https://launchpad.net/ubuntu/+archive/test-rebuild-20181222/+build/16089555 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos02-arm64-042 4.4.0-142-generic #168-Ubuntu SMP Wed Jan 16 21:00:53 UTC 2019 aarch64 Buildd toolchain package versions: launchpad-buildd_167 python-lpbuildd_167 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.6 dpkg-dev_1.18.4ubuntu1.5 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 20 Feb 08:46:07 ntpdate[1845]: adjust time server 10.211.37.1 offset -0.001620 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=bionic --arch=arm64 PACKAGEBUILD-16089555 --image-type chroot /home/buildd/filecache-default/ba8da4cd8f224e5b98b45e770e42ce881cefd998 Creating target for build PACKAGEBUILD-16089555 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=bionic --arch=arm64 PACKAGEBUILD-16089555 Starting target for build PACKAGEBUILD-16089555 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=bionic --arch=arm64 PACKAGEBUILD-16089555 'deb http://ftpmaster.internal/ubuntu bionic main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu bionic-security main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu bionic-updates main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-16089555 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=bionic --arch=arm64 PACKAGEBUILD-16089555 Updating target for build PACKAGEBUILD-16089555 Get:1 http://ftpmaster.internal/ubuntu bionic InRelease [242 kB] Get:2 http://ftpmaster.internal/ubuntu bionic-security InRelease [88.7 kB] Get:3 http://ftpmaster.internal/ubuntu bionic-updates InRelease [88.7 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main arm64 Packages [975 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main Translation-en [516 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/universe arm64 Packages [8316 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/universe Translation-en [4941 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/multiverse arm64 Packages [126 kB] Get:9 http://ftpmaster.internal/ubuntu bionic-security/main arm64 Packages [198 kB] Get:10 http://ftpmaster.internal/ubuntu bionic-security/main Translation-en [100 kB] Get:11 http://ftpmaster.internal/ubuntu bionic-security/universe arm64 Packages [127 kB] Get:12 http://ftpmaster.internal/ubuntu bionic-security/universe Translation-en [71.2 kB] Get:13 http://ftpmaster.internal/ubuntu bionic-security/multiverse arm64 Packages [1444 B] Get:14 http://ftpmaster.internal/ubuntu bionic-security/multiverse Translation-en [1848 B] Get:15 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 Packages [429 kB] Get:16 http://ftpmaster.internal/ubuntu bionic-updates/main Translation-en [196 kB] Get:17 http://ftpmaster.internal/ubuntu bionic-updates/restricted arm64 Packages [672 B] Get:18 http://ftpmaster.internal/ubuntu bionic-updates/restricted Translation-en [3076 B] Get:19 http://ftpmaster.internal/ubuntu bionic-updates/universe arm64 Packages [623 kB] Get:20 http://ftpmaster.internal/ubuntu bionic-updates/universe Translation-en [189 kB] Get:21 http://ftpmaster.internal/ubuntu bionic-updates/multiverse arm64 Packages [2380 B] Get:22 http://ftpmaster.internal/ubuntu bionic-updates/multiverse Translation-en [3452 B] Fetched 17.2 MB in 8s (2296 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt base-files binutils binutils-aarch64-linux-gnu binutils-common bsdutils cpp cpp-7 dpkg dpkg-dev e2fslibs e2fsprogs fdisk g++ g++-7 gcc gcc-7 gcc-7-base gcc-8-base gpg gpg-agent gpgconf gpgv libapparmor1 libapt-pkg5.0 libasan4 libatomic1 libbinutils libblkid1 libcc1-0 libcom-err2 libcomerr2 libcryptsetup12 libdpkg-perl libext2fs2 libfdisk1 libgcc-7-dev libgcc1 libgcrypt20 libgomp1 libitm1 libkmod2 liblsan0 libmount1 libncurses5 libncursesw5 libperl5.26 libpng16-16 libprocps6 libsmartcols1 libss2 libssl1.1 libstdc++-7-dev libstdc++6 libsystemd0 libtinfo5 libtsan0 libubsan0 libudev1 libuuid1 linux-libc-dev mount ncurses-base ncurses-bin openssl perl perl-base perl-modules-5.26 pkgbinarymangler procps systemd systemd-sysv tar tzdata ubuntu-keyring util-linux 76 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 45.3 MB of archives. After this operation, 273 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 base-files arm64 10.1ubuntu2.4 [60.0 kB] Get:2 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 bsdutils arm64 1:2.31.1-0.4ubuntu3.3 [54.7 kB] Get:3 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 tar arm64 1.29b-2ubuntu0.1 [207 kB] Get:4 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 dpkg arm64 1.19.0.5ubuntu2.1 [1095 kB] Get:5 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libext2fs2 arm64 1.44.1-1ubuntu1.1 [138 kB] Get:6 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 e2fsprogs arm64 1.44.1-1ubuntu1.1 [345 kB] Get:7 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 ncurses-bin arm64 6.1-1ubuntu1.18.04 [154 kB] Get:8 http://ftpmaster.internal/ubuntu bionic-security/main arm64 libperl5.26 arm64 5.26.1-6ubuntu0.3 [3326 kB] Get:9 http://ftpmaster.internal/ubuntu bionic-security/main arm64 perl arm64 5.26.1-6ubuntu0.3 [201 kB] Get:10 http://ftpmaster.internal/ubuntu bionic-security/main arm64 perl-base arm64 5.26.1-6ubuntu0.3 [1236 kB] Get:11 http://ftpmaster.internal/ubuntu bionic-security/main arm64 perl-modules-5.26 all 5.26.1-6ubuntu0.3 [2763 kB] Get:12 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libuuid1 arm64 2.31.1-0.4ubuntu3.3 [18.7 kB] Get:13 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libblkid1 arm64 2.31.1-0.4ubuntu3.3 [105 kB] Get:14 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libfdisk1 arm64 2.31.1-0.4ubuntu3.3 [138 kB] Get:15 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libmount1 arm64 2.31.1-0.4ubuntu3.3 [115 kB] Get:16 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libncurses5 arm64 6.1-1ubuntu1.18.04 [77.0 kB] Get:17 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libtinfo5 arm64 6.1-1ubuntu1.18.04 [71.0 kB] Get:18 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libncursesw5 arm64 6.1-1ubuntu1.18.04 [96.4 kB] Get:19 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libsmartcols1 arm64 2.31.1-0.4ubuntu3.3 [70.9 kB] Get:20 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 fdisk arm64 2.31.1-0.4ubuntu3.3 [95.1 kB] Get:21 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 util-linux arm64 2.31.1-0.4ubuntu3.3 [818 kB] Get:22 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 ncurses-base all 6.1-1ubuntu1.18.04 [17.8 kB] Get:23 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libtsan0 arm64 8.2.0-1ubuntu2~18.04 [269 kB] Get:24 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 liblsan0 arm64 8.2.0-1ubuntu2~18.04 [120 kB] Get:25 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libitm1 arm64 8.2.0-1ubuntu2~18.04 [24.4 kB] Get:26 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libgomp1 arm64 8.2.0-1ubuntu2~18.04 [69.6 kB] Get:27 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 gcc-8-base arm64 8.2.0-1ubuntu2~18.04 [18.3 kB] Get:28 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libgcc1 arm64 1:8.2.0-1ubuntu2~18.04 [34.3 kB] Get:29 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libcc1-0 arm64 8.2.0-1ubuntu2~18.04 [36.5 kB] Get:30 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libatomic1 arm64 8.2.0-1ubuntu2~18.04 [9156 B] Get:31 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libstdc++6 arm64 8.2.0-1ubuntu2~18.04 [372 kB] Get:32 http://ftpmaster.internal/ubuntu bionic-security/main arm64 libudev1 arm64 237-3ubuntu10.13 [45.5 kB] Get:33 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libapt-pkg5.0 arm64 1.6.8 [763 kB] Get:34 http://ftpmaster.internal/ubuntu bionic-security/main arm64 libgcrypt20 arm64 1.8.1-4ubuntu1.1 [325 kB] Get:35 http://ftpmaster.internal/ubuntu bionic-security/main arm64 gpgv arm64 2.2.4-1ubuntu1.2 [166 kB] Get:36 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 ubuntu-keyring all 2018.09.18.1~18.04.0 [22.4 kB] Get:37 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 apt arm64 1.6.8 [1130 kB] Get:38 http://ftpmaster.internal/ubuntu bionic-security/main arm64 libapparmor1 arm64 2.12-4ubuntu5.1 [28.4 kB] Get:39 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libcryptsetup12 arm64 2:2.0.2-1ubuntu1.1 [112 kB] Get:40 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libkmod2 arm64 24-1ubuntu3.2 [32.7 kB] Get:41 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 mount arm64 2.31.1-0.4ubuntu3.3 [97.8 kB] Get:42 http://ftpmaster.internal/ubuntu bionic-security/main arm64 libprocps6 arm64 2:3.3.12-3ubuntu1.1 [28.6 kB] Get:43 http://ftpmaster.internal/ubuntu bionic-security/main arm64 procps arm64 2:3.3.12-3ubuntu1.1 [207 kB] Get:44 http://ftpmaster.internal/ubuntu bionic-security/main arm64 systemd arm64 237-3ubuntu10.13 [2551 kB] Get:45 http://ftpmaster.internal/ubuntu bionic-security/main arm64 libsystemd0 arm64 237-3ubuntu10.13 [171 kB] Get:46 http://ftpmaster.internal/ubuntu bionic-security/main arm64 systemd-sysv arm64 237-3ubuntu10.13 [12.0 kB] Get:47 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libcom-err2 arm64 1.44.1-1ubuntu1.1 [8684 B] Get:48 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libss2 arm64 1.44.1-1ubuntu1.1 [9992 B] Get:49 http://ftpmaster.internal/ubuntu bionic-security/main arm64 libssl1.1 arm64 1.1.0g-2ubuntu4.3 [916 kB] Get:50 http://ftpmaster.internal/ubuntu bionic-security/main arm64 openssl arm64 1.1.0g-2ubuntu4.3 [504 kB] Get:51 http://ftpmaster.internal/ubuntu bionic-security/main arm64 tzdata all 2018i-0ubuntu0.18.04 [189 kB] Get:52 http://ftpmaster.internal/ubuntu bionic-security/main arm64 libpng16-16 arm64 1.6.34-1ubuntu0.18.04.1 [162 kB] Get:53 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 binutils-aarch64-linux-gnu arm64 2.30-21ubuntu1~18.04 [2183 kB] Get:54 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libbinutils arm64 2.30-21ubuntu1~18.04 [429 kB] Get:55 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 binutils arm64 2.30-21ubuntu1~18.04 [3368 B] Get:56 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 binutils-common arm64 2.30-21ubuntu1~18.04 [193 kB] Get:57 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libubsan0 arm64 7.3.0-27ubuntu1~18.04 [117 kB] Get:58 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libasan4 arm64 7.3.0-27ubuntu1~18.04 [335 kB] Get:59 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 g++-7 arm64 7.3.0-27ubuntu1~18.04 [6147 kB] Get:60 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 gcc-7 arm64 7.3.0-27ubuntu1~18.04 [5999 kB] Get:61 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libstdc++-7-dev arm64 7.3.0-27ubuntu1~18.04 [1463 kB] Get:62 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libgcc-7-dev arm64 7.3.0-27ubuntu1~18.04 [834 kB] Get:63 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 cpp-7 arm64 7.3.0-27ubuntu1~18.04 [5330 kB] Get:64 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 gcc-7-base arm64 7.3.0-27ubuntu1~18.04 [19.0 kB] Get:65 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 cpp arm64 4:7.3.0-3ubuntu2.1 [27.6 kB] Get:66 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 dpkg-dev all 1.19.0.5ubuntu2.1 [608 kB] Get:67 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libdpkg-perl all 1.19.0.5ubuntu2.1 [211 kB] Get:68 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 e2fslibs arm64 1.44.1-1ubuntu1.1 [2712 B] Get:69 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 gcc arm64 4:7.3.0-3ubuntu2.1 [5200 B] Get:70 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 g++ arm64 4:7.3.0-3ubuntu2.1 [1560 B] Get:71 http://ftpmaster.internal/ubuntu bionic-security/main arm64 gpg arm64 2.2.4-1ubuntu1.2 [400 kB] Get:72 http://ftpmaster.internal/ubuntu bionic-security/main arm64 gpgconf arm64 2.2.4-1ubuntu1.2 [106 kB] Get:73 http://ftpmaster.internal/ubuntu bionic-security/main arm64 gpg-agent arm64 2.2.4-1ubuntu1.2 [190 kB] Get:74 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libcomerr2 arm64 1.44.1-1ubuntu1.1 [2712 B] Get:75 http://ftpmaster.internal/ubuntu bionic-security/main arm64 linux-libc-dev arm64 4.15.0-45.48 [978 kB] Get:76 http://ftpmaster.internal/ubuntu bionic-security/main arm64 pkgbinarymangler all 138.18.04.0 [52.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 45.3 MB in 2s (26.6 MB/s) (Reading database ... 12590 files and directories currently installed.) Preparing to unpack .../base-files_10.1ubuntu2.4_arm64.deb ... Unpacking base-files (10.1ubuntu2.4) over (10.1ubuntu2) ... Setting up base-files (10.1ubuntu2.4) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Installing new version of config file /etc/update-motd.d/50-motd-news ... (Reading database ... 12592 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.31.1-0.4ubuntu3.3_arm64.deb ... Unpacking bsdutils (1:2.31.1-0.4ubuntu3.3) over (1:2.31.1-0.4ubuntu3) ... Setting up bsdutils (1:2.31.1-0.4ubuntu3.3) ... (Reading database ... 12592 files and directories currently installed.) Preparing to unpack .../tar_1.29b-2ubuntu0.1_arm64.deb ... Unpacking tar (1.29b-2ubuntu0.1) over (1.29b-2) ... Setting up tar (1.29b-2ubuntu0.1) ... (Reading database ... 12592 files and directories currently installed.) 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Kernel reported to sbuild: 4.4.0-142-generic #168-Ubuntu SMP Wed Jan 16 21:00:53 UTC 2019 aarch64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-042.buildd +==============================================================================+ | t-coffee 11.00.8cbe486-6 (arm64) 20 Feb 2019 08:47 | +==============================================================================+ Package: t-coffee Version: 11.00.8cbe486-6 Source Version: 11.00.8cbe486-6 Distribution: bionic Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 I: NOTICE: Log filtering will replace 'build/t-coffee-XQc_Xm/t-coffee-11.00.8cbe486' with '<>' I: NOTICE: Log filtering will replace 'build/t-coffee-XQc_Xm' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-16089555/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- t-coffee_11.00.8cbe486-6.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-4zeC8L/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-4zeC8L/apt_archive ./ InRelease Get:2 copy:/<>/resolver-4zeC8L/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-4zeC8L/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-4zeC8L/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-4zeC8L/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (97.9 kB/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-4zeC8L/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 ... 12597 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 10) Filtered Build-Depends: debhelper (>= 10) dpkg-deb: building package 'sbuild-build-depends-t-coffee-dummy' in '/<>/resolver-kvORGq/apt_archive/sbuild-build-depends-t-coffee-dummy.deb'. Ign:1 copy:/<>/resolver-kvORGq/apt_archive ./ InRelease Get:2 copy:/<>/resolver-kvORGq/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-kvORGq/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-kvORGq/apt_archive ./ Sources [209 B] Get:5 copy:/<>/resolver-kvORGq/apt_archive ./ Packages [527 B] Fetched 2855 B in 0s (71.4 kB/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 libbsd0 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libicu60 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 libbsd0 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libicu60 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf sbuild-build-depends-t-coffee-dummy 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 16.1 MB of archives. After this operation, 61.8 MB of additional disk space will be used. Get:1 copy:/<>/resolver-kvORGq/apt_archive ./ sbuild-build-depends-t-coffee-dummy 0.invalid.0 [856 B] Get:2 http://ftpmaster.internal/ubuntu bionic/main arm64 libbsd0 arm64 0.8.7-1 [36.4 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main arm64 bsdmainutils arm64 11.1.2ubuntu1 [175 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main arm64 groff-base arm64 1.22.3-10 [1152 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main arm64 libpipeline1 arm64 1.5.0-1 [22.0 kB] Get:6 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 man-db arm64 2.8.3-2ubuntu0.1 [993 kB] Get:7 http://ftpmaster.internal/ubuntu bionic-security/main arm64 libmagic-mgc arm64 1:5.32-2ubuntu0.1 [184 kB] Get:8 http://ftpmaster.internal/ubuntu bionic-security/main arm64 libmagic1 arm64 1:5.32-2ubuntu0.1 [61.9 kB] Get:9 http://ftpmaster.internal/ubuntu bionic-security/main arm64 file arm64 1:5.32-2ubuntu0.1 [21.8 kB] Get:10 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 libglib2.0-0 arm64 2.56.3-0ubuntu0.18.04.1 [982 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/main arm64 libicu60 arm64 60.2-3ubuntu3 [7985 kB] Get:12 http://ftpmaster.internal/ubuntu bionic-security/main arm64 libxml2 arm64 2.9.4+dfsg1-6.1ubuntu1.2 [548 kB] Get:13 http://ftpmaster.internal/ubuntu bionic-security/main arm64 gettext-base arm64 0.19.8.1-6ubuntu0.1 [46.7 kB] Get:14 http://ftpmaster.internal/ubuntu bionic/main arm64 libsigsegv2 arm64 2.12-1 [14.1 kB] Get:15 http://ftpmaster.internal/ubuntu bionic/main arm64 m4 arm64 1.4.18-1 [185 kB] Get:16 http://ftpmaster.internal/ubuntu bionic/main arm64 autoconf all 2.69-11 [322 kB] Get:17 http://ftpmaster.internal/ubuntu bionic/main arm64 autotools-dev all 20180224.1 [39.6 kB] Get:18 http://ftpmaster.internal/ubuntu bionic/main arm64 automake all 1:1.15.1-3ubuntu2 [509 kB] Get:19 http://ftpmaster.internal/ubuntu bionic-security/main arm64 autopoint all 0.19.8.1-6ubuntu0.1 [412 kB] Get:20 http://ftpmaster.internal/ubuntu bionic/main arm64 libtool all 2.4.6-2 [194 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main arm64 dh-autoreconf all 17 [15.8 kB] Get:22 http://ftpmaster.internal/ubuntu bionic-security/main arm64 libarchive-zip-perl all 1.60-1ubuntu0.1 [84.6 kB] Get:23 http://ftpmaster.internal/ubuntu bionic/main arm64 libfile-stripnondeterminism-perl all 0.040-1.1~build1 [13.8 kB] Get:24 http://ftpmaster.internal/ubuntu bionic/main arm64 libtimedate-perl all 2.3000-2 [37.5 kB] Get:25 http://ftpmaster.internal/ubuntu bionic/main arm64 dh-strip-nondeterminism all 0.040-1.1~build1 [5208 B] Get:26 http://ftpmaster.internal/ubuntu bionic/main arm64 libcroco3 arm64 0.6.12-2 [68.2 kB] Get:27 http://ftpmaster.internal/ubuntu bionic-security/main arm64 gettext arm64 0.19.8.1-6ubuntu0.1 [824 kB] Get:28 http://ftpmaster.internal/ubuntu bionic/main arm64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:29 http://ftpmaster.internal/ubuntu bionic/main arm64 po-debconf all 1.0.20 [232 kB] Get:30 http://ftpmaster.internal/ubuntu bionic-updates/main arm64 debhelper all 11.1.6ubuntu2 [902 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 16.1 MB in 1s (27.8 MB/s) Selecting previously unselected package libbsd0:arm64. (Reading database ... 12597 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.8.7-1_arm64.deb ... Unpacking libbsd0:arm64 (0.8.7-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2ubuntu1_arm64.deb ... Unpacking bsdmainutils (11.1.2ubuntu1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.3-10_arm64.deb ... Unpacking groff-base (1.22.3-10) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../03-libpipeline1_1.5.0-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.0-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.8.3-2ubuntu0.1_arm64.deb ... Unpacking man-db (2.8.3-2ubuntu0.1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.32-2ubuntu0.1_arm64.deb ... Unpacking libmagic-mgc (1:5.32-2ubuntu0.1) ... 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Selecting previously unselected package sbuild-build-depends-t-coffee-dummy. Preparing to unpack .../29-sbuild-build-depends-t-coffee-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-t-coffee-dummy (0.invalid.0) ... Setting up libicu60:arm64 (60.2-3ubuntu3) ... Setting up libarchive-zip-perl (1.60-1ubuntu0.1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:arm64 (2.12-1) ... Setting up groff-base (1.22.3-10) ... Setting up libglib2.0-0:arm64 (2.56.3-0ubuntu0.18.04.1) ... No schema files found: doing nothing. Setting up gettext-base (0.19.8.1-6ubuntu0.1) ... Setting up libpipeline1:arm64 (1.5.0-1) ... Setting up m4 (1.4.18-1) ... Setting up libbsd0:arm64 (0.8.7-1) ... Setting up libxml2:arm64 (2.9.4+dfsg1-6.1ubuntu1.2) ... Setting up libmagic-mgc (1:5.32-2ubuntu0.1) ... Setting up libmagic1:arm64 (1:5.32-2ubuntu0.1) ... Setting up libcroco3:arm64 (0.6.12-2) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... Setting up autotools-dev (20180224.1) ... Setting up bsdmainutils (11.1.2ubuntu1) ... 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 (0.19.8.1-6ubuntu0.1) ... Setting up libfile-stripnondeterminism-perl (0.040-1.1~build1) ... Setting up gettext (0.19.8.1-6ubuntu0.1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.32-2ubuntu0.1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15.1-3ubuntu2) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.8.3-2ubuntu0.1) ... Not building database; man-db/auto-update is not 'true'. Setting up libtool (2.4.6-2) ... Setting up po-debconf (1.0.20) ... Setting up dh-autoreconf (17) ... Setting up dh-strip-nondeterminism (0.040-1.1~build1) ... Setting up debhelper (11.1.6ubuntu2) ... Setting up sbuild-build-depends-t-coffee-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-142-generic arm64 (aarch64) Toolchain package versions: binutils_2.30-21ubuntu1~18.04 dpkg-dev_1.19.0.5ubuntu2.1 g++-7_7.3.0-27ubuntu1~18.04 gcc-7_7.3.0-27ubuntu1~18.04 libc6-dev_2.27-3ubuntu1 libstdc++-7-dev_7.3.0-27ubuntu1~18.04 libstdc++6_8.2.0-1ubuntu2~18.04 linux-libc-dev_4.15.0-45.48 Package versions: adduser_3.116ubuntu1 advancecomp_2.1-1 apt_1.6.8 autoconf_2.69-11 automake_1:1.15.1-3ubuntu2 autopoint_0.19.8.1-6ubuntu0.1 autotools-dev_20180224.1 base-files_10.1ubuntu2.4 base-passwd_3.5.44 bash_4.4.18-2ubuntu1 binutils_2.30-21ubuntu1~18.04 binutils-aarch64-linux-gnu_2.30-21ubuntu1~18.04 binutils-common_2.30-21ubuntu1~18.04 bsdmainutils_11.1.2ubuntu1 bsdutils_1:2.31.1-0.4ubuntu3.3 build-essential_12.4ubuntu1 bzip2_1.0.6-8.1 ca-certificates_20180409 coreutils_8.28-1ubuntu1 cpp_4:7.3.0-3ubuntu2.1 cpp-7_7.3.0-27ubuntu1~18.04 dash_0.5.8-2.10 debconf_1.5.66 debhelper_11.1.6ubuntu2 debianutils_4.8.4 dh-autoreconf_17 dh-strip-nondeterminism_0.040-1.1~build1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu3 dpkg_1.19.0.5ubuntu2.1 dpkg-dev_1.19.0.5ubuntu2.1 e2fslibs_1.44.1-1ubuntu1.1 e2fsprogs_1.44.1-1ubuntu1.1 fakeroot_1.22-2ubuntu1 fdisk_2.31.1-0.4ubuntu3.3 file_1:5.32-2ubuntu0.1 findutils_4.6.0+git+20170828-2 g++_4:7.3.0-3ubuntu2.1 g++-7_7.3.0-27ubuntu1~18.04 gcc_4:7.3.0-3ubuntu2.1 gcc-7_7.3.0-27ubuntu1~18.04 gcc-7-base_7.3.0-27ubuntu1~18.04 gcc-8-base_8.2.0-1ubuntu2~18.04 gettext_0.19.8.1-6ubuntu0.1 gettext-base_0.19.8.1-6ubuntu0.1 gpg_2.2.4-1ubuntu1.2 gpg-agent_2.2.4-1ubuntu1.2 gpgconf_2.2.4-1ubuntu1.2 gpgv_2.2.4-1ubuntu1.2 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5ubuntu1 hostname_3.20 init_1.51 init-system-helpers_1.51 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.12-4ubuntu5.1 libapt-pkg5.0_1.6.8 libarchive-zip-perl_1.60-1ubuntu0.1 libargon2-0_0~20161029-1.1 libasan4_7.3.0-27ubuntu1~18.04 libassuan0_2.5.1-2 libatomic1_8.2.0-1ubuntu2~18.04 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.2-1ubuntu1 libaudit1_1:2.8.2-1ubuntu1 libbinutils_2.30-21ubuntu1~18.04 libblkid1_2.31.1-0.4ubuntu3.3 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3ubuntu1 libc-dev-bin_2.27-3ubuntu1 libc6_2.27-3ubuntu1 libc6-dev_2.27-3ubuntu1 libcap-ng0_0.7.7-3.1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-1ubuntu2~18.04 libcom-err2_1.44.1-1ubuntu1.1 libcomerr2_1.44.1-1ubuntu1.1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1ubuntu1.1 libdb5.3_5.3.28-13.1ubuntu1 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu3 libdpkg-perl_1.19.0.5ubuntu2.1 libext2fs2_1.44.1-1ubuntu1.1 libfakeroot_1.22-2ubuntu1 libfdisk1_2.31.1-0.4ubuntu3.3 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.040-1.1~build1 libgcc-7-dev_7.3.0-27ubuntu1~18.04 libgcc1_1:8.2.0-1ubuntu2~18.04 libgcrypt20_1.8.1-4ubuntu1.1 libgdbm-compat4_1.14.1-6 libgdbm5_1.14.1-6 libglib2.0-0_2.56.3-0ubuntu0.18.04.1 libgmp10_2:6.1.2+dfsg-2 libgnutls30_3.5.18-1ubuntu1 libgomp1_8.2.0-1ubuntu2~18.04 libgpg-error0_1.27-6 libhogweed4_3.4-1 libicu60_60.2-3ubuntu3 libidn11_1.33-2.1ubuntu1 libidn2-0_2.0.4-1.1build2 libip4tc0_1.6.1-2ubuntu2 libisl19_0.19-1 libitm1_8.2.0-1ubuntu2~18.04 libjson-c3_0.12.1-1.3 libkmod2_24-1ubuntu3.2 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblsan0_8.2.0-1ubuntu2~18.04 liblz4-1_0.0~r131-2ubuntu3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-2ubuntu0.1 libmagic1_1:5.32-2ubuntu0.1 libmount1_2.31.1-0.4ubuntu3.3 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1-1ubuntu1.18.04 libncursesw5_6.1-1ubuntu1.18.04 libnettle6_3.4-1 libnpth0_1.5-3 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.6ubuntu2 libpam-modules-bin_1.1.8-3.6ubuntu2 libpam-runtime_1.1.8-3.6ubuntu2 libpam0g_1.1.8-3.6ubuntu2 libpcre3_2:8.39-9 libperl5.26_5.26.1-6ubuntu0.3 libpipeline1_1.5.0-1 libpng16-16_1.6.34-1ubuntu0.18.04.1 libprocps6_2:3.3.12-3ubuntu1.1 libreadline7_7.0-3 libseccomp2_2.3.1-2.1ubuntu4 libselinux1_2.7-2build2 libsemanage-common_2.7-2build2 libsemanage1_2.7-2build2 libsepol1_2.7-1 libsigsegv2_2.12-1 libslang2_2.3.1a-3ubuntu1 libsmartcols1_2.31.1-0.4ubuntu3.3 libsqlite3-0_3.22.0-1 libss2_1.44.1-1ubuntu1.1 libssl1.1_1.1.0g-2ubuntu4.3 libstdc++-7-dev_7.3.0-27ubuntu1~18.04 libstdc++6_8.2.0-1ubuntu2~18.04 libsystemd0_237-3ubuntu10.13 libtasn1-6_4.13-2 libtimedate-perl_2.3000-2 libtinfo5_6.1-1ubuntu1.18.04 libtool_2.4.6-2 libtsan0_8.2.0-1ubuntu2~18.04 libubsan0_7.3.0-27ubuntu1~18.04 libudev1_237-3ubuntu10.13 libunistring2_0.9.9-0ubuntu1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.31.1-0.4ubuntu3.3 libxml2_2.9.4+dfsg1-6.1ubuntu1.2 libzstd1_1.3.3+dfsg-2ubuntu1 linux-libc-dev_4.15.0-45.48 lockfile-progs_0.1.17build1 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-1 make_4.1-9.1ubuntu1 man-db_2.8.3-2ubuntu0.1 mawk_1.3.3-17ubuntu3 mount_2.31.1-0.4ubuntu3.3 multiarch-support_2.27-3ubuntu1 ncurses-base_6.1-1ubuntu1.18.04 ncurses-bin_6.1-1ubuntu1.18.04 openssl_1.1.0g-2ubuntu4.3 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-2ubuntu1 perl_5.26.1-6ubuntu0.3 perl-base_5.26.1-6ubuntu0.3 perl-modules-5.26_5.26.1-6ubuntu0.3 pinentry-curses_1.1.0-1 pkgbinarymangler_138.18.04.0 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-3ubuntu1.1 readline-common_7.0-3 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 systemd_237-3ubuntu10.13 systemd-sysv_237-3ubuntu10.13 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 tar_1.29b-2ubuntu0.1 tzdata_2018i-0ubuntu0.18.04 ubuntu-keyring_2018.09.18.1~18.04.0 util-linux_2.31.1-0.4ubuntu3.3 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- 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 t-coffee-11.00.8cbe486 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 disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-16089555 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-16089555 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-16089555 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 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-source --before-build t-coffee-11.00.8cbe486 dpkg-buildpackage: info: host architecture arm64 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 -j4 -O -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/CUSTOM_evaluate_for_struc.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dev_lib/dev1.c dev_lib/dev1.c: In function ‘void aln2hitMat(Alignment*, char*)’: dev_lib/dev1.c:89:43: warning: too many arguments for format [-Wformat-extra-args] fprintf (stdout, "Process positions\n", i); ^ make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/evaluate_for_domain.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/evaluate_dirichlet.c dp_lib/evaluate_dirichlet.c: In function ‘Mixture* read_dirichlet(char*)’: dp_lib/evaluate_dirichlet.c:317:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%f\n", &f); ~~~~~~^~~~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:319:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%f", &f); ~~~~~~^~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:323:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%f", &f); ~~~~~~^~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:326:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "\n"); ~~~~~~^~~~~~~~~~ make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/evaluate_for_struc.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/showpair.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/fsa_dp.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/pavie_dp.c dp_lib/pavie_dp.c: In function ‘double** pavie_seq2pavie_aln(Sequence*, char*, char*)’: dp_lib/pavie_dp.c:127:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s\n",mat_list[nch++]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/pavie_dp.c: In function ‘char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)’: dp_lib/pavie_dp.c:1079:15: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system (command); ~~~~~~~~^~~~~~~~~ dp_lib/pavie_dp.c:1081:14: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system (command); ~~~~~~~^~~~~~~~~ dp_lib/pavie_dp.c: In function ‘Alignment* pavie_seq2pavie_msa(Sequence*, char*, char*)’: dp_lib/pavie_dp.c:1365:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s", mat); ~~~~~~~^~~~~~~~~~~~~~~ make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_domain_dp.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_domain_dp_drivers.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_cdna_fasta_nw.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_clean_maln.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_est.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_fasta_sw.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_generic_fasta_nw.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_fasta_nw.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/evaluate.c dp_lib/evaluate.c: In function ‘Alignment* fork_triplet_coffee_evaluate_output(Alignment*, Constraint_list*, int)’: dp_lib/evaluate.c:808:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d ", &res); ~~~~~~~^~~~~~~~~~~~~~~~~ dp_lib/evaluate.c:813:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%f %f", &sseq, &mseq); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate.c:818:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%f %f", &sseq, &mseq); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate.c: In function ‘float** initialise_aa_physico_chemical_property_table(int*)’: dp_lib/evaluate.c:5644:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%f %c %*s",&v1, &c1 ); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_mm_nw.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_gotoh_sw.c dp_lib/util_dp_gotoh_sw.c: In function ‘int gotoh_pair_wise_sw(Alignment*, int*, int**, Constraint_list*)’: dp_lib/util_dp_gotoh_sw.c:391:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread ( &k, sizeof (TRACE_TYPE), 1, long_trace); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_ssec_pwaln.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_gotoh_nw.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_sim.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_graph_maln.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC fastal/diagonal.c fastal/diagonal.c: In function ‘int seq_pair2blast_diagonal2(char*, char*, Diagonal**, int*, int, int, int)’: fastal/diagonal.c:434:8: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ~~~~~~^~~~~~~~~~~~~~~ fastal/diagonal.c:439:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/diagonal.c:440:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/diagonal.c:441:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_drivers.c dp_lib/util_dp_drivers.c: In function ‘Constraint_list* align_pdb_pair_2(char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:968:10: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* align_pdb_pair(char*, char*, char*, char*, Constraint_list*, Job_TC*)’: dp_lib/util_dp_drivers.c:996:10: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* hh_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1037:8: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1048:9: warning: ignoring return value of ‘char* tmpnam(char*)’, declared with attribute warn_unused_result [-Wunused-result] tmpnam(aln1); ~~~~~~^~~~~~ dp_lib/util_dp_drivers.c:1049:9: warning: ignoring return value of ‘char* tmpnam(char*)’, declared with attribute warn_unused_result [-Wunused-result] tmpnam(aln2); ~~~~~~^~~~~~ dp_lib/util_dp_drivers.c:1052:9: warning: ignoring return value of ‘char* tmpnam(char*)’, declared with attribute warn_unused_result [-Wunused-result] tmpnam(hhfile); ~~~~~~^~~~~~~~ dp_lib/util_dp_drivers.c:1099:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets (buf2, 10000, fp); ~~~~~~^~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* profile_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1253:6: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* pdbid_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1388:8: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* pdb_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1445:8: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* thread_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1577:8: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* lsqman_pair(char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1652:8: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* sap_pair(char*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1744:10: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1792:10: warning: ignoring return value of ‘char* getcwd(char*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] getcwd (cdir, sizeof(char)*1000); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1793:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (get_cache_dir()); ~~~~~~^~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1813:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~^~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* rnapdb_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1927:6: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* method2pw_cl(TC_method*, Constraint_list*)’: dp_lib/util_dp_drivers.c:340:18: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] Constraint_list *method2pw_cl (TC_method *M, Constraint_list *CL) ^~~~~~~~~~~~ In file included from /usr/include/stdio.h:862:0, from dp_lib/util_dp_drivers.c:27: /usr/include/aarch64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 __bos (__s), __fmt, __va_arg_pack ()); ^ dp_lib/util_dp_drivers.c:340:18: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] Constraint_list *method2pw_cl (TC_method *M, Constraint_list *CL) ^~~~~~~~~~~~ In file included from /usr/include/stdio.h:862:0, from dp_lib/util_dp_drivers.c:27: /usr/include/aarch64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 __bos (__s), __fmt, __va_arg_pack ()); ^ dp_lib/util_dp_drivers.c:340:18: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] Constraint_list *method2pw_cl (TC_method *M, Constraint_list *CL) ^~~~~~~~~~~~ In file included from /usr/include/stdio.h:862:0, from dp_lib/util_dp_drivers.c:27: /usr/include/aarch64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 __bos (__s), __fmt, __va_arg_pack ()); ^ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* seq_msa(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1485:19: warning: ‘%s’ directive writing up to 500 bytes into a region of size between 445 and 945 [-Wformat-overflow=] Constraint_list * seq_msa (TC_method *M , char *in_seq, Constraint_list *CL) ^~~~~~~ In file included from /usr/include/stdio.h:862:0, from dp_lib/util_dp_drivers.c:27: /usr/include/aarch64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output 71 or more bytes (assuming 5068) into a destination of size 1000 __bos (__s), __fmt, __va_arg_pack ()); ^ dp_lib/util_dp_drivers.c: In function ‘Alignment* stack_progressive_aln(Alignment*, Constraint_list*, int, int)’: dp_lib/util_dp_drivers.c:3225:12: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] Alignment *stack_progressive_aln(Alignment *A, Constraint_list *CL, int gop, int gep) ^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:862:0, from dp_lib/util_dp_drivers.c:27: /usr/include/aarch64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 __bos (__s), __fmt, __va_arg_pack ()); ^ make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC fastal/fastal_opt_parsing.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC fastal/iteration.c fastal/iteration.c: In function ‘void split_set(FILE*, Fastal_profile*, Fastal_profile*, char*, int, int*, char*)’: fastal/iteration.c:185:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , alignment_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c: In function ‘void iterate(Fastal_param*, void*, char*, char*, int)’: fastal/iteration.c:310:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , alignment_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:435:8: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(command); ~~~~~~^~~~~~~~~ fastal/iteration.c: In function ‘void write_iterated_aln(char*, char*, char*, char*, int*, int, char*, int*, int)’: fastal/iteration.c:501:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(alnline, ALNLINE_LENGTH , old_aln_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:504:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(alnline, ALNLINE_LENGTH , old_aln_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:535:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(alnline, ALNLINE_LENGTH, old_aln_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c: In function ‘void edit2seq_pattern(FILE*, char*, char*)’: fastal/iteration.c:563:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:565:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:567:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:569:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC dp_lib/util_dp_suboptimal_nw.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC fastal/scoring.c fastal/scoring.c: In function ‘double calculate_sum_of_pairs_score_affine(char*, int**, double, double)’: fastal/scoring.c:76:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, alignment_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:78:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, alignment_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:82:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, alignment_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c: In function ‘void compute_ref_alignments(char*, char*, int, int)’: fastal/scoring.c:384:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, seq_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:398:9: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(aln_command); ~~~~~~^~~~~~~~~~~~~ fastal/scoring.c: In function ‘void make_ref_alignment(char*, char*, char*, int)’: fastal/scoring.c:488:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, seq_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:502:8: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(command); ~~~~~~^~~~~~~~~ fastal/scoring.c: In function ‘double agreement_score(char*, char*)’: fastal/scoring.c:583:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, result); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:584:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, result); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:585:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, result); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c: In function ‘int complete_agreement_score(char*, const char*)’: fastal/scoring.c:601:5: warning: ‘%s’ directive writing up to 255 bytes into a region of size 199 [-Wformat-overflow=] int complete_agreement_score(char *aln_file_name, const char *ref_directory) ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:862:0, from fastal/scoring.c:28: /usr/include/aarch64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output 2 or more bytes (assuming 257) into a destination of size 200 __bos (__s), __fmt, __va_arg_pack ()); ^ make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC fastal/tree.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC io_lib/pb_util_read_seq_util.c io_lib/pb_util_read_seq_util.c: In function ‘void getstr(char*, char*)’: io_lib/pb_util_read_seq_util.c:269:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(outstr, 100, stdin); ~~~~~^~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_seq_util.c: In function ‘double getreal(char*, double, double, double)’: io_lib/pb_util_read_seq_util.c:280:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, MAXLINE, stdin); ~~~~~^~~~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_seq_util.c: In function ‘int getint(char*, int, int, int)’: io_lib/pb_util_read_seq_util.c:305:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, MAXLINE, stdin); ~~~~~^~~~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_seq_util.c: In function ‘void do_system()’: io_lib/pb_util_read_seq_util.c:327:9: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(line); ~~~~~~^~~~~~ make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC io_lib/pb_util_read_sequence.c io_lib/pb_util_read_sequence.c: In function ‘void get_clustal_seq(char*, char*, int*, char*, int)’: io_lib/pb_util_read_sequence.c:144:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE+1,fin); /* read the title line...ignore it */ ~~~~~^~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_sequence.c:149:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] for(i=1;i>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC fastal/parttree.c fastal/parttree.c: In function ‘int** make_distance_matrix_sim(FILE*, long int*, int*, int, int**)’: fastal/parttree.c:695:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 500, aln_f); ~~~~~^~~~~~~~~~~~~~~~~~ fastal/parttree.c:701:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 500, aln_f); ~~~~~^~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function ‘void get_table(short int*, FILE*, long int)’: fastal/parttree.c:848:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, tables_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:859:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, tables_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function ‘int euclidean_dist(FILE*, long int, long int, short int*, short int*, int)’: fastal/parttree.c:891:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:903:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:906:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:912:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function ‘int euclidean_dist_half(FILE*, long int, short int*, short int*, int)’: fastal/parttree.c:951:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:962:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, ktup_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC km_coffee/Stack.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC fastal/fastal.c fastal/fastal.c: In function ‘int seq_pair2blast_diagonal(char*, char*, int**, int*, int, int, int)’: fastal/fastal.c:1924:8: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c:1929:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1930:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1931:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1976:9: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c:1980:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1981:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1982:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 300, diag_f); ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function ‘int seq_pair2blat_diagonal(char*, char*, int**, int*, int, int, int)’: fastal/fastal.c:2115:8: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c: In function ‘int seq_pair2blastz_diagonal(char*, char*, int**, int*, int, int, int)’: fastal/fastal.c:2262:8: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c: In function ‘void file_pos2profile(FILE*, long int, Fastal_profile*, int, Fastal_param*)’: fastal/fastal.c:3201:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets (line, LINE_LENGTH , seq_file); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function ‘void profile_file2profile(Fastal_profile*, FILE*, long int, Fastal_param*)’: fastal/fastal.c:3323:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3326:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3329:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3331:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3333:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, profile_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3352:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , profile_f); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function ‘void edit_seq2aligned_seq(char*, FILE*, long int, FILE*)’: fastal/fastal.c:3502:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets (line, LINE_LENGTH , sequence_file); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function ‘void edit2alignment(FILE*, long int*, FILE*, long int*, int, int, char*, int, FILE*, int, FILE*)’: fastal/fastal.c:3575:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3577:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3579:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3581:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3643:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(aligned_sequence, alignment_length+3, edit_seq_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC km_coffee/classes.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC km_coffee/Vector.c km_coffee/Vector.c: In function ‘void print_vecs(VectorSet*, char*)’: km_coffee/Vector.c:869:26: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=] fprintf(out_F, "%i ", i); ^ make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC km_coffee/km_coffee.c km_coffee/km_coffee.c: In function ‘int km_coffee_align3(char*, int, int, char*, char*, int, int, int, char*)’: km_coffee/km_coffee.c:491:7: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir(km_tmp_dir); ~~~~~^~~~~~~~~~~~ make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC km_coffee/km_util.c km_coffee/km_util.c: In function ‘char* my_make_temp_dir(char*, char*)’: km_coffee/km_util.c:96:70: warning: format ‘%s’ expects a matching ‘char*’ argument [-Wformat=] fprintf(stderr, "This error was caused by '%s' in '%s'\n", function); ^ make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC io_lib/io_func.c io_lib/io_func.c: In function ‘int output_raw_score(Alignment*, Alignment*, char*)’: io_lib/io_func.c:1235:17: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] if (!A)return NULL; ^~~~ io_lib/io_func.c: In function ‘int** read_matrice(char*)’: io_lib/io_func.c:511:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "\n"); ~~~~~~~^~~~~~~~~~~ io_lib/io_func.c: In function ‘void get_rgb_values(int, Color*)’: io_lib/io_func.c:971:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s %f %f %f", html_code[classC], &ps_code[classC][0], &ps_code[classC][1],&ps_code[classC][2]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC km_coffee/kmeans.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/aln_compare.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/hsearch.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/random.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC io_lib/tree_util.c io_lib/tree_util.c: In function ‘tnode* tree_scan(Alignment*, NT_node, char*, char*)’: io_lib/tree_util.c:836:43: warning: too many arguments for format [-Wformat-extra-args] fprintf (stdout, "Process positions\n", i); ^ io_lib/tree_util.c: In function ‘FILE* create_tree(NT_node, NT_node, int*, int*, int*, tnode***, FILE*)’: io_lib/tree_util.c:2803:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%f",&dist); ~~~~~~^~~~~~~~~~~~~~~ io_lib/tree_util.c:2811:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%f",&bootstrap); ~~~~~~^~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/reformat_struc.c util_lib/reformat_struc.c: In function ‘Ca_trace* simple_read_ca_trace(char*)’: util_lib/reformat_struc.c:326:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%*s" ); ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:328:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%*s" ); ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:334:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%*s %*s %c %*c %d %*f %*f %*f\n",&res,&res_num); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat_struc.c:361:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%*s" ); ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:363:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%*s" ); ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:372:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-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); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC t_coffee_lib/t_coffee.c t_coffee_lib/t_coffee.c: In function ‘int batch_main(int, char**)’: t_coffee_lib/t_coffee.c:3956:14: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system (command); ~~~~~~~^~~~~~~~~ t_coffee_lib/t_coffee.c:3970:14: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system (command); ~~~~~~~^~~~~~~~~ t_coffee_lib/t_coffee.c:3984:14: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system (command); ~~~~~~~^~~~~~~~~ make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/util_aln_analyze.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/util_analyse_constraints_list.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/aln_convertion_util.c util_lib/aln_convertion_util.c: In function ‘Alignment* extract_aln3(Alignment*, char*)’: util_lib/aln_convertion_util.c:7269:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets ( line, VERY_LONG_STRING,fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7288:31: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] if ( c=='#' || c=='!')fgets ( line, VERY_LONG_STRING,fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7292:13: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets ( line, VERY_LONG_STRING,fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c: In function ‘int handle_X_template_files(X_template*, char*)’: util_lib/aln_convertion_util.c:5657:5: warning: ‘%s’ directive writing up to 500 bytes into a region of size 91 [-Wformat-overflow=] int handle_X_template_files ( X_template *T, char *mode) ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:862:0, from util_lib/aln_convertion_util.c:27: /usr/include/aarch64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output between 10 and 510 bytes into a destination of size 100 __bos (__s), __fmt, __va_arg_pack ()); ^ make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/reformat.c util_lib/reformat.c: In function ‘void modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)’: util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:10953:35: note: in expansion of macro ‘ATOI_ACTION’ (D1->A)=aln2bootstrap (D1->A, ATOI_ACTION (1)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:10958:32: note: in expansion of macro ‘ATOI_ACTION’ (D1->A)=aln2sample (D1->A, ATOI_ACTION (1)); ^~~~~~~~~~~ util_lib/reformat.c:11157:36: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(2))D=atof (ACTION(2)); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11183:38: note: in expansion of macro ‘ATOI_ACTION’ else TS=treelist2sub_seq((D1->S),ATOI_ACTION(1)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11282:38: note: in expansion of macro ‘ATOI_ACTION’ else TS=treelist2sub_seq((D1->S),ATOI_ACTION(2)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11283:34: note: in expansion of macro ‘ATOI_ACTION’ treelist2lti (D1->S,TS, (int)ATOI_ACTION(1), stdout ); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11290:38: note: in expansion of macro ‘ATOI_ACTION’ else TS=treelist2sub_seq((D1->S),ATOI_ACTION(1)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11297:35: note: in expansion of macro ‘ATOI_ACTION’ D1->S=treelist2sub_seq (D1->S,ATOI_ACTION(1)); ^~~~~~~~~~~ util_lib/reformat.c:11325:27: warning: null argument where non-null required (argument 1) [-Wnonnull] ng=atoi(ACTION (2))+1; ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11444:44: note: in expansion of macro ‘ATOI_ACTION’ D1->T= aln2km_tree(D1->A, (ACTION(1)), ATOI_ACTION(2)); ^~~~~~~~~~~ util_lib/reformat.c:11530:47: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+1))max=atof(ACTION(na+1)); ^ util_lib/reformat.c:11531:47: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+2))enb=atoi(ACTION(na+2)); ^ util_lib/reformat.c:11539:47: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+1))max=atof(ACTION(na+1)); ^ util_lib/reformat.c:11540:47: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+2))enb=atoi(ACTION(na+2)); ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:11669:37: note: in expansion of macro ‘ATOI_ACTION’ D1->A=aln2conservation ( D1->A, ATOI_ACTION (1), ACTION (2)); ^~~~~~~~~~~ util_lib/reformat.c:12301:36: warning: null argument where non-null required (argument 1) [-Wnonnull] else if (strstr (ACTION(1), "h")) ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12308:10: note: in expansion of macro ‘ATOI_ACTION’ F->t=ATOI_ACTION(2); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12309:10: note: in expansion of macro ‘ATOI_ACTION’ F->f=ATOI_ACTION(3); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12310:11: note: in expansion of macro ‘ATOI_ACTION’ F->p1=ATOI_ACTION(4); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12311:11: note: in expansion of macro ‘ATOI_ACTION’ F->p2=ATOI_ACTION(5); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12312:11: note: in expansion of macro ‘ATOI_ACTION’ F->p3=ATOI_ACTION(6); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12313:11: note: in expansion of macro ‘ATOI_ACTION’ F->p3=ATOI_ACTION(7); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12336:34: note: in expansion of macro ‘ATOI_ACTION’ D1->A=unalign_aln (D1->A,SA, ATOI_ACTION(1)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12476:10: note: in expansion of macro ‘ATOI_ACTION’ if (!ATOI_ACTION(1))myexit(fprintf_error (stderr,"-kmeans ")); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12477:19: note: in expansion of macro ‘ATOI_ACTION’ km_seq (D1->A,ATOI_ACTION (1),ACTION(2),ACTION(3)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12481:27: note: in expansion of macro ‘ATOI_ACTION’ D1->A=gap_trim (D1->A,ATOI_ACTION(1)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:12488:34: note: in expansion of macro ‘ATOI_ACTION’ D1->A=trim_RNA(D1->A, D2->S, ATOI_ACTION(1)); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:13008:7: note: in expansion of macro ‘ATOI_ACTION’ t=ATOI_ACTION(1); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:13009:7: note: in expansion of macro ‘ATOI_ACTION’ f=ATOI_ACTION(2); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:13010:8: note: in expansion of macro ‘ATOI_ACTION’ p1=ATOI_ACTION(3); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:13011:8: note: in expansion of macro ‘ATOI_ACTION’ p2=ATOI_ACTION(4); ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ util_lib/reformat.c:13012:8: note: in expansion of macro ‘ATOI_ACTION’ p3=ATOI_ACTION(5); ^~~~~~~~~~~ util_lib/reformat.c: In function ‘int is_pdb_name(char*)’: util_lib/reformat.c:1502:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%d", &result); ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘char* get_pdb_id(char*)’: util_lib/reformat.c:1540:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "\n%s\n", buf); ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int format_is_msf(char*)’: util_lib/reformat.c:2092:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp , "%s", buf); ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Weights* get_amps_sd_scores(char*)’: util_lib/reformat.c:3590:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", buf2); ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3597:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", buf2); ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3606:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", buf2); ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3612:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s",W->seq_name[a]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:3614:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", buf2); ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3625:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "\n"); ~~~~~~~^~~~~~~~~~~ util_lib/reformat.c: In function ‘Structure* read_rna_struc_number(Alignment*, char*)’: util_lib/reformat.c:3898:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%c\n%d\n",&x, &(ST)->tot_list); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:3901:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-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: In function ‘Sequence* get_struc_gor(char*)’: util_lib/reformat.c:4098:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s %d", name, &len); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4119:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s %d\n",S->name[S->nseq], &(S->len[S->nseq])); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4124:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, " %*c %c %*f %*f %*f\n",&(S->seq[S->nseq][a])); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Sequence* get_sequence_dali(char*)’: util_lib/reformat.c:4161:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s",name); ~~~~~~~^~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Sequence* get_dialign_sequence(char*)’: util_lib/reformat.c:4236:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] {fscanf (fp, "%s",name); ~~~~~~~^~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Sequence* get_swissprot_sequence(char*, char*)’: util_lib/reformat.c:5281:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets (buf, LONG_STRING, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:5300:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets (buf, LONG_STRING, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int fscanf_seq_name(FILE*, char*)’: util_lib/reformat.c:5319:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s", name); ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int get_amps_seq_name(char**, char*)’: util_lib/reformat.c:5672:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] {fscanf (fp, "%*d >%s", name[nseq++]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Alignment* read_gotoh_aln(char*, Alignment*)’: util_lib/reformat.c:5721:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(buf, VERY_LONG_STRING, fp); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:5743:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(buf, VERY_LONG_STRING, fp); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘float output_maln_pval(char*, Alignment*)’: util_lib/reformat.c:5941:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s",string); ~~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Alignment* similarities_file2aln(char*)’: util_lib/reformat.c:6106:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s %d", name,&i); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int** read_blast_matrix(char*)’: util_lib/reformat.c:13557:13: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s ", buf); ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:13570:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%d ", &value); ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:13595:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "\n"); ~~~~~~^~~~~~~~~~ util_lib/reformat.c: In function ‘int** read_blast_matrix_old(char*)’: util_lib/reformat.c:13620:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets ( sbuf, VERY_LONG_STRING, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:13637:13: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s ", buf); ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:13650:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%d ", &value); ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:13677:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "\n"); ~~~~~~^~~~~~~~~~ util_lib/reformat.c: In function ‘int** read_pavie_matrix(char*)’: util_lib/reformat.c:13788:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets ( sbuf, VERY_LONG_STRING, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/util.c util_lib/util.c: In function ‘FILE* hsort_file(FILE*, int, int, size_t, int, int, int (*)(const void*, const void*, int, int, size_t), void* (*)(void*, void*, size_t))’: util_lib/util.c:281:11: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread( rra, size, len,fp); /*rra=ra[--l]*/ ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c:286:11: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread( rra, size, len,fp); /*rra=ra[ir]*/ ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c:289:11: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread( rrb, size, len,fp); /*rrb=ra[0]*/ ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c:306:15: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (ra_j, size, len, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:311:11: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (ra_j_1, size, len, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘void* bsearch_file(const void*, int*, int, int, FILE*, int, int, size_t, int (*)(const void*, const void*, int, int, size_t))’: util_lib/util.c:420:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread ( key2, el_size, entry_len,fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘FILE* get_number_list_in_file(FILE*, int*, int*, int*)’: util_lib/util.c:847:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%d",&list[n[0]++]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int quantile(int, char**)’: util_lib/util.c:906:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s %s\n", s1, s2); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int** input_array_int(char*)’: util_lib/util.c:1262:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d\n", &len); ~~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/util.c:1266:13: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%d ", &len2); ~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/util.c:1269:8: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%d ", &array[a][b]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:1270:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "\n"); ~~~~~~~^~~~~~~~~~ util_lib/util.c: In function ‘int perl_strstr(char*, char*)’: util_lib/util.c:1925:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d", &r); ~~~~~~~^~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* count_strings_in_file(char*, char*)’: util_lib/util.c:5090:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s\n",list[n]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int get_cl_param(int, char**, FILE**, const char*, int*, const char*, int, int, const char*, ...)’: util_lib/util.c:6571:2: warning: second parameter of ‘va_start’ not last named argument [-Wvarargs] va_start (ap, usage); ^~~~~~~~ util_lib/util.c: In function ‘char** get_parameter(char*, int*, char*)’: util_lib/util.c:6838:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets ( line, VERY_LONG_STRING,fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘FILE* set_fp_id(FILE*, char*)’: util_lib/util.c:6858:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s", string); ~~~~~~~^~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int** get_file_block_pattern(char*, int*, int)’: util_lib/util.c:7214:11: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets ( line, lline,fp); ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util.c:7244:11: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets ( line, lline,fp); ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int check_for_update(char*)’: util_lib/util.c:7331:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "Version_%f", &new_version); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/util_domain_constraints_list.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/util_dps.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/util_job_handling.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/util_declare.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/util_make_tree.c make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' CC util_lib/util_constraints_list.c util_lib/util_constraints_list.c: In function ‘Constraint_list* fork_read_n_constraint_list(char**, int, char*, char*, char*, char*, FILE*, Constraint_list*, char*, int)’: util_lib/util_constraints_list.c:2163:81: warning: too many arguments for format [-Wformat-extra-args] fprintf ( local_stderr, "\n\t--- Process Method/Library/Aln %s", fname[a], ns); ^ util_lib/util_constraints_list.c: In function ‘Constraint_list* read_constraint_list_file(Constraint_list*, char*)’: util_lib/util_constraints_list.c:2775:76: warning: too many arguments for format [-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: In function ‘Job_TC* submit_lib_job(Job_TC*)’: util_lib/util_constraints_list.c:577:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (tdir); ~~~~~~^~~~~~ util_lib/util_constraints_list.c:580:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~^~~~~~ util_lib/util_constraints_list.c: In function ‘char* method_file_tag2value(char*, char*)’: util_lib/util_constraints_list.c:1140:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets ( line,LONG_STRING, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘TC_method* method_file2TC_method(char*)’: util_lib/util_constraints_list.c:1182:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets ( line,LONG_STRING, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘int read_cpu_in_list(char*)’: util_lib/util_constraints_list.c:2525:20: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] if ( c=='C')fscanf( fp, "PU %d\n", &cpu); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘int read_seq_in_list(char*, int*, char***, char***, Genomic_info**)’: util_lib/util_constraints_list.c:2833:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d\n", &max_nseq); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2838:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%*s %d %*s\n", &l); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2870:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s %d %s\n", name, &seq_len, sequence); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2895:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets (line , 200 , fp); ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘Constraint_list* nfork_relax_constraint_list_4gp(Constraint_list*)’: util_lib/util_constraints_list.c:3903:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%d ", &CL->residue_index[s][r][a+WE]); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘char* make_aln_command(TC_method*, char*, char*)’: util_lib/util_constraints_list.c:1262:7: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 499 and 999 [-Wformat-overflow=] char *make_aln_command(TC_method *m, char *seq, char *aln) ^~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:862:0, from util_lib/util_constraints_list.c:29: /usr/include/aarch64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output 6 or more bytes (assuming 4503) into a destination of size 1000 __bos (__s), __fmt, __va_arg_pack ()); ^ util_lib/util_constraints_list.c: In function ‘Distance_matrix* seq2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)’: util_lib/util_constraints_list.c:4787:18: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] Distance_matrix *seq2distance_matrix (Constraint_list *CL, Alignment *A,char *mode, char *sim_mode, int print) ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:862:0, from util_lib/util_constraints_list.c:29: /usr/include/aarch64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 __bos (__s), __fmt, __va_arg_pack ()); ^ util_lib/util_constraints_list.c:4787:18: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] Distance_matrix *seq2distance_matrix (Constraint_list *CL, Alignment *A,char *mode, char *sim_mode, int print) ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:862:0, from util_lib/util_constraints_list.c:29: /usr/include/aarch64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 __bos (__s), __fmt, __va_arg_pack ()); ^ util_lib/util_constraints_list.c: In function ‘Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)’: util_lib/util_constraints_list.c:611:9: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] Job_TC* method2job_list ( char *method_name,Sequence *S, char *weight, char *lib_list, Distance_matrix *DM, Constraint_list *CL) ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:862:0, from util_lib/util_constraints_list.c:29: /usr/include/aarch64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 __bos (__s), __fmt, __va_arg_pack ()); ^ util_lib/util_constraints_list.c:611:9: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] Job_TC* method2job_list ( char *method_name,Sequence *S, char *weight, char *lib_list, Distance_matrix *DM, Constraint_list *CL) ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:862:0, from util_lib/util_constraints_list.c:29: /usr/include/aarch64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 __bos (__s), __fmt, __va_arg_pack ()); ^ util_lib/util_constraints_list.c:611:9: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 499 and 999 [-Wformat-overflow=] Job_TC* method2job_list ( char *method_name,Sequence *S, char *weight, char *lib_list, Distance_matrix *DM, Constraint_list *CL) ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:862:0, from util_lib/util_constraints_list.c:29: /usr/include/aarch64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output 6 or more bytes (assuming 4503) into a destination of size 1000 __bos (__s), __fmt, __va_arg_pack ()); ^ util_lib/util_constraints_list.c:611:9: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 499 and 999 [-Wformat-overflow=] Job_TC* method2job_list ( char *method_name,Sequence *S, char *weight, char *lib_list, Distance_matrix *DM, Constraint_list *CL) ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:862:0, from util_lib/util_constraints_list.c:29: /usr/include/aarch64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output 6 or more bytes (assuming 4503) into a destination of size 1000 __bos (__s), __fmt, __va_arg_pack ()); ^ util_lib/util_constraints_list.c:611:9: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 499 and 999 [-Wformat-overflow=] Job_TC* method2job_list ( char *method_name,Sequence *S, char *weight, char *lib_list, Distance_matrix *DM, Constraint_list *CL) ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:862:0, from util_lib/util_constraints_list.c:29: /usr/include/aarch64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output 6 or more bytes (assuming 4503) into a destination of size 1000 __bos (__s), __fmt, __va_arg_pack ()); ^ util_lib/util_constraints_list.c:611:9: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] Job_TC* method2job_list ( char *method_name,Sequence *S, char *weight, char *lib_list, Distance_matrix *DM, Constraint_list *CL) ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:862:0, from util_lib/util_constraints_list.c:29: /usr/include/aarch64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 __bos (__s), __fmt, __va_arg_pack ()); ^ util_lib/util_constraints_list.c:611:9: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] Job_TC* method2job_list ( char *method_name,Sequence *S, char *weight, char *lib_list, Distance_matrix *DM, Constraint_list *CL) ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:862:0, from util_lib/util_constraints_list.c:29: /usr/include/aarch64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 __bos (__s), __fmt, __va_arg_pack ()); ^ util_lib/util_constraints_list.c:611:9: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 499 and 999 [-Wformat-overflow=] Job_TC* method2job_list ( char *method_name,Sequence *S, char *weight, char *lib_list, Distance_matrix *DM, Constraint_list *CL) ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:862:0, from util_lib/util_constraints_list.c:29: /usr/include/aarch64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output 6 or more bytes (assuming 4503) into a destination of size 1000 __bos (__s), __fmt, __va_arg_pack ()); ^ make[2]: Leaving directory '/<>/t_coffee_source' make[2]: Entering directory '/<>/t_coffee_source' Linking... dp_lib/util_dp_drivers.o: In function `hh_pair(TC_method*, char*, Constraint_list*)': ./t_coffee_source/dp_lib/util_dp_drivers.c:1048: warning: the use of `tmpnam' is dangerous, better use `mkstemp' 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_installdocs -a -O--sourcedirectory=t_coffee_source dh_installchangelogs -a -O--sourcedirectory=t_coffee_source debian/rules override_dh_installexamples make[1]: Entering directory '/<>' dh_installexamples mkdir -p /<>/debian/t-coffee/usr/share/doc/t-coffee/examples; cp -aR example/* /<>/debian/t-coffee/usr/share/doc/t-coffee/examples/; make[1]: Leaving directory '/<>' dh_installman -a -O--sourcedirectory=t_coffee_source dh_perl -a -O--sourcedirectory=t_coffee_source dh_link -a -O--sourcedirectory=t_coffee_source dh_strip_nondeterminism -a -O--sourcedirectory=t_coffee_source debian/rules override_dh_compress make[1]: Entering directory '/<>' #Compressing most of the files in examples/ makes them unusable dh_compress -Xt-coffee-examples ( cd debian/t-coffee-examples/ && \ chmod 644 usr/share/doc/t-coffee-examples/changelog.Debian && \ gzip -9 -n usr/share/doc/t-coffee-examples/changelog.Debian ) || true /bin/sh: 1: cd: can't cd to debian/t-coffee-examples/ make[1]: Leaving directory '/<>' dh_fixperms -a -O--sourcedirectory=t_coffee_source dh_missing -a -O--sourcedirectory=t_coffee_source dh_strip -a -O--sourcedirectory=t_coffee_source dh_makeshlibs -a -O--sourcedirectory=t_coffee_source dh_shlibdeps -a -O--sourcedirectory=t_coffee_source dh_installdeb -a -O--sourcedirectory=t_coffee_source dh_gencontrol -a -O--sourcedirectory=t_coffee_source dh_md5sums -a -O--sourcedirectory=t_coffee_source dh_builddeb -a -O--sourcedirectory=t_coffee_source INFO: pkgstriptranslations version 138.18.04.0 pkgstriptranslations: processing t-coffee (in debian/t-coffee); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/t-coffee/DEBIAN/control, package t-coffee, directory debian/t-coffee pkgstripfiles: Truncating usr/share/doc/t-coffee/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package t-coffee ... pkgstripfiles: No PNG files. dpkg-deb: building package 't-coffee' in '../t-coffee_11.00.8cbe486-6_arm64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../t-coffee_11.00.8cbe486-6_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build t-coffee-11.00.8cbe486 dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20190220-0849 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ t-coffee_11.00.8cbe486-6_arm64.changes: --------------------------------------- Format: 1.8 Date: Mon, 28 Aug 2017 15:27:17 +0200 Source: t-coffee Binary: t-coffee t-coffee-examples Architecture: arm64 Version: 11.00.8cbe486-6 Distribution: bionic Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: t-coffee - Multiple Sequence Alignment t-coffee-examples - annotated examples for the use of T-Coffee Closes: 853677 Changes: t-coffee (11.00.8cbe486-6) unstable; urgency=medium . * Standards-Version: 4.1.0 (no changes needed) * Fix some string assignments which fail build with gcc-7 Closes: #853677 * d/rules: do not parse d/changelog Checksums-Sha1: 8af6d98214337f152653ee989490c6bea69e37dc 5081 t-coffee_11.00.8cbe486-6_arm64.buildinfo 3ef21b0b291a7127d0e5fae9676dfd4702d0a221 1840456 t-coffee_11.00.8cbe486-6_arm64.deb Checksums-Sha256: eb0549b36de460b31e2670747dbd5d629959ca5164420cbc6cd71e7eefccb8cd 5081 t-coffee_11.00.8cbe486-6_arm64.buildinfo c7be9a209f85c298c586c3d47cff307b996a161318b2a06ab1ff58ef8c20cc13 1840456 t-coffee_11.00.8cbe486-6_arm64.deb Files: fae3cc0e6d3eeeae0edd1a56abcac97f 5081 science optional t-coffee_11.00.8cbe486-6_arm64.buildinfo 0eb6197f7b1626b0f08e822651009ba7 1840456 science optional t-coffee_11.00.8cbe486-6_arm64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ t-coffee_11.00.8cbe486-6_arm64.deb ---------------------------------- new debian package, version 2.0. size 1840456 bytes: control archive=5788 bytes. 1681 bytes, 30 lines control 16530 bytes, 196 lines md5sums Package: t-coffee Version: 11.00.8cbe486-6 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 3619 Depends: libc6 (>= 2.27), libgcc1 (>= 1:3.0), libstdc++6 (>= 4.1.1) Recommends: amap-align, clustalo, clustalw, dialign-tx, fsa, kalign, libsoap-lite-perl, libxml-simple-perl, mafft, muscle, mustang, ncbi-blast+, poa, prank, probcons, proda, tm-align Suggests: boxshade, seaview, t-coffee-examples Section: science Priority: optional Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html Description: Multiple Sequence Alignment T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can mix sequences and structures. . T-Coffee allows the combination of a collection of multiple/pairwise, global or local alignments into a single model. It can also estimate the level of consistency of each position within the new alignment with the rest of the alignments. See the pre-print for more information . T-Coffee has a special called M-Coffee that makes it possible to combine the output of many multiple sequence alignment packages. In its published version, it uses MUSCLE, PROBCONS, POA, DiAlign-TS, MAFFT, Clustal W, PCMA and T-Coffee. A special version has been made for Debian, DM-Coffee, that uses only free software by replacing Clustal W by Kalign. Using the 8 Methods of M-Coffee can sometimes be a bit heavy. You can use a subset of your favorite methods if you prefer. drwxr-xr-x root/root 0 2017-08-28 13:27 ./ drwxr-xr-x root/root 0 2017-08-28 13:27 ./usr/ drwxr-xr-x root/root 0 2017-08-28 13:27 ./usr/bin/ -rwxr-xr-x root/root 2535648 2017-08-28 13:27 ./usr/bin/t_coffee drwxr-xr-x root/root 0 2017-08-28 13:27 ./usr/share/ drwxr-xr-x root/root 0 2017-08-28 13:27 ./usr/share/doc/ drwxr-xr-x root/root 0 2017-08-28 13:27 ./usr/share/doc/t-coffee/ -rw-r--r-- root/root 1744 2017-08-28 13:27 ./usr/share/doc/t-coffee/README.Debian -rw-r--r-- root/root 261 2017-08-28 13:27 ./usr/share/doc/t-coffee/README.test -rw-r--r-- root/root 1864 2017-08-28 13:27 ./usr/share/doc/t-coffee/changelog.Debian.gz -rw-r--r-- root/root 1432 2017-08-28 13:27 ./usr/share/doc/t-coffee/copyright drwxr-xr-x root/root 0 2017-08-28 13:27 ./usr/share/doc/t-coffee/examples/ -rw-r--r-- root/root 4306 2014-08-12 20:07 ./usr/share/doc/t-coffee/examples/1D4V-1.pdb.gz -rw-r--r-- root/root 6980 2014-08-12 20:07 ./usr/share/doc/t-coffee/examples/1D4V-2.pdb.gz -rw-r--r-- root/root 6897 2014-08-12 20:07 ./usr/share/doc/t-coffee/examples/1D4V-3.pdb.gz -rw-r--r-- root/root 6197 2014-08-12 20:07 ./usr/share/doc/t-coffee/examples/1EXT-1.pdb.gz -rw-r--r-- root/root 6843 2014-08-12 20:07 ./usr/share/doc/t-coffee/examples/1EXT-2.pdb.gz -rw-r--r-- root/root 7091 2014-08-12 20:07 ./usr/share/doc/t-coffee/examples/1EXT-3.pdb.gz -rw-r--r-- root/root 4649 2014-08-12 20:07 ./usr/share/doc/t-coffee/examples/1EXT-4.pdb.gz -rw-r--r-- root/root 5371 2014-08-12 20:07 ./usr/share/doc/t-coffee/examples/1JMA-1.pdb.gz -rw-r--r-- root/root 6619 2014-08-12 20:07 ./usr/share/doc/t-coffee/examples/1JMA-2.pdb.gz -rw-r--r-- root/root 4986 2014-08-12 20:07 ./usr/share/doc/t-coffee/examples/1OQE-1.pdb.gz -rw-r--r-- root/root 5031 2014-08-12 20:07 ./usr/share/doc/t-coffee/examples/1SG1-1.pdb.gz -rw-r--r-- root/root 6468 2014-08-12 20:07 ./usr/share/doc/t-coffee/examples/1SG1-2.pdb.gz -rw-r--r-- root/root 6340 2014-08-12 20:07 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+------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build-Space: 52024 Build-Time: 116 Distribution: bionic Host Architecture: arm64 Install-Time: 22 Job: t-coffee_11.00.8cbe486-6.dsc Machine Architecture: arm64 Package: t-coffee Package-Time: 141 Source-Version: 11.00.8cbe486-6 Space: 52024 Status: successful Version: 11.00.8cbe486-6 -------------------------------------------------------------------------------- Finished at 20190220-0849 Build needed 00:02:21, 52024k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=bionic --arch=arm64 PACKAGEBUILD-16089555 Scanning for processes to kill in build PACKAGEBUILD-16089555