https://launchpad.net/ubuntu/+source/t-coffee/13.41.0.28bdc39+dfsg-4/+build/19472633 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-024 4.4.0-177-generic #207-Ubuntu SMP Mon Mar 16 01:17:51 UTC 2020 aarch64 Buildd toolchain package versions: launchpad-buildd_188 python-lpbuildd_188 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_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.7 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 18 Jun 00:27:10 ntpdate[1945]: adjust time server 10.211.37.1 offset 0.000170 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19472633 --image-type chroot /home/buildd/filecache-default/a77e1afdcf3761e08e999e63510e3d2f5c5a8a8d Creating target for build PACKAGEBUILD-19472633 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19472633 Starting target for build PACKAGEBUILD-19472633 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19472633 'deb http://ftpmaster.internal/ubuntu groovy main universe' 'deb http://ftpmaster.internal/ubuntu groovy-security main universe' 'deb http://ftpmaster.internal/ubuntu groovy-updates main universe' 'deb http://ftpmaster.internal/ubuntu groovy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-19472633 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19472633 Updating target for build PACKAGEBUILD-19472633 Get:1 http://ftpmaster.internal/ubuntu groovy InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu groovy-security InRelease [89.1 kB] Get:3 http://ftpmaster.internal/ubuntu groovy-updates InRelease [89.1 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main armhf Packages [937 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main Translation-en [508 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/universe armhf Packages [8424 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/universe Translation-en [5187 kB] Get:9 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf Packages [73.7 kB] Get:10 http://ftpmaster.internal/ubuntu groovy-proposed/main Translation-en [44.8 kB] Get:11 http://ftpmaster.internal/ubuntu groovy-proposed/universe armhf Packages [793 kB] Get:12 http://ftpmaster.internal/ubuntu groovy-proposed/universe Translation-en [421 kB] Fetched 17.0 MB in 6s (2814 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-arm-linux-gnueabihf binutils-common bsdutils bzip2 ca-certificates cpp-9 dash debconf debianutils dpkg dpkg-dev e2fsprogs fdisk g++-9 gcc-10-base gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv gzip libacl1 libapparmor1 libapt-pkg6.0 libargon2-1 libasan5 libassuan0 libatomic1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libext2fs2 libfdisk1 libgcc-9-dev libgcc-s1 libgmp10 libgnutls30 libgomp1 libgpg-error0 libidn2-0 libjson-c4 libkmod2 libmount1 libncurses6 libncursesw6 libnpth0 libperl5.30 libprocps8 libseccomp2 libsmartcols1 libsqlite3-0 libss2 libstdc++-9-dev libstdc++6 libsystemd0 libtinfo6 libubsan1 libudev1 libunistring2 libuuid1 libzstd1 linux-libc-dev login logsave make mount ncurses-base ncurses-bin passwd perl perl-base perl-modules-5.30 pkgbinarymangler procps systemd systemd-sysv systemd-timesyncd sysvinit-utils tzdata ubuntu-keyring util-linux 101 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 55.9 MB of archives. After this operation, 556 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libcrypt-dev armhf 1:4.4.16-1ubuntu1 [120 kB] Get:2 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libcrypt1 armhf 1:4.4.16-1ubuntu1 [93.4 kB] Get:3 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libc6-dev armhf 2.31-0ubuntu10 [1914 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libc-dev-bin armhf 2.31-0ubuntu10 [63.6 kB] Get:5 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf linux-libc-dev armhf 5.4.0-37.41 [1085 kB] Get:6 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libatomic1 armhf 10.1.0-4ubuntu1 [7208 B] Get:7 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libubsan1 armhf 10.1.0-4ubuntu1 [121 kB] Get:8 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libgomp1 armhf 10.1.0-4ubuntu1 [86.8 kB] Get:9 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf gcc-10-base armhf 10.1.0-4ubuntu1 [20.1 kB] Get:10 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libgcc-s1 armhf 10.1.0-4ubuntu1 [36.1 kB] Get:11 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libcc1-0 armhf 10.1.0-4ubuntu1 [34.6 kB] Get:12 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libstdc++6 armhf 10.1.0-4ubuntu1 [440 kB] Get:13 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libc6 armhf 2.31-0ubuntu10 [2133 kB] Get:14 http://ftpmaster.internal/ubuntu groovy/main armhf base-files armhf 11ubuntu7 [59.7 kB] Get:15 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf bsdutils armhf 1:2.35.1-5ubuntu2 [78.9 kB] Get:16 http://ftpmaster.internal/ubuntu groovy/main armhf debianutils armhf 4.11 [84.3 kB] Get:17 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf dpkg armhf 1.19.7ubuntu4 [1083 kB] Get:18 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf perl-modules-5.30 all 5.30.3-4 [2740 kB] Get:19 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libperl5.30 armhf 5.30.3-4 [3281 kB] Get:20 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf perl armhf 5.30.3-4 [223 kB] Get:21 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf perl-base armhf 5.30.3-4 [1410 kB] Get:22 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf bzip2 armhf 1.0.8-3 [31.8 kB] Get:23 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libbz2-1.0 armhf 1.0.8-3 [31.0 kB] Get:24 http://ftpmaster.internal/ubuntu groovy/main armhf debconf all 1.5.74 [121 kB] Get:25 http://ftpmaster.internal/ubuntu groovy/main armhf dash armhf 0.5.10.2-7 [79.2 kB] Get:26 http://ftpmaster.internal/ubuntu groovy/main armhf gzip armhf 1.10-2ubuntu1 [90.8 kB] Get:27 http://ftpmaster.internal/ubuntu groovy/main armhf login armhf 1:4.8.1-1ubuntu6 [217 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main armhf ncurses-bin armhf 6.2-1 [164 kB] Get:29 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libblkid1 armhf 2.35.1-5ubuntu2 [120 kB] Get:30 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libuuid1 armhf 2.35.1-5ubuntu2 [21.5 kB] Get:31 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libfdisk1 armhf 2.35.1-5ubuntu2 [159 kB] Get:32 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libmount1 armhf 2.35.1-5ubuntu2 [132 kB] Get:33 http://ftpmaster.internal/ubuntu groovy/main armhf libncurses6 armhf 6.2-1 [79.7 kB] Get:34 http://ftpmaster.internal/ubuntu groovy/main armhf libncursesw6 armhf 6.2-1 [106 kB] Get:35 http://ftpmaster.internal/ubuntu groovy/main armhf libtinfo6 armhf 6.2-1 [73.6 kB] Get:36 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libsmartcols1 armhf 2.35.1-5ubuntu2 [84.3 kB] Get:37 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf fdisk armhf 2.35.1-5ubuntu2 [113 kB] Get:38 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf util-linux armhf 2.35.1-5ubuntu2 [985 kB] Get:39 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libc-bin armhf 2.31-0ubuntu10 [492 kB] Get:40 http://ftpmaster.internal/ubuntu groovy/main armhf ncurses-base all 6.2-1 [18.7 kB] Get:41 http://ftpmaster.internal/ubuntu groovy/main armhf sysvinit-utils armhf 2.96-3ubuntu1 [19.1 kB] Get:42 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf systemd-sysv armhf 245.6-1ubuntu1 [10.3 kB] Get:43 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf systemd-timesyncd armhf 245.6-1ubuntu1 [27.9 kB] Get:44 http://ftpmaster.internal/ubuntu groovy/main armhf libacl1 armhf 2.2.53-8 [16.0 kB] Get:45 http://ftpmaster.internal/ubuntu groovy/main armhf libapparmor1 armhf 2.13.3-7ubuntu6 [29.2 kB] Get:46 http://ftpmaster.internal/ubuntu groovy/main armhf libcap2 armhf 1:2.34-2 [15.6 kB] Get:47 http://ftpmaster.internal/ubuntu groovy/main armhf libargon2-1 armhf 0~20171227-0.2build20.10.0 [20.0 kB] Get:48 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libudev1 armhf 245.6-1ubuntu1 [67.3 kB] Get:49 http://ftpmaster.internal/ubuntu groovy/main armhf libdevmapper1.02.1 armhf 2:1.02.167-1ubuntu3 [118 kB] Get:50 http://ftpmaster.internal/ubuntu groovy/main armhf libjson-c4 armhf 0.13.1+dfsg-9 [25.8 kB] Get:51 http://ftpmaster.internal/ubuntu groovy/main armhf libcryptsetup12 armhf 2:2.3.1-1ubuntu1 [172 kB] Get:52 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libgmp10 armhf 2:6.2.0+dfsg-6 [192 kB] Get:53 http://ftpmaster.internal/ubuntu groovy/main armhf libunistring2 armhf 0.9.10-4 [359 kB] Get:54 http://ftpmaster.internal/ubuntu groovy/main armhf libidn2-0 armhf 2.3.0-1 [49.9 kB] Get:55 http://ftpmaster.internal/ubuntu groovy/main armhf libgnutls30 armhf 3.6.13-4ubuntu2 [769 kB] Get:56 http://ftpmaster.internal/ubuntu groovy/main armhf libgpg-error0 armhf 1.38-1 [54.2 kB] Get:57 http://ftpmaster.internal/ubuntu groovy/main armhf libkmod2 armhf 27+20200310-2ubuntu1 [38.2 kB] Get:58 http://ftpmaster.internal/ubuntu groovy/main armhf libseccomp2 armhf 2.4.3-1ubuntu3 [32.5 kB] Get:59 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf mount armhf 2.35.1-5ubuntu2 [112 kB] Get:60 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf systemd armhf 245.6-1ubuntu1 [3649 kB] Get:61 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libsystemd0 armhf 245.6-1ubuntu1 [247 kB] Get:62 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libzstd1 armhf 1.4.5+dfsg-2 [276 kB] Get:63 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libapt-pkg6.0 armhf 2.1.6 [757 kB] Get:64 http://ftpmaster.internal/ubuntu groovy/main armhf gpgv armhf 2.2.20-1ubuntu1 [170 kB] Get:65 http://ftpmaster.internal/ubuntu groovy/main armhf ubuntu-keyring all 2020.06.17.1 [22.2 kB] Get:66 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf apt armhf 2.1.6 [1244 kB] Get:67 http://ftpmaster.internal/ubuntu groovy/main armhf logsave armhf 1.45.6-1ubuntu1 [9676 B] Get:68 http://ftpmaster.internal/ubuntu groovy/main armhf libext2fs2 armhf 1.45.6-1ubuntu1 [170 kB] Get:69 http://ftpmaster.internal/ubuntu groovy/main armhf e2fsprogs armhf 1.45.6-1ubuntu1 [510 kB] Get:70 http://ftpmaster.internal/ubuntu groovy/main armhf libcap-ng0 armhf 0.7.9-2.2 [9764 B] Get:71 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libdebconfclient0 armhf 0.252ubuntu1 [5716 B] Get:72 http://ftpmaster.internal/ubuntu groovy/main armhf passwd armhf 1:4.8.1-1ubuntu6 [749 kB] Get:73 http://ftpmaster.internal/ubuntu groovy/main armhf libcom-err2 armhf 1.45.6-1ubuntu1 [8708 B] Get:74 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libprocps8 armhf 2:3.3.16-5ubuntu1 [29.6 kB] Get:75 http://ftpmaster.internal/ubuntu groovy/main armhf libss2 armhf 1.45.6-1ubuntu1 [9384 B] Get:76 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf procps armhf 2:3.3.16-5ubuntu1 [222 kB] Get:77 http://ftpmaster.internal/ubuntu groovy/main armhf ca-certificates all 20190110ubuntu2 [145 kB] Get:78 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libsqlite3-0 armhf 3.32.2-2 [469 kB] Get:79 http://ftpmaster.internal/ubuntu groovy/main armhf tzdata all 2020a-0ubuntu1 [293 kB] Get:80 http://ftpmaster.internal/ubuntu groovy/main armhf libctf0 armhf 2.34-7ubuntu1 [37.1 kB] Get:81 http://ftpmaster.internal/ubuntu groovy/main armhf binutils-arm-linux-gnueabihf armhf 2.34-7ubuntu1 [2093 kB] Get:82 http://ftpmaster.internal/ubuntu groovy/main armhf libbinutils armhf 2.34-7ubuntu1 [317 kB] Get:83 http://ftpmaster.internal/ubuntu groovy/main armhf binutils armhf 2.34-7ubuntu1 [3364 B] Get:84 http://ftpmaster.internal/ubuntu groovy/main armhf binutils-common armhf 2.34-7ubuntu1 [207 kB] Get:85 http://ftpmaster.internal/ubuntu groovy/main armhf libctf-nobfd0 armhf 2.34-7ubuntu1 [38.0 kB] Get:86 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libasan5 armhf 9.3.0-14ubuntu1 [387 kB] Get:87 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf g++-9 armhf 9.3.0-14ubuntu1 [6690 kB] Get:88 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf gcc-9 armhf 9.3.0-14ubuntu1 [6556 kB] Get:89 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libstdc++-9-dev armhf 9.3.0-14ubuntu1 [1783 kB] Get:90 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libgcc-9-dev armhf 9.3.0-14ubuntu1 [685 kB] Get:91 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf cpp-9 armhf 9.3.0-14ubuntu1 [5878 kB] Get:92 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf gcc-9-base armhf 9.3.0-14ubuntu1 [19.5 kB] Get:93 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf dpkg-dev all 1.19.7ubuntu4 [679 kB] Get:94 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libdpkg-perl all 1.19.7ubuntu4 [230 kB] Get:95 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf make armhf 4.3-3 [156 kB] Get:96 http://ftpmaster.internal/ubuntu groovy/main armhf libassuan0 armhf 2.5.3-7.1 [29.2 kB] Get:97 http://ftpmaster.internal/ubuntu groovy/main armhf libnpth0 armhf 1.6-2 [6772 B] Get:98 http://ftpmaster.internal/ubuntu groovy/main armhf gpg armhf 2.2.20-1ubuntu1 [427 kB] Get:99 http://ftpmaster.internal/ubuntu groovy/main armhf gpgconf armhf 2.2.20-1ubuntu1 [107 kB] Get:100 http://ftpmaster.internal/ubuntu groovy/main armhf gpg-agent armhf 2.2.20-1ubuntu1 [195 kB] Get:101 http://ftpmaster.internal/ubuntu groovy/main armhf pkgbinarymangler all 146 [31.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 55.9 MB in 2s (31.1 MB/s) (Reading database ... 12562 files and directories currently installed.) 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Installing new version of config file /etc/mke2fs.conf ... Setting up fdisk (2.35.1-5ubuntu2) ... Setting up libasan5:armhf (9.3.0-14ubuntu1) ... Setting up perl (5.30.3-4) ... Setting up libdpkg-perl (1.19.7ubuntu4) ... Setting up procps (2:3.3.16-5ubuntu1) ... Installing new version of config file /etc/sysctl.conf ... Removing obsolete conffile /etc/sysctl.d/10-link-restrictions.conf ... Setting up cpp-9 (9.3.0-14ubuntu1) ... Setting up libc6-dev:armhf (2.31-0ubuntu10) ... Setting up libcryptsetup12:armhf (2:2.3.1-1ubuntu1) ... Setting up binutils-arm-linux-gnueabihf (2.34-7ubuntu1) ... Setting up binutils (2.34-7ubuntu1) ... Setting up dpkg-dev (1.19.7ubuntu4) ... Setting up libgcc-9-dev:armhf (9.3.0-14ubuntu1) ... Setting up gcc-9 (9.3.0-14ubuntu1) ... Setting up libstdc++-9-dev:armhf (9.3.0-14ubuntu1) ... Setting up g++-9 (9.3.0-14ubuntu1) ... Setting up systemd-timesyncd (245.6-1ubuntu1) ... Installing new version of config file /etc/dhcp/dhclient-exit-hooks.d/timesyncd ... Setting up systemd (245.6-1ubuntu1) ... Installing new version of config file /etc/systemd/journald.conf ... Initializing machine ID from KVM UUID. Setting up systemd-sysv (245.6-1ubuntu1) ... Processing triggers for libc-bin (2.31-0ubuntu10) ... Processing triggers for ca-certificates (20190110ubuntu2) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19472633 armhf groovy-proposed -c chroot:build-PACKAGEBUILD-19472633 --arch=armhf --dist=groovy-proposed --nolog t-coffee_13.41.0.28bdc39+dfsg-4.dsc Initiating build PACKAGEBUILD-19472633 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-177-generic #207-Ubuntu SMP Mon Mar 16 01:17:51 UTC 2020 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-024.buildd +==============================================================================+ | t-coffee 13.41.0.28bdc39+dfsg-4 (armhf) 18 Jun 2020 00:28 | +==============================================================================+ Package: t-coffee Version: 13.41.0.28bdc39+dfsg-4 Source Version: 13.41.0.28bdc39+dfsg-4 Distribution: groovy-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/t-coffee-fTibWw/t-coffee-13.41.0.28bdc39+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/t-coffee-fTibWw' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19472633/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- t-coffee_13.41.0.28bdc39+dfsg-4.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-Af6WHg/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-Af6WHg/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Af6WHg/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-Af6WHg/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Af6WHg/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-Af6WHg/apt_archive ./ Packages [528 B] Fetched 2861 B in 0s (88.3 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-Af6WHg/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 (63.4 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12563 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper-compat (= 12) Filtered Build-Depends: debhelper-compat (= 12) dpkg-deb: building package 'sbuild-build-depends-t-coffee-dummy' in '/<>/resolver-h69bld/apt_archive/sbuild-build-depends-t-coffee-dummy.deb'. Ign:1 copy:/<>/resolver-h69bld/apt_archive ./ InRelease Get:2 copy:/<>/resolver-h69bld/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-h69bld/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-h69bld/apt_archive ./ Sources [212 B] Get:5 copy:/<>/resolver-h69bld/apt_archive ./ Packages [528 B] Fetched 2859 B in 0s (78.2 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 dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libicu66 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc 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 dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libicu66 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-t-coffee-dummy 0 upgraded, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 16.5 MB of archives. After this operation, 61.1 MB of additional disk space will be used. Get:1 copy:/<>/resolver-h69bld/apt_archive ./ sbuild-build-depends-t-coffee-dummy 0.invalid.0 [860 B] Get:2 http://ftpmaster.internal/ubuntu groovy/main armhf libbsd0 armhf 0.10.0-1 [49.8 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main armhf bsdmainutils armhf 11.1.2ubuntu3 [176 kB] Get:4 http://ftpmaster.internal/ubuntu groovy/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main armhf groff-base armhf 1.22.4-5 [759 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main armhf libpipeline1 armhf 1.5.2-2build1 [23.5 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/main armhf man-db armhf 2.9.2-1 [1082 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/main armhf libmagic-mgc armhf 1:5.38-5 [218 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main armhf libmagic1 armhf 1:5.38-5 [68.4 kB] Get:10 http://ftpmaster.internal/ubuntu groovy/main armhf file armhf 1:5.38-5 [22.4 kB] Get:11 http://ftpmaster.internal/ubuntu groovy/main armhf libelf1 armhf 0.176-1.1build1 [41.3 kB] Get:12 http://ftpmaster.internal/ubuntu groovy/main armhf libglib2.0-0 armhf 2.64.3-1 [1124 kB] Get:13 http://ftpmaster.internal/ubuntu groovy/main armhf libicu66 armhf 66.1-2ubuntu2 [8222 kB] Get:14 http://ftpmaster.internal/ubuntu groovy/main armhf libxml2 armhf 2.9.10+dfsg-5 [546 kB] Get:15 http://ftpmaster.internal/ubuntu groovy/main armhf gettext-base armhf 0.19.8.1-10build1 [46.0 kB] Get:16 http://ftpmaster.internal/ubuntu groovy/main armhf libsigsegv2 armhf 2.12-2 [13.1 kB] Get:17 http://ftpmaster.internal/ubuntu groovy/main armhf m4 armhf 1.4.18-4 [187 kB] Get:18 http://ftpmaster.internal/ubuntu groovy/main armhf autoconf all 2.69-11.1 [321 kB] Get:19 http://ftpmaster.internal/ubuntu groovy/main armhf autotools-dev all 20180224.1 [39.6 kB] Get:20 http://ftpmaster.internal/ubuntu groovy/main armhf automake all 1:1.16.2-1ubuntu1 [521 kB] Get:21 http://ftpmaster.internal/ubuntu groovy/main armhf autopoint all 0.19.8.1-10build1 [412 kB] Get:22 http://ftpmaster.internal/ubuntu groovy/main armhf libtool all 2.4.6-14 [161 kB] Get:23 http://ftpmaster.internal/ubuntu groovy/main armhf dh-autoreconf all 19 [16.1 kB] Get:24 http://ftpmaster.internal/ubuntu groovy/main armhf libdebhelper-perl all 13.1ubuntu1 [64.0 kB] Get:25 http://ftpmaster.internal/ubuntu groovy/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] Get:26 http://ftpmaster.internal/ubuntu groovy/main armhf libsub-override-perl all 0.09-2 [9532 B] Get:27 http://ftpmaster.internal/ubuntu groovy/main armhf libfile-stripnondeterminism-perl all 1.8.1-1 [17.1 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main armhf dh-strip-nondeterminism all 1.8.1-1 [5232 B] Get:29 http://ftpmaster.internal/ubuntu groovy/main armhf dwz armhf 0.13-5 [153 kB] Get:30 http://ftpmaster.internal/ubuntu groovy/main armhf libcroco3 armhf 0.6.13-1 [70.5 kB] Get:31 http://ftpmaster.internal/ubuntu groovy/main armhf gettext armhf 0.19.8.1-10build1 [835 kB] Get:32 http://ftpmaster.internal/ubuntu groovy/main armhf intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:33 http://ftpmaster.internal/ubuntu groovy/main armhf po-debconf all 1.0.21 [233 kB] Get:34 http://ftpmaster.internal/ubuntu groovy/main armhf debhelper all 13.1ubuntu1 [885 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 16.5 MB in 1s (31.1 MB/s) Selecting previously unselected package libbsd0:armhf. (Reading database ... 12563 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.10.0-1_armhf.deb ... Unpacking libbsd0:armhf (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2ubuntu3_armhf.deb ... Unpacking bsdmainutils (11.1.2ubuntu3) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-5_armhf.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../04-libpipeline1_1.5.2-2build1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.2-2build1) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.9.2-1_armhf.deb ... Unpacking man-db (2.9.2-1) ... 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Setting up libdebhelper-perl (13.1ubuntu1) ... Setting up libmagic1:armhf (1:5.38-5) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up file (1:5.38-5) ... Setting up autotools-dev (20180224.1) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up autopoint (0.19.8.1-10build1) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libbsd0:armhf (0.10.0-1) ... Setting up libelf1:armhf (0.176-1.1build1) ... Setting up libxml2:armhf (2.9.10+dfsg-5) ... Setting up libfile-stripnondeterminism-perl (1.8.1-1) ... Setting up libtool (2.4.6-14) ... Setting up m4 (1.4.18-4) ... Setting up bsdmainutils (11.1.2ubuntu3) ... 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 libcroco3:armhf (0.6.13-1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.8.1-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-5) ... Setting up automake (1:1.16.2-1ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-10build1) ... Setting up man-db (2.9.2-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up dh-autoreconf (19) ... Setting up debhelper (13.1ubuntu1) ... Setting up sbuild-build-depends-t-coffee-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-0ubuntu10) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-177-generic arm64 (armv7l) Toolchain package versions: binutils_2.34-7ubuntu1 dpkg-dev_1.19.7ubuntu4 g++-9_9.3.0-14ubuntu1 gcc-9_9.3.0-14ubuntu1 libc6-dev_2.31-0ubuntu10 libstdc++-9-dev_9.3.0-14ubuntu1 libstdc++6_10.1.0-4ubuntu1 linux-libc-dev_5.4.0-37.41 Package versions: adduser_3.118ubuntu2 advancecomp_2.1-2.1build1 apt_2.1.6 autoconf_2.69-11.1 automake_1:1.16.2-1ubuntu1 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu7 base-passwd_3.5.47 bash_5.0-6ubuntu1 binutils_2.34-7ubuntu1 binutils-arm-linux-gnueabihf_2.34-7ubuntu1 binutils-common_2.34-7ubuntu1 bsdmainutils_11.1.2ubuntu3 bsdutils_1:2.35.1-5ubuntu2 build-essential_12.8ubuntu1 bzip2_1.0.8-3 ca-certificates_20190110ubuntu2 coreutils_8.30-3ubuntu2 cpp_4:9.3.0-1ubuntu2 cpp-9_9.3.0-14ubuntu1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.1ubuntu1 debianutils_4.11 dh-autoreconf_19 dh-strip-nondeterminism_1.8.1-1 diffutils_1:3.7-3 dpkg_1.19.7ubuntu4 dpkg-dev_1.19.7ubuntu4 dwz_0.13-5 e2fsprogs_1.45.6-1ubuntu1 fakeroot_1.24-1 fdisk_2.35.1-5ubuntu2 file_1:5.38-5 findutils_4.7.0-1ubuntu1 g++_4:9.3.0-1ubuntu2 g++-9_9.3.0-14ubuntu1 gcc_4:9.3.0-1ubuntu2 gcc-10-base_10.1.0-4ubuntu1 gcc-9_9.3.0-14ubuntu1 gcc-9-base_9.3.0-14ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gpg_2.2.20-1ubuntu1 gpg-agent_2.2.20-1ubuntu1 gpgconf_2.2.20-1ubuntu1 gpgv_2.2.20-1ubuntu1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2ubuntu1 hostname_3.23 init_1.57 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapparmor1_2.13.3-7ubuntu6 libapt-pkg6.0_2.1.6 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2build20.10.0 libasan5_9.3.0-14ubuntu1 libassuan0_2.5.3-7.1 libatomic1_10.1.0-4ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu6 libaudit1_1:2.8.5-2ubuntu6 libbinutils_2.34-7ubuntu1 libblkid1_2.35.1-5ubuntu2 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-3 libc-bin_2.31-0ubuntu10 libc-dev-bin_2.31-0ubuntu10 libc6_2.31-0ubuntu10 libc6-dev_2.31-0ubuntu10 libcap-ng0_0.7.9-2.2 libcap2_1:2.34-2 libcc1-0_10.1.0-4ubuntu1 libcom-err2_1.45.6-1ubuntu1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1ubuntu1 libcrypt1_1:4.4.16-1ubuntu1 libcryptsetup12_2:2.3.1-1ubuntu1 libctf-nobfd0_2.34-7ubuntu1 libctf0_2.34-7ubuntu1 libdb5.3_5.3.28+dfsg1-0.6ubuntu2 libdebconfclient0_0.252ubuntu1 libdebhelper-perl_13.1ubuntu1 libdevmapper1.02.1_2:1.02.167-1ubuntu3 libdpkg-perl_1.19.7ubuntu4 libelf1_0.176-1.1build1 libext2fs2_1.45.6-1ubuntu1 libfakeroot_1.24-1 libfdisk1_2.35.1-5ubuntu2 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.8.1-1 libgcc-9-dev_9.3.0-14ubuntu1 libgcc-s1_10.1.0-4ubuntu1 libgcrypt20_1.8.5-5ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.3-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.13-4ubuntu2 libgomp1_10.1.0-4ubuntu1 libgpg-error0_1.38-1 libhogweed5_3.5.1+really3.5.1-2 libicu66_66.1-2ubuntu2 libidn2-0_2.3.0-1 libip4tc2_1.8.4-3ubuntu2 libisl22_0.22.1-1 libjson-c4_0.13.1+dfsg-9 libkmod2_27+20200310-2ubuntu1 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.1-5ubuntu2 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-2 libp11-kit0_0.23.20-1build1 libpam-modules_1.3.1-5ubuntu4 libpam-modules-bin_1.3.1-5ubuntu4 libpam-runtime_1.3.1-5ubuntu4 libpam0g_1.3.1-5ubuntu4 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12build1 libperl5.30_5.30.3-4 libpipeline1_1.5.2-2build1 libpng16-16_1.6.37-2 libprocps8_2:3.3.16-5ubuntu1 libreadline8_8.0-4 libseccomp2_2.4.3-1ubuntu3 libselinux1_3.0-1build2 libsemanage-common_3.0-1build2 libsemanage1_3.0-1build2 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.35.1-5ubuntu2 libsqlite3-0_3.32.2-2 libss2_1.45.6-1ubuntu1 libssl1.1_1.1.1f-1ubuntu2 libstdc++-9-dev_9.3.0-14ubuntu1 libstdc++6_10.1.0-4ubuntu1 libsub-override-perl_0.09-2 libsystemd0_245.6-1ubuntu1 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.1.0-4ubuntu1 libuchardet0_0.0.7-1 libudev1_245.6-1ubuntu1 libunistring2_0.9.10-4 libuuid1_2.35.1-5ubuntu2 libxml2_2.9.10+dfsg-5 libzstd1_1.4.5+dfsg-2 linux-libc-dev_5.4.0-37.41 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu6 logsave_1.45.6-1ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.3-3 man-db_2.9.2-1 mawk_1.3.4.20200120-2 mount_2.35.1-5ubuntu2 ncurses-base_6.2-1 ncurses-bin_6.2-1 openssl_1.1.1f-1ubuntu2 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu6 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-3build1 pkgbinarymangler_146 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.16-5ubuntu1 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-t-coffee-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 systemd_245.6-1ubuntu1 systemd-sysv_245.6-1ubuntu1 systemd-timesyncd_245.6-1ubuntu1 sysvinit-utils_2.96-3ubuntu1 tar_1.30+dfsg-7 tzdata_2020a-0ubuntu1 ubuntu-keyring_2020.06.17.1 util-linux_2.35.1-5ubuntu2 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Wed Jun 17 19:39:09 2020 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./t-coffee_13.41.0.28bdc39+dfsg-4.dsc dpkg-source: info: extracting t-coffee in t-coffee-13.41.0.28bdc39+dfsg dpkg-source: info: unpacking t-coffee_13.41.0.28bdc39+dfsg.orig.tar.xz dpkg-source: info: unpacking t-coffee_13.41.0.28bdc39+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying probconsrna.patch dpkg-source: info: applying bypass_legacy_blast.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 verbose_build dpkg-source: info: applying increase_max_pid.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=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-19472633 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19472633 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19472633 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 13.41.0.28bdc39+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --sourcedirectory=t_coffee_source debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/t-coffee-13.41.0.28bdc39+dfsg' rm -rf t_coffee_source/*.o t_coffee_source/t_coffee bin/t_coffee example/ph_tree_scan.txt bin/t_coffee rm -rf t_coffee_source/TMalign find . -name "*.o" -delete find . -name "*.deps" -delete chmod 644 example/* make[1]: Leaving directory '/<>/t-coffee-13.41.0.28bdc39+dfsg' dh_autoreconf_clean -O--sourcedirectory=t_coffee_source dh_clean -O--sourcedirectory=t_coffee_source debian/rules binary-arch dh binary-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 '/<>/t-coffee-13.41.0.28bdc39+dfsg' dh_auto_build -- USER_BIN=../bin/ FCC="gfortran -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong" 'CC=$(CXX)' all cd t_coffee_source && make -j4 "INSTALL=install --strip-program=true" USER_BIN=../bin/ "FCC=gfortran -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong" CC=\$\(CXX\) all make[2]: Entering directory '/<>/t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source' CC dev_lib/dev1.c CC dp_lib/CUSTOM_evaluate_for_struc.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dev_lib/dev1.deps -c -o dev_lib/dev1.o dev_lib/dev1.c CC dp_lib/evaluate.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/CUSTOM_evaluate_for_struc.deps -c -o dp_lib/CUSTOM_evaluate_for_struc.o dp_lib/CUSTOM_evaluate_for_struc.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate.deps -c -o dp_lib/evaluate.o dp_lib/evaluate.c CC dp_lib/evaluate_dirichlet.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_dirichlet.deps -c -o dp_lib/evaluate_dirichlet.o dp_lib/evaluate_dirichlet.c In file included from ./io_lib_header.h:33, from dp_lib/CUSTOM_evaluate_for_struc.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, from dev_lib/dev1.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/evaluate_dirichlet.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/evaluate.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ dev_lib/dev1.c: In function ‘void aln2hitMat(Alignment*, char*)’: dev_lib/dev1.c:89:19: warning: too many arguments for format [-Wformat-extra-args] 89 | fprintf (stdout, "Process positions\n", i); | ^~~~~~~~~~~~~~~~~~~~~ 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] 317 | 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] 319 | 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] 323 | 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] 326 | fscanf(fp, "\n"); | ~~~~~~^~~~~~~~~~ CC dp_lib/evaluate_for_domain.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_domain.deps -c -o dp_lib/evaluate_for_domain.o dp_lib/evaluate_for_domain.c dp_lib/evaluate.c: In function ‘Alignment* msa2distances(Alignment*, Constraint_list*, float, float, int)’: dp_lib/evaluate.c:3070:53: warning: format ‘%f’ expects argument of type ‘double’, but argument 4 has type ‘int’ [-Wformat=] 3070 | fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); | ~~~~^ ~~~ | | | | double int | %3.2d dp_lib/evaluate.c:3070:67: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘double’ [-Wformat=] 3070 | fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); | ~~^ ~~~~~~~ | | | | int double | %3f dp_lib/evaluate.c:3070:79: warning: format ‘%f’ expects argument of type ‘double’, but argument 6 has type ‘int’ [-Wformat=] 3070 | fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); | ~~~^ ~~~~~~~~ | | | | double int | %.3d dp_lib/evaluate.c:3070:95: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘double’ [-Wformat=] 3070 | fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); | ~~^ ~~~~~~ | | | | int double | %3f CC dp_lib/evaluate_for_struc.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_struc.deps -c -o dp_lib/evaluate_for_struc.o dp_lib/evaluate_for_struc.c In file included from ./io_lib_header.h:33, from dp_lib/evaluate_for_domain.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/evaluate.c: In function ‘Alignment* fork_triplet_coffee_evaluate_output(Alignment*, Constraint_list*, int)’: dp_lib/evaluate.c:809:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 809 | fscanf (fp, "%d ", &res); | ~~~~~~~^~~~~~~~~~~~~~~~~ dp_lib/evaluate.c:814:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 814 | fscanf (fp, "%f %f", &sseq, &mseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate.c:819:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 819 | fscanf (fp, "%f %f", &sseq, &mseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/evaluate_for_struc.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/evaluate.c: In function ‘float** initialise_aa_physico_chemical_property_table(int*)’: dp_lib/evaluate.c:7626:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 7626 | fscanf (fp, "%f %c %*s",&v1, &c1 ); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/fsa_dp.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/fsa_dp.deps -c -o dp_lib/fsa_dp.o dp_lib/fsa_dp.c CC dp_lib/pavie_dp.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/pavie_dp.deps -c -o dp_lib/pavie_dp.o dp_lib/pavie_dp.c In file included from ./io_lib_header.h:33, from dp_lib/fsa_dp.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/pavie_dp.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ 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] 127 | 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] 1079 | 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] 1081 | 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] 1365 | fscanf (fp, "%s", mat); | ~~~~~~~^~~~~~~~~~~~~~~ dp_lib/pavie_dp.c: In function ‘char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)’: dp_lib/pavie_dp.c:1078:33: warning: ‘%s’ directive writing up to 999 bytes into a region of size 996 [-Wformat-overflow=] 1078 | sprintf ( command, "cp %s %s", mat_name[a], latest); | ^~ ~~~~~~ In file included from /usr/include/stdio.h:867, from dp_lib/pavie_dp.c:27: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 1004) into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/pavie_dp.c:1080:30: warning: ‘%s’ directive writing up to 999 bytes into a region of size 997 [-Wformat-overflow=] 1080 | sprintf ( command, "cp %s %s", latest, current); | ^~ ~~~~~~ In file included from /usr/include/stdio.h:867, from dp_lib/pavie_dp.c:27: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 2003 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/showpair.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/showpair.deps -c -o dp_lib/showpair.o dp_lib/showpair.c In file included from ./io_lib_header.h:33, from dp_lib/showpair.c:32: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_domain_dp.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp.deps -c -o dp_lib/util_domain_dp.o dp_lib/util_domain_dp.c CC dp_lib/util_domain_dp_drivers.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp_drivers.deps -c -o dp_lib/util_domain_dp_drivers.o dp_lib/util_domain_dp_drivers.c CC dp_lib/util_dp_cdna_fasta_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_cdna_fasta_nw.deps -c -o dp_lib/util_dp_cdna_fasta_nw.o dp_lib/util_dp_cdna_fasta_nw.c In file included from ./io_lib_header.h:33, from dp_lib/util_domain_dp.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_domain_dp_drivers.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_cdna_fasta_nw.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_clean_maln.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_clean_maln.deps -c -o dp_lib/util_dp_clean_maln.o dp_lib/util_dp_clean_maln.c CC dp_lib/util_dp_drivers.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_drivers.deps -c -o dp_lib/util_dp_drivers.o dp_lib/util_dp_drivers.c In file included from ./io_lib_header.h:33, from dp_lib/util_dp_clean_maln.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_drivers.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_est.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_est.deps -c -o dp_lib/util_dp_est.o dp_lib/util_dp_est.c CC dp_lib/util_dp_fasta_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_nw.deps -c -o dp_lib/util_dp_fasta_nw.o dp_lib/util_dp_fasta_nw.c In file included from ./io_lib_header.h:33, from dp_lib/util_dp_est.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_fasta_sw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_sw.deps -c -o dp_lib/util_dp_fasta_sw.o dp_lib/util_dp_fasta_sw.c dp_lib/util_dp_drivers.c: In function ‘char* seq_file2msa_file(char*, char*, char*)’: dp_lib/util_dp_drivers.c:1014:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1014 | chdir (dir); | ~~~~~~^~~~~ dp_lib/util_dp_drivers.c:1028:16: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1028 | chdir (cdir); | ~~~~~~~~~^~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* align_pdb_pair_2(char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1080:10: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1080 | 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:1108:10: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1108 | 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:1149:8: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1149 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1160:9: warning: ignoring return value of ‘char* tmpnam(char*)’, declared with attribute warn_unused_result [-Wunused-result] 1160 | tmpnam(aln1); | ~~~~~~^~~~~~ dp_lib/util_dp_drivers.c:1161:9: warning: ignoring return value of ‘char* tmpnam(char*)’, declared with attribute warn_unused_result [-Wunused-result] 1161 | tmpnam(aln2); | ~~~~~~^~~~~~ dp_lib/util_dp_drivers.c:1164:9: warning: ignoring return value of ‘char* tmpnam(char*)’, declared with attribute warn_unused_result [-Wunused-result] 1164 | tmpnam(hhfile); | ~~~~~~^~~~~~~~ dp_lib/util_dp_drivers.c:1211:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 1211 | fgets (buf2, 10000, fp); | ~~~~~~^~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_fasta_nw.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* profile_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1280:6: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1280 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1363:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1363 | fscanf (fp, "%s", bufname); | ~~~~~~~^~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* profile_pair_decomposed(TC_method*, char*, Constraint_list*, char*)’: dp_lib/util_dp_drivers.c:1445:7: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1445 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* profile_subset_pair_old(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1581:7: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1581 | 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:1717:8: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1717 | 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:1774:8: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1774 | 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:1906:8: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1906 | 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:1981:8: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1981 | 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:2073:10: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2073 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2121:10: warning: ignoring return value of ‘char* getcwd(char*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] 2121 | getcwd (cdir, sizeof(char)*1000); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2122:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2122 | chdir (get_cache_dir()); | ~~~~~~^~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2142:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2142 | 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:2256:6: warning: ignoring return value of ‘int atoi(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2256 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_fasta_sw.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_generic_fasta_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_generic_fasta_nw.deps -c -o dp_lib/util_dp_generic_fasta_nw.o dp_lib/util_dp_generic_fasta_nw.c In file included from ./io_lib_header.h:33, from dp_lib/util_dp_generic_fasta_nw.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* method2pw_cl(TC_method*, Constraint_list*)’: dp_lib/util_dp_drivers.c:382:24: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 382 | sprintf ( mat, "%s", (strm(m, "default"))?"dna_idmat":m); | ^~ In file included from /usr/include/stdio.h:867, from dp_lib/util_dp_drivers.c:27: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:373:23: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 373 | sprintf ( mat, "%s", (strm(m, "default"))?"blosum62mt":m); | ^~ In file included from /usr/include/stdio.h:867, from dp_lib/util_dp_drivers.c:27: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:386:41: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 386 | if ( M->matrix[0])sprintf ( mat, "%s", M->matrix); | ^~ In file included from /usr/include/stdio.h:867, from dp_lib/util_dp_drivers.c:27: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_gotoh_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_nw.deps -c -o dp_lib/util_dp_gotoh_nw.o dp_lib/util_dp_gotoh_nw.c dp_lib/util_dp_drivers.c: In function ‘Alignment* realign_block(Alignment*, int, int, char*)’: dp_lib/util_dp_drivers.c:921:25: warning: ‘ -infile=’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 921 | sprintf ( command, "%s -infile=%s -outfile=%s %s", script,seq_name, aln_name, TO_NULL_DEVICE); | ^~~~~~~~~ In file included from /usr/include/stdio.h:867, from dp_lib/util_dp_drivers.c:27: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 38 or more bytes (assuming 1037) into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_gotoh_nw.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_gotoh_sw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_sw.deps -c -o dp_lib/util_dp_gotoh_sw.o dp_lib/util_dp_gotoh_sw.c dp_lib/util_dp_drivers.c: In function ‘Constraint_list* seq_msa(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1854:80: warning: ‘%s’ directive writing up to 500 bytes into a region of size between 445 and 945 [-Wformat-overflow=] 1854 | sprintf ( command, "t_coffee -other_pg tc_generic_method.pl -mode=%s -method=%s %s %s%s %s %s%s -tmpdir=%s %s %s", M->executable, M->executable2, M->param1,M->in_flag,infile,M->param2,M->out_flag,outfile,get_tmp_4_tcoffee(),db,M->param); | ^~ In file included from /usr/include/stdio.h:867, from dp_lib/util_dp_drivers.c:27: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 71 or more bytes (assuming 6067) into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_gotoh_sw.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ 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] 391 | fread ( &k, sizeof (TRACE_TYPE), 1, long_trace); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_mm_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_mm_nw.deps -c -o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_mm_nw.c In file included from ./io_lib_header.h:33, from dp_lib/util_dp_mm_nw.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_sim.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_sim.deps -c -o dp_lib/util_dp_sim.o dp_lib/util_dp_sim.c In file included from ./io_lib_header.h:33, from dp_lib/util_dp_sim.c:32: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Alignment* stack_progressive_aln(Alignment*, Constraint_list*, int, int)’: dp_lib/util_dp_drivers.c:3717:25: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 3717 | sprintf ( dp_mode, "%s", CL->dp_mode); | ^~ In file included from /usr/include/stdio.h:867, from dp_lib/util_dp_drivers.c:27: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_ssec_pwaln.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_ssec_pwaln.deps -c -o dp_lib/util_dp_ssec_pwaln.o dp_lib/util_dp_ssec_pwaln.c In file included from ./io_lib_header.h:33, from dp_lib/util_dp_ssec_pwaln.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_graph_maln.c CC dp_lib/util_dp_suboptimal_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_suboptimal_nw.deps -c -o dp_lib/util_dp_suboptimal_nw.o dp_lib/util_dp_suboptimal_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_graph_maln.deps -c -o dp_lib/util_graph_maln.o dp_lib/util_graph_maln.c In file included from ./io_lib_header.h:33, from dp_lib/util_graph_maln.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_suboptimal_nw.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC fastal/diagonal.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF fastal/diagonal.deps -c -o fastal/diagonal.o fastal/diagonal.c In file included from ./io_lib_header.h:33, from fastal/diagonal.c:31: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ 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] 434 | 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] 439 | 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] 440 | 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] 441 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ CC fastal/fastal.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF fastal/fastal.deps -c -o fastal/fastal.o fastal/fastal.c CC fastal/fastal_opt_parsing.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF fastal/fastal_opt_parsing.deps -c -o fastal/fastal_opt_parsing.o fastal/fastal_opt_parsing.c In file included from ./io_lib_header.h:33, from fastal/fastal.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC fastal/iteration.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF fastal/iteration.deps -c -o fastal/iteration.o fastal/iteration.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] 1924 | 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] 1929 | 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] 1930 | 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] 1931 | 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] 1976 | 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] 1980 | 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] 1981 | 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] 1982 | 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] 2115 | 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] 2262 | 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] 3201 | 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] 3323 | 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] 3326 | 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] 3329 | 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] 3331 | 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] 3333 | 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] 3352 | 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] 3502 | 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] 3575 | 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] 3577 | 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] 3579 | 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] 3581 | 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] 3643 | fgets(aligned_sequence, alignment_length+3, edit_seq_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from fastal/iteration.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ 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] 185 | 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] 310 | 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] 435 | 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] 501 | 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] 504 | 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] 535 | 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] 563 | 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] 565 | 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] 567 | 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] 569 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC fastal/parttree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF fastal/parttree.deps -c -o fastal/parttree.o fastal/parttree.c In file included from ./io_lib_header.h:33, from fastal/parttree.c:36: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ 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] 695 | 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] 701 | 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] 848 | 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] 859 | 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] 891 | 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] 903 | 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] 906 | 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] 912 | 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] 951 | 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] 962 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ CC fastal/scoring.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF fastal/scoring.deps -c -o fastal/scoring.o fastal/scoring.c In file included from ./io_lib_header.h:33, from fastal/scoring.c:37: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ 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] 76 | 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] 78 | 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] 82 | 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] 384 | 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] 398 | 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] 488 | 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] 502 | 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] 583 | 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] 584 | 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] 585 | fgets(line, LINE_LENGTH, result); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c: In function ‘int complete_agreement_score(char*, const char*)’: fastal/scoring.c:624:28: warning: ‘%s’ directive writing up to 499 bytes into a region of size 200 [-Wformat-overflow=] 624 | sprintf(ref_file_name, "%s/%s",directory, dp->d_name); | ^~ ~~~~~~~~~ In file included from /usr/include/stdio.h:867, from fastal/scoring.c:28: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 2 and 756 bytes into a destination of size 200 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC fastal/tree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF fastal/tree.deps -c -o fastal/tree.o fastal/tree.c In file included from ./io_lib_header.h:33, from fastal/tree.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC io_lib/io_func.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF io_lib/io_func.deps -c -o io_lib/io_func.o io_lib/io_func.c In file included from ./io_lib_header.h:33, from io_lib/io_func.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ 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] 1235 | if (!A)return NULL; | ^~~~ io_lib/io_func.c: In function ‘int aln2compressed_ps(Alignment*, char*)’: io_lib/io_func.c:2076:1: warning: no return statement in function returning non-void [-Wreturn-type] 2076 | } | ^ CC io_lib/pb_util_read_seq_util.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_seq_util.deps -c -o io_lib/pb_util_read_seq_util.o io_lib/pb_util_read_seq_util.c 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] 511 | 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] 971 | fscanf (fp, "%s %f %f %f", html_code[classC], &ps_code[classC][0], &ps_code[classC][1],&ps_code[classC][2]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from io_lib/pb_util_read_seq_util.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ 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] 269 | 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] 280 | 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] 305 | fgets(line, MAXLINE, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ CC io_lib/pb_util_read_sequence.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_sequence.deps -c -o io_lib/pb_util_read_sequence.o io_lib/pb_util_read_sequence.c In file included from ./io_lib_header.h:33, from io_lib/pb_util_read_sequence.c:35: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ 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] 144 | 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] 149 | for(i=1;i>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF io_lib/tree_util.deps -c -o io_lib/tree_util.o io_lib/tree_util.c In file included from ./io_lib_header.h:33, from io_lib/tree_util.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ io_lib/tree_util.c: In function ‘tnode* tree_scan(Alignment*, NT_node, char*, char*)’: io_lib/tree_util.c:836:19: warning: too many arguments for format [-Wformat-extra-args] 836 | fprintf (stdout, "Process positions\n", i); | ^~~~~~~~~~~~~~~~~~~~~ io_lib/tree_util.c: In function ‘Alignment* phylotrim(Alignment*, NT_node, char*, char*, char*)’: io_lib/tree_util.c:1299:1: warning: no return statement in function returning non-void [-Wreturn-type] 1299 | } | ^ io_lib/tree_util.c: In function ‘tnode* no_rec_free_tree(NT_node)’: io_lib/tree_util.c:2317:1: warning: no return statement in function returning non-void [-Wreturn-type] 2317 | } | ^ io_lib/tree_util.c: In function ‘int node_sort(char*, NT_node)’: io_lib/tree_util.c:6273:1: warning: no return statement in function returning non-void [-Wreturn-type] 6273 | } | ^ io_lib/tree_util.c: In function ‘int treelist2leafgroup(Sequence*, Sequence*, char*)’: io_lib/tree_util.c:6566:1: warning: no return statement in function returning non-void [-Wreturn-type] 6566 | } | ^ io_lib/tree_util.c: In function ‘int count_tree_groups(Sequence*, char*)’: io_lib/tree_util.c:6669:1: warning: no return statement in function returning non-void [-Wreturn-type] 6669 | } | ^ io_lib/tree_util.c: In function ‘int treelist2splits(Sequence*, Sequence*)’: io_lib/tree_util.c:7047:1: warning: no return statement in function returning non-void [-Wreturn-type] 7047 | } | ^ io_lib/tree_util.c: In function ‘int treelist2splits_old(Sequence*, Sequence*)’: io_lib/tree_util.c:7131:1: warning: no return statement in function returning non-void [-Wreturn-type] 7131 | } | ^ io_lib/tree_util.c: In function ‘int treelist2frame(Sequence*, Sequence*)’: io_lib/tree_util.c:7204:1: warning: no return statement in function returning non-void [-Wreturn-type] 7204 | } | ^ io_lib/tree_util.c: In function ‘char* graph2cons_d(long unsigned int, int)’: io_lib/tree_util.c:10163:27: warning: NULL used in arithmetic [-Wpointer-arith] 10163 | while ((c=rn_c(s))!=NULL) | ^~~~ io_lib/tree_util.c: In function ‘long unsigned int insert_gap_in_graph_d(long unsigned int)’: io_lib/tree_util.c:10181:20: warning: converting to non-pointer type ‘long unsigned int’ from NULL [-Wconversion-null] 10181 | unsigned long pn=NULL; | ^~~~ io_lib/tree_util.c:10183:22: warning: converting to non-pointer type ‘long unsigned int’ from NULL [-Wconversion-null] 10183 | if (!start) return NULL; | ^~~~ io_lib/tree_util.c:10196:14: warning: passing NULL to non-pointer argument 2 of ‘void wn_c(long unsigned int, long unsigned int)’ [-Wconversion-null] 10196 | wn_c(n,NULL); | ^~~~ io_lib/tree_util.c:9947:46: note: declared here 9947 | void wn_c (unsigned long n, unsigned long t); | ~~~~~~~~~~~~~~^ io_lib/tree_util.c: In function ‘FILE* create_tree(NT_node, NT_node, int*, int*, int*, tnode***, FILE*)’: io_lib/tree_util.c:3973:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 3973 | fscanf(fp,"%f",&dist); | ~~~~~~^~~~~~~~~~~~~~~ io_lib/tree_util.c:3981:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 3981 | fscanf(fp,"%f",&bootstrap); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ io_lib/tree_util.c: In function ‘int check_node(ALN_node, char*)’: io_lib/tree_util.c:9772:1: warning: control reaches end of non-void function [-Wreturn-type] 9772 | } | ^ CC km_coffee/Stack.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF km_coffee/Stack.deps -c -o km_coffee/Stack.o km_coffee/Stack.c CC km_coffee/Vector.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF km_coffee/Vector.deps -c -o km_coffee/Vector.o km_coffee/Vector.c CC km_coffee/classes.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF km_coffee/classes.deps -c -o km_coffee/classes.o km_coffee/classes.c CC km_coffee/km_coffee.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF km_coffee/km_coffee.deps -c -o km_coffee/km_coffee.o km_coffee/km_coffee.c In file included from ./io_lib_header.h:33, from km_coffee/km_coffee.c:43: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ km_coffee/km_coffee.c: In function ‘void traverse_km_tree(KM_node*, int*, const SeqSet*, char*, int, int, int, char*)’: km_coffee/km_coffee.c:148:25: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 148 | sprintf(command, "%li",current->id); | ~~^ ~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i km_coffee/km_coffee.c:157:38: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 157 | sprintf(command,"t_coffee -in %li -output fasta_aln -outfile %li.fa -n_core %i -gapopen %i -gapext %i -method %s -quiet >/dev/null 2>/dev/null", current->id, current->id, n_cores, gapopen, gapext, method); | ~~^ ~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i km_coffee/km_coffee.c:157:69: warning: format ‘%li’ expects argument of type ‘long int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 157 | sprintf(command,"t_coffee -in %li -output fasta_aln -outfile %li.fa -n_core %i -gapopen %i -gapext %i -method %s -quiet >/dev/null 2>/dev/null", current->id, current->id, n_cores, gapopen, gapext, method); | ~~^ ~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i km_coffee/km_coffee.c:159:38: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 159 | sprintf(command,"t_coffee -in %li -output fasta_aln -outfile %s -n_core %i -gapopen %i -gapext %i -method %s -quiet >/dev/null 2>/dev/null ", current->id, out_f, n_cores, gapopen, gapext, method); | ~~^ ~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i km_coffee/km_coffee.c:169:25: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 169 | sprintf(command, "%li",current->id); | ~~^ ~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i km_coffee/km_coffee.c:172:38: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 172 | sprintf(command,"t_coffee -in %li -output fasta_aln -outfile %li.fa -n_core %i -gapopen %i -gapext %i -method %s -quiet >/dev/null 2>/dev/null", current->id, current->id, n_cores, gapopen, gapext, method); | ~~^ ~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i km_coffee/km_coffee.c:172:69: warning: format ‘%li’ expects argument of type ‘long int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 172 | sprintf(command,"t_coffee -in %li -output fasta_aln -outfile %li.fa -n_core %i -gapopen %i -gapext %i -method %s -quiet >/dev/null 2>/dev/null", current->id, current->id, n_cores, gapopen, gapext, method); | ~~^ ~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i km_coffee/km_coffee.c:174:38: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 174 | sprintf(command,"t_coffee -in %li -output fasta_aln -outfile %s -n_core %i -gapopen %i -gapext %i -method %s -quiet >/dev/null 2>/dev/null ", current->id, out_f, n_cores, gapopen, gapext, method); | ~~^ ~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i km_coffee/km_coffee.c:185:25: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 185 | sprintf(command, "%li.fa",current->id); | ~~^ ~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i km_coffee/km_coffee.c:195:80: warning: format ‘%li’ expects argument of type ‘long int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 195 | sprintf(command, "t_coffee -output fasta_aln -method %s -quiet -outfile %li.fa -n_core %i -gapopen %i -profile FILE::prf.fa ", method, current->id,n_cores, gapopen); | ~~^ ~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i km_coffee/km_coffee.c:201:24: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 201 | fprintf(prf_F, "%li.fa\n", current->children[j]->id); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i 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] 491 | chdir(km_tmp_dir); | ~~~~~^~~~~~~~~~~~ CC km_coffee/km_util.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF km_coffee/km_util.deps -c -o km_coffee/km_util.o km_coffee/km_util.c km_coffee/km_util.c: In function ‘void* my_malloc(size_t)’: km_coffee/km_util.c:49:62: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 49 | fprintf(stderr, "ERROR: Could not allocate space of size %li\n", size); | ~~^ ~~~~ | | | | | size_t {aka unsigned int} | long int | %i km_coffee/km_util.c: In function ‘void* my_calloc(size_t, size_t)’: km_coffee/km_util.c:61:62: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 61 | fprintf(stderr, "ERROR: Could not allocate space of size %li\n", size*num); | ~~^ ~~~~~~~~ | | | | long int size_t {aka unsigned int} | %i km_coffee/km_util.c: In function ‘void* my_realloc(void*, size_t)’: km_coffee/km_util.c:74:62: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 74 | fprintf(stderr, "ERROR: Could not allocate space of size %li\n", size); | ~~^ ~~~~ | | | | | size_t {aka unsigned int} | long int | %i km_coffee/km_util.c: In function ‘char* my_make_temp_dir(char*, char*)’: km_coffee/km_util.c:96:55: warning: format ‘%s’ expects a matching ‘char*’ argument [-Wformat=] 96 | fprintf(stderr, "This error was caused by '%s' in '%s'\n", function); | ~^ | | | char* CC km_coffee/kmeans.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF km_coffee/kmeans.deps -c -o km_coffee/kmeans.o km_coffee/kmeans.c CC t_coffee_lib/t_coffee.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF t_coffee_lib/t_coffee.deps -c -o t_coffee_lib/t_coffee.o t_coffee_lib/t_coffee.c In file included from ./io_lib_header.h:33, from t_coffee_lib/t_coffee.c:35: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/aln_compare.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_compare.deps -c -o util_lib/aln_compare.o util_lib/aln_compare.c In file included from ./io_lib_header.h:33, from util_lib/aln_compare.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ t_coffee_lib/t_coffee.c: In function ‘char** km_coffee(int, char**)’: t_coffee_lib/t_coffee.c:6577:1: warning: no return statement in function returning non-void [-Wreturn-type] 6577 | } | ^ t_coffee_lib/t_coffee.c: In function ‘Alignment* t_coffee_dpa(int, char**)’: t_coffee_lib/t_coffee.c:7172:57: warning: too many arguments for format [-Wformat-extra-args] 7172 | else { w=seq2dpa_weight (S, "longuest");fprintf ( le, "default longuest\n", dpa_weight);} | ^~~~~~~~~~~~~~~~~~~~ t_coffee_lib/t_coffee.c: In function ‘int run_other_pg(int, char**)’: t_coffee_lib/t_coffee.c:6139:30: warning: control reaches end of non-void function [-Wreturn-type] 6139 | unpack_all_perl_script (argv[0]+strlen ("unpack_")); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ t_coffee_lib/t_coffee.c: In function ‘Alignment* km_align_seq_slow(char*, Alignment*, int, char**, int, int)’: t_coffee_lib/t_coffee.c:6816:1: warning: control reaches end of non-void function [-Wreturn-type] 6816 | } | ^ CC util_lib/aln_convertion_util.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_convertion_util.deps -c -o util_lib/aln_convertion_util.o util_lib/aln_convertion_util.c In file included from ./io_lib_header.h:33, from util_lib/aln_convertion_util.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ util_lib/aln_convertion_util.c: In function ‘int trim_aln_file(char*, char*, char*, char*)’: util_lib/aln_convertion_util.c:3105:62: warning: NULL used in arithmetic [-Wpointer-arith] 3105 | while ((get_next_fasta_sequence(fp, &name, &comment,&seq)!=NULL)) | ^~~~ util_lib/aln_convertion_util.c: In function ‘Alignment* aln2conservation(Alignment*, int, char*)’: util_lib/aln_convertion_util.c:4511:1: warning: no return statement in function returning non-void [-Wreturn-type] 4511 | } | ^ util_lib/aln_convertion_util.c: In function ‘Alignment* aln2N_replicate(Alignment*, char*, char*)’: util_lib/aln_convertion_util.c:7762:1: warning: no return statement in function returning non-void [-Wreturn-type] 7762 | } | ^ util_lib/aln_convertion_util.c: In function ‘Alignment* extract_aln3(Alignment*, char*)’: util_lib/aln_convertion_util.c:7524:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 7524 | fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7543:31: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 7543 | if ( c=='#' || c=='!')fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7547:13: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 7547 | fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/hsearch.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/hsearch.deps -c -o util_lib/hsearch.o util_lib/hsearch.c t_coffee_lib/t_coffee.c: In function ‘int batch_main(int, char**)’: t_coffee_lib/t_coffee.c:5662:45: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 982 and 991 [-Wformat-overflow=] 5662 | sprintf ( split_name, "%s.split.%d.%s", F->name, b,split_format); | ^~ ~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from t_coffee_lib/t_coffee.c:27: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 10 or more bytes (assuming 1018) into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from util_lib/hsearch.c:35: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/random.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/random.deps -c -o util_lib/random.o util_lib/random.c CC util_lib/reformat.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat.deps -c -o util_lib/reformat.o util_lib/reformat.c In file included from ./io_lib_header.h:33, from util_lib/reformat.c:35: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ util_lib/reformat.c: In function ‘int output_suchard_aln(char*, Alignment*)’: util_lib/reformat.c:7551:1: warning: no return statement in function returning non-void [-Wreturn-type] 7551 | } | ^ 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] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:11400:35: note: in expansion of macro ‘ATOI_ACTION’ 11400 | (D1->A)=aln2bootstrap (D1->A, ATOI_ACTION (1)); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:11406:32: note: in expansion of macro ‘ATOI_ACTION’ 11406 | (D1->A)=aln2sample (D1->A, ATOI_ACTION (1)); | ^~~~~~~~~~~ util_lib/reformat.c:11639:41: warning: null argument where non-null required (argument 1) [-Wnonnull] 11639 | if (ACTION (3))D=atof (ACTION(3)); | ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:11673:38: note: in expansion of macro ‘ATOI_ACTION’ 11673 | 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] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:11772:38: note: in expansion of macro ‘ATOI_ACTION’ 11772 | 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] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:11773:34: note: in expansion of macro ‘ATOI_ACTION’ 11773 | 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] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:11780:38: note: in expansion of macro ‘ATOI_ACTION’ 11780 | 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] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:11787:35: note: in expansion of macro ‘ATOI_ACTION’ 11787 | D1->S=treelist2sub_seq (D1->S,ATOI_ACTION(1)); | ^~~~~~~~~~~ util_lib/reformat.c:11815:27: warning: null argument where non-null required (argument 1) [-Wnonnull] 11815 | ng=atoi(ACTION (2))+1; | ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:11843:31: note: in expansion of macro ‘ATOI_ACTION’ 11843 | tree2bucket (D2->T, D1->S,ATOI_ACTION(1), ACTION(2)); | ^~~~~~~~~~~ util_lib/reformat.c:11855:29: warning: null argument where non-null required (argument 1) [-Wnonnull] 11855 | int shuf=atoi (ACTION(1)); | ^ util_lib/reformat.c:11856:27: warning: null argument where non-null required (argument 1) [-Wnonnull] 11856 | int n=atoi (ACTION (2)); | ^ util_lib/reformat.c:11862:29: warning: null argument where non-null required (argument 1) [-Wnonnull] 11862 | int shuf=atoi (ACTION(1)); | ^ util_lib/reformat.c:11873:29: warning: null argument where non-null required (argument 1) [-Wnonnull] 11873 | int shuf=atoi (ACTION(1)); | ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:12001:44: note: in expansion of macro ‘ATOI_ACTION’ 12001 | D1->T= aln2km_tree(D1->A, (ACTION(1)), ATOI_ACTION(2)); | ^~~~~~~~~~~ util_lib/reformat.c:12090:32: warning: null argument where non-null required (argument 1) [-Wnonnull] 12090 | else max=atof(ACTION(na+1)); | ^ util_lib/reformat.c:12093:32: warning: null argument where non-null required (argument 1) [-Wnonnull] 12093 | else enb=atoi(ACTION(na+2)); | ^ util_lib/reformat.c:12105:77: warning: null argument where non-null required (argument 1) [-Wnonnull] 12105 | if (ACTION(na+1)&& !strm (ACTION(na+1), "def"))max=atof(ACTION(na+1)); | ^ util_lib/reformat.c:12106:77: warning: null argument where non-null required (argument 1) [-Wnonnull] 12106 | if (ACTION(na+2)&& !strm (ACTION(na+2), "def"))enb=atoi(ACTION(na+2)); | ^ util_lib/reformat.c:12114:78: warning: null argument where non-null required (argument 1) [-Wnonnull] 12114 | if (ACTION(na+1) && !strm (ACTION(na+1), "def"))max=atof(ACTION(na+1)); | ^ util_lib/reformat.c:12115:78: warning: null argument where non-null required (argument 1) [-Wnonnull] 12115 | if (ACTION(na+2) && !strm (ACTION(na+2), "def"))enb=atoi(ACTION(na+2)); | ^ util_lib/reformat.c:12149:30: warning: null argument where non-null required (argument 1) [-Wnonnull] 12149 | radius=atof(ACTION(1)); | ^ util_lib/reformat.c:12157:33: warning: null argument where non-null required (argument 1) [-Wnonnull] 12157 | threshold=atof(ACTION(2)); | ^ util_lib/reformat.c:12164:27: warning: null argument where non-null required (argument 1) [-Wnonnull] 12164 | min=atoi(ACTION(3)); | ^ util_lib/reformat.c:12201:32: warning: null argument where non-null required (argument 1) [-Wnonnull] 12201 | else max=atof(ACTION(na+1)); | ^ util_lib/reformat.c:12204:32: warning: null argument where non-null required (argument 1) [-Wnonnull] 12204 | else enb=atoi(ACTION(na+2)); | ^ util_lib/reformat.c:12216:77: warning: null argument where non-null required (argument 1) [-Wnonnull] 12216 | if (ACTION(na+1)&& !strm (ACTION(na+1), "def"))max=atof(ACTION(na+1)); | ^ util_lib/reformat.c:12217:77: warning: null argument where non-null required (argument 1) [-Wnonnull] 12217 | if (ACTION(na+2)&& !strm (ACTION(na+2), "def"))enb=atoi(ACTION(na+2)); | ^ util_lib/reformat.c:12225:78: warning: null argument where non-null required (argument 1) [-Wnonnull] 12225 | if (ACTION(na+1) && !strm (ACTION(na+1), "def"))max=atof(ACTION(na+1)); | ^ util_lib/reformat.c:12226:78: warning: null argument where non-null required (argument 1) [-Wnonnull] 12226 | if (ACTION(na+2) && !strm (ACTION(na+2), "def"))enb=atoi(ACTION(na+2)); | ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:12275:44: note: in expansion of macro ‘ATOI_ACTION’ 12275 | float results=shuff (D1->S, ACTION (1),ATOI_ACTION(2)); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:12395:37: note: in expansion of macro ‘ATOI_ACTION’ 12395 | D1->A=aln2conservation ( D1->A, ATOI_ACTION (1), ACTION (2)); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:12519:31: note: in expansion of macro ‘ATOI_ACTION’ 12519 | D1->A=shuffle_aln (D1->A, ATOI_ACTION(1), ACTION(2), ACTION (3)); | ^~~~~~~~~~~ util_lib/reformat.c:13030:36: warning: null argument where non-null required (argument 1) [-Wnonnull] 13030 | else if (strstr (ACTION(1), "h")) | ^ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13037:10: note: in expansion of macro ‘ATOI_ACTION’ 13037 | F->t=ATOI_ACTION(2); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13038:10: note: in expansion of macro ‘ATOI_ACTION’ 13038 | F->f=ATOI_ACTION(3); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13039:11: note: in expansion of macro ‘ATOI_ACTION’ 13039 | F->p1=ATOI_ACTION(4); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13040:11: note: in expansion of macro ‘ATOI_ACTION’ 13040 | F->p2=ATOI_ACTION(5); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13041:11: note: in expansion of macro ‘ATOI_ACTION’ 13041 | F->p3=ATOI_ACTION(6); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13042:11: note: in expansion of macro ‘ATOI_ACTION’ 13042 | F->p3=ATOI_ACTION(7); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13065:34: note: in expansion of macro ‘ATOI_ACTION’ 13065 | 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] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13205:10: note: in expansion of macro ‘ATOI_ACTION’ 13205 | 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] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13206:19: note: in expansion of macro ‘ATOI_ACTION’ 13206 | 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] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13210:27: note: in expansion of macro ‘ATOI_ACTION’ 13210 | 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] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13217:34: note: in expansion of macro ‘ATOI_ACTION’ 13217 | 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] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13745:7: note: in expansion of macro ‘ATOI_ACTION’ 13745 | t=ATOI_ACTION(1); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13746:7: note: in expansion of macro ‘ATOI_ACTION’ 13746 | f=ATOI_ACTION(2); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13747:8: note: in expansion of macro ‘ATOI_ACTION’ 13747 | p1=ATOI_ACTION(3); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13748:8: note: in expansion of macro ‘ATOI_ACTION’ 13748 | p2=ATOI_ACTION(4); | ^~~~~~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] 43 | #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) | ^ util_lib/reformat.c:13749:8: note: in expansion of macro ‘ATOI_ACTION’ 13749 | p3=ATOI_ACTION(5); | ^~~~~~~~~~~ util_lib/reformat.c: In function ‘int output_header_mat(int**, char*)’: util_lib/reformat.c:14453:1: warning: no return statement in function returning non-void [-Wreturn-type] 14453 | } | ^ util_lib/reformat.c: In function ‘Sequence* quick_read_seq(char*)’: util_lib/reformat.c:1332:1: warning: control reaches end of non-void function [-Wreturn-type] 1332 | } | ^ util_lib/reformat.c: In function ‘Alignment* quick_read_aln_static(char*)’: util_lib/reformat.c:1371:1: warning: control reaches end of non-void function [-Wreturn-type] 1371 | } | ^ util_lib/reformat.c: In function ‘Alignment* quick_read_aln(char*)’: util_lib/reformat.c:1413:1: warning: control reaches end of non-void function [-Wreturn-type] 1413 | } | ^ util_lib/reformat.c: In function ‘int read_nameseq(char*, char***, char***, char***)’: util_lib/reformat.c:1427:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1427 | fscanf (fp, "#NAMESEQ_01\n"); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1428:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1428 | fscanf (fp, "# %d\n", &nseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1438:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1438 | fscanf (fp, "%d %d ", &l1, &l2); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1441:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1441 | fscanf (fp, "%s %s\n", nam[0][nseq], seq[0][nseq]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1446:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1446 | fscanf (fp, "%d ", &l1); | ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c:1448:15: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 1448 | fgets (com[0][nseq],l1, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int read_nameseq_old(char*, char***, char***, char***)’: util_lib/reformat.c:1472:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1472 | fscanf (fp, "#NAMESEQ_01\n"); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1473:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1473 | fscanf (fp, "# %d\n", &nseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1483:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1483 | fscanf (fp, "%d %d ", &l1, &l2); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1486:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1486 | fscanf (fp, "%s %s\n", nam[0][nseq], seq[0][nseq]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1491:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1491 | fscanf (fp, "%d ", &l1); | ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c:1493:15: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 1493 | fgets (com[0][nseq],l1, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int is_pdb_name(char*)’: util_lib/reformat.c:1788:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1788 | fscanf ( fp, "%d", &result); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘char* get_pdb_id(char*)’: util_lib/reformat.c:1826:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1826 | fscanf ( fp, "\n%s\n", buf); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int fast_format_determination(char*)’: util_lib/reformat.c:2507:1: warning: control reaches end of non-void function [-Wreturn-type] 2507 | } | ^ util_lib/reformat.c: In function ‘Weights* get_amps_sd_scores(char*)’: util_lib/reformat.c:3948:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 3948 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3955:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 3955 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3964:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 3964 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3970:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 3970 | fscanf ( fp, "%s",W->seq_name[a]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:3972:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 3972 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3983:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 3983 | fscanf ( fp, "\n"); | ~~~~~~~^~~~~~~~~~~ util_lib/reformat.c: In function ‘Structure* read_rna_struc_number(Alignment*, char*)’: util_lib/reformat.c:4256:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 4256 | fscanf ( fp, "%c\n%d\n",&x, &(ST)->tot_list); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4259:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 4259 | 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:4486:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 4486 | fscanf ( fp, "%s %d", name, &len); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4507:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 4507 | fscanf ( fp, "%s %d\n",S->name[S->nseq], &(S->len[S->nseq])); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4512:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 4512 | 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:4549:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 4549 | fscanf (fp, "%s",name); | ~~~~~~~^~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Sequence* get_dialign_sequence(char*)’: util_lib/reformat.c:4624:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 4624 | {fscanf (fp, "%s",name); | ~~~~~~~^~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int get_next_fasta_sequence(FILE*, char**, char**, char**)’: util_lib/reformat.c:5264:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 5264 | fgets (line, ml,fp); | ~~~~~~^~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int fscanf_seq_name(FILE*, char*)’: util_lib/reformat.c:5724:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 5724 | fscanf (fp, "%s", name); | ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int get_amps_seq_name(char**, char*)’: util_lib/reformat.c:6077:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 6077 | {fscanf (fp, "%*d >%s", name[nseq++]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Alignment* read_gotoh_aln(char*, Alignment*)’: util_lib/reformat.c:6126:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 6126 | fgets(buf, VERY_LONG_STRING, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:6148:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 6148 | fgets(buf, VERY_LONG_STRING, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘float output_maln_pval(char*, Alignment*)’: util_lib/reformat.c:6346:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 6346 | fscanf ( fp, "%s",string); | ~~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Alignment* similarities_file2aln(char*)’: util_lib/reformat.c:6511:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 6511 | fscanf (fp, "%s %d", name,&i); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int** read_blast_matrix(char*)’: util_lib/reformat.c:14294:13: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 14294 | fscanf ( fp, "%s ", buf); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:14307:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 14307 | fscanf ( fp, "%d ", &value); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14332:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 14332 | fscanf(fp, "\n"); | ~~~~~~^~~~~~~~~~ util_lib/reformat.c: In function ‘int** read_blast_matrix_old(char*)’: util_lib/reformat.c:14357:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 14357 | fgets ( sbuf, VERY_LONG_STRING, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14374:13: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 14374 | fscanf ( fp, "%s ", buf); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:14387:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 14387 | fscanf ( fp, "%d ", &value); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14414:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 14414 | fscanf(fp, "\n"); | ~~~~~~^~~~~~~~~~ util_lib/reformat.c: In function ‘int** read_pavie_matrix(char*)’: util_lib/reformat.c:14525:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 14525 | fgets ( sbuf, VERY_LONG_STRING, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/reformat_struc.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat_struc.deps -c -o util_lib/reformat_struc.o util_lib/reformat_struc.c In file included from ./io_lib_header.h:33, from util_lib/reformat_struc.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ util_lib/reformat_struc.c: In function ‘void bfactor2x_in_pdb(char*, char*, float*)’: util_lib/reformat_struc.c:125:18: warning: too many arguments for format [-Wformat-extra-args] 125 | fprintf (out, "ATOM ", lw[1]);//ATOM | ^~~~~~~~ util_lib/reformat_struc.c: In function ‘Ca_trace* simple_read_ca_trace(char*)’: util_lib/reformat_struc.c:370:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 370 | 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] 372 | fscanf ( fp, "%*s" ); | ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:378:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 378 | fscanf (fp, "%*s %*s %c %*c %d %*f %*f %*f\n",&res,&res_num); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat_struc.c:405:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 405 | fscanf ( fp, "%*s" ); | ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:407:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 407 | fscanf ( fp, "%*s" ); | ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:416:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 416 | fscanf (fp, "%*s %s %s %*c %d %f %f %f\n",A->type, A->res,&A->res_num, &A->x, &A->y, &A->z); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/util.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/util.deps -c -o util_lib/util.o util_lib/util.c In file included from ./io_lib_header.h:33, from util_lib/util.c:52: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ util_lib/util.c: In function ‘int cherry(int, char**)’: util_lib/util.c:1009:1: warning: no return statement in function returning non-void [-Wreturn-type] 1009 | } | ^ util_lib/util.c: In function ‘int dump_nfc(char*, char*)’: util_lib/util.c:4456:1: warning: no return statement in function returning non-void [-Wreturn-type] 4456 | } | ^ util_lib/util.c: In function ‘int set_nproc(int)’: util_lib/util.c:5489:1: warning: no return statement in function returning non-void [-Wreturn-type] 5489 | } | ^ util_lib/util.c: In function ‘char* vremove3(char*, char*)’: util_lib/util.c:6938:1: warning: no return statement in function returning non-void [-Wreturn-type] 6938 | } | ^ 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] 281 | 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] 286 | 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] 289 | 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] 306 | 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] 311 | 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] 420 | 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] 847 | fscanf ( fp, "%d",&list[n[0]++]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int quantile(int, char**)’: util_lib/util.c:1321:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1321 | fscanf ( fp, "%s %s\n", s1, s2); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int** input_array_int(char*)’: util_lib/util.c:1805:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1805 | fscanf (fp, "%d\n", &len); | ~~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/util.c:1809:13: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1809 | fscanf(fp, "%d ", &len2); | ~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/util.c:1812:8: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1812 | fscanf(fp, "%d ", &array[a][b]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:1813:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 1813 | fscanf (fp, "\n"); | ~~~~~~~^~~~~~~~~~ util_lib/util.c: In function ‘int perl_strstr(char*, char*)’: util_lib/util.c:2468:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 2468 | fscanf (fp, "%d", &r); | ~~~~~~~^~~~~~~~~~~~~~ util_lib/util.c: In function ‘int printf_system_direct_check(char*, ...)’: util_lib/util.c:4440:19: warning: control reaches end of non-void function [-Wreturn-type] 4440 | printf_exit ( EXIT_FAILURE, stderr, "ERROR: Could not run %s\n", buf); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* count_strings_in_file(char*, char*)’: util_lib/util.c:5761:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 5761 | fscanf (fp, "%s\n",list[n]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* redirect_stderr(char*)’: util_lib/util.c:6301:12: warning: ignoring return value of ‘FILE* freopen(const char*, const char*, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 6301 | freopen(stderr_file, "w", stderr); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* redirect_stdout(char*)’: util_lib/util.c:6344:12: warning: ignoring return value of ‘FILE* freopen(const char*, const char*, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 6344 | freopen(stdout_file, "w", stdout); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 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:7645:2: warning: second parameter of ‘va_start’ not last named argument [-Wvarargs] 7645 | va_start (ap, usage); | ^~~~~~~~ util_lib/util.c: In function ‘char** get_parameter(char*, int*, char*)’: util_lib/util.c:7912:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 7912 | fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘FILE* set_fp_id(FILE*, char*)’: util_lib/util.c:7932:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 7932 | fscanf ( fp, "%s", string); | ~~~~~~~^~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int** get_file_block_pattern(char*, int*, int)’: util_lib/util.c:8319:11: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 8319 | fgets ( line, lline,fp); | ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util.c:8349:11: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 8349 | fgets ( line, lline,fp); | ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int check_for_update(char*)’: util_lib/util.c:8436:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 8436 | fscanf ( fp, "Version_%f", &new_version); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int check_internet_connection(int)’: util_lib/util.c:8528:10: warning: control reaches end of non-void function [-Wreturn-type] 8528 | myexit (EXIT_FAILURE); | ~~~~~~~^~~~~~~~~~~~~~ util_lib/util.c: In function ‘int km_main(int, char**)’: util_lib/util.c:10533:1: warning: control reaches end of non-void function [-Wreturn-type] 10533 | } | ^ util_lib/aln_convertion_util.c: In function ‘float** get_weight(Alignment*, Sequence*, char*)’: util_lib/aln_convertion_util.c:12147:32: warning: ‘ -w ’ directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 12147 | sprintf ( command, "%s %s -w %s", program, seq_name, weight_name); | ^~~~ In file included from /usr/include/stdio.h:867, from util_lib/aln_convertion_util.c:27: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 6 or more bytes (assuming 1005) into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:12141:32: warning: ‘ -i ’ directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 12141 | sprintf ( command, "%s %s -i %s -w %s", program, seq_name, aln_name, weight_name); | ^~~~ In file included from /usr/include/stdio.h:867, from util_lib/aln_convertion_util.c:27: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 10 or more bytes (assuming 1009) into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/util_aln_analyze.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/util_aln_analyze.deps -c -o util_lib/util_aln_analyze.o util_lib/util_aln_analyze.c In file included from ./io_lib_header.h:33, from util_lib/util_aln_analyze.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ util_lib/util_aln_analyze.c: In function ‘Alignment* sar_analyze(Alignment*, Alignment*, char*)’: util_lib/util_aln_analyze.c:713:1: warning: no return statement in function returning non-void [-Wreturn-type] 713 | } | ^ util_lib/util_aln_analyze.c: In function ‘Alignment* or_scan(Alignment*, Alignment*, char*)’: util_lib/util_aln_analyze.c:4480:1: warning: no return statement in function returning non-void [-Wreturn-type] 4480 | } | ^ 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:13639:27: warning: ‘ -method ’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 13639 | sprintf ( command, "%s -method %s -aln %s -tree %s -dmatrix %s -weightfile %s %s",method_4_msa_weights, action_list[1],aln_name, tree_name, dist_matrix_name,weight_name, TO_NULL_DEVICE); | ^~~~~~~~~ In file included from /usr/include/stdio.h:867, from util_lib/reformat.c:27: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 64 or more bytes (assuming 3059) into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)’ at util_lib/reformat.c:11638:17: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* get_cache_4_tcoffee()’: util_lib/util.c:5385:42: warning: ‘/cache/’ directive writing 7 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5385 | else sprintf ( cache_4_tcoffee, "%s/cache/", get_dir_4_tcoffee()); | ^~~~~~~ In file included from /usr/include/stdio.h:867, from util_lib/util.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 8 and 1007 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* get_plugins_4_tcoffee()’: util_lib/util.c:5435:43: warning: ‘/plugins/’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5435 | else sprintf (plugins_4_tcoffee, "%s/plugins/%s/", get_dir_4_tcoffee(), get_os()); | ^~~~~~~~~ In file included from /usr/include/stdio.h:867, from util_lib/util.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 11 and 1109 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/util_analyse_constraints_list.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/util_analyse_constraints_list.deps -c -o util_lib/util_analyse_constraints_list.o util_lib/util_analyse_constraints_list.c In file included from ./io_lib_header.h:33, from util_lib/util_analyse_constraints_list.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/util_constraints_list.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/util_constraints_list.deps -c -o util_lib/util_constraints_list.o util_lib/util_constraints_list.c In file included from ./io_lib_header.h:33, from util_lib/util_constraints_list.c:37: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ util_lib/util.c: In function ‘char* long_tmpnam_2(char*)’: util_lib/util.c:6826:22: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 0 and 9999 [-Wformat-overflow=] 6826 | sprintf (buf, "%s/%s%d%s",tmpdir,root2, file++,set_file2remove_extension (NULL, GET)); | ^~ In file included from /usr/include/stdio.h:867, from util_lib/util.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 3 or more bytes (assuming 10101) into a destination of size 10000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘Constraint_list* unfreeze_constraint_list(Constraint_list*)’: util_lib/util_constraints_list.c:1311:1: warning: no return statement in function returning non-void [-Wreturn-type] 1311 | } | ^ 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:2224:28: warning: too many arguments for format [-Wformat-extra-args] 2224 | 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:2851:19: warning: too many arguments for format [-Wformat-extra-args] 2851 | x=sscanf (buf, "%s %d %d %d %d %d",arg, &length, &r1,&r2,&we,&cons,&misc); | ^~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* ultrashort_tmpnam_2(char*)’: util_lib/util.c:6858:22: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 0 and 9999 [-Wformat-overflow=] 6858 | sprintf (buf, "%s/%s%d%s",tmpdir,root2, file++,set_file2remove_extension (NULL, GET)); | ^~ In file included from /usr/include/stdio.h:867, from util_lib/util.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 3 or more bytes (assuming 10101) into a destination of size 10000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘Job_TC* submit_lib_job(Job_TC*)’: util_lib/util_constraints_list.c:582:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 582 | chdir (tdir); | ~~~~~~^~~~~~ util_lib/util_constraints_list.c:585:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 585 | chdir (cdir); | ~~~~~~^~~~~~ util_lib/util_constraints_list.c: In function ‘char* method_file_tag2value(char*, char*)’: util_lib/util_constraints_list.c:1150:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 1150 | 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:1193:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 1193 | 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:2599:20: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 2599 | 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:2917:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 2917 | fscanf (fp, "%d\n", &max_nseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2922:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 2922 | fscanf (fp, "%*s %d %*s\n", &l); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2954:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 2954 | fscanf ( fp, "%s %d %s\n", name, &seq_len, sequence); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2979:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 2979 | 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:4053:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 4053 | fscanf (fp, "%d ", &CL->residue_index[s][r][a+WE]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* short_tmpnam_2(char*)’: util_lib/util.c:6889:22: warning: ‘%s’ directive writing up to 99 bytes into a region of size between 0 and 9999 [-Wformat-overflow=] 6889 | sprintf (buf, "%s%d%s",root2, file++,set_file2remove_extension (NULL, GET)); | ^~ In file included from /usr/include/stdio.h:867, from util_lib/util.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 2 and 10110 bytes into a destination of size 10000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* get_mcoffee_4_tcoffee()’: util_lib/util.c:5400:44: warning: ‘/mcoffee/’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5400 | else sprintf ( mcoffee_4_tcoffee, "%s/mcoffee/", get_dir_4_tcoffee()); | ^~~~~~~~~ In file included from /usr/include/stdio.h:867, from util_lib/util.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 10 and 1009 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* get_methods_4_tcoffee()’: util_lib/util.c:5413:44: warning: ‘/methods/’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5413 | else sprintf ( methods_4_tcoffee, "%s/methods/", get_dir_4_tcoffee()); | ^~~~~~~~~ In file included from /usr/include/stdio.h:867, from util_lib/util.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 10 and 1009 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* get_cache_4_tcoffee()’: util_lib/util.c:5385:42: warning: ‘/cache/’ directive writing 7 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5385 | else sprintf ( cache_4_tcoffee, "%s/cache/", get_dir_4_tcoffee()); | ^~~~~~~ In file included from /usr/include/stdio.h:867, from util_lib/util.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 8 and 1007 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘char* make_aln_command(TC_method*, char*, char*)’: util_lib/util_constraints_list.c:1286:21: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 499 and 999 [-Wformat-overflow=] 1286 | sprintf ( buf, "%s %s %s%s %s %s%s %s", m->executable, m->param1, m->in_flag, seq,m->param2, m->out_flag,aln, m->param); | ^~ In file included from /usr/include/stdio.h:867, from util_lib/util_constraints_list.c:29: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output 6 or more bytes (assuming 4503) into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/util_declare.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/util_declare.deps -c -o util_lib/util_declare.o util_lib/util_declare.c In file included from ./io_lib_header.h:33, from util_lib/util_declare.c:37: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ util_lib/util_constraints_list.c: In function ‘Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)’: util_lib/util_constraints_list.c:4922:19: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 4922 | sprintf ( mode, "%s", (CL && in_mode==NULL)?CL->distance_matrix_mode:in_mode); | ^~ In file included from /usr/include/stdio.h:867, from util_lib/util_constraints_list.c:29: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:4923:23: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 4923 | sprintf ( sim_mode, "%s", (CL && in_sim_mode==NULL)?CL->distance_matrix_sim_mode:in_sim_mode); | ^~ In file included from /usr/include/stdio.h:867, from util_lib/util_constraints_list.c:29: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/util_domain_constraints_list.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/util_domain_constraints_list.deps -c -o util_lib/util_domain_constraints_list.o util_lib/util_domain_constraints_list.c In file included from ./io_lib_header.h:33, from util_lib/util_domain_constraints_list.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/util_dps.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/util_dps.deps -c -o util_lib/util_dps.o util_lib/util_dps.c In file included from ./io_lib_header.h:33, from util_lib/util_dps.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/util_job_handling.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/util_job_handling.deps -c -o util_lib/util_job_handling.o util_lib/util_job_handling.c util_lib/util.c: In function ‘char** standard_initialisation(char**, int*)’: util_lib/util.c:5400:44: warning: ‘/mcoffee/’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5400 | else sprintf ( mcoffee_4_tcoffee, "%s/mcoffee/", get_dir_4_tcoffee()); | ^~~~~~~~~ In file included from /usr/include/stdio.h:867, from util_lib/util.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 10 and 1009 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:5413:44: warning: ‘/methods/’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5413 | else sprintf ( methods_4_tcoffee, "%s/methods/", get_dir_4_tcoffee()); | ^~~~~~~~~ In file included from /usr/include/stdio.h:867, from util_lib/util.c:32: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 10 and 1009 bytes into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from util_lib/util_job_handling.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/util_make_tree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/t-coffee-13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wno-write-strings -I. -MD -MF util_lib/util_make_tree.deps -c -o util_lib/util_make_tree.o util_lib/util_make_tree.c In file included from ./io_lib_header.h:33, from util_lib/util_make_tree.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ util_lib/util_make_tree.c: In function ‘tnode* redundate(Sequence*, NT_node, char*, char*)’: util_lib/util_make_tree.c:66:1: warning: no return statement in function returning non-void [-Wreturn-type] 66 | } | ^ util_lib/util_make_tree.c: In function ‘char* seq2co_aln_file(char*, char*)’: util_lib/util_make_tree.c:124:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 124 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:127:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 127 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘char* seq2mafft_aln_file(char*, char*)’: util_lib/util_make_tree.c:157:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 157 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:160:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 160 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘char* seq2cw_aln_file(char*, char*)’: util_lib/util_make_tree.c:190:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 190 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:192:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 192 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘char* prf_pair2cw_aln_file(char*, char*, char*)’: util_lib/util_make_tree.c:223:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 223 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:226:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 226 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2fftns1_dnd(Sequence*)’: util_lib/util_make_tree.c:1855:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1855 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1868:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1868 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2fftns2_dnd(Sequence*)’: util_lib/util_make_tree.c:1884:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1884 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1897:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1897 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2mafft_dnd(Sequence*)’: util_lib/util_make_tree.c:1913:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1913 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1926:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1926 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2parttree_dnd(Sequence*)’: util_lib/util_make_tree.c:1943:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1943 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1956:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1956 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2dpparttree_dnd(Sequence*)’: util_lib/util_make_tree.c:1973:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1973 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1988:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1988 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2fastparttree_dnd(Sequence*)’: util_lib/util_make_tree.c:2006:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2006 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2019:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2019 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2cwquick_dnd(Sequence*)’: util_lib/util_make_tree.c:2035:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2035 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2043:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2043 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2cw_dnd(Sequence*)’: util_lib/util_make_tree.c:2060:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2060 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2068:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2068 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* aln2cw_tree(Alignment*)’: util_lib/util_make_tree.c:2088:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2088 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2095:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2095 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2cw_tree(Sequence*)’: util_lib/util_make_tree.c:2110:9: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2110 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2119:12: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 2119 | chdir (cdir); | ~~~~~~~~~^~~~~~ 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:694:24: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 694 | sprintf ( aln_mode, "%s", method->aln_mode); | ^~ In file included from /usr/include/stdio.h:867, from util_lib/util_constraints_list.c:29: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:695:24: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 695 | sprintf ( out_mode, "%s", method->out_mode); | ^~ In file included from /usr/include/stdio.h:867, from util_lib/util_constraints_list.c:29: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Linking... g++ dev_lib/dev1.o dp_lib/CUSTOM_evaluate_for_struc.o dp_lib/evaluate.o dp_lib/evaluate_dirichlet.o dp_lib/evaluate_for_domain.o dp_lib/evaluate_for_struc.o dp_lib/fsa_dp.o dp_lib/pavie_dp.o dp_lib/showpair.o dp_lib/util_domain_dp.o dp_lib/util_domain_dp_drivers.o dp_lib/util_dp_cdna_fasta_nw.o dp_lib/util_dp_clean_maln.o dp_lib/util_dp_drivers.o dp_lib/util_dp_est.o dp_lib/util_dp_fasta_nw.o dp_lib/util_dp_fasta_sw.o dp_lib/util_dp_generic_fasta_nw.o dp_lib/util_dp_gotoh_nw.o dp_lib/util_dp_gotoh_sw.o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_sim.o dp_lib/util_dp_ssec_pwaln.o dp_lib/util_dp_suboptimal_nw.o dp_lib/util_graph_maln.o fastal/diagonal.o fastal/fastal.o fastal/fastal_opt_parsing.o fastal/iteration.o fastal/parttree.o fastal/scoring.o fastal/tree.o io_lib/io_func.o io_lib/pb_util_read_seq_util.o io_lib/pb_util_read_sequence.o io_lib/tree_util.o km_coffee/Stack.o km_coffee/Vector.o km_coffee/classes.o km_coffee/km_coffee.o km_coffee/km_util.o km_coffee/kmeans.o t_coffee_lib/t_coffee.o util_lib/aln_compare.o util_lib/aln_convertion_util.o util_lib/hsearch.o util_lib/random.o util_lib/reformat.o util_lib/reformat_struc.o util_lib/util.o util_lib/util_aln_analyze.o util_lib/util_analyse_constraints_list.o util_lib/util_constraints_list.o util_lib/util_declare.o util_lib/util_domain_constraints_list.o util_lib/util_dps.o util_lib/util_job_handling.o util_lib/util_make_tree.o -o t_coffee -lm -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now /usr/bin/ld: dp_lib/util_dp_drivers.o: in function `hh_pair(TC_method*, char*, Constraint_list*)': ./t_coffee_source/dp_lib/util_dp_drivers.c:1160: warning: the use of `tmpnam' is dangerous, better use `mkstemp' make[2]: Leaving directory '/<>/t-coffee-13.41.0.28bdc39+dfsg/t_coffee_source' make[1]: Leaving directory '/<>/t-coffee-13.41.0.28bdc39+dfsg' dh_auto_test -a -O--sourcedirectory=t_coffee_source create-stamp debian/debhelper-build-stamp 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 '/<>/t-coffee-13.41.0.28bdc39+dfsg' dh_installexamples for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/share/doc/*` ; do \ sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/<>/t-coffee-13.41.0.28bdc39+dfsg' dh_installman -a -O--sourcedirectory=t_coffee_source dh_installinit -a -O--sourcedirectory=t_coffee_source dh_installsystemduser -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 '/<>/t-coffee-13.41.0.28bdc39+dfsg' #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 '/<>/t-coffee-13.41.0.28bdc39+dfsg' dh_fixperms -a -O--sourcedirectory=t_coffee_source dh_missing -a -O--sourcedirectory=t_coffee_source dh_dwz -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 dpkg-shlibdeps: warning: debian/t-coffee/usr/bin/t_coffee contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin 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 146 INFO: pkgstriptranslations version 146 pkgstriptranslations: processing t-coffee (in debian/t-coffee); do_strip: , oemstrip: pkgstriptranslations: processing t-coffee-dbgsym (in debian/.debhelper/t-coffee/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/t-coffee/dbgsym-root/DEBIAN/control, package t-coffee-dbgsym, directory debian/.debhelper/t-coffee/dbgsym-root dpkg-deb: building package 't-coffee-dbgsym' in 'debian/.debhelper/scratch-space/build-t-coffee/t-coffee-dbgsym_13.41.0.28bdc39+dfsg-4_armhf.deb'. 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_13.41.0.28bdc39+dfsg-4_armhf.deb'. Renaming t-coffee-dbgsym_13.41.0.28bdc39+dfsg-4_armhf.deb to t-coffee-dbgsym_13.41.0.28bdc39+dfsg-4_armhf.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../t-coffee_13.41.0.28bdc39+dfsg-4_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20200618-0030 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ t-coffee_13.41.0.28bdc39+dfsg-4_armhf.changes: ---------------------------------------------- Format: 1.8 Date: Wed, 17 Jun 2020 20:34:34 +0200 Source: t-coffee Binary: t-coffee Architecture: armhf Version: 13.41.0.28bdc39+dfsg-4 Distribution: groovy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Etienne Mollier Description: t-coffee - Multiple Sequence Alignment Closes: 962974 Changes: t-coffee (13.41.0.28bdc39+dfsg-4) unstable; urgency=medium . * Team upload. * Increase MAX_N_PID to 4194304. (Closes: #962974) * Updated the homepage, following permanent redirection. Checksums-Sha1: 38c9083a1d827cca6d5390f7154c0746f8ce273a 2767264 t-coffee-dbgsym_13.41.0.28bdc39+dfsg-4_armhf.ddeb a139498d5c3b12dc661cc078b0a5c4a8ca9f1ff2 5081 t-coffee_13.41.0.28bdc39+dfsg-4_armhf.buildinfo 525c7608134131df95802e9844321587f1e22056 871196 t-coffee_13.41.0.28bdc39+dfsg-4_armhf.deb Checksums-Sha256: 9f6049f568c3e6dbdefaa1756abe7c71fea08226a9f0814a9dea984235e1cb75 2767264 t-coffee-dbgsym_13.41.0.28bdc39+dfsg-4_armhf.ddeb ee3ecd99a526597baf6d820b6ab87fe4b68f3c5877669ee8334e6569515e821b 5081 t-coffee_13.41.0.28bdc39+dfsg-4_armhf.buildinfo 79739ed131d59930c057e58935e6811201e67d492c16b39c32055a4b2047333b 871196 t-coffee_13.41.0.28bdc39+dfsg-4_armhf.deb Files: 02b0e997f0ea6ec194487afac693c5f2 2767264 debug optional t-coffee-dbgsym_13.41.0.28bdc39+dfsg-4_armhf.ddeb e138b48dc60e5883eb6eb161371e2fa5 5081 science optional t-coffee_13.41.0.28bdc39+dfsg-4_armhf.buildinfo f3ea428e242d1e175eb52137a7137615 871196 science optional t-coffee_13.41.0.28bdc39+dfsg-4_armhf.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ t-coffee_13.41.0.28bdc39+dfsg-4_armhf.deb ----------------------------------------- new debian package, version 2.0. size 871196 bytes: control archive=1432 bytes. 1673 bytes, 30 lines control 473 bytes, 7 lines md5sums Package: t-coffee Version: 13.41.0.28bdc39+dfsg-4 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1912 Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.5), libstdc++6 (>= 4.3.0) 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/tcoffee/index.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 2020-06-17 18:34 ./ drwxr-xr-x root/root 0 2020-06-17 18:34 ./usr/ drwxr-xr-x root/root 0 2020-06-17 18:34 ./usr/bin/ -rwxr-xr-x root/root 1932668 2020-06-17 18:34 ./usr/bin/t_coffee drwxr-xr-x root/root 0 2020-06-17 18:34 ./usr/share/ drwxr-xr-x root/root 0 2020-06-17 18:34 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-06-17 18:34 ./usr/share/doc/t-coffee/ -rw-r--r-- root/root 1744 2020-06-17 18:34 ./usr/share/doc/t-coffee/README.Debian -rw-r--r-- root/root 261 2020-06-17 18:34 ./usr/share/doc/t-coffee/README.test -rw-r--r-- root/root 1412 2020-06-17 18:34 ./usr/share/doc/t-coffee/changelog.Debian.gz -rw-r--r-- root/root 1571 2020-06-17 18:34 ./usr/share/doc/t-coffee/copyright -rw-r--r-- root/root 2586 2020-06-17 18:34 ./usr/share/doc/t-coffee/run-unit-test drwxr-xr-x root/root 0 2020-06-17 18:34 ./usr/share/man/ drwxr-xr-x root/root 0 2020-06-17 18:34 ./usr/share/man/man1/ -rw-r--r-- root/root 1463 2020-06-17 18:34 ./usr/share/man/man1/t_coffee.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 57768 Build-Time: 125 Distribution: groovy-proposed Host Architecture: armhf Install-Time: 19 Job: t-coffee_13.41.0.28bdc39+dfsg-4.dsc Machine Architecture: arm64 Package: t-coffee Package-Time: 147 Source-Version: 13.41.0.28bdc39+dfsg-4 Space: 57768 Status: successful Version: 13.41.0.28bdc39+dfsg-4 -------------------------------------------------------------------------------- Finished at 20200618-0030 Build needed 00:02:27, 57768k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19472633 Scanning for processes to kill in build PACKAGEBUILD-19472633