https://launchpad.net/ubuntu/+source/mafft/7.453-1/+build/19107320 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux riscv64-qemu-lcy01-022 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... 3 Apr 09:23:37 ntpdate[290387]: adjust time server 10.211.37.1 offset -0.002661 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19107320 --image-type chroot /home/buildd/filecache-default/88ad86cb2b525f1abddded96eadf8014548f7845 Creating target for build PACKAGEBUILD-19107320 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19107320 Starting target for build PACKAGEBUILD-19107320 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19107320 'deb http://ftpmaster.internal/ubuntu focal main universe' Overriding sources.list in build-PACKAGEBUILD-19107320 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19107320 Updating target for build PACKAGEBUILD-19107320 Ign:1 http://archive-team.internal/bootstrap/riscv64 focal InRelease Get:2 http://ftpmaster.internal/ubuntu focal InRelease [265 kB] Get:3 http://archive-team.internal/bootstrap/riscv64 focal Release [760 B] Get:4 http://ftpmaster.internal/ubuntu focal-proposed InRelease [265 kB] Ign:5 http://archive-team.internal/bootstrap/riscv64 focal Release.gpg Get:6 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 Packages [1034 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main riscv64 Packages [642 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main Translation-en [501 kB] Get:9 http://ftpmaster.internal/ubuntu focal/universe riscv64 Packages [4846 kB] Get:10 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5127 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 Packages [19.8 kB] Get:12 http://ftpmaster.internal/ubuntu focal-proposed/main Translation-en [15.7 kB] Get:13 http://ftpmaster.internal/ubuntu focal-proposed/universe riscv64 Packages [83.4 kB] Get:14 http://ftpmaster.internal/ubuntu focal-proposed/universe Translation-en [96.3 kB] Fetched 12.9 MB in 26s (492 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: coreutils liblocale-gettext-perl libperl5.30 libtext-charwidth-perl libtext-iconv-perl perl-base 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 6037 kB of archives. After this operation, 6144 B of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu focal/main riscv64 coreutils riscv64 8.30-3ubuntu2 [1158 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main riscv64 perl-base riscv64 5.30.0-9build1 [1419 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main riscv64 liblocale-gettext-perl riscv64 1.07-4 [16.5 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main riscv64 libtext-charwidth-perl riscv64 0.04-10 [9460 B] Get:5 http://ftpmaster.internal/ubuntu focal/main riscv64 libtext-iconv-perl riscv64 1.7-7 [13.2 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main riscv64 libperl5.30 riscv64 5.30.0-9build1 [3422 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6037 kB in 2s (3863 kB/s) (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../coreutils_8.30-3ubuntu2_riscv64.deb ... Unpacking coreutils (8.30-3ubuntu2) over (8.30-3ubuntu2) ... Setting up coreutils (8.30-3ubuntu2) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../perl-base_5.30.0-9build1_riscv64.deb ... Unpacking perl-base (5.30.0-9build1) over (5.30.0-9build1) ... Setting up perl-base (5.30.0-9build1) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-4_riscv64.deb ... Unpacking liblocale-gettext-perl (1.07-4) over (1.07-4) ... Preparing to unpack .../libtext-charwidth-perl_0.04-10_riscv64.deb ... Unpacking libtext-charwidth-perl (0.04-10) over (0.04-10) ... Preparing to unpack .../libtext-iconv-perl_1.7-7_riscv64.deb ... Unpacking libtext-iconv-perl (1.7-7) over (1.7-7) ... Preparing to unpack .../libperl5.30_5.30.0-9build1_riscv64.deb ... Unpacking libperl5.30:riscv64 (5.30.0-9build1) over (5.30.0-9build1) ... Setting up libtext-iconv-perl (1.7-7) ... Setting up libtext-charwidth-perl (0.04-10) ... Setting up libperl5.30:riscv64 (5.30.0-9build1) ... Setting up liblocale-gettext-perl (1.07-4) ... Processing triggers for libc-bin (2.31-0ubuntu6~riscv64.1) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19107320 riscv64 focal -c chroot:build-PACKAGEBUILD-19107320 --arch=riscv64 --dist=focal --nolog mafft_7.453-1.dsc Initiating build PACKAGEBUILD-19107320 with 4 jobs across 4 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-lcy01-022 +==============================================================================+ | mafft 7.453-1 (riscv64) Fri, 03 Apr 2020 09:26:10 +0000 | +==============================================================================+ Package: mafft Version: 7.453-1 Source Version: 7.453-1 Distribution: focal Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19107320/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/mafft-HjKokO/resolver-zpDxB1' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- mafft_7.453-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/mafft-HjKokO/mafft-7.453' with '<>' I: NOTICE: Log filtering will replace 'build/mafft-HjKokO' 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 [454 B] Fetched 1780 B in 1s (3084 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 17.0 MB of archives. After this operation, 67.6 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [880 B] Get:2 http://ftpmaster.internal/ubuntu focal/main riscv64 libbsd0 riscv64 0.10.0-1 [42.0 kB] Get:3 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 libglib2.0-0 riscv64 2.64.1-1 [1125 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main riscv64 bsdmainutils riscv64 11.1.2ubuntu3 [176 kB] Get:5 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libuchardet0 riscv64 0.0.6-3build1 [64.9 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main riscv64 groff-base riscv64 1.22.4-4build1 [816 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main riscv64 libpipeline1 riscv64 1.5.2-2build1 [23.9 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main riscv64 man-db riscv64 2.9.1-1 [1075 kB] Get:9 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 dwz riscv64 0.13-5 [147 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main riscv64 libmagic-mgc riscv64 1:5.38-4 [218 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main riscv64 libmagic1 riscv64 1:5.38-4 [70.5 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main riscv64 file riscv64 1:5.38-4 [22.5 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main riscv64 libelf1 riscv64 0.176-1.1build1 [41.8 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main riscv64 tzdata all 2019c-3ubuntu1 [294 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main riscv64 libicu66 riscv64 66.1-2ubuntu2 [8406 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main riscv64 libxml2 riscv64 2.9.10+dfsg-4build1 [558 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main riscv64 gettext-base riscv64 0.19.8.1-10build1 [47.4 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main riscv64 libsigsegv2 riscv64 2.12-2 [13.0 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main riscv64 m4 riscv64 1.4.18-4 [188 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main riscv64 autoconf all 2.69-11.1 [321 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main riscv64 autotools-dev all 20180224.1 [39.6 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main riscv64 automake all 1:1.16.1-4ubuntu6 [522 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main riscv64 autopoint all 0.19.8.1-10build1 [412 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main riscv64 libtool all 2.4.6-13 [161 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main riscv64 dh-autoreconf all 19 [16.1 kB] Get:26 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libdebhelper-perl all 12.10ubuntu1 [62.1 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main riscv64 libarchive-zip-perl all 1.67-2 [90.5 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main riscv64 libsub-override-perl all 0.09-2 [9532 B] Get:29 http://ftpmaster.internal/ubuntu focal/main riscv64 libfile-stripnondeterminism-perl all 1.6.3-2 [16.0 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main riscv64 dh-strip-nondeterminism all 1.6.3-2 [5228 B] Get:31 http://ftpmaster.internal/ubuntu focal/main riscv64 libcroco3 riscv64 0.6.13-1 [71.1 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main riscv64 gettext riscv64 0.19.8.1-10build1 [844 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main riscv64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main riscv64 po-debconf all 1.0.21 [233 kB] Get:35 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 debhelper all 12.10ubuntu1 [877 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 17.0 MB in 4s (4164 kB/s) Selecting previously unselected package libbsd0:riscv64. (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.10.0-1_riscv64.deb ... Unpacking libbsd0:riscv64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2ubuntu3_riscv64.deb ... Unpacking bsdmainutils (11.1.2ubuntu3) ... Selecting previously unselected package libuchardet0:riscv64. Preparing to unpack .../02-libuchardet0_0.0.6-3build1_riscv64.deb ... Unpacking libuchardet0:riscv64 (0.0.6-3build1) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-4build1_riscv64.deb ... Unpacking groff-base (1.22.4-4build1) ... Selecting previously unselected package libpipeline1:riscv64. Preparing to unpack .../04-libpipeline1_1.5.2-2build1_riscv64.deb ... Unpacking libpipeline1:riscv64 (1.5.2-2build1) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.9.1-1_riscv64.deb ... 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Unpacking libcroco3:riscv64 (0.6.13-1) ... Selecting previously unselected package gettext. Preparing to unpack .../30-gettext_0.19.8.1-10build1_riscv64.deb ... Unpacking gettext (0.19.8.1-10build1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../31-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../32-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../33-debhelper_12.10ubuntu1_all.deb ... Unpacking debhelper (12.10ubuntu1) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../34-sbuild-build-depends-main-dummy_0.invalid.0_riscv64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libpipeline1:riscv64 (1.5.2-2build1) ... Setting up libmagic-mgc (1:5.38-4) ... Setting up libarchive-zip-perl (1.67-2) ... Setting up libglib2.0-0:riscv64 (2.64.1-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (12.10ubuntu1) ... Setting up libmagic1:riscv64 (1:5.38-4) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up file (1:5.38-4) ... Setting up tzdata (2019c-3ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Apr 3 09:28:15 UTC 2020. Universal Time is now: Fri Apr 3 09:28:15 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 (0.0.6-3build1) ... 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 (1.6.3-2) ... Setting up libtool (2.4.6-13) ... 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 (1.6.3-2) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4build1) ... Setting up libxml2:riscv64 (2.9.10+dfsg-4build1) ... Setting up automake (1:1.16.1-4ubuntu6) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.9.1-1) ... 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 (12.10ubuntu1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-0ubuntu6~riscv64.1) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any) +------------------------------------------------------------------------------+ | 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_2.34-5ubuntu1 dpkg-dev_1.19.7ubuntu3 g++-9_9.3.0-8ubuntu1 gcc-9_9.3.0-8ubuntu1 libc6-dev_2.31-0ubuntu6~riscv64.1 libstdc++-9-dev_9.3.0-8ubuntu1 libstdc++6_10-20200324-1ubuntu1 linux-libc-dev_5.4.0-21.25 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1build1 apt_2.0.1 autoconf_2.69-11.1 automake_1:1.16.1-4ubuntu6 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu4 base-passwd_3.5.47 bash_5.0-6ubuntu1 binutils_2.34-5ubuntu1 binutils-common_2.34-5ubuntu1 binutils-riscv64-linux-gnu_2.34-5ubuntu1 bsdmainutils_11.1.2ubuntu3 bsdutils_1:2.34-0.1ubuntu8 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110ubuntu1 coreutils_8.30-3ubuntu2 cpp_4:9.3.0-1ubuntu2 cpp-9_9.3.0-8ubuntu1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.10ubuntu1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dpkg_1.19.7ubuntu3 dpkg-dev_1.19.7ubuntu3 dwz_0.13-5 e2fsprogs_1.45.5-2ubuntu1 fakeroot_1.24-1 file_1:5.38-4 findutils_4.7.0-1ubuntu1 g++_4:9.3.0-1ubuntu2 g++-9_9.3.0-8ubuntu1 gcc_4:9.3.0-1ubuntu2 gcc-10-base_10-20200324-1ubuntu1 gcc-8-base_8.4.0-3ubuntu1 gcc-9_9.3.0-8ubuntu1 gcc-9-base_9.3.0-8ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gpg_2.2.19-3ubuntu2 gpg-agent_2.2.19-3ubuntu2 gpgconf_2.2.19-3ubuntu2 gpgv_2.2.19-3ubuntu2 grep_3.4-1 groff-base_1.22.4-4build1 gzip_1.10-0ubuntu4 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-6 libapt-pkg6.0_2.0.1 libarchive-zip-perl_1.67-2 libassuan0_2.5.3-7ubuntu2 libatomic1_10-20200324-1ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu6 libaudit1_1:2.8.5-2ubuntu6 libbinutils_2.34-5ubuntu1 libblkid1_2.34-0.1ubuntu8 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.31-0ubuntu6~riscv64.1 libc-dev-bin_2.31-0ubuntu6~riscv64.1 libc6_2.31-0ubuntu6~riscv64.1 libc6-dev_2.31-0ubuntu6~riscv64.1 libcap-ng0_0.7.9-2.1build1 libcc1-0_10-20200324-1ubuntu1 libcom-err2_1.45.5-2ubuntu1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10ubuntu4 libcrypt1_1:4.4.10-10ubuntu4 libctf-nobfd0_2.34-5ubuntu1 libctf0_2.34-5ubuntu1 libdb5.3_5.3.28+dfsg1-0.6ubuntu2 libdebconfclient0_0.251ubuntu1 libdebhelper-perl_12.10ubuntu1 libdpkg-perl_1.19.7ubuntu3 libelf1_0.176-1.1build1 libext2fs2_1.45.5-2ubuntu1 libfakeroot_1.24-1 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.6.3-2 libgcc-9-dev_9.3.0-8ubuntu1 libgcc-s1_10-20200324-1ubuntu1 libgcc1_1:10-20200324-1ubuntu1 libgcrypt20_1.8.5-5ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.1-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.11.1-2ubuntu2 libgomp1_10-20200324-1ubuntu1 libgpg-error0_1.37-1 libgpm2_1.20.7-5 libhogweed5_3.5.1+really3.5.1-2 libicu66_66.1-2ubuntu2 libidn2-0_2.2.0-2 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_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1ubuntu8 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncursesw6_6.2-0ubuntu2 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-1 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_5.30.0-9build1 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_2.34-0.1ubuntu8 libsqlite3-0_3.31.1-4 libss2_1.45.5-2ubuntu1 libssl1.1_1.1.1d-2ubuntu6 libstdc++-9-dev_9.3.0-8ubuntu1 libstdc++6_10-20200324-1ubuntu1 libsub-override-perl_0.09-2 libsystemd0_244.3-1ubuntu1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtinfo6_6.2-0ubuntu2 libtool_2.4.6-13 libuchardet0_0.0.6-3build1 libudev1_244.3-1ubuntu1 libunistring2_0.9.10-2 libuuid1_2.34-0.1ubuntu8 libxml2_2.9.10+dfsg-4build1 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.4.0-21.25 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu3 logsave_1.45.5-2ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mount_2.34-0.1ubuntu8 ncurses-base_6.2-0ubuntu2 ncurses-bin_6.2-0ubuntu2 openssl_1.1.1d-2ubuntu6 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu3 patch_2.7.6-6 perl_5.30.0-9build1 perl-base_5.30.0-9build1 perl-modules-5.30_5.30.0-9build1 pinentry-curses_1.1.0-3build1 pkgbinarymangler_144 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_2.96-2.1ubuntu1 tar_1.30+dfsg-7 tzdata_2019c-3ubuntu1 ubuntu-keyring_2020.02.11.1 util-linux_2.34-0.1ubuntu8 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: mafft Binary: mafft Architecture: any Version: 7.453-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Homepage: https://mafft.cbrc.jp/alignment/software/ Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/mafft Vcs-Git: https://salsa.debian.org/med-team/mafft.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 12) Package-List: mafft deb science optional arch=any Checksums-Sha1: 06fd525754dbef00769c6feebcbf52a7d27e6c70 612421 mafft_7.453.orig.tar.gz e6f22bbef0e589f3d520808043678c8b6acfa20c 6692 mafft_7.453-1.debian.tar.xz Checksums-Sha256: 4c05dfc4d173c9a139fcaa9373fbc2c8d6a59f410a7971f7acc6268be628b1f9 612421 mafft_7.453.orig.tar.gz a84ae8eb57f4058ebd46987bf7fa0732536d0c55551917f57e31a56ad1569196 6692 mafft_7.453-1.debian.tar.xz Files: 45a8f0f459acd6a8ffc6efd46d5f60ab 612421 mafft_7.453.orig.tar.gz 584a8e3a89dc17da6f834d75cdf658eb 6692 mafft_7.453-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJHBAEBCAAxFiEEhMGXeonn7+0+XKYuL9i+2sAg7tEFAl3WuzcTHG1vZWxsZXJA ZGViaWFuLm9yZwAKCRAv2L7awCDu0bUpD/4lJNRDslMja96CZi8NfwU8vhuBT5Ye gAlK3yt1QKqFEoKNHh0DvXBC6P2/9cbI33C9VZrhoaV+jAB9fuylP/BliSCipg2U dNi1JuOzeMRmN3iIgyf1sg/72uk2c2hfEjs8ywGzqc/Y7MQOdpBrHlxqXf0Evjuf RC6x5ygeX1TlS7+AHUwkqhelmNTKQWRLPIcPCDT25gtoc6SrQww5j7jYyi/RkiBU w/DLZ23fGYHLKsnPOqxGs6QDWIqupQa2d3jiVLRZbaOzaE1/WjEufWB4ZZl2ArB7 GordUqvkAwy6IfwiYR9rWGjDo8+eK0efE0SZaz2QAtmtnodKBDgbVevneRSCzMsv dN7yq1+iV11N2oLiDHVqr1jKgG0BqMisHwyzDxURvtbReNV1LgCbF1NVIBi+3rZD 5fsStMQ18K5DK38aP9K7IQgEDhSC4uxPSG1FxW7tNoaooEOyp9IHNy87YO80wyZ5 NwDliG86APNj0wlIWfZ15LPsA7++cv7VzA0WJIrMpL09Z5YdyM0e8Zsc8aWjZCg1 mM33bnqjzaKn8QnFx4ykap94Op7f3Lgoj6lLJ2j5M+QLbznBFOAnWY2zpwc4rXec 2qkpRa7fCi0vKHjmDiGCVMP5LsR96m2pQSe6zdxHF2esNJSRPUxv8Kftm7fYlEe7 4Ve4ROs0XHDncg== =x4pu -----END PGP SIGNATURE----- gpgv: Signature made Thu Nov 21 16:28:39 2019 UTC gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1 gpgv: issuer "moeller@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./mafft_7.453-1.dsc dpkg-source: info: extracting mafft in /<> dpkg-source: info: unpacking mafft_7.453.orig.tar.gz dpkg-source: info: unpacking mafft_7.453-1.debian.tar.xz Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-19107320 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19107320 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19107320 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 mafft dpkg-buildpackage: info: source version 7.453-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture riscv64 fakeroot debian/rules clean dh clean --sourcedirectory=core dh_auto_clean -O--sourcedirectory=core cd core && make -j4 clean make[1]: Entering directory '/<>/core' rm -f *.o *.a *.exe *~ mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore replaceu restoreu setdirection makedirectionlist version mafft mafft-homologs.rb mafft-sparsecore.rb libdisttbfast.so libdisttbfast.dylib libdisttbfast.dll *.gcda *.gcno make[1]: Leaving directory '/<>/core' dh_autoreconf_clean -O--sourcedirectory=core debian/rules override_dh_clean make[1]: Entering directory '/<>' rm -rf binaries/* scripts/* dh_clean make[1]: Leaving directory '/<>' debian/rules build-arch dh build-arch --sourcedirectory=core dh_update_autotools_config -a -O--sourcedirectory=core dh_autoreconf -a -O--sourcedirectory=core dh_auto_configure -a -O--sourcedirectory=core debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- \ PREFIX=/usr/lib/mafft \ ENABLE_MULTITHREAD=-Denablemultithread \ LIBDIR=/usr/lib/mafft/lib/mafft \ CFLAGS="-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" \ LDFLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now" cd core && make -j4 "INSTALL=install --strip-program=true" PREFIX=/usr/lib/mafft ENABLE_MULTITHREAD=-Denablemultithread LIBDIR=/usr/lib/mafft/lib/mafft "CFLAGS=-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/<>/core' cp mafftash_premafft.tmpl mafftash_premafft.pl cp seekquencer_premafft.tmpl seekquencer_premafft.pl gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mtxutl.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c io.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mltaln9.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tddis.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from tddis.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from mltaln9.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from io.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ io.c: In function ‘PreRead’: io.c:1097:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 1097 | fgets( b, B-1, fp ); *locnjob = atoi( b ); | ^~~~~~~~~~~~~~~~~~~ io.c:1102:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 1102 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:1106:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 1106 | fgets( b, B-1, fp ); nleni = atoi( b ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘FRead’: io.c:1142:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 1142 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:1232:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 1232 | fgets( b, B-1, fp ); nlen[i] = atoi( b ); /* seq i no nagasa */ | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘readhat2_doublehalf_part_pointer’: io.c:2667:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2667 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2668:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2668 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) | ^~~~~~~~~~~~~~~~~ io.c:2673:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2673 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function ‘readhat2_doublehalf_pointer’: io.c:2703:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2703 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2704:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2704 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) | ^~~~~~~~~~~~~~~~~ io.c:2709:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2709 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function ‘readhat2_doublehalf’: io.c:2737:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2737 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2738:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2738 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); | ^~~~~~~~~~~~~~~~~ io.c:2739:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2739 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function ‘readhat2_double’: io.c:2767:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2767 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2768:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2768 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); | ^~~~~~~~~~~~~~~~~ io.c:2769:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2769 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function ‘readhat2_int’: io.c:2797:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2797 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2798:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2798 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); | ^~~~~~~~~~~~~~~~~ io.c:2799:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2799 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function ‘readhat2_pointer’: io.c:2828:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2828 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2829:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2829 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); | ^~~~~~~~~~~~~~~~~ io.c:2830:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2830 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function ‘readhat2’: io.c:2858:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2858 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2859:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2859 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); | ^~~~~~~~~~~~~~~~~ io.c:2860:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2860 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function ‘ReadFasta_sub’: io.c:3060:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3060 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3075:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3075 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadSsearch’: io.c:3094:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3094 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadBlastm7_avscore’: io.c:3222:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3222 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3229:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3229 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3230:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3230 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadBlastm7_scoreonly’: io.c:3345:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3345 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3352:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3352 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3353:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3353 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadBlastm7’: io.c:3463:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3463 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3470:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3470 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3471:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3471 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadFasta34noalign’: io.c:3495:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3495 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadFasta34m10_nuc’: io.c:3532:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3532 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3558:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3558 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadFasta34m10’: io.c:3671:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3671 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3695:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3695 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadFasta34m10_scoreonly_nucbk’: io.c:3798:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3798 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadFasta34m10_scoreonly_nuc’: io.c:3848:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3848 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadFasta34m10_scoreonly’: io.c:3909:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3909 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadFasta34’: io.c:3965:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3965 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3991:10: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3991 | fgets( b, B-1, fp ); // initn: | ^~~~~~~~~~~~~~~~~~~ io.c:3994:10: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3994 | fgets( b, B-1, fp ); // Smith-Waterman score | ^~~~~~~~~~~~~~~~~~~ io.c:4006:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 4006 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadFasta3’: io.c:4028:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 4028 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadFasta’: io.c:4053:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 4053 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadOpt’: io.c:4090:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 4090 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadOpt2’: io.c:4111:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 4111 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘readOtherOptions’: io.c:4207:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 4207 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘loadaamtx’: io.c:5465:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5465 | fgets( inorder, 999, mf ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ io.c:5497:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5497 | fgets( line, 999, mf ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5520:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5520 | fgets( line, 999, mf ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c: In function ‘readsubalignmentstable’: io.c:5676:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5676 | fgets( line, linelen-1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ io.c:5697:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5697 | fgets( line, linelen-1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ io.c: In function ‘readmccaskill’: io.c:5751:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5751 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5761:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5761 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c: In function ‘readpairfoldalign’: io.c:5820:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5820 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5833:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5833 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5840:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5840 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5854:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5854 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5860:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5860 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c: In function ‘readexternalanchors’: io.c:6298:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 6298 | fgets( buf, 9999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ mltaln9.c: In function ‘check_guidetreefile’: mltaln9.c:2802:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2802 | fgets( string, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c: In function ‘readlocalhomtable2_single_bin_noseek’: mltaln9.c:15112:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 15112 | fread( &size, sizeof( int ), 1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c:15113:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 15113 | fread( &opt, sizeof( double ), 1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c:15116:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 15116 | fread( m, size*sizeof( int ), 3, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c:15152:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 15152 | fread( &c, sizeof( char ), 1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c constants.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from constants.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from constants.c:7: blosum.c: In function ‘overridematrix’: blosum.c:369:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 369 | fgets( buf, 499, fp ); | ^~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nj.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from nj.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c partSalignmm.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from partSalignmm.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from /usr/include/stdio.h:867, from mltaln.h:13, from mltaln9.c:1: In function ‘fgets’, inlined from ‘check_guidetreefile’ at mltaln9.c:2802:2: /usr/include/riscv64-linux-gnu/bits/stdio2.h:263:9: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 263 | return __fgets_chk_warn (__s, __bos (__s), __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Lalignmm.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from Lalignmm.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rna.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from rna.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Salignmm.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from Salignmm.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ rna.c: In function ‘rnaalifoldcall’: rna.c:225:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 225 | system( cmd ); | ^~~~~~~~~~~~~ rna.c:245:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 245 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ rna.c:285:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 285 | system( cmd ); | ^~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Dalignmm.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from Dalignmm.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Falign.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from Falign.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Falign_localhom.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from Falign_localhom.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Galign11.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from Galign11.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Lalign11.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from Lalign11.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c genalign11.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from genalign11.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c MSalignmm.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fftFunctions.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from MSalignmm.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from fftFunctions.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fft.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from fft.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tditeration.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from tditeration.c:9: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dvtditr.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from dvtditr.c:4: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ dvtditr.c: In function ‘main’: dvtditr.c:1020:5: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 1020 | system( "cp infile.tree GuideTree" ); // tekitou | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c defs.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from defs.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c SAalignmm.c -o SAalignmm.o In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from SAalignmm.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c treeOperation.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from treeOperation.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c addfunctions.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from addfunctions.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dndfast7.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from dndfast7.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ dndfast7.c: In function ‘main’: dndfast7.c:326:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 326 | system( com ); | ^~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dndblast.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sextet5.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from dndblast.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from sextet5.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-distance.c dndblast.c: In function ‘main’: dndblast.c:201:4: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 201 | system( com ); | ^~~~~~~~~~~~~ dndblast.c:382:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 382 | system( com ); | ^~~~~~~~~~~~~ In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from mafft-distance.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c MSalign11.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c suboptalign11.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from MSalign11.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from suboptalign11.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pairlocalalignmain.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from pairlocalalignmain.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pairlocalalign.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from pairlocalalign.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ pairlocalalign.c: In function ‘calllast_once’: pairlocalalign.c:1055:3: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 1055 | system( command ); | ^~~~~~~~~~~~~~~~~ pairlocalalign.c:1091:3: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 1091 | system( command ); | ^~~~~~~~~~~~~~~~~ pairlocalalign.c: In function ‘readlastresx’: pairlocalalign.c:607:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 607 | fgets( gett, 9999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function ‘calllast_fast’: pairlocalalign.c:980:3: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 980 | system( command ); | ^~~~~~~~~~~~~~~~~ pairlocalalign.c: In function ‘lastcallthread’: pairlocalalign.c:871:5: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 871 | system( command ); | ^~~~~~~~~~~~~~~~~ pairlocalalign.c: In function ‘readlastresx_singleq’: pairlocalalign.c:373:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 373 | fgets( gett, 9999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function ‘readhat4’: pairlocalalign.c:1531:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 1531 | fgets( oneline, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1543:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 1543 | fgets( oneline, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function ‘recalllara’: pairlocalalign.c:1244:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 1244 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function ‘callmxscarna_giving_bpp’: pairlocalalign.c:1407:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 1407 | system( com ); | ^~~~~~~~~~~~~ pairlocalalign.c:1409:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 1409 | system( com ); | ^~~~~~~~~~~~~ pairlocalalign.c:1429:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 1429 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1450:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 1450 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1464:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 1464 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1484:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 1484 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1486:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 1486 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function ‘calldafs_giving_bpp’: pairlocalalign.c:1290:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 1290 | system( com ); | ^~~~~~~~~~~~~ pairlocalalign.c:1292:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 1292 | system( com ); | ^~~~~~~~~~~~~ pairlocalalign.c:1312:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 1312 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1333:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 1333 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1343:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 1343 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1363:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 1363 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1365:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 1365 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1367:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 1367 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function ‘pairalign_node’: pairlocalalign.c:3438:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 3438 | system( "rm -rf hat3dir" ); // toriaezu | ^~~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:3439:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 3439 | system( "mkdir hat3dir" ); // toriaezu | ^~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:3444:3: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 3444 | system( fn ); | ^~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c multi2hat3s.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from multi2hat3s.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pairash.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c addsingle.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from pairash.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from addsingle.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ pairash.c: In function ‘prepareash’: pairash.c:639:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 639 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:681:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 681 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function ‘callrash’: pairash.c:485:3: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 485 | system( com ); | ^~~~~~~~~~~~~ pairash.c: In function ‘readrash’: pairash.c:277:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 277 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:284:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 284 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:289:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 289 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:294:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 294 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function ‘preparetmalign’: pairash.c:530:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 530 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:576:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 576 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:587:4: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 587 | system( command ); | ^~~~~~~~~~~~~~~~~ pairash.c: In function ‘checkcbeta’: pairash.c:321:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 321 | fgets( linec, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function ‘calltmalign’: pairash.c:347:3: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 347 | system( com ); | ^~~~~~~~~~~~~ pairash.c:356:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 356 | fgets( com, 100, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairash.c: In function ‘readtmalign’: pairash.c:228:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 228 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:232:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 232 | fgets( line, nlenmax*2, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:235:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 235 | fgets( line, nlenmax*2, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:238:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 238 | fgets( line, nlenmax*2, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function ‘callrash.isra.0’: pairash.c:428:29: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 9999 [-Wformat-overflow=] 428 | sprintf( cachefile, "%s/%s.%s.rash", cachedir, fname1, fname2 ); | ^ In file included from /usr/include/stdio.h:867, from mltaln.h:13, from pairash.c:1: /usr/include/riscv64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output 8 or more bytes (assuming 10007) into a destination of size 10000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:484:22: warning: ‘%s’ directive writing up to 9999 bytes into a region of size 9996 [-Wformat-overflow=] 484 | sprintf( com, "cat %s > %s.rashout", cachefile, pairid ); | ^~ ~~~~~~~~~ In file included from /usr/include/stdio.h:867, from mltaln.h:13, from pairash.c:1: /usr/include/riscv64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 16 and 11014 bytes into a destination of size 10000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function ‘calltmalign.isra.0’: pairash.c:346:27: warning: ‘%s’ directive writing up to 9999 bytes into a region of size 9991 [-Wformat-overflow=] 346 | sprintf( com, "mkdir -p %s", cachedir ); | ^~ ~~~~~~~~ In file included from /usr/include/stdio.h:867, from mltaln.h:13, from pairash.c:1: /usr/include/riscv64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 10 and 10009 bytes into a destination of size 10000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:349:31: warning: ‘-’ directive writing 1 byte into a region of size between 0 and 9999 [-Wformat-overflow=] 349 | sprintf( cachefile, "%s/%s%s-%s%s", cachedir, fname1, chain1, fname2, chain2 ); | ^ In file included from /usr/include/stdio.h:867, from mltaln.h:13, from pairash.c:1: /usr/include/riscv64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output 3 or more bytes (assuming 10002) into a destination of size 10000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -o maffttext2hex maffttext2hex.c -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread maffttext2hex.c: In function ‘main’: maffttext2hex.c:55:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 55 | fgets( (char *)buf, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function ‘preparetmalign.constprop’: pairash.c:586:29: warning: ‘%s’ directive writing up to 999 bytes into a region of size 996 [-Wformat-overflow=] 586 | sprintf( command, "cp %s %s.pdb", sline, fname ); | ^~ ~~~~~ In file included from /usr/include/stdio.h:867, from mltaln.h:13, from pairash.c:1: /usr/include/riscv64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output 9 or more bytes (assuming 1008) into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:588:44: warning: ‘%s’ directive writing up to 999 bytes into a region of size 983 [-Wformat-overflow=] 588 | sprintf( command, "perl \"%s/clean.pl\" %s.pdb", whereispairalign, fname ); | ^~ ~~~~~ In file included from /usr/include/stdio.h:867, from mltaln.h:13, from pairash.c:1: /usr/include/riscv64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output 22 or more bytes (assuming 1021) into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -o hex2maffttext hex2maffttext.c -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c splittbfast.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from splittbfast.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ splittbfast.c: In function ‘main’: gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c disttbfast.c splittbfast.c:3218:3: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 3218 | system( com ); | ^~~~~~~~~~~~~ In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from disttbfast.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ disttbfast.c: In function ‘disttbfast’: disttbfast.c:4133:6: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 4133 | system( "cp infile.tree GuideTree" ); // tekitou | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tbfast.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from tbfast.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ tbfast.c: In function ‘main’: tbfast.c:3190:5: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 3190 | system( "cp infile.tree GuideTree" ); // tekitou | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nodepair.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from nodepair.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-profile.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from mafft-profile.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c f2cl.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from f2cl.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ f2cl.c: In function ‘main’: f2cl.c:287:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 287 | fgets( gett, B-1, orderfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mccaskillwrap.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from mccaskillwrap.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ mccaskillwrap.c: In function ‘main’: mccaskillwrap.c:372:4: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 372 | system( "tr -d '\\r' < _mccaskillinorg > _mccaskillin" ); // for cygwin, wakaran | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mccaskillwrap.c: In function ‘athread’: mccaskillwrap.c:115:3: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 115 | system( com ); | ^~~~~~~~~~~~~ mccaskillwrap.c:117:3: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 117 | system( com ); | ^~~~~~~~~~~~~ mccaskillwrap.c:129:3: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 129 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ mccaskillwrap.c:155:4: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 155 | system( com ); | ^~~~~~~~~~~~~ mccaskillwrap.c: In function ‘readrawmccaskill’: mccaskillwrap.c:46:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 46 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c contrafoldwrap.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from contrafoldwrap.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ contrafoldwrap.c: In function ‘readcontrafold’: contrafoldwrap.c:57:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 57 | fgets( gett, 9999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c countlen.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from countlen.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c seq2regtable.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from seq2regtable.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c regtable2seq.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from regtable2seq.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ regtable2seq.c: In function ‘readereg’: regtable2seq.c:69:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 69 | fgets( gett, 999, regfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ regtable2seq.c:97:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 97 | fgets( gett, 999, regfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ regtable2seq.c: In function ‘readreg’: regtable2seq.c:120:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 120 | fgets( gett, 999, regfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c score.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from score.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c getlag.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from getlag.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dndpre.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from dndpre.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c setcore.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from setcore.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c replaceu.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from replaceu.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c restoreu.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from restoreu.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c setdirection.c In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from setdirection.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ restoreu.c: In function ‘main’: restoreu.c:177:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 177 | fgets( gett, 999, dlfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c makedirectionlist.c gcc -o version version.c -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread setdirection.c: In function ‘main’: setdirection.c:132:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 132 | fgets( line, 99, difp ); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from makedirectionlist.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ In file included from /usr/include/riscv64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, from version.c:1: /usr/include/features.h:187:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 187 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ sed "s:_LIBDIR:/usr/lib/mafft/lib/mafft:" mafft.tmpl > mafft sed "s:_BINDIR:/usr/lib/mafft/bin:" mafft-homologs.tmpl > mafft-homologs.rb sed "s:_BINDIR:/usr/lib/mafft/bin:" mafft-sparsecore.tmpl > mafft-sparsecore.rb gcc -o dvtditr mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o MSalignmm.o fftFunctions.o fft.o tditeration.o dvtditr.o defs.o SAalignmm.o treeOperation.o addfunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o dndfast7 dndfast7.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o dndblast dndblast.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o sextet5 io.o constants.o mtxutl.o mltaln9.o tddis.o sextet5.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o mafft-distance io.o constants.o mtxutl.o mltaln9.o tddis.o mafft-distance.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o pairlocalalign mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o MSalignmm.o Galign11.o Lalign11.o genalign11.o MSalign11.o suboptalign11.o SAalignmm.o pairlocalalignmain.o pairlocalalign.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o multi2hat3s mtxutl.o io.o mltaln9.o tddis.o constants.o multi2hat3s.o defs.o fft.o fftFunctions.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o pairash mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o MSalignmm.o Galign11.o Lalign11.o genalign11.o MSalign11.o suboptalign11.o SAalignmm.o pairash.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o addsingle mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o addsingle.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o splittbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o splittbfast.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o disttbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o disttbfast.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o tbfast mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o tbfast.o defs.o fft.o fftFunctions.o addfunctions.o pairlocalalign.o MSalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o nodepair mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o nodepair.o defs.o fft.o fftFunctions.o addfunctions.o pairlocalalign.o MSalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o mafft-profile io.o mtxutl.o mltaln9.o tddis.o constants.o partSalignmm.o MSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o SAalignmm.o Galign11.o Lalign11.o genalign11.o Falign.o Falign_localhom.o fftFunctions.o fft.o mafft-profile.o defs.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o f2cl mtxutl.o io.o f2cl.o constants.o defs.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o mccaskillwrap mtxutl.o io.o mccaskillwrap.o constants.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o contrafoldwrap mtxutl.o io.o contrafoldwrap.o constants.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o countlen mtxutl.o io.o countlen.o defs.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o seq2regtable mtxutl.o io.o seq2regtable.o defs.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o regtable2seq mtxutl.o io.o regtable2seq.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o score io.o mtxutl.o mltaln9.o score.o constants.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o getlag mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o Dalignmm.o getlag.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o dndpre dndpre.o io.o constants.o mtxutl.o mltaln9.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o setcore mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o setcore.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o replaceu mtxutl.o io.o replaceu.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o restoreu mtxutl.o io.o restoreu.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o setdirection mtxutl.o io.o setdirection.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o makedirectionlist mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o makedirectionlist.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lm -lpthread cp mafft mafft-homologs.rb mafft-sparsecore.rb ../scripts chmod 755 ../scripts/* cp mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore replaceu restoreu setdirection makedirectionlist version ../binaries chmod 755 ../binaries/* cp mafft.1 mafft-homologs.1 ../binaries done. make[2]: Leaving directory '/<>/core' make[1]: Leaving directory '/<>' dh_auto_test -a -O--sourcedirectory=core create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --sourcedirectory=core dh_testroot -a -O--sourcedirectory=core dh_prep -a -O--sourcedirectory=core debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install -- PREFIX=/usr/lib/mafft MANDIR=/usr/share/man/man1 LIBDIR=/usr/lib/mafft/lib/mafft cd core && make -j4 install DESTDIR=/<>/debian/mafft AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" PREFIX=/usr/lib/mafft MANDIR=/usr/share/man/man1 LIBDIR=/usr/lib/mafft/lib/mafft make[2]: Entering directory '/<>/core' cp mafft mafft-homologs.rb mafft-sparsecore.rb ../scripts chmod 755 ../scripts/* cp mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore replaceu restoreu setdirection makedirectionlist version ../binaries chmod 755 ../binaries/* cp mafft.1 mafft-homologs.1 ../binaries done. mkdir -p /<>/debian/mafft/usr/lib/mafft/lib/mafft chmod 755 /<>/debian/mafft/usr/lib/mafft/lib/mafft mkdir -p /<>/debian/mafft/usr/lib/mafft/bin chmod 755 /<>/debian/mafft/usr/lib/mafft/bin chmod 755 mafft mafft-homologs.rb mafft-sparsecore.rb install --strip-program=true mafft mafft-homologs.rb mafft-sparsecore.rb /<>/debian/mafft/usr/lib/mafft/bin install: WARNING: ignoring --strip-program option as -s option was not specified chmod 755 dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore replaceu restoreu setdirection makedirectionlist version ||: # in MinGW, it's ok if this fails install --strip-program=true -s dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore replaceu restoreu setdirection makedirectionlist version /<>/debian/mafft/usr/lib/mafft/lib/mafft install --strip-program=true mafftash_premafft.pl seekquencer_premafft.pl /<>/debian/mafft/usr/lib/mafft/lib/mafft install: WARNING: ignoring --strip-program option as -s option was not specified install --strip-program=true -m 644 mafft.1 mafft-homologs.1 /<>/debian/mafft/usr/lib/mafft/lib/mafft install: WARNING: ignoring --strip-program option as -s option was not specified ( cd /<>/debian/mafft/usr/lib/mafft/bin; \ rm -f linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi; \ rm -f mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi mafft-nwns mafft-nwnsi mafft-xinsi mafft-qinsi mafft-randomcore.rb ; \ ln -s mafft linsi; ln -s mafft ginsi; ln -s mafft fftns; \ ln -s mafft fftnsi; ln -s mafft nwns; ln -s mafft nwnsi; \ ln -s mafft einsi; \ ln -s mafft mafft-linsi; ln -s mafft mafft-ginsi; ln -s mafft mafft-fftns; \ ln -s mafft mafft-fftnsi; ln -s mafft mafft-nwns; ln -s mafft mafft-nwnsi; \ ln -s mafft mafft-einsi; ln -s mafft mafft-xinsi; ln -s mafft mafft-qinsi;\ rm -f mafft-profile mafft-profile.exe; ln -s /usr/lib/mafft/lib/mafft/mafft-profile .; \ rm -f mafft-distance mafft-distance.exe; ln -s /usr/lib/mafft/lib/mafft/mafft-distance . ) mkdir -p /<>/debian/mafft/usr/share/man/man1 chmod 755 /<>/debian/mafft/usr/share/man/man1 install --strip-program=true -m 644 mafft.1 mafft-homologs.1 /<>/debian/mafft/usr/share/man/man1 install: WARNING: ignoring --strip-program option as -s option was not specified make[2]: Leaving directory '/<>/core' rm debian/mafft/usr/lib/mafft/lib/mafft/*.1 make[1]: Leaving directory '/<>' dh_installdocs -a -O--sourcedirectory=core dh_installchangelogs -a -O--sourcedirectory=core dh_installman -a -O--sourcedirectory=core dh_installinit -a -O--sourcedirectory=core dh_installsystemduser -a -O--sourcedirectory=core dh_perl -a -O--sourcedirectory=core dh_link -a -O--sourcedirectory=core dh_strip_nondeterminism -a -O--sourcedirectory=core debian/rules override_dh_compress make[1]: Entering directory '/<>' dh_compress -X test/sample make[1]: Leaving directory '/<>' dh_fixperms -a -O--sourcedirectory=core dh_missing -a -O--sourcedirectory=core dh_dwz -a -O--sourcedirectory=core dh_strip -a -O--sourcedirectory=core dh_makeshlibs -a -O--sourcedirectory=core dh_shlibdeps -a -O--sourcedirectory=core dh_installdeb -a -O--sourcedirectory=core dh_gencontrol -a -O--sourcedirectory=core dh_md5sums -a -O--sourcedirectory=core dh_builddeb -a -O--sourcedirectory=core INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing mafft (in debian/mafft); do_strip: , oemstrip: pkgstriptranslations: processing mafft-dbgsym (in debian/.debhelper/mafft/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/mafft/DEBIAN/control, package mafft, directory debian/mafft pkgstripfiles: Truncating usr/share/doc/mafft/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package mafft ... pkgstripfiles: No PNG files. dpkg-deb: building package 'mafft' in '../mafft_7.453-1_riscv64.deb'. pkgstripfiles: processing control file: debian/.debhelper/mafft/dbgsym-root/DEBIAN/control, package mafft-dbgsym, directory debian/.debhelper/mafft/dbgsym-root dpkg-deb: building package 'mafft-dbgsym' in 'debian/.debhelper/scratch-space/build-mafft/mafft-dbgsym_7.453-1_riscv64.deb'. Renaming mafft-dbgsym_7.453-1_riscv64.deb to mafft-dbgsym_7.453-1_riscv64.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../mafft_7.453-1_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 2020-04-03T09:37:24Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ mafft_7.453-1_riscv64.changes: ------------------------------ Format: 1.8 Date: Thu, 21 Nov 2019 17:27:17 +0100 Source: mafft Binary: mafft Architecture: riscv64 Version: 7.453-1 Distribution: focal Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Steffen Moeller Description: mafft - Multiple alignment program for amino acid or nucleotide sequences Changes: mafft (7.453-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version: 4.4.1 * Trim trailing whitespace. * Use secure URI in Homepage field. * Set fields Upstream-Name, Upstream-Contact in debian/copyright. * Remove obsolete fields Name, Contact from debian/upstream/metadata. Checksums-Sha1: ab5987613ba9aba7a1a98c2d31249a50b959031a 8336448 mafft-dbgsym_7.453-1_riscv64.ddeb 85b10fd53c278909ec8570232f21f270343632de 5008 mafft_7.453-1_riscv64.buildinfo b268d9cd5d88015d66186bca550b8b746d51fa37 916212 mafft_7.453-1_riscv64.deb Checksums-Sha256: 3a1bb49f9db4422aed4a42bd9ca592d3af38d9912001e01260de21f041900006 8336448 mafft-dbgsym_7.453-1_riscv64.ddeb 31418fb81ffb032a65f88a01e0f78914129f366b343b9f448530a2adfb9fa004 5008 mafft_7.453-1_riscv64.buildinfo c6faefaf3174e8daa37aef365b13f459bf9839e73545be1d845e508324d04f40 916212 mafft_7.453-1_riscv64.deb Files: f65753924e1db9857136e44f5f37d2ef 8336448 debug optional mafft-dbgsym_7.453-1_riscv64.ddeb 7bb236358c63cabe2b32ef87aaf067d3 5008 science optional mafft_7.453-1_riscv64.buildinfo de5cfc4cbf8d5f4692b380daf6e036d4 916212 science optional mafft_7.453-1_riscv64.deb /<>/mafft_7.453-1_riscv64.changes.new could not be renamed to /<>/mafft_7.453-1_riscv64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: mafft Binary: mafft Architecture: riscv64 Version: 7.453-1 Checksums-Md5: f65753924e1db9857136e44f5f37d2ef 8336448 mafft-dbgsym_7.453-1_riscv64.ddeb de5cfc4cbf8d5f4692b380daf6e036d4 916212 mafft_7.453-1_riscv64.deb Checksums-Sha1: ab5987613ba9aba7a1a98c2d31249a50b959031a 8336448 mafft-dbgsym_7.453-1_riscv64.ddeb b268d9cd5d88015d66186bca550b8b746d51fa37 916212 mafft_7.453-1_riscv64.deb Checksums-Sha256: 3a1bb49f9db4422aed4a42bd9ca592d3af38d9912001e01260de21f041900006 8336448 mafft-dbgsym_7.453-1_riscv64.ddeb c6faefaf3174e8daa37aef365b13f459bf9839e73545be1d845e508324d04f40 916212 mafft_7.453-1_riscv64.deb Build-Origin: Ubuntu Build-Architecture: riscv64 Build-Date: Fri, 03 Apr 2020 09:37:14 +0000 Build-Path: /<> Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.69-11.1), automake (= 1:1.16.1-4ubuntu6), autopoint (= 0.19.8.1-10build1), autotools-dev (= 20180224.1), base-files (= 11ubuntu4), base-passwd (= 3.5.47), bash (= 5.0-6ubuntu1), binutils (= 2.34-5ubuntu1), binutils-common (= 2.34-5ubuntu1), binutils-riscv64-linux-gnu (= 2.34-5ubuntu1), bsdmainutils (= 11.1.2ubuntu3), bsdutils (= 1:2.34-0.1ubuntu8), build-essential (= 12.8ubuntu1), bzip2 (= 1.0.8-2), coreutils (= 8.30-3ubuntu2), cpp (= 4:9.3.0-1ubuntu2), cpp-9 (= 9.3.0-8ubuntu1), dash (= 0.5.10.2-6), debconf (= 1.5.73), debhelper (= 12.10ubuntu1), debianutils (= 4.9.1), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.6.3-2), diffutils (= 1:3.7-3), dpkg (= 1.19.7ubuntu3), dpkg-dev (= 1.19.7ubuntu3), dwz (= 0.13-5), file (= 1:5.38-4), findutils (= 4.7.0-1ubuntu1), g++ (= 4:9.3.0-1ubuntu2), g++-9 (= 9.3.0-8ubuntu1), gcc (= 4:9.3.0-1ubuntu2), gcc-10-base (= 10-20200324-1ubuntu1), gcc-9 (= 9.3.0-8ubuntu1), gcc-9-base (= 9.3.0-8ubuntu1), gettext (= 0.19.8.1-10build1), gettext-base (= 0.19.8.1-10build1), grep (= 3.4-1), groff-base (= 1.22.4-4build1), gzip (= 1.10-0ubuntu4), hostname (= 3.23), init-system-helpers (= 1.57), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-6), libarchive-zip-perl (= 1.67-2), libatomic1 (= 10-20200324-1ubuntu1), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-2ubuntu6), libaudit1 (= 1:2.8.5-2ubuntu6), libbinutils (= 2.34-5ubuntu1), libblkid1 (= 2.34-0.1ubuntu8), libbsd0 (= 0.10.0-1), libbz2-1.0 (= 1.0.8-2), libc-bin (= 2.31-0ubuntu6~riscv64.1), libc-dev-bin (= 2.31-0ubuntu6~riscv64.1), libc6 (= 2.31-0ubuntu6~riscv64.1), libc6-dev (= 2.31-0ubuntu6~riscv64.1), libcap-ng0 (= 0.7.9-2.1build1), libcc1-0 (= 10-20200324-1ubuntu1), libcroco3 (= 0.6.13-1), libcrypt-dev (= 1:4.4.10-10ubuntu4), libcrypt1 (= 1:4.4.10-10ubuntu4), libctf-nobfd0 (= 2.34-5ubuntu1), libctf0 (= 2.34-5ubuntu1), libdb5.3 (= 5.3.28+dfsg1-0.6ubuntu2), libdebconfclient0 (= 0.251ubuntu1), libdebhelper-perl (= 12.10ubuntu1), libdpkg-perl (= 1.19.7ubuntu3), libelf1 (= 0.176-1.1build1), libffi7 (= 3.3-4), libfile-stripnondeterminism-perl (= 1.6.3-2), libgcc-9-dev (= 9.3.0-8ubuntu1), libgcc-s1 (= 10-20200324-1ubuntu1), libgcc1 (= 1:10-20200324-1ubuntu1), libgcrypt20 (= 1.8.5-5ubuntu1), libgdbm-compat4 (= 1.18.1-5), libgdbm6 (= 1.18.1-5), libglib2.0-0 (= 2.64.1-1), libgmp10 (= 2:6.2.0+dfsg-4), libgomp1 (= 10-20200324-1ubuntu1), libgpg-error0 (= 1.37-1), libicu66 (= 66.1-2ubuntu2), libisl22 (= 0.22.1-1), liblz4-1 (= 1.9.2-2), liblzma5 (= 5.2.4-1), libmagic-mgc (= 1:5.38-4), libmagic1 (= 1:5.38-4), libmount1 (= 2.34-0.1ubuntu8), 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 (= 5.30.0-9build1), libpipeline1 (= 1.5.2-2build1), libselinux1 (= 3.0-1build2), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.34-0.1ubuntu8), libstdc++-9-dev (= 9.3.0-8ubuntu1), libstdc++6 (= 10-20200324-1ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 244.3-1ubuntu1), libtinfo6 (= 6.2-0ubuntu2), libtool (= 2.4.6-13), libuchardet0 (= 0.0.6-3build1), libudev1 (= 244.3-1ubuntu1), libunistring2 (= 0.9.10-2), libuuid1 (= 2.34-0.1ubuntu8), libxml2 (= 2.9.10+dfsg-4build1), libzstd1 (= 1.4.4+dfsg-3), linux-libc-dev (= 5.4.0-21.25), login (= 1:4.8.1-1ubuntu3), lsb-base (= 11.1.0ubuntu2), m4 (= 1.4.18-4), make (= 4.2.1-1.2), man-db (= 2.9.1-1), mawk (= 1.3.4.20200120-2), ncurses-base (= 6.2-0ubuntu2), ncurses-bin (= 6.2-0ubuntu2), patch (= 2.7.6-6), perl (= 5.30.0-9build1), perl-base (= 5.30.0-9build1), perl-modules-5.30 (= 5.30.0-9build1), po-debconf (= 1.0.21), sed (= 4.7-1), sensible-utils (= 0.0.12+nmu1), sysvinit-utils (= 2.96-2.1ubuntu1), tar (= 1.30+dfsg-7), tzdata (= 2019c-3ubuntu1), util-linux (= 2.34-0.1ubuntu8), xz-utils (= 5.2.4-1), zlib1g (= 1:1.2.11.dfsg-2ubuntu1) Environment: DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1574353637" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ mafft_7.453-1_riscv64.deb ------------------------- new Debian package, version 2.0. size 916212 bytes: control archive=2392 bytes. 1467 bytes, 31 lines control 3783 bytes, 54 lines md5sums Package: mafft Version: 7.453-1 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 8110 Depends: libc6 (>= 2.27), perl:any Recommends: blast2, libwww-perl, lynx, ruby Enhances: t-coffee Section: science Priority: optional Homepage: https://mafft.cbrc.jp/alignment/software/ Description: Multiple alignment program for amino acid or nucleotide sequences MAFFT is a multiple sequence alignment program which offers three accuracy-oriented methods: * L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information), * G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information), * E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences), and five speed-oriented methods: * FFT-NS-i (iterative refinement method; two cycles only), * FFT-NS-i (iterative refinement method; max. 1000 iterations), * FFT-NS-2 (fast; progressive method), * FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree), * NW-NS-PartTree-1 (recommended for ∼50,000 sequences; progressive method with the PartTree algorithm). drwxr-xr-x root/root 0 2019-11-21 16:27 ./ drwxr-xr-x root/root 0 2019-11-21 16:27 ./usr/ drwxr-xr-x root/root 0 2019-11-21 16:27 ./usr/bin/ lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/bin/mafft -> ../lib/mafft/bin/mafft lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/bin/mafft-homologs -> ../lib/mafft/bin/mafft-homologs.rb lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/bin/mafft-profile -> ../lib/mafft/bin/mafft-profile drwxr-xr-x root/root 0 2019-11-21 16:27 ./usr/lib/ drwxr-xr-x root/root 0 2019-11-21 16:27 ./usr/lib/mafft/ drwxr-xr-x root/root 0 2019-11-21 16:27 ./usr/lib/mafft/bin/ lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/lib/mafft/bin/einsi -> mafft lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/lib/mafft/bin/fftns -> mafft lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/lib/mafft/bin/fftnsi -> mafft lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/lib/mafft/bin/ginsi -> mafft lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/lib/mafft/bin/linsi -> mafft -rwxr-xr-x root/root 105464 2019-11-21 16:27 ./usr/lib/mafft/bin/mafft lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/lib/mafft/bin/mafft-distance -> ../lib/mafft/mafft-distance lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/lib/mafft/bin/mafft-einsi -> mafft lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/lib/mafft/bin/mafft-fftns -> mafft lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/lib/mafft/bin/mafft-fftnsi -> mafft lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/lib/mafft/bin/mafft-ginsi -> mafft -rwxr-xr-x root/root 11551 2019-11-21 16:27 ./usr/lib/mafft/bin/mafft-homologs.rb lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/lib/mafft/bin/mafft-linsi -> mafft lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/lib/mafft/bin/mafft-nwns -> mafft lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/lib/mafft/bin/mafft-nwnsi -> mafft lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/lib/mafft/bin/mafft-profile -> ../lib/mafft/mafft-profile lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/lib/mafft/bin/mafft-qinsi -> mafft -rwxr-xr-x root/root 7788 2019-11-21 16:27 ./usr/lib/mafft/bin/mafft-sparsecore.rb lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/lib/mafft/bin/mafft-xinsi -> mafft lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/lib/mafft/bin/nwns -> mafft lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/lib/mafft/bin/nwnsi -> mafft drwxr-xr-x root/root 0 2019-11-21 16:27 ./usr/lib/mafft/lib/ drwxr-xr-x root/root 0 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/ -rwxr-xr-x root/root 401008 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/addsingle -rwxr-xr-x root/root 224648 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/contrafoldwrap -rwxr-xr-x root/root 68400 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/countlen -rwxr-xr-x root/root 409248 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/disttbfast -rwxr-xr-x root/root 232856 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/dndblast -rwxr-xr-x root/root 232864 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/dndfast7 -rwxr-xr-x root/root 224648 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/dndpre -rwxr-xr-x root/root 409296 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/dvtditr -rwxr-xr-x root/root 126000 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/f2cl -rwxr-xr-x root/root 368192 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/getlag -rwxr-xr-x root/root 10424 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/hex2maffttext -rwxr-xr-x root/root 232832 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/mafft-distance -rwxr-xr-x root/root 368192 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/mafft-profile -rwxr-xr-x root/root 10475 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/mafftash_premafft.pl -rwxr-xr-x root/root 10432 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/maffttext2hex -rwxr-xr-x root/root 380456 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/makedirectionlist -rwxr-xr-x root/root 228752 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/mccaskillwrap -rwxr-xr-x root/root 241176 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/multi2hat3s -rwxr-xr-x root/root 409200 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/nodepair -rwxr-xr-x root/root 376408 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/pairash -rwxr-xr-x root/root 396904 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/pairlocalalign -rwxr-xr-x root/root 171264 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/regtable2seq -rwxr-xr-x root/root 171264 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/replaceu -rwxr-xr-x root/root 171264 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/restoreu -rwxr-xr-x root/root 224640 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/score -rwxr-xr-x root/root 15541 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/seekquencer_premafft.pl -rwxr-xr-x root/root 68400 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/seq2regtable -rwxr-xr-x root/root 368208 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/setcore -rwxr-xr-x root/root 171264 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/setdirection -rwxr-xr-x root/root 232840 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/sextet5 -rwxr-xr-x root/root 384616 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/splittbfast -rwxr-xr-x root/root 442048 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/tbfast -rwxr-xr-x root/root 6240 2019-11-21 16:27 ./usr/lib/mafft/lib/mafft/version drwxr-xr-x root/root 0 2019-11-21 16:27 ./usr/share/ drwxr-xr-x root/root 0 2019-11-21 16:27 ./usr/share/doc/ drwxr-xr-x root/root 0 2019-11-21 16:27 ./usr/share/doc/mafft/ -rw-r--r-- root/root 1029 2019-11-21 16:27 ./usr/share/doc/mafft/changelog.Debian.gz -rw-r--r-- root/root 2013 2019-11-21 16:27 ./usr/share/doc/mafft/copyright drwxr-xr-x root/root 0 2019-11-21 16:27 ./usr/share/doc/mafft/test/ -rw-r--r-- root/root 16616 2019-11-08 07:45 ./usr/share/doc/mafft/test/sample -rw-r--r-- root/root 30112 2019-11-08 07:45 ./usr/share/doc/mafft/test/sample.dpparttree -rw-r--r-- root/root 28816 2019-11-08 07:45 ./usr/share/doc/mafft/test/sample.fftns2 -rw-r--r-- root/root 28996 2019-11-08 07:45 ./usr/share/doc/mafft/test/sample.fftnsi -rw-r--r-- root/root 29896 2019-11-08 07:45 ./usr/share/doc/mafft/test/sample.gins1 -rw-r--r-- root/root 29572 2019-11-08 07:45 ./usr/share/doc/mafft/test/sample.ginsi -rw-r--r-- root/root 41380 2019-11-08 07:45 ./usr/share/doc/mafft/test/sample.ginsi.allowshift -rw-r--r-- root/root 28888 2019-11-08 07:45 ./usr/share/doc/mafft/test/sample.lins1 -rw-r--r-- root/root 29500 2019-11-08 07:45 ./usr/share/doc/mafft/test/sample.linsi -rw-r--r-- root/root 30112 2019-11-08 07:45 ./usr/share/doc/mafft/test/sample.parttree -rw-r--r-- root/root 1502 2019-11-08 07:45 ./usr/share/doc/mafft/test/samplerna -rw-r--r-- root/root 1916 2019-11-08 07:45 ./usr/share/doc/mafft/test/samplerna.qinsi -rw-r--r-- root/root 1916 2019-11-08 07:45 ./usr/share/doc/mafft/test/samplerna.xinsi -rw-r--r-- root/root 908 2019-11-08 07:45 ./usr/share/doc/mafft/test/script drwxr-xr-x root/root 0 2019-11-21 16:27 ./usr/share/man/ drwxr-xr-x root/root 0 2019-11-21 16:27 ./usr/share/man/man1/ lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/share/man/man1/einsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/share/man/man1/fftns.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/share/man/man1/fftnsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/share/man/man1/ginsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/share/man/man1/linsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/share/man/man1/mafft-einsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/share/man/man1/mafft-fftns.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/share/man/man1/mafft-fftnsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/share/man/man1/mafft-ginsi.1.gz -> mafft.1.gz -rw-r--r-- root/root 2130 2019-11-21 16:27 ./usr/share/man/man1/mafft-homologs.1.gz lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/share/man/man1/mafft-linsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2019-11-21 16:27 ./usr/share/man/man1/mafft-profile.1.gz -> mafft.1.gz -rw-r--r-- root/root 4421 2019-11-21 16:27 ./usr/share/man/man1/mafft.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: riscv64 Build Type: any Build-Space: 157760 Build-Time: 524 Distribution: focal Host Architecture: riscv64 Install-Time: 113 Job: mafft_7.453-1.dsc Machine Architecture: riscv64 Package: mafft Package-Time: 674 Source-Version: 7.453-1 Space: 157760 Status: successful Version: 7.453-1 -------------------------------------------------------------------------------- Finished at 2020-04-03T09:37:24Z Build needed 00:11:14, 157760k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19107320 Scanning for processes to kill in build PACKAGEBUILD-19107320 RUN: /usr/share/launchpad-buildd/bin/in-target umount-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19107320 Stopping target for build PACKAGEBUILD-19107320 RUN: /usr/share/launchpad-buildd/bin/in-target remove-build --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19107320 Removing build PACKAGEBUILD-19107320