncurses5:amd64. Preparing to unpack .../02-libncurses5_6.1+20180210-2_amd64.deb ... Unpacking libncurses5:amd64 (6.1+20180210-2) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../03-libedit2_3.1-20170329-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20170329-1) ... Selecting previously unselected package libllvm6.0:amd64. Preparing to unpack .../04-libllvm6.0_1%3a6.0-3_amd64.deb ... Unpacking libllvm6.0:amd64 (1:6.0-3) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../05-libobjc4_8-20180425-1_amd64.deb ... Unpacking libobjc4:amd64 (8-20180425-1) ... Selecting previously unselected package libobjc-7-dev:amd64. Preparing to unpack .../06-libobjc-7-dev_7.3.0-17_amd64.deb ... Unpacking libobjc-7-dev:amd64 (7.3.0-17) ... Selecting previously unselected package libc6-i386. Preparing to unpack .../07-libc6-i386_2.27-3_amd64.deb ... Unpacking libc6-i386 (2.27-3) ... Selecting previously unselected package lib32gcc1. Preparing to unpack .../08-lib32gcc1_1%3a8-20180425-1_amd64.deb ... Unpacking lib32gcc1 (1:8-20180425-1) ... Selecting previously unselected package lib32stdc++6. Preparing to unpack .../09-lib32stdc++6_8-20180425-1_amd64.deb ... Unpacking lib32stdc++6 (8-20180425-1) ... Selecting previously unselected package libclang-common-6.0-dev. Preparing to unpack .../10-libclang-common-6.0-dev_1%3a6.0-3_amd64.deb ... Unpacking libclang-common-6.0-dev (1:6.0-3) ... Selecting previously unselected package libclang1-6.0:amd64. Preparing to unpack .../11-libclang1-6.0_1%3a6.0-3_amd64.deb ... Unpacking libclang1-6.0:amd64 (1:6.0-3) ... Selecting previously unselected package clang-6.0. Preparing to unpack .../12-clang-6.0_1%3a6.0-3_amd64.deb ... Unpacking clang-6.0 (1:6.0-3) ... Setting up libncurses5:amd64 (6.1+20180210-2) ... Setting up libobjc4:amd64 (8-20180425-1) ... Setting up libc6-i386 (2.27-3) ... Setting up libbsd0:amd64 (0.8.7-1) ... Setting up libobjc-7-dev:amd64 (7.3.0-17) ... Processing triggers for libc-bin (2.27-3) ... Setting up lib32gcc1 (1:8-20180425-1) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up libedit2:amd64 (3.1-20170329-1) ... Setting up libllvm6.0:amd64 (1:6.0-3) ... Setting up libclang1-6.0:amd64 (1:6.0-3) ... Setting up lib32stdc++6 (8-20180425-1) ... Setting up libclang-common-6.0-dev (1:6.0-3) ... Setting up clang-6.0 (1:6.0-3) ... Processing triggers for libc-bin (2.27-3) ... 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 8' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-6.0 g++-4.6 + ln -s clang-6.0 gcc-4.6 + ln -s clang-6.0 cpp-4.6 + ln -s clang-6.0 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++-6.0 g++-4.7 + ln -s clang-6.0 gcc-4.7 + ln -s clang-6.0 cpp-4.7 + ln -s clang-6.0 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++-6.0 g++-4.8 + ln -s clang-6.0 gcc-4.8 + ln -s clang-6.0 cpp-4.8 + ln -s clang-6.0 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++-6.0 g++-4.9 + ln -s clang-6.0 gcc-4.9 + ln -s clang-6.0 cpp-4.9 + ln -s clang-6.0 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++-6.0 g++-5 + ln -s clang-6.0 gcc-5 + ln -s clang-6.0 cpp-5 + ln -s clang-6.0 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++-6.0 g++-6 + ln -s clang-6.0 gcc-6 + ln -s clang-6.0 cpp-6 + ln -s clang-6.0 gcc + echo 'gcc-6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-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++-6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-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++-7 gcc-7 cpp-7 gcc + ln -s clang++-6.0 g++-7 + ln -s clang-6.0 gcc-7 + ln -s clang-6.0 cpp-7 + ln -s clang-6.0 gcc + echo 'gcc-7 hold' + dpkg --set-selections + echo 'g++-7 hold' + dpkg --set-selections + for VERSION in $VERSIONS + rm -f g++-8 gcc-8 cpp-8 gcc + ln -s clang++-6.0 g++-8 + ln -s clang-6.0 gcc-8 + ln -s clang-6.0 cpp-8 + ln -s clang-6.0 gcc + echo 'gcc-8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-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++-8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-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 + cd - /build/t-coffee-dRXsY0 + 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/clang60'. 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 11.00.8cbe486-6 (dsc) [2173 B] Get:2 http://127.0.0.1:9999/debian unstable/main t-coffee 11.00.8cbe486-6 (tar) [3526 kB] Get:3 http://127.0.0.1:9999/debian unstable/main t-coffee 11.00.8cbe486-6 (diff) [15.9 kB] Fetched 3544 kB in 0s (20.0 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/t-coffee-dRXsY0/t-coffee-11.00.8cbe486' with '<>' I: NOTICE: Log filtering will replace 'build/t-coffee-dRXsY0' 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-FQhQ1r/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-FQhQ1r/apt_archive ./ InRelease Get:2 copy:/<>/resolver-FQhQ1r/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-FQhQ1r/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-FQhQ1r/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-FQhQ1r/apt_archive ./ Packages [432 B] Fetched 1738 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 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-FQhQ1r/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10771 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-FQhQ1r/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-FQhQ1r/apt_archive ./ InRelease Get:2 copy:/<>/resolver-FQhQ1r/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-FQhQ1r/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-FQhQ1r/apt_archive ./ Sources [486 B] Get:5 copy:/<>/resolver-FQhQ1r/apt_archive ./ Packages [565 B] Fetched 2014 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 dwz gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev 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 19.7 MB of archives. After this operation, 66.6 MB of additional disk space will be used. Get:1 copy:/<>/resolver-FQhQ1r/apt_archive ./ sbuild-build-depends-t-coffee-dummy 0.invalid.0 [856 B] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 bsdmainutils amd64 11.1.2 [190 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 groff-base amd64 1.22.3-10 [1176 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libpipeline1 amd64 1.5.0-1 [29.0 kB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 man-db amd64 2.8.3-2 [1180 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libmagic-mgc amd64 1:5.33-2 [234 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libmagic1 amd64 1:5.33-2 [113 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 file amd64 1:5.33-2 [65.6 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 gettext-base amd64 0.19.8.1-6 [122 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 m4 amd64 1.4.18-1 [202 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 autoconf all 2.69-11 [341 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:14 http://127.0.0.1:9999/debian unstable/main amd64 automake all 1:1.15.1-3.1 [736 kB] Get:15 http://127.0.0.1:9999/debian unstable/main amd64 autopoint all 0.19.8.1-6 [434 kB] Get:16 http://127.0.0.1:9999/debian unstable/main amd64 libtool all 2.4.6-2.1 [547 kB] Get:17 http://127.0.0.1:9999/debian unstable/main amd64 dh-autoreconf all 17 [16.5 kB] Get:18 http://127.0.0.1:9999/debian unstable/main amd64 libarchive-zip-perl all 1.60-1 [95.6 kB] Get:19 http://127.0.0.1:9999/debian unstable/main amd64 libfile-stripnondeterminism-perl all 0.041-1 [19.9 kB] Get:20 http://127.0.0.1:9999/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:21 http://127.0.0.1:9999/debian unstable/main amd64 dh-strip-nondeterminism all 0.041-1 [12.0 kB] Get:22 http://127.0.0.1:9999/debian unstable/main amd64 libglib2.0-0 amd64 2.56.1-2 [2928 kB] Get:23 http://127.0.0.1:9999/debian unstable/main amd64 libicu57 amd64 57.1-9 [7698 kB] Get:24 http://127.0.0.1:9999/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-6.1 [725 kB] Get:25 http://127.0.0.1:9999/debian unstable/main amd64 libcroco3 amd64 0.6.12-2 [144 kB] Get:26 http://127.0.0.1:9999/debian unstable/main amd64 gettext amd64 0.19.8.1-6 [1302 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 11.2.1 [1013 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.7 MB in 0s (96.2 MB/s) Selecting previously unselected package bsdmainutils. (Reading database ... 10771 files and directories currently installed.) Preparing to unpack .../00-bsdmainutils_11.1.2_amd64.deb ... Unpacking bsdmainutils (11.1.2) ... Selecting previously unselected package groff-base. Preparing to unpack .../01-groff-base_1.22.3-10_amd64.deb ... Unpacking groff-base (1.22.3-10) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../02-libpipeline1_1.5.0-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.0-1) ... Selecting previously unselected package man-db. Preparing to unpack .../03-man-db_2.8.3-2_amd64.deb ... Unpacking man-db (2.8.3-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.33-2_amd64.deb ... Unpacking libmagic-mgc (1:5.33-2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../05-libmagic1_1%3a5.33-2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.33-2) ... Selecting previously unselected package file. 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Setting up libpipeline1:amd64 (1.5.0-1) ... Setting up m4 (1.4.18-1) ... Setting up libicu57:amd64 (57.1-9) ... Setting up libxml2:amd64 (2.9.4+dfsg1-6.1) ... Setting up libmagic-mgc (1:5.33-2) ... Setting up libmagic1:amd64 (1:5.33-2) ... Setting up libcroco3:amd64 (0.6.12-2) ... Processing triggers for libc-bin (2.27-3) ... Setting up autotools-dev (20180224.1) ... Setting up bsdmainutils (11.1.2) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up autopoint (0.19.8.1-6) ... Setting up libfile-stripnondeterminism-perl (0.041-1) ... Setting up gettext (0.19.8.1-6) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.33-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15.1-3.1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.8.3-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libtool (2.4.6-2.1) ... Setting up po-debconf (1.0.20) ... Setting up dh-autoreconf (17) ... Setting up dh-strip-nondeterminism (0.041-1) ... Setting up debhelper (11.2.1) ... Setting up sbuild-build-depends-t-coffee-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.27-3) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-5-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.30-16 dpkg-dev_1.19.0.5 g++-7_7.3.0-17 gcc-7_7.3.0-17 libc6-dev_2.27-3 libstdc++-7-dev_7.3.0-17 libstdc++6_8-20180425-1 linux-libc-dev_4.15.17-1 Package versions: adduser_3.117 apt_1.6.1 autoconf_2.69-11 automake_1:1.15.1-3.1 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1 base-passwd_3.5.45 bash_4.4.18-2 binutils_2.30-16 binutils-common_2.30-16 binutils-x86-64-linux-gnu_2.30-16 bsdmainutils_11.1.2 bsdutils_1:2.31.1-0.5 build-essential_12.5 bzip2_1.0.6-8.1 clang-6.0_1:6.0-3 coreutils_8.28-1 cpp_4:7.3.0-3 cpp-7_7.3.0-17 dash_0.5.8-2.10 debconf_1.5.66 debfoster_2.7-2.1+b1 debhelper_11.2.1 debian-archive-keyring_2017.7 debianutils_4.8.4 dh-autoreconf_17 dh-strip-nondeterminism_0.041-1 diffutils_1:3.6-1 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 e2fslibs_1.44.1-2 e2fsprogs_1.44.1-2 eatmydata_105-6 fakeroot_1.22-2 fdisk_2.31.1-0.5 file_1:5.33-2 findutils_4.6.0+git+20171230-2 g++_4:7.3.0-3 g++-7_7.3.0-17 gcc_4:7.3.0-3 gcc-6-base_6.4.0-17 gcc-7_7.3.0-17 gcc-7-base_7.3.0-17 gcc-8-base_8-20180425-1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gpgv_2.2.5-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5+b1 hostname_3.20 init-system-helpers_1.51 intltool-debian_0.35.0+20060710.4 lib32gcc1_1:8-20180425-1 lib32stdc++6_8-20180425-1 libacl1_2.2.52-3+b1 libapt-pkg5.0_1.6.1 libarchive-zip-perl_1.60-1 libasan4_7.3.0-17 libatomic1_8-20180425-1 libattr1_1:2.4.47-2+b2 libaudit-common_1:2.8.3-1 libaudit1_1:2.8.3-1 libbinutils_2.30-16 libblkid1_2.31.1-0.5 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3 libc-dev-bin_2.27-3 libc6_2.27-3 libc6-dev_2.27-3 libc6-i386_2.27-3 libcap-ng0_0.7.9-1 libcc1-0_8-20180425-1 libcilkrts5_7.3.0-17 libclang-common-6.0-dev_1:6.0-3 libclang1-6.0_1:6.0-3 libcom-err2_1.44.1-2 libcomerr2_1.44.1-2 libcroco3_0.6.12-2 libdb5.3_5.3.28-13.1+b1 libdebconfclient0_0.243 libdpkg-perl_1.19.0.5 libeatmydata1_105-6 libedit2_3.1-20170329-1 libext2fs2_1.44.1-2 libfakeroot_1.22-2 libfdisk1_2.31.1-0.5 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.041-1 libgc1c2_1:7.4.2-8.2 libgcc-7-dev_7.3.0-17 libgcc1_1:8-20180425-1 libgcrypt20_1.8.2-2 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libglib2.0-0_2.56.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8-20180425-1 libgpg-error0_1.29-4 libhogweed4_3.4-1 libicu57_57.1-9 libidn2-0_2.0.4-1.1 libisl15_0.18-4 libisl19_0.19-1 libitm1_8-20180425-1 libjsoncpp1_1.7.4-3 libllvm6.0_1:6.0-3 liblsan0_8-20180425-1 liblz4-1_1.8.1.2-1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.33-2 libmagic1_1:5.33-2 libmount1_2.31.1-0.5 libmpc3_1.1.0-1 libmpfr4_3.1.6-1 libmpfr6_4.0.1-1 libmpx2_8-20180425-1 libncurses5_6.1+20180210-2 libncursesw5_6.1+20180210-2 libnettle6_3.4-1 libobjc-7-dev_7.3.0-17 libobjc4_8-20180425-1 libp11-kit0_0.23.10-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam0g_1.1.8-3.7 libpcre3_2:8.39-9 libperl5.26_5.26.2-3 libpipeline1_1.5.0-1 libquadmath0_8-20180425-1 libseccomp2_2.3.3-1 libselinux1_2.7-2+b2 libsemanage-common_2.7-2 libsemanage1_2.7-2+b2 libsepol1_2.7-1 libsigsegv2_2.12-2 libsmartcols1_2.31.1-0.5 libss2_1.44.1-2 libstdc++-7-dev_7.3.0-17 libstdc++6_8-20180425-1 libsystemd0_238-4 libtasn1-6_4.13-2 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180210-2 libtinfo6_6.1+20180210-2 libtool_2.4.6-2.1 libtsan0_8-20180425-1 libubsan0_7.3.0-17 libudev1_238-4 libunistring2_0.9.8-1 libustr-1.0-1_1.0.4-6 libuuid1_2.31.1-0.5 libxml2_2.9.4+dfsg1-6.1 libzstd1_1.3.4+dfsg-1 linux-libc-dev_4.15.17-1 login_1:4.5-1 m4_1.4.18-1 make_4.2.1-1 man-db_2.8.3-2 mawk_1.3.3-17+b3 mount_2.31.1-0.5 multiarch-support_2.27-3 ncurses-base_6.1+20180210-2 ncurses-bin_6.1+20180210-2 passwd_1:4.5-1 patch_2.7.6-2 perl_5.26.2-3 perl-base_5.26.2-3 perl-modules-5.26_5.26.2-3 po-debconf_1.0.20 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-t-coffee-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-1 util-linux_2.31.1-0.5 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Mon Aug 28 13:29:39 2017 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./t-coffee_11.00.8cbe486-6.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_11.00.8cbe486-6.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 dpkg-source: info: applying gcc-7.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-91556204-385a-498b-a1ed-cdaf0a56abfb 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 11.00.8cbe486-6 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 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_clean -O--sourcedirectory=t_coffee_source debian/rules build-arch dh build-arch --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 cd t_coffee_source && make -j8 -Oline -i USER_BIN=../bin/ "FCC=gfortran -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong" all make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/evaluate_dirichlet.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 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_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); ^ 5 warnings and 1 error generated. make[2]: [makefile:11: dp_lib/evaluate_dirichlet.o] Error 1 (ignored) make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/CUSTOM_evaluate_for_struc.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 1 warning generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dev_lib/dev1.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ dev_lib/dev1.c:89:42: warning: data argument not used by format string [-Wformat-extra-args] fprintf (stdout, "Process positions\n", i); ~~~~~~~~~~~~~~~~~~~~~ ^ 2 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/evaluate_for_domain.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 1 warning generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_domain_dp.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 1 warning generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/showpair.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 1 warning generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_domain_dp_drivers.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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/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)) ^ == 2 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_est.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 1 warning generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_clean_maln.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 1 warning generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/pavie_dp.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 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/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); ^~~~~~ ~~~~~~~ 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); ^ ( ) dp_lib/pavie_dp.c:1365:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf (fp, "%s", mat); ^~~~~~ ~~~~~~~~~~~~~ 7 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_cdna_fasta_nw.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 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; ^ ( ) 3 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_fasta_sw.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ 1 warning generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/evaluate_for_struc.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 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) ~~~~~~~~~~~~^~~~~~~~~~~~~ ~~~~ 2 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_generic_fasta_nw.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 1 warning generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_gotoh_sw.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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_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); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/fsa_dp.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 1 warning generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_mm_nw.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 1 warning generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_fasta_nw.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ dp_lib/util_dp_fasta_nw.c:157:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int *p; ^~~~~~~~~ 2 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_ssec_pwaln.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 1 warning generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_graph_maln.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 1 warning generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC fastal/diagonal.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 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); ^~~~~ ~~~~~~~~~~~~~~~~~ 5 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC fastal/fastal_opt_parsing.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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") ^ ~~~~~~~~~~ 1 warning generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_sim.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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:173:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int d; ^~~~~~~~~ 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 */ ^~ = nullptr dp_lib/util_dp_sim.c:481:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] { register int i, j; /* row and column indices */ ^~~~~~~~~ dp_lib/util_dp_sim.c:481:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] { register int i, j; /* row and column indices */ ^~~~~~~~~ dp_lib/util_dp_sim.c:482:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int c; /* best score at current point */ ^~~~~~~~~ dp_lib/util_dp_sim.c:483:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int f; /* best score ending with insertion */ ^~~~~~~~~ dp_lib/util_dp_sim.c:484:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int d; /* best score ending with deletion */ ^~~~~~~~~ dp_lib/util_dp_sim.c:485:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p; /* best score at (i-1, j-1) */ ^~~~~~~~~ dp_lib/util_dp_sim.c:486:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int ci, cj; /* end-point associated with c */ ^~~~~~~~~ dp_lib/util_dp_sim.c:486:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int ci, cj; /* end-point associated with c */ ^~~~~~~~~ dp_lib/util_dp_sim.c:487:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int di, dj; /* end-point associated with d */ ^~~~~~~~~ dp_lib/util_dp_sim.c:487:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int di, dj; /* end-point associated with d */ ^~~~~~~~~ dp_lib/util_dp_sim.c:488:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int fi, fj; /* end-point associated with f */ ^~~~~~~~~ dp_lib/util_dp_sim.c:488:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int fi, fj; /* end-point associated with f */ ^~~~~~~~~ dp_lib/util_dp_sim.c:489:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pi, pj; /* end-point associated with p */ ^~~~~~~~~ dp_lib/util_dp_sim.c:489:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pi, pj; /* end-point associated with p */ ^~~~~~~~~ dp_lib/util_dp_sim.c:562:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] { register int i, j; /* row and column indices */ ^~~~~~~~~ dp_lib/util_dp_sim.c:562:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] { register int i, j; /* row and column indices */ ^~~~~~~~~ dp_lib/util_dp_sim.c:563:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int c; /* best score at current point */ ^~~~~~~~~ dp_lib/util_dp_sim.c:564:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int f; /* best score ending with insertion */ ^~~~~~~~~ dp_lib/util_dp_sim.c:565:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int d; /* best score ending with deletion */ ^~~~~~~~~ dp_lib/util_dp_sim.c:566:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p; /* best score at (i-1, j-1) */ ^~~~~~~~~ dp_lib/util_dp_sim.c:567:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int ci, cj; /* end-point associated with c */ ^~~~~~~~~ dp_lib/util_dp_sim.c:567:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int ci, cj; /* end-point associated with c */ ^~~~~~~~~ dp_lib/util_dp_sim.c:568:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int di=0, dj=0; /* end-point associated with d */ ^~~~~~~~~ dp_lib/util_dp_sim.c:568:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int di=0, dj=0; /* end-point associated with d */ ^~~~~~~~~ dp_lib/util_dp_sim.c:569:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int fi, fj; /* end-point associated with f */ ^~~~~~~~~ dp_lib/util_dp_sim.c:569:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int fi, fj; /* end-point associated with f */ ^~~~~~~~~ dp_lib/util_dp_sim.c:570:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pi, pj; /* end-point associated with p */ ^~~~~~~~~ dp_lib/util_dp_sim.c:570:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pi, pj; /* end-point associated with p */ ^~~~~~~~~ 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 dp_lib/util_dp_sim.c:786:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] { register int i, j; /* row and column indices */ ^~~~~~~~~ dp_lib/util_dp_sim.c:786:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] { register int i, j; /* row and column indices */ ^~~~~~~~~ dp_lib/util_dp_sim.c:787:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int c; /* best score at current point */ ^~~~~~~~~ dp_lib/util_dp_sim.c:788:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int f; /* best score ending with insertion */ ^~~~~~~~~ dp_lib/util_dp_sim.c:789:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int d; /* best score ending with deletion */ ^~~~~~~~~ dp_lib/util_dp_sim.c:790:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p; /* best score at (i-1, j-1) */ ^~~~~~~~~ dp_lib/util_dp_sim.c:791:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int ci, cj; /* end-point associated with c */ ^~~~~~~~~ dp_lib/util_dp_sim.c:791:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int ci, cj; /* end-point associated with c */ ^~~~~~~~~ dp_lib/util_dp_sim.c:792:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int di, dj; /* end-point associated with d */ ^~~~~~~~~ dp_lib/util_dp_sim.c:792:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int di, dj; /* end-point associated with d */ ^~~~~~~~~ dp_lib/util_dp_sim.c:793:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int fi, fj; /* end-point associated with f */ ^~~~~~~~~ dp_lib/util_dp_sim.c:793:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int fi, fj; /* end-point associated with f */ ^~~~~~~~~ dp_lib/util_dp_sim.c:794:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pi, pj; /* end-point associated with p */ ^~~~~~~~~ dp_lib/util_dp_sim.c:794:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pi, pj; /* end-point associated with p */ ^~~~~~~~~ dp_lib/util_dp_sim.c:864:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j; ^~~~~~~~~ dp_lib/util_dp_sim.c:864:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j; ^~~~~~~~~ dp_lib/util_dp_sim.c:883:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ dp_lib/util_dp_sim.c:911:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j; ^~~~~~~~~ dp_lib/util_dp_sim.c:911:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j; ^~~~~~~~~ dp_lib/util_dp_sim.c:912:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int c, e, d, s; ^~~~~~~~~ dp_lib/util_dp_sim.c:912:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int c, e, d, s; ^~~~~~~~~ dp_lib/util_dp_sim.c:912:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int c, e, d, s; ^~~~~~~~~ dp_lib/util_dp_sim.c:912:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int c, e, d, s; ^~~~~~~~~ 55 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC fastal/iteration.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 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/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); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 11 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_gotoh_nw.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 1 warning generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC fastal/scoring.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 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); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ 11 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC fastal/tree.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 1 warning generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC io_lib/pb_util_read_seq_util.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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/pb_util_read_seq_util.c:68:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register void *ret; ^~~~~~~~~ io_lib/pb_util_read_seq_util.c:91:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register void *ret; ^~~~~~~~~ io_lib/pb_util_read_seq_util.c:191:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p; ^~~~~~~~~ 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:240:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register char *s = str; ^~~~~~~~~ io_lib/pb_util_read_seq_util.c:258:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register char *s = str; ^~~~~~~~~ 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); ^~~~~ ~~~~~~~~~~~~~~~~~~~~ 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/pb_util_read_seq_util.c:356:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ 12 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_drivers.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 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)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ 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] 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); ^~~~~ ~~~~~~~~~~~~~~~ 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)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ 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)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ 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:1722:13: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int a; ^~~~~~~~~ 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)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~ 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]) ~~~~~^~~~~~~~~ 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")) ~~ ~~~~^~~~~~~ 23 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC km_coffee/Stack.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC fastal/parttree.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 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); ^~~~~ ~~~~~~~~~~~~~~~~ fastal/parttree.c:757:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int *p; ^~~~~~~~~ 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); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ 12 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/evaluate.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 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.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/evaluate.c: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 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 ); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~ 7 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC io_lib/pb_util_read_sequence.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ io_lib/pb_util_read_sequence.c:79:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ io_lib/pb_util_read_sequence.c:80:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int c; ^~~~~~~~~ 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;i>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC km_coffee/classes.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC km_coffee/km_util.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] km_coffee/km_util.c:96:55: warning: more '%' conversions than data arguments [-Wformat] fprintf(stderr, "This error was caused by '%s' in '%s'\n", function); ~^ 1 warning generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC km_coffee/km_coffee.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] In file included from km_coffee/km_coffee.c:44: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ km_coffee/km_coffee.c:491:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] chdir(km_tmp_dir); ^~~~~ ~~~~~~~~~~ 2 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_suboptimal_nw.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 1 warning generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC io_lib/io_func.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ io_lib/io_func.c:511:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "\n"); ^~~~~~ ~~~~~~~~ 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/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. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC fastal/fastal.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 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); ^~~~~ ~~~~~~~~~~~~~~~~~ fastal/fastal.c:2115:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system(blast_command); ^~~~~~ ~~~~~~~~~~~~~ fastal/fastal.c:2262:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system(blast_command); ^~~~~~ ~~~~~~~~~~~~~ fastal/fastal.c:3201:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] 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); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 24 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/hsearch.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] In file included from util_lib/hsearch.c:35: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ 1 warning generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/random.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC km_coffee/Vector.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] km_coffee/Vector.c:869:25: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] fprintf(out_F, "%i ", i); ~~ ^ %zu 1 warning generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/aln_compare.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] In file included from util_lib/aln_compare.c:35: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ 1 warning generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC km_coffee/kmeans.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/util_analyse_constraints_list.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 1 warning generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/reformat_struc.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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_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" ); ^~~~~~ ~~~~~~~~~ 7 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC t_coffee_lib/t_coffee.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] In file included from t_coffee_lib/t_coffee.c:36: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ t_coffee_lib/t_coffee.c:3956:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system (command); ^~~~~~ ~~~~~~~ t_coffee_lib/t_coffee.c:3970:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system (command); ^~~~~~ ~~~~~~~ t_coffee_lib/t_coffee.c:3984:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] system (command); ^~~~~~ ~~~~~~~ t_coffee_lib/t_coffee.c:6306:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ t_coffee_lib/t_coffee.c:6545:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ 6 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/util_domain_constraints_list.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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_domain_constraints_list.c:52:11: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] while (e=extract_entry (CL)) ~^~~~~~~~~~~~~~~~~~~ util_lib/util_domain_constraints_list.c:52:11: note: place parentheses around the assignment to silence this warning while (e=extract_entry (CL)) ^ ( ) util_lib/util_domain_constraints_list.c:52:11: note: use '==' to turn this assignment into an equality comparison while (e=extract_entry (CL)) ^ == 2 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/util_dps.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 1 warning generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC io_lib/tree_util.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] In file included from io_lib/tree_util.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ io_lib/tree_util.c:836:42: warning: data argument not used by format string [-Wformat-extra-args] fprintf (stdout, "Process positions\n", i); ~~~~~~~~~~~~~~~~~~~~~ ^ io_lib/tree_util.c:1205:23: warning: implicit conversion from 'double' to 'int' changes value from 1.0E-4 to 0 [-Wliteral-conversion] reset_boot_tree (RT,0.0001); ~~~~~~~~~~~~~~~ ^~~~~~ io_lib/tree_util.c:2803:10: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(fp,"%f",&dist); ^~~~~~ ~~~~~~~~~~~~~ io_lib/tree_util.c:2811:6: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(fp,"%f",&bootstrap); ^~~~~~ ~~~~~~~~~~~~~~~~~~ io_lib/tree_util.c:4252:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ io_lib/tree_util.c:4478:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ io_lib/tree_util.c:4581:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ io_lib/tree_util.c:4959:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ io_lib/tree_util.c:5043:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ io_lib/tree_util.c:5116:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 11 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/util_job_handling.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 1 warning generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/util_declare.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 1 warning generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/util_make_tree.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] } ^ util_lib/util_make_tree.c:727:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ 3 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/util_constraints_list.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 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_constraints_list.c:1294:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 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); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ 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_constraints_list.c:2838:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf (fp, "%*s %d %*s\n", &l); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~ util_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); ^~~~~ ~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: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_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_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); ~~~~~^~~~~~~ ~ 17 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/util_aln_analyze.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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/util_aln_analyze.c:713:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ util_lib/util_aln_analyze.c:4480:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 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; ^ ( ) 5 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/aln_convertion_util.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] In file included from util_lib/aln_convertion_util.c:34: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ util_lib/aln_convertion_util.c:4453:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ util_lib/aln_convertion_util.c:4549:26: warning: address of array 'T->template_file' will always evaluate to 'true' [-Wpointer-bool-conversion] else if ( T && T->template_file && T->template_file[0]) ~~ ~~~^~~~~~~~~~~~~ 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] } ^ 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")) ~~~^~~~ ~~ 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]); ^ ( ) 13 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/reformat.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] In file included from util_lib/reformat.c:36: In file included from ./util_lib_header.h:30: ./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment] /* */ ^ util_lib/reformat.c:1356:23: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] else if (format_val = fast_format_determination(file)) ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1356:23: note: place parentheses around the assignment to silence this warning else if (format_val = fast_format_determination(file)) ^ ( ) util_lib/reformat.c:1356:23: note: use '==' to turn this assignment into an equality comparison else if (format_val = fast_format_determination(file)) ^ == util_lib/reformat.c:1502:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "%d", &result); ^~~~~~ ~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1540:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf ( fp, "\n%s\n", buf); ^~~~~~ ~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1692:12: 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 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/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); ^~~~~~ ~~~~~~~~~~~~~~ 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/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/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: note: put the semicolon on a separate line to silence this warning 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/reformat.c:7124:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 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"); ^~~~~~ ~~~~~~~~ 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); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ 45 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/util.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 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] /* */ ^ 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/util.c:97:1: warning: '/*' within block comment [-Wcomment] /* */ ^ 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]*/ ^~~~~ ~~~~~~~~~~~~~~~~~ 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.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/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); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~ 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); ^~~~~~ ~~~~~~~~~~~~~~~~ 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.c:3827:1: warning: control may reach end of non-void function [-Wreturn-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.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 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.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.c:6465:17: warning: '/*' within block comment [-Wcomment] * /*Flag* / &garbage ,\ ^ util_lib/util.c:6466:17: warning: '/*' within block comment [-Wcomment] * /*TYPE* / "S" ,\ ^ util_lib/util.c:6467:17: warning: '/*' within block comment [-Wcomment] * /*OPTIONAL?* / OPTIONAL ,\ ^ 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.c: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:6472:17: 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" \ ^ util_lib/util.c:6571:16: warning: second argument to 'va_start' is not the last named parameter [-Wvarargs] va_start (ap, usage); ^ 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); ^~~~~~ ~~~~~~~~~~~~~~~~ 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.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] } ^ 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.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]; ~ ~^ 46 warnings generated. make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' Linking... clang: error: no such file or directory: 'dp_lib/evaluate_dirichlet.o' make[2]: [makefile:8: 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 make: *** [debian/rules:11: binary-arch] Error 25 dpkg-buildpackage: error: fakeroot debian/rules binary-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2018-05-02T13:28:47Z 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: 27840 Build-Time: 15 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 7 Job: t-coffee_11.00.8cbe486-6 Machine Architecture: amd64 Package: t-coffee Package-Time: 36 Source-Version: 11.00.8cbe486-6 Space: 27840 Status: attempted Version: 11.00.8cbe486-6 -------------------------------------------------------------------------------- Finished at 2018-05-02T13:28:47Z Build needed 00:00:36, 27840k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 37.833815198s