https://launchpad.net/ubuntu/+source/t-coffee/13.41.0.28bdc39+dfsg-4/+build/19472635 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux riscv64-qemu-lcy01-007 5.4.0-21-generic #25-Ubuntu SMP Tue Mar 31 01:57:06 UTC 2020 riscv64 Buildd toolchain package versions: launchpad-buildd_188 python-lpbuildd_188 sbuild_0.79.0-1ubuntu1 git_1:2.25.1-1ubuntu1 dpkg-dev_1.19.7ubuntu2 python-debian_0.1.36build1. Syncing the system clock with the buildd NTP service... 17 Jun 23:52:52 ntpdate[1935171]: adjust time server 10.211.37.1 offset -0.000425 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=groovy --arch=riscv64 PACKAGEBUILD-19472635 --image-type chroot /home/buildd/filecache-default/f3eb94e98b295919e6c8d0c40a2cb7b393a0119c Creating target for build PACKAGEBUILD-19472635 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=groovy --arch=riscv64 PACKAGEBUILD-19472635 Starting target for build PACKAGEBUILD-19472635 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=groovy --arch=riscv64 PACKAGEBUILD-19472635 '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-19472635 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=groovy --arch=riscv64 PACKAGEBUILD-19472635 Updating target for build PACKAGEBUILD-19472635 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 riscv64 Packages [883 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main Translation-en [508 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/universe riscv64 Packages [8110 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/universe Translation-en [5187 kB] Get:9 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 Packages [58.9 kB] Get:10 http://ftpmaster.internal/ubuntu groovy-proposed/main Translation-en [44.8 kB] Get:11 http://ftpmaster.internal/ubuntu groovy-proposed/universe riscv64 Packages [770 kB] Get:12 http://ftpmaster.internal/ubuntu groovy-proposed/universe Translation-en [415 kB] Fetched 16.5 MB in 28s (600 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be REMOVED: libgcc1* The following packages will be upgraded: apt base-files binutils binutils-common binutils-riscv64-linux-gnu bzip2 ca-certificates cpp-9 dash debconf debianutils dpkg dpkg-dev e2fsprogs g++-9 gcc-10-base gcc-8-base gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv gzip libacl1 libapt-pkg6.0 libassuan0 libatomic1 libbinutils libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libctf-nobfd0 libctf0 libdebconfclient0 libdpkg-perl libext2fs2 libgcc-9-dev libgcc-s1 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgpm2 libidn2-0 libncursesw6 libnpth0 libperl5.30 libsqlite3-0 libss2 libssl1.1 libstdc++-9-dev libstdc++6 libsystemd0 libtinfo6 libudev1 libunistring2 libzstd1 linux-libc-dev login logsave make ncurses-base ncurses-bin openssl passwd perl perl-base perl-modules-5.30 pkgbinarymangler sysvinit-utils ubuntu-keyring 79 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. Need to get 53.6 MB of archives. After this operation, 226 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 libcrypt-dev riscv64 1:4.4.16-1ubuntu1 [204 kB] Get:2 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 libcrypt1 riscv64 1:4.4.16-1ubuntu1 [94.2 kB] Get:3 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 libc6-dev riscv64 2.31-0ubuntu10 [3658 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 libc-dev-bin riscv64 2.31-0ubuntu10 [62.5 kB] Get:5 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 linux-libc-dev riscv64 5.4.0-27.31 [1063 kB] Get:6 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 libatomic1 riscv64 10.1.0-4ubuntu2 [7472 B] Get:7 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 libgomp1 riscv64 10.1.0-4ubuntu2 [83.5 kB] Get:8 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 gcc-10-base riscv64 10.1.0-4ubuntu2 [20.2 kB] Get:9 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 libgcc-s1 riscv64 10.1.0-4ubuntu2 [40.4 kB] Get:10 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 libcc1-0 riscv64 10.1.0-4ubuntu2 [38.1 kB] Get:11 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 libstdc++6 riscv64 10.1.0-4ubuntu2 [506 kB] Get:12 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 libc6 riscv64 2.31-0ubuntu10 [2268 kB] Get:13 http://ftpmaster.internal/ubuntu groovy/main riscv64 base-files riscv64 11ubuntu7 [59.7 kB] Get:14 http://ftpmaster.internal/ubuntu groovy/main riscv64 debianutils riscv64 4.11 [84.5 kB] Get:15 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 dpkg riscv64 1.19.7ubuntu4 [1090 kB] Get:16 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 perl-modules-5.30 all 5.30.3-4 [2740 kB] Get:17 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 libperl5.30 riscv64 5.30.3-4 [3444 kB] Get:18 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 perl riscv64 5.30.3-4 [223 kB] Get:19 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 perl-base riscv64 5.30.3-4 [1421 kB] Get:20 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 bzip2 riscv64 1.0.8-3 [32.6 kB] Get:21 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 libbz2-1.0 riscv64 1.0.8-3 [34.5 kB] Get:22 http://ftpmaster.internal/ubuntu groovy/main riscv64 debconf all 1.5.74 [121 kB] Get:23 http://ftpmaster.internal/ubuntu groovy/main riscv64 dash riscv64 0.5.10.2-7 [82.0 kB] Get:24 http://ftpmaster.internal/ubuntu groovy/main riscv64 gzip riscv64 1.10-2ubuntu1 [91.7 kB] Get:25 http://ftpmaster.internal/ubuntu groovy/main riscv64 login riscv64 1:4.8.1-1ubuntu6 [216 kB] Get:26 http://ftpmaster.internal/ubuntu groovy/main riscv64 ncurses-bin riscv64 6.2-1 [166 kB] Get:27 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 libc-bin riscv64 2.31-0ubuntu10 [511 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main riscv64 ncurses-base all 6.2-1 [18.7 kB] Get:29 http://ftpmaster.internal/ubuntu groovy/main riscv64 sysvinit-utils riscv64 2.96-3ubuntu1 [19.6 kB] Get:30 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 libsystemd0 riscv64 245.6-1ubuntu1 [240 kB] Get:31 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 libudev1 riscv64 245.6-1ubuntu1 [66.8 kB] Get:32 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 libzstd1 riscv64 1.4.5+dfsg-2 [340 kB] Get:33 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 libapt-pkg6.0 riscv64 2.1.6 [804 kB] Get:34 http://ftpmaster.internal/ubuntu groovy/main riscv64 libgpg-error0 riscv64 1.38-1 [55.2 kB] Get:35 http://ftpmaster.internal/ubuntu groovy/main riscv64 gpgv riscv64 2.2.20-1ubuntu1 [181 kB] Get:36 http://ftpmaster.internal/ubuntu groovy/main riscv64 ubuntu-keyring all 2020.06.17.1 [22.2 kB] Get:37 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 libgmp10 riscv64 2:6.2.0+dfsg-6 [232 kB] Get:38 http://ftpmaster.internal/ubuntu groovy/main riscv64 libunistring2 riscv64 0.9.10-4 [361 kB] Get:39 http://ftpmaster.internal/ubuntu groovy/main riscv64 libidn2-0 riscv64 2.3.0-1 [50.5 kB] Get:40 http://ftpmaster.internal/ubuntu groovy/main riscv64 libgnutls30 riscv64 3.6.13-4ubuntu2 [721 kB] Get:41 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 apt riscv64 2.1.6 [1231 kB] Get:42 http://ftpmaster.internal/ubuntu groovy/main riscv64 logsave riscv64 1.45.6-1ubuntu1 [9708 B] Get:43 http://ftpmaster.internal/ubuntu groovy/main riscv64 libext2fs2 riscv64 1.45.6-1ubuntu1 [175 kB] Get:44 http://ftpmaster.internal/ubuntu groovy/main riscv64 e2fsprogs riscv64 1.45.6-1ubuntu1 [496 kB] Get:45 http://ftpmaster.internal/ubuntu groovy/main riscv64 libacl1 riscv64 2.2.53-8 [16.4 kB] Get:46 http://ftpmaster.internal/ubuntu groovy/main riscv64 libcap-ng0 riscv64 0.7.9-2.2 [9948 B] Get:47 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 libdebconfclient0 riscv64 0.252ubuntu1 [5704 B] Get:48 http://ftpmaster.internal/ubuntu groovy/main riscv64 libncursesw6 riscv64 6.2-1 [116 kB] Get:49 http://ftpmaster.internal/ubuntu groovy/main riscv64 libtinfo6 riscv64 6.2-1 [78.7 kB] Get:50 http://ftpmaster.internal/ubuntu groovy/main riscv64 passwd riscv64 1:4.8.1-1ubuntu6 [751 kB] Get:51 http://ftpmaster.internal/ubuntu groovy/main riscv64 libcom-err2 riscv64 1.45.6-1ubuntu1 [8564 B] Get:52 http://ftpmaster.internal/ubuntu groovy/main riscv64 libss2 riscv64 1.45.6-1ubuntu1 [9820 B] Get:53 http://ftpmaster.internal/ubuntu groovy/main riscv64 libssl1.1 riscv64 1.1.1f-1ubuntu2 [967 kB] Get:54 http://ftpmaster.internal/ubuntu groovy/main riscv64 openssl riscv64 1.1.1f-1ubuntu2 [595 kB] Get:55 http://ftpmaster.internal/ubuntu groovy/main riscv64 ca-certificates all 20190110ubuntu2 [145 kB] Get:56 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 libsqlite3-0 riscv64 3.32.2-2 [488 kB] Get:57 http://ftpmaster.internal/ubuntu groovy/main riscv64 libctf0 riscv64 2.34-7ubuntu1 [39.9 kB] Get:58 http://ftpmaster.internal/ubuntu groovy/main riscv64 binutils-riscv64-linux-gnu riscv64 2.34-7ubuntu1 [646 kB] Get:59 http://ftpmaster.internal/ubuntu groovy/main riscv64 libbinutils riscv64 2.34-7ubuntu1 [279 kB] Get:60 http://ftpmaster.internal/ubuntu groovy/main riscv64 binutils riscv64 2.34-7ubuntu1 [3288 B] Get:61 http://ftpmaster.internal/ubuntu groovy/main riscv64 binutils-common riscv64 2.34-7ubuntu1 [199 kB] Get:62 http://ftpmaster.internal/ubuntu groovy/main riscv64 libctf-nobfd0 riscv64 2.34-7ubuntu1 [40.7 kB] Get:63 http://ftpmaster.internal/ubuntu groovy/main riscv64 g++-9 riscv64 9.3.0-13ubuntu1 [6931 kB] Get:64 http://ftpmaster.internal/ubuntu groovy/main riscv64 gcc-9 riscv64 9.3.0-13ubuntu1 [6789 kB] Get:65 http://ftpmaster.internal/ubuntu groovy/main riscv64 libstdc++-9-dev riscv64 9.3.0-13ubuntu1 [3670 kB] Get:66 http://ftpmaster.internal/ubuntu groovy/main riscv64 libgcc-9-dev riscv64 9.3.0-13ubuntu1 [405 kB] Get:67 http://ftpmaster.internal/ubuntu groovy/main riscv64 cpp-9 riscv64 9.3.0-13ubuntu1 [6047 kB] Get:68 http://ftpmaster.internal/ubuntu groovy/main riscv64 gcc-9-base riscv64 9.3.0-13ubuntu1 [19.6 kB] Get:69 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 dpkg-dev all 1.19.7ubuntu4 [679 kB] Get:70 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 libdpkg-perl all 1.19.7ubuntu4 [230 kB] Get:71 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 make riscv64 4.3-3 [158 kB] Get:72 http://ftpmaster.internal/ubuntu groovy/universe riscv64 gcc-8-base riscv64 8.4.0-4ubuntu1 [18.4 kB] Get:73 http://ftpmaster.internal/ubuntu groovy/main riscv64 libassuan0 riscv64 2.5.3-7.1 [30.6 kB] Get:74 http://ftpmaster.internal/ubuntu groovy/main riscv64 libnpth0 riscv64 1.6-2 [6832 B] Get:75 http://ftpmaster.internal/ubuntu groovy/main riscv64 gpg riscv64 2.2.20-1ubuntu1 [439 kB] Get:76 http://ftpmaster.internal/ubuntu groovy/main riscv64 gpgconf riscv64 2.2.20-1ubuntu1 [110 kB] Get:77 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Updating certificates in /etc/ssl/certs... 0 added, 1 removed; done. Setting up perl (5.30.3-4) ... Setting up libdpkg-perl (1.19.7ubuntu4) ... Setting up cpp-9 (9.3.0-13ubuntu1) ... Setting up libc6-dev:riscv64 (2.31-0ubuntu10) ... Setting up gcc-9 (9.3.0-13ubuntu1) ... Setting up libstdc++-9-dev:riscv64 (9.3.0-13ubuntu1) ... Setting up dpkg-dev (1.19.7ubuntu4) ... Setting up g++-9 (9.3.0-13ubuntu1) ... 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-19472635 riscv64 groovy-proposed -c chroot:build-PACKAGEBUILD-19472635 --arch=riscv64 --dist=groovy-proposed --nolog t-coffee_13.41.0.28bdc39+dfsg-4.dsc Initiating build PACKAGEBUILD-19472635 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 5.4.0-21-generic #25-Ubuntu SMP Tue Mar 31 01:57:06 UTC 2020 riscv64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on riscv64-qemu-lcy01-007.buildd +==============================================================================+ | t-coffee 13.41.0.28bdc39+dfsg-4 (riscv64) Wed, 17 Jun 2020 23:58:29 +0000 | +==============================================================================+ Package: t-coffee Version: 13.41.0.28bdc39+dfsg-4 Source Version: 13.41.0.28bdc39+dfsg-4 Distribution: groovy-proposed Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19472635/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/t-coffee-ay47St/resolver-hQLRoV' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- t-coffee_13.41.0.28bdc39+dfsg-4.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/t-coffee-ay47St/t-coffee-13.41.0.28bdc39+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/t-coffee-ay47St' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 12), build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [369 B] Get:5 copy:/<>/apt_archive ./ Packages [453 B] Fetched 1779 B in 0s (4440 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libgpm2 Use 'apt autoremove' to remove it. 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 tzdata 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-main-dummy tzdata 0 upgraded, 35 newly installed, 0 to remove and 0 not upgraded. Need to get 17.1 MB of archives. After this operation, 67.7 MB of additional disk space will be used. 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Setting up libglib2.0-0:riscv64 (2.64.3-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.1ubuntu1) ... Setting up libmagic1:riscv64 (1:5.38-5) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up file (1:5.38-5) ... Setting up tzdata (2020a-0ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Jun 17 23:59:54 UTC 2020. Universal Time is now: Wed Jun 17 23:59:54 UTC 2020. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20180224.1) ... Setting up libsigsegv2:riscv64 (2.12-2) ... Setting up autopoint (0.19.8.1-10build1) ... Setting up libuchardet0:riscv64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libbsd0:riscv64 (0.10.0-1) ... Setting up libelf1:riscv64 (0.176-1.1build1) ... Setting up libfile-stripnondeterminism-perl (1.8.1-1) ... Setting up libtool (2.4.6-14) ... Setting up libicu66:riscv64 (66.1-2ubuntu2) ... 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 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 libxml2:riscv64 (2.9.10+dfsg-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 man-db (2.9.2-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcroco3:riscv64 (0.6.13-1) ... Setting up gettext (0.19.8.1-10build1) ... 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-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-0ubuntu10) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-21-generic #25-Ubuntu SMP Tue Mar 31 01:57:06 UTC 2020 riscv64 (riscv64) Toolchain package versions: binutils_2.34-7ubuntu1 dpkg-dev_1.19.7ubuntu4 g++-9_9.3.0-13ubuntu1 gcc-9_9.3.0-13ubuntu1 libc6-dev_2.31-0ubuntu10 libstdc++-9-dev_9.3.0-13ubuntu1 libstdc++6_10.1.0-4ubuntu2 linux-libc-dev_5.4.0-27.31 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-common_2.34-7ubuntu1 binutils-riscv64-linux-gnu_2.34-7ubuntu1 bsdmainutils_11.1.2ubuntu3 bsdutils_1:2.34-0.1ubuntu9 build-essential_12.8ubuntu1 bzip2_1.0.8-3 ca-certificates_20190110ubuntu2 coreutils_8.30-3ubuntu2 cpp_4:9.3.0-1ubuntu2 cpp-9_9.3.0-13ubuntu1 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 file_1:5.38-5 findutils_4.7.0-1ubuntu1 g++_4:9.3.0-1ubuntu2 g++-9_9.3.0-13ubuntu1 gcc_4:9.3.0-1ubuntu2 gcc-10-base_10.1.0-4ubuntu2 gcc-8-base_8.4.0-4ubuntu1 gcc-9_9.3.0-13ubuntu1 gcc-9-base_9.3.0-13ubuntu1 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-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapt-pkg6.0_2.1.6 libarchive-zip-perl_1.68-1 libassuan0_2.5.3-7.1 libatomic1_10.1.0-4ubuntu2 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu6 libaudit1_1:2.8.5-2ubuntu6 libbinutils_2.34-7ubuntu1 libblkid1_2.34-0.1ubuntu9 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 libcc1-0_10.1.0-4ubuntu2 libcom-err2_1.45.6-1ubuntu1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1ubuntu1 libcrypt1_1:4.4.16-1ubuntu1 libctf-nobfd0_2.34-7ubuntu1 libctf0_2.34-7ubuntu1 libdb5.3_5.3.28+dfsg1-0.6ubuntu2 libdebconfclient0_0.252ubuntu1 libdebhelper-perl_13.1ubuntu1 libdpkg-perl_1.19.7ubuntu4 libelf1_0.176-1.1build1 libext2fs2_1.45.6-1ubuntu1 libfakeroot_1.24-1 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.8.1-1 libgcc-9-dev_9.3.0-13ubuntu1 libgcc-s1_10.1.0-4ubuntu2 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_10.1.0-4ubuntu2 libgpg-error0_1.38-1 libgpm2_1.20.7-6 libhogweed5_3.5.1+really3.5.1-2 libicu66_66.1-2ubuntu2 libidn2-0_2.3.0-1 libisl22_0.22.1-1 liblocale-gettext-perl_1.07-4 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_2.34-0.1ubuntu9 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 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 libreadline8_8.0-4 libselinux1_3.0-1build2 libsemanage-common_3.0-1build2 libsemanage1_3.0-1build2 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1ubuntu9 libsqlite3-0_3.32.2-2 libss2_1.45.6-1ubuntu1 libssl1.1_1.1.1f-1ubuntu2 libstdc++-9-dev_9.3.0-13ubuntu1 libstdc++6_10.1.0-4ubuntu2 libsub-override-perl_0.09-2 libsystemd0_245.6-1ubuntu1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtinfo6_6.2-1 libtool_2.4.6-14 libuchardet0_0.0.7-1 libudev1_245.6-1ubuntu1 libunistring2_0.9.10-4 libuuid1_2.34-0.1ubuntu9 libxml2_2.9.10+dfsg-5 libzstd1_1.4.5+dfsg-2 linux-libc-dev_5.4.0-27.31 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_2.34-0.1ubuntu9 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 readline-common_8.0-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3ubuntu1 tar_1.30+dfsg-7 tzdata_2020a-0ubuntu1 ubuntu-keyring_2020.06.17.1 util-linux_2.34-0.1ubuntu9 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: t-coffee Binary: t-coffee, t-coffee-examples Architecture: any all Version: 13.41.0.28bdc39+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille Homepage: http://www.tcoffee.org/Projects/tcoffee/index.html Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/t-coffee Vcs-Git: https://salsa.debian.org/med-team/t-coffee.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 12) Package-List: t-coffee deb science optional arch=any t-coffee-examples deb science optional arch=all Checksums-Sha1: fab3dbecabca6c0248a8c8a0336f5995be3b4e3f 3229824 t-coffee_13.41.0.28bdc39+dfsg.orig.tar.xz 40c1a9f0ea7b599343d3a16f965b32e0ef77faec 17124 t-coffee_13.41.0.28bdc39+dfsg-4.debian.tar.xz Checksums-Sha256: a1b37c67caba574ccf53c38279863dffa67d62232e017317754b5eb29db60746 3229824 t-coffee_13.41.0.28bdc39+dfsg.orig.tar.xz 36b1a1da7837f2206d5892bca66d9a9257a349cedadb7124302bd2f1491c4a00 17124 t-coffee_13.41.0.28bdc39+dfsg-4.debian.tar.xz Files: 74a867b32054875c3ce5f2a11767d610 3229824 t-coffee_13.41.0.28bdc39+dfsg.orig.tar.xz f284e548233a1d9726e0a0a0baedb510 17124 t-coffee_13.41.0.28bdc39+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl7qcV0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHNaQ//bgReo0RgFiZiS7+jiL6sZz3j8nI+n9gU g2tKwflXxBbo0COzy9lBqIimUOiTtX4rXx8gCPWoz8YmAWUy/5T2LuXrKO5Pt4Ks HRfyNNjucPMD1zEB1SgaCBvMfee+i20aQmxl2TFFSSohNf1V/IrYZH/Dd2PEUzc2 D+3c5aCFirl5WZyv4KprhCF2TzGuSICsbE4TZlwcp5T5T7uM/QJsUMLokUAmn1ye mv/sVETbsyxIADtKyfdXOuoZH1okbA9jdBGLooGbrNQCVeCGHrqo23S/kTMpXYQM nvJaIhDS5vfobvvrFSbX6ZkqQGxW/RiuKRq4PlAzCkeBQ+ulpQJcVufRgaBfkRQM YNuRUaIyQcTV/O7ASaFbPgkhr0cTfdo7FNYsGPKUYdQXnvlzQpmVyzdoIniaHauY kqPPlW+XjugzX9CEH2wcEB9N+a8yidaBe2S1QnzUag6FMdSsqDWLlPHkxKsEBnJz RzoWw2C8RFU/15UMjmEoKPPsFBEHtuTKDcdDe4vAhX6euNe+cUfaQQi8vmqOUmFh hZefSInhUASz9FyXmujj1n7fVhGdaDDuCF4aiCVSrhQ3nkQVfY+47dTeGAe77VFM u2PLTsVb+hB57esbmXz6QuRy2cn7fHcjmPKZCaLckl24iYD3pZpjCml+BF1U3lH8 bjebJZT+Iiw= =LR+J -----END PGP SIGNATURE----- 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 /<> 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 disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=8 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-19472635 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19472635 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19472635 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot 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 riscv64 debian/rules clean dh clean --sourcedirectory=t_coffee_source debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -rf t_coffee_source/*.o t_coffee_source/t_coffee bin/t_coffee example/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 '/<>' 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 '/<>' dh_auto_build -- USER_BIN=../bin/ FCC="gfortran -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong" 'CC=$(CXX)' all cd t_coffee_source && make -j8 "INSTALL=install --strip-program=true" USER_BIN=../bin/ "FCC=gfortran -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong" CC=\$\(CXX\) all make[2]: Entering directory '/<>/t_coffee_source' CC dev_lib/dev1.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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/CUSTOM_evaluate_for_struc.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 CC dp_lib/evaluate.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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=/<>=. -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 CC dp_lib/evaluate_for_domain.c CC dp_lib/evaluate_for_struc.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 CC dp_lib/fsa_dp.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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=/<>=. -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/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 dp_lib/pavie_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/evaluate_for_struc.c:34: ./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/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/evaluate_for_domain.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"); | ~~~~~~^~~~~~~~~~ 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/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/showpair.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 CC dp_lib/util_domain_dp.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 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/riscv64-linux-gnu/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/riscv64-linux-gnu/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/util_domain_dp_drivers.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 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/showpair.c:32: ./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.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 ‘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 ); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 | ^~~~~~~ CC dp_lib/util_dp_cdna_fasta_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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_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=/<>=. -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=/<>=. -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 CC dp_lib/util_dp_est.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 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 | ^~~~~~~ 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_fasta_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 CC dp_lib/util_dp_fasta_sw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_generic_fasta_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 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); | ~~~~~~^~~~~~~~~~~~~~~~~ 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_nw.c:34: ./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_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_gotoh_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 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 | ^~~~~~~ CC dp_lib/util_dp_gotoh_sw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 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 | ^~~~~~~ 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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/riscv64-linux-gnu/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/riscv64-linux-gnu/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/riscv64-linux-gnu/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_mm_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 CC dp_lib/util_dp_sim.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 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/riscv64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_ssec_pwaln.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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_mm_nw.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_sim.c:32: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_suboptimal_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 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 | ^~~~~~~ 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/riscv64-linux-gnu/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_suboptimal_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_graph_maln.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 CC fastal/diagonal.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 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 | ^~~~~~~ CC fastal/fastal.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 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); | ~~~~~^~~~~~~~~~~~~~~~~~~ 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/fastal_opt_parsing.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 CC fastal/iteration.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC fastal/parttree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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/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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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=/<>=. -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 CC fastal/tree.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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/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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/riscv64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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=/<>=. -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 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/riscv64-linux-gnu/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 io_lib/pb_util_read_seq_util.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 CC io_lib/pb_util_read_sequence.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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/io_func.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 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/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; | ^~~~ 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/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 | } | ^ 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]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ 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>=. -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 CC km_coffee/Stack.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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=/<>=. -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 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 | ^~~~~~~ CC km_coffee/classes.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ CC km_coffee/km_coffee.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 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 | } | ^ km_coffee/Vector.c: In function ‘void print_vecs(VectorSet*, char*)’: km_coffee/Vector.c:869:20: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 869 | fprintf(out_F, "%i ", i); | ~^ ~ | | | | int size_t {aka long unsigned int} | %li CC km_coffee/km_util.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 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 ‘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/kmeans.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 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 t_coffee_lib/t_coffee.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 CC util_lib/aln_compare.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 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 | ^~~~~~~ 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 | ^~~~~~~ CC util_lib/aln_convertion_util.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 CC util_lib/hsearch.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 ‘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 | } | ^ 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 | ^~~~~~~ CC util_lib/random.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 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/reformat.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 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)) | ^~~~ CC util_lib/reformat_struc.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 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 | } | ^ 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 | ^~~~~~~ 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_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); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/util.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 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)); | ^~~~~~~~~~~ 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/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)); | ^~~~~~~~~~~ CC util_lib/util_aln_analyze.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 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); | ^~~~~~~~~~~ CC util_lib/util_analyse_constraints_list.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 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/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 | } | ^ 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/riscv64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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 | } | ^ 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 | ^~~~~~~ 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 | ^~~~~~~ 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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/util_constraints_list.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 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_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.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_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/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 | } | ^ 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_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); | ^~~~~~~~~~~~~~~~~~~ CC util_lib/util_declare.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 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]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 ‘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/riscv64-linux-gnu/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_domain_constraints_list.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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=/<>=. -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=/<>=. -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 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=/<>=. -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 ‘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/riscv64-linux-gnu/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/riscv64-linux-gnu/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.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/riscv64-linux-gnu/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/riscv64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/riscv64-linux-gnu/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/riscv64-linux-gnu/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.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/riscv64-linux-gnu/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.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/riscv64-linux-gnu/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.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/riscv64-linux-gnu/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/riscv64-linux-gnu/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/riscv64-linux-gnu/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/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); | ^~~~ 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/riscv64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from util_lib/aln_convertion_util.c:27: /usr/include/riscv64-linux-gnu/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/riscv64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/riscv64-linux-gnu/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/riscv64-linux-gnu/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** 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/riscv64-linux-gnu/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/riscv64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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_source' make[1]: Leaving directory '/<>' 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 '/<>' 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 '/<>' 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 '/<>' #Compressing most of the files in examples/ makes them unusable dh_compress -Xt-coffee-examples ( cd debian/t-coffee-examples/ && \ chmod 644 usr/share/doc/t-coffee-examples/changelog.Debian && \ gzip -9 -n usr/share/doc/t-coffee-examples/changelog.Debian ) || true /bin/sh: 1: cd: can't cd to debian/t-coffee-examples/ make[1]: Leaving directory '/<>' dh_fixperms -a -O--sourcedirectory=t_coffee_source dh_missing -a -O--sourcedirectory=t_coffee_source dh_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 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/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 8 cpus) for package t-coffee ... pkgstripfiles: No PNG files. dpkg-deb: building package 't-coffee' in '../t-coffee_13.41.0.28bdc39+dfsg-4_riscv64.deb'. 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_riscv64.deb'. Renaming t-coffee-dbgsym_13.41.0.28bdc39+dfsg-4_riscv64.deb to t-coffee-dbgsym_13.41.0.28bdc39+dfsg-4_riscv64.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../t-coffee_13.41.0.28bdc39+dfsg-4_riscv64.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 2020-06-18T00:06:50Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ t-coffee_13.41.0.28bdc39+dfsg-4_riscv64.changes: ------------------------------------------------ Format: 1.8 Date: Wed, 17 Jun 2020 20:34:34 +0200 Source: t-coffee Binary: t-coffee Architecture: riscv64 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. 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t-coffee_13.41.0.28bdc39+dfsg-4_riscv64.deb /<>/t-coffee_13.41.0.28bdc39+dfsg-4_riscv64.changes.new could not be renamed to /<>/t-coffee_13.41.0.28bdc39+dfsg-4_riscv64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: t-coffee Binary: t-coffee t-coffee-examples Architecture: riscv64 Version: 13.41.0.28bdc39+dfsg-4 Checksums-Md5: d8fe62a89f676b79eb181354913fbd74 2619196 t-coffee-dbgsym_13.41.0.28bdc39+dfsg-4_riscv64.ddeb 0fecf56a17b9d3a3c4469bc06ed76b63 959092 t-coffee_13.41.0.28bdc39+dfsg-4_riscv64.deb Checksums-Sha1: 442e9868ad197f348f35150b4f9ecccf66dadfe9 2619196 t-coffee-dbgsym_13.41.0.28bdc39+dfsg-4_riscv64.ddeb f1b94b56045572fb3dc53940e428dd1dd2e165e7 959092 t-coffee_13.41.0.28bdc39+dfsg-4_riscv64.deb Checksums-Sha256: e89ef88a4ad995692739b40ca498b67e63e34228ae61db3a5706c0840583de44 2619196 t-coffee-dbgsym_13.41.0.28bdc39+dfsg-4_riscv64.ddeb 958482d1b7afccc3cb143f944f7c7c7d383f39018e3b730fc4cfd3ce82ad5c15 959092 t-coffee_13.41.0.28bdc39+dfsg-4_riscv64.deb Build-Origin: Ubuntu Build-Architecture: riscv64 Build-Date: Thu, 18 Jun 2020 00:06:44 +0000 Build-Path: /<> Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: 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-common (= 2.34-7ubuntu1), binutils-riscv64-linux-gnu (= 2.34-7ubuntu1), bsdmainutils (= 11.1.2ubuntu3), bsdutils (= 1:2.34-0.1ubuntu9), build-essential (= 12.8ubuntu1), bzip2 (= 1.0.8-3), coreutils (= 8.30-3ubuntu2), cpp (= 4:9.3.0-1ubuntu2), cpp-9 (= 9.3.0-13ubuntu1), 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), file (= 1:5.38-5), findutils (= 4.7.0-1ubuntu1), g++ (= 4:9.3.0-1ubuntu2), g++-9 (= 9.3.0-13ubuntu1), gcc (= 4:9.3.0-1ubuntu2), gcc-10-base (= 10.1.0-4ubuntu2), gcc-9 (= 9.3.0-13ubuntu1), gcc-9-base (= 9.3.0-13ubuntu1), gettext (= 0.19.8.1-10build1), gettext-base (= 0.19.8.1-10build1), grep (= 3.4-1), groff-base (= 1.22.4-5), gzip (= 1.10-2ubuntu1), hostname (= 3.23), init-system-helpers (= 1.57), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-8), libarchive-zip-perl (= 1.68-1), libatomic1 (= 10.1.0-4ubuntu2), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-2ubuntu6), libaudit1 (= 1:2.8.5-2ubuntu6), libbinutils (= 2.34-7ubuntu1), libblkid1 (= 2.34-0.1ubuntu9), 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), libcc1-0 (= 10.1.0-4ubuntu2), libcroco3 (= 0.6.13-1), libcrypt-dev (= 1:4.4.16-1ubuntu1), libcrypt1 (= 1:4.4.16-1ubuntu1), libctf-nobfd0 (= 2.34-7ubuntu1), libctf0 (= 2.34-7ubuntu1), libdb5.3 (= 5.3.28+dfsg1-0.6ubuntu2), libdebconfclient0 (= 0.252ubuntu1), libdebhelper-perl (= 13.1ubuntu1), libdpkg-perl (= 1.19.7ubuntu4), libelf1 (= 0.176-1.1build1), libffi7 (= 3.3-4), libfile-stripnondeterminism-perl (= 1.8.1-1), libgcc-9-dev (= 9.3.0-13ubuntu1), libgcc-s1 (= 10.1.0-4ubuntu2), 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), libgomp1 (= 10.1.0-4ubuntu2), libgpg-error0 (= 1.38-1), libicu66 (= 66.1-2ubuntu2), libisl22 (= 0.22.1-1), liblz4-1 (= 1.9.2-2), liblzma5 (= 5.2.4-1), libmagic-mgc (= 1:5.38-5), libmagic1 (= 1:5.38-5), libmount1 (= 2.34-0.1ubuntu9), libmpc3 (= 1.1.0-1), libmpfr6 (= 4.0.2-1), 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), libselinux1 (= 3.0-1build2), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.34-0.1ubuntu9), libstdc++-9-dev (= 9.3.0-13ubuntu1), libstdc++6 (= 10.1.0-4ubuntu2), libsub-override-perl (= 0.09-2), libsystemd0 (= 245.6-1ubuntu1), libtinfo6 (= 6.2-1), libtool (= 2.4.6-14), libuchardet0 (= 0.0.7-1), libudev1 (= 245.6-1ubuntu1), libunistring2 (= 0.9.10-4), libuuid1 (= 2.34-0.1ubuntu9), libxml2 (= 2.9.10+dfsg-5), libzstd1 (= 1.4.5+dfsg-2), linux-libc-dev (= 5.4.0-27.31), login (= 1:4.8.1-1ubuntu6), 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), ncurses-base (= 6.2-1), ncurses-bin (= 6.2-1), patch (= 2.7.6-6), perl (= 5.30.3-4), perl-base (= 5.30.3-4), perl-modules-5.30 (= 5.30.3-4), po-debconf (= 1.0.21), sed (= 4.7-1), sensible-utils (= 0.0.12+nmu1), sysvinit-utils (= 2.96-3ubuntu1), tar (= 1.30+dfsg-7), tzdata (= 2020a-0ubuntu1), util-linux (= 2.34-0.1ubuntu9), xz-utils (= 5.2.4-1), zlib1g (= 1:1.2.11.dfsg-2ubuntu1) Environment: DEB_BUILD_OPTIONS="parallel=8" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1592418874" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ t-coffee_13.41.0.28bdc39+dfsg-4_riscv64.deb ------------------------------------------- new Debian package, version 2.0. size 959092 bytes: control archive=1436 bytes. 1675 bytes, 30 lines control 473 bytes, 7 lines md5sums Package: t-coffee Version: 13.41.0.28bdc39+dfsg-4 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 2222 Depends: libc6 (>= 2.27), libgcc-s1 (>= 3.0), libstdc++6 (>= 4.1.1) Recommends: amap-align, clustalo, clustalw, dialign-tx, fsa, kalign, libsoap-lite-perl, libxml-simple-perl, mafft, muscle, mustang, ncbi-blast+, poa, prank, probcons, proda, tm-align Suggests: boxshade, seaview, t-coffee-examples Section: science Priority: optional Homepage: http://www.tcoffee.org/Projects/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 2250592 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: riscv64 Build Type: any Build-Space: 119144 Build-Time: 393 Distribution: groovy-proposed Host Architecture: riscv64 Install-Time: 80 Job: t-coffee_13.41.0.28bdc39+dfsg-4.dsc Machine Architecture: riscv64 Package: t-coffee Package-Time: 501 Source-Version: 13.41.0.28bdc39+dfsg-4 Space: 119144 Status: successful Version: 13.41.0.28bdc39+dfsg-4 -------------------------------------------------------------------------------- Finished at 2020-06-18T00:06:50Z Build needed 00:08:21, 119144k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=groovy --arch=riscv64 PACKAGEBUILD-19472635 Scanning for processes to kill in build PACKAGEBUILD-19472635 RUN: /usr/share/launchpad-buildd/bin/in-target umount-chroot --backend=chroot --series=groovy --arch=riscv64 PACKAGEBUILD-19472635 Stopping target for build PACKAGEBUILD-19472635 RUN: /usr/share/launchpad-buildd/bin/in-target remove-build --backend=chroot --series=groovy --arch=riscv64 PACKAGEBUILD-19472635 Removing build PACKAGEBUILD-19472635