https://launchpad.net/ubuntu/+archive/test-rebuild-20240502-noble/+build/28269765 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-032 5.4.0-177-generic #197-Ubuntu SMP Thu Mar 28 22:45:47 UTC 2024 x86_64 Buildd toolchain package versions: launchpad-buildd_237~660~ubuntu20.04.1 python3-lpbuildd_237~660~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 5 May 22:30:22 ntpdate[1851]: adjust time server 10.131.248.1 offset 0.000223 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-28269765 --image-type chroot /home/buildd/filecache-default/1fe94ca8758119221c8de2550665a1bb335bd6a9 Creating target for build PACKAGEBUILD-28269765 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-28269765 Starting target for build PACKAGEBUILD-28269765 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-28269765 'deb http://ftpmaster.internal/ubuntu noble main universe' Overriding sources.list in build-PACKAGEBUILD-28269765 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-28269765 Updating target for build PACKAGEBUILD-28269765 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [256 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 Packages [1401 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main Translation-en [513 kB] Get:4 http://ftpmaster.internal/ubuntu noble/universe amd64 Packages [15.0 MB] Get:5 http://ftpmaster.internal/ubuntu noble/universe Translation-en [5982 kB] Fetched 23.2 MB in 3s (8238 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libnsl-dev libperl5.36 libtirpc-dev libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0* libdb5.3* libext2fs2* libgdbm-compat4* libgdbm6* libgnutls30* libhogweed6* libnettle8* libnpth0* libpng16-16* libreadline8* libssl3* libtirpc3* usrmerge* The following NEW packages will be installed: cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-13-x86-64-linux-gnu gcc-14-base gcc-x86-64-linux-gnu libapt-pkg6.0t64 libdb5.3t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64 libgnutls30t64 libhogweed6t64 libnettle8t64 libnpth0t64 libperl5.38t64 libpng16-16t64 libreadline8t64 libssl3t64 libtirpc3t64 libunistring5 perl-modules-5.38 The following packages will be upgraded: advancecomp apt apt-utils base-files base-passwd bash bash-completion binutils binutils-common binutils-x86-64-linux-gnu bsdextrautils bsdutils bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot findutils g++ g++-13 gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep gzip hostname init init-system-helpers krb5-locales libacl1 libapparmor1 libargon2-1 libasan8 libassuan0 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgmp10 libgomp1 libgpg-error-l10n libgpg-error0 libgpm2 libgprofng0 libgssapi-krb5-2 libhwasan0 libidn2-0 libip4tc2 libisl23 libitm1 libjansson4 libjson-c5 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblockfile-bin liblockfile1 liblsan0 liblz4-1 liblzma5 libmd0 libmount1 libmpc3 libmpfr6 libncursesw6 libnsl-dev libnsl2 libnss-nis libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libproc2-0 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libss2 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtasn1-6 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtsan2 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev lockfile-progs login logsave lto-disabled-list make mawk mount ncurses-base ncurses-bin openssl optipng passwd patch perl perl-base pinentry-curses procps psmisc readline-common rpcsvc-proto sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 177 upgraded, 23 newly installed, 14 to remove and 0 not upgraded. Need to get 121 MB of archives. After this operation, 78.2 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc-common all 1.3.4+ds-1.1build1 [8094 B] Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc-dev amd64 1.3.4+ds-1.1build1 [193 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libnsl-dev amd64 1.3.0-3build3 [70.5 kB] Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libnsl2 amd64 1.3.0-3build3 [41.4 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.1build1 [82.6 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 libgssapi-krb5-2 amd64 1.20.1-6ubuntu2 [142 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libkrb5-3 amd64 1.20.1-6ubuntu2 [347 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libk5crypto3 amd64 1.20.1-6ubuntu2 [81.7 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libkrb5support0 amd64 1.20.1-6ubuntu2 [33.5 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 libacl1 amd64 2.3.2-1build1 [16.8 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 libapparmor1 amd64 4.0.0-beta3-0ubuntu3 [49.5 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 libaudit-common all 1:3.1.2-2.1build1 [5736 B] Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libcap-ng0 amd64 0.8.4-2build2 [15.2 kB] Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 libaudit1 amd64 1:3.1.2-2.1build1 [46.9 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libblkid1 amd64 2.39.3-9ubuntu6 [123 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libcap2 amd64 1:2.66-5ubuntu2 [30.0 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt-dev amd64 1:4.4.36-4build1 [112 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt1 amd64 1:4.4.36-4build1 [82.3 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libgpg-error-l10n all 1.47-3build2 [8064 B] Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libgpg-error0 amd64 1.47-3build2 [70.0 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libgcrypt20 amd64 1.10.3-2build1 [532 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 liblzma5 amd64 5.6.1+really5.4.5-1 [127 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libzstd1 amd64 1.5.5+dfsg2-2build1 [299 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 libkmod2 amd64 31+20240202-2ubuntu7 [51.7 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 liblz4-1 amd64 1.9.4-1build1 [63.0 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-8-0 amd64 10.42-4ubuntu2 [227 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 libselinux1 amd64 3.5-2ubuntu2 [79.6 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 libmount1 amd64 2.39.3-9ubuntu6 [134 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 perl-modules-5.38 all 5.38.2-3.2build2 [3110 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-7 [734 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 libgdbm6t64 amd64 1.23-5.1build1 [34.4 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 libgdbm-compat4t64 amd64 1.23-5.1build1 [6710 B] Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 libperl5.38t64 amd64 5.38.2-3.2build2 [4873 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 perl amd64 5.38.2-3.2build2 [231 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 perl-base amd64 5.38.2-3.2build2 [1823 kB] Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 liblocale-gettext-perl amd64 1.07-6ubuntu5 [15.8 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 libtext-iconv-perl amd64 1.7-8build3 [13.5 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 libtext-charwidth-perl amd64 0.04-11build3 [9358 B] Get:39 http://ftpmaster.internal/ubuntu noble/universe amd64 libnss-nisplus amd64 1.3-5build1 [22.4 kB] Get:40 http://ftpmaster.internal/ubuntu noble/universe amd64 libnss-nis amd64 3.1-0ubuntu7 [26.5 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 libc-dev-bin amd64 2.39-0ubuntu8 [20.4 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 rpcsvc-proto amd64 1.4.2-0ubuntu7 [67.4 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 libc6-dev amd64 2.39-0ubuntu8 [2124 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 libc6 amd64 2.39-0ubuntu8 [3265 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 libc-bin amd64 2.39-0ubuntu8 [682 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 openssl amd64 3.0.13-0ubuntu3 [1002 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 libsystemd-shared amd64 255.4-1ubuntu8 [2067 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 libcryptsetup12 amd64 2:2.7.0-1ubuntu4 [266 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 libssl3t64 amd64 3.0.13-0ubuntu3 [1936 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 systemd-dev all 255.4-1ubuntu8 [104 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 systemd-sysv amd64 255.4-1ubuntu8 [11.9 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 systemd amd64 255.4-1ubuntu8 [3471 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 libsystemd0 amd64 255.4-1ubuntu8 [429 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 libpam-modules-bin amd64 1.5.3-5ubuntu5 [51.9 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 libpam-modules amd64 1.5.3-5ubuntu5 [279 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 libnettle8t64 amd64 3.9.1-2.2build1 [182 kB] Get:57 http://ftpmaster.internal/ubuntu noble/main amd64 libhogweed6t64 amd64 3.9.1-2.2build1 [199 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 libp11-kit0 amd64 0.25.3-4ubuntu2 [299 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 libunistring5 amd64 1.1-2build1 [535 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main amd64 libgnutls30t64 amd64 3.8.3-1.1ubuntu3 [998 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 libapt-pkg6.0t64 amd64 2.7.14build2 [985 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main amd64 bzip2 amd64 1.0.8-5.1 [34.5 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main amd64 libbz2-1.0 amd64 1.0.8-5.1 [34.3 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-14-base amd64 14-20240412-0ubuntu1 [47.6 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-s1 amd64 14-20240412-0ubuntu1 [78.5 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++6 amd64 14-20240412-0ubuntu1 [795 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main amd64 libudev1 amd64 255.4-1ubuntu8 [174 kB] Get:68 http://ftpmaster.internal/ubuntu noble/main amd64 libxxhash0 amd64 0.8.2-2build1 [24.1 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main amd64 zlib1g amd64 1:1.3.dfsg-3.1ubuntu2 [62.8 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2ubuntu6 [253 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main amd64 libffi8 amd64 3.4.6-1build1 [24.7 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main amd64 libidn2-0 amd64 2.3.7-2build1 [66.2 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main amd64 libtasn1-6 amd64 4.19.0-3build1 [43.9 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main amd64 libdebconfclient0 amd64 0.271ubuntu3 [11.4 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main amd64 base-passwd amd64 3.6.3build1 [51.1 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main amd64 libassuan0 amd64 2.5.6-1build1 [37.3 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main amd64 libsqlite3-0 amd64 3.45.1-1ubuntu2 [701 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main amd64 gpg amd64 2.4.4-2ubuntu17 [565 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main amd64 libreadline8t64 amd64 8.2-4build1 [153 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main amd64 readline-common all 8.2-4build1 [56.5 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main amd64 libncursesw6 amd64 6.4+20240113-1ubuntu2 [148 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main amd64 libtinfo6 amd64 6.4+20240113-1ubuntu2 [108 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main amd64 gpg-agent amd64 2.4.4-2ubuntu17 [227 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main amd64 gpgconf amd64 2.4.4-2ubuntu17 [103 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main amd64 pinentry-curses amd64 1.2.1-3ubuntu5 [35.2 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main amd64 init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main amd64 libnpth0t64 amd64 1.6-3.1build1 [8378 B] Get:88 http://ftpmaster.internal/ubuntu noble/main amd64 gpgv amd64 2.4.4-2ubuntu17 [157 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main amd64 ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main amd64 libseccomp2 amd64 2.5.5-1ubuntu3 [50.3 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main amd64 apt-utils amd64 2.7.14build2 [217 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main amd64 apt amd64 2.7.14build2 [1375 kB] Get:93 http://ftpmaster.internal/ubuntu noble/main amd64 debconf-i18n all 1.5.86ubuntu1 [205 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main amd64 debconf all 1.5.86ubuntu1 [124 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main amd64 libpam0g amd64 1.5.3-5ubuntu5 [67.7 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main amd64 libargon2-1 amd64 0~20190702+dfsg-4build1 [20.8 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main amd64 libdevmapper1.02.1 amd64 2:1.02.185-3ubuntu3 [139 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main amd64 libjson-c5 amd64 0.17-1build1 [35.3 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main amd64 libuuid1 amd64 2.39.3-9ubuntu6 [35.2 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main amd64 libfdisk1 amd64 2.39.3-9ubuntu6 [146 kB] Get:101 http://ftpmaster.internal/ubuntu noble/main amd64 mount amd64 2.39.3-9ubuntu6 [118 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main amd64 libcom-err2 amd64 1.47.0-2.4~exp1ubuntu4 [22.8 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main amd64 libkeyutils1 amd64 1.6.3-3build1 [9490 B] Get:104 http://ftpmaster.internal/ubuntu noble/main amd64 linux-libc-dev amd64 6.8.0-31.31 [1598 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main amd64 base-files amd64 13ubuntu10 [73.6 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main amd64 debianutils amd64 5.17build1 [89.9 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main amd64 bash amd64 5.2.21-2ubuntu4 [794 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main amd64 bsdutils amd64 1:2.39.3-9ubuntu6 [95.0 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main amd64 coreutils amd64 9.4-3ubuntu6 [1412 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main amd64 tar amd64 1.35+dfsg-3build1 [253 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main amd64 dpkg amd64 1.22.6ubuntu6 [1283 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main amd64 dash amd64 0.5.12-6ubuntu5 [89.8 kB] Get:113 http://ftpmaster.internal/ubuntu noble/main amd64 diffutils amd64 1:3.10-1build1 [177 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main amd64 findutils amd64 4.9.0-5build1 [298 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main amd64 grep amd64 3.11-4build1 [162 kB] Get:116 http://ftpmaster.internal/ubuntu noble/main amd64 gzip amd64 1.12-1ubuntu3 [98.8 kB] Get:117 http://ftpmaster.internal/ubuntu noble/main amd64 hostname amd64 3.23+nmu2ubuntu2 [11.1 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main amd64 login amd64 1:4.13+dfsg1-4ubuntu3 [202 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main amd64 ncurses-bin amd64 6.4+20240113-1ubuntu2 [188 kB] Get:120 http://ftpmaster.internal/ubuntu noble/main amd64 sed amd64 4.9-2build1 [193 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main amd64 util-linux amd64 2.39.3-9ubuntu6 [1127 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main amd64 ncurses-base all 6.4+20240113-1ubuntu2 [25.5 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main amd64 sysvinit-utils amd64 3.08-6ubuntu3 [34.2 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main amd64 logsave amd64 1.47.0-2.4~exp1ubuntu4 [22.5 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main amd64 libext2fs2t64 amd64 1.47.0-2.4~exp1ubuntu4 [222 kB] Get:126 http://ftpmaster.internal/ubuntu noble/main amd64 e2fsprogs amd64 1.47.0-2.4~exp1ubuntu4 [601 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main amd64 optipng amd64 0.7.8+ds-1build2 [110 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main amd64 libpng16-16t64 amd64 1.6.43-5build1 [187 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main amd64 init amd64 1.66ubuntu1 [6186 B] Get:130 http://ftpmaster.internal/ubuntu noble/main amd64 libsmartcols1 amd64 2.39.3-9ubuntu6 [64.8 kB] Get:131 http://ftpmaster.internal/ubuntu noble/main amd64 uuid-runtime amd64 2.39.3-9ubuntu6 [33.1 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main amd64 libattr1 amd64 1:2.5.2-1build1 [11.3 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main amd64 libmd0 amd64 1.1.0-2build1 [27.0 kB] Get:134 http://ftpmaster.internal/ubuntu noble/main amd64 libpam-runtime all 1.5.3-5ubuntu5 [40.8 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main amd64 libsemanage-common all 3.5-1build5 [10.1 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main amd64 libsepol2 amd64 3.5-2build1 [303 kB] Get:137 http://ftpmaster.internal/ubuntu noble/main amd64 libsemanage2 amd64 3.5-1build5 [93.2 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main amd64 passwd amd64 1:4.13+dfsg1-4ubuntu3 [845 kB] Get:139 http://ftpmaster.internal/ubuntu noble/main amd64 libproc2-0 amd64 2:4.0.4-4ubuntu3 [59.1 kB] Get:140 http://ftpmaster.internal/ubuntu noble/main amd64 libss2 amd64 1.47.0-2.4~exp1ubuntu4 [17.0 kB] Get:141 http://ftpmaster.internal/ubuntu noble/main amd64 mawk amd64 1.3.4.20240123-1build1 [127 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main amd64 procps amd64 2:4.0.4-4ubuntu3 [708 kB] Get:143 http://ftpmaster.internal/ubuntu noble/main amd64 sensible-utils all 0.0.22 [22.5 kB] Get:144 http://ftpmaster.internal/ubuntu noble/main amd64 ca-certificates all 20240203 [159 kB] Get:145 http://ftpmaster.internal/ubuntu noble/main amd64 krb5-locales all 1.20.1-6ubuntu2 [13.8 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main amd64 tzdata all 2024a-2ubuntu1 [273 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main amd64 bash-completion all 1:2.11-8 [180 kB] Get:148 http://ftpmaster.internal/ubuntu noble/main amd64 bsdextrautils amd64 2.39.3-9ubuntu6 [73.8 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main amd64 libgpm2 amd64 1.20.7-11 [14.1 kB] Get:150 http://ftpmaster.internal/ubuntu noble/main amd64 libip4tc2 amd64 1.8.10-3ubuntu2 [23.3 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main amd64 libjansson4 amd64 2.14-2build2 [32.8 kB] Get:152 http://ftpmaster.internal/ubuntu noble/main amd64 psmisc amd64 23.7-1build1 [179 kB] Get:153 http://ftpmaster.internal/ubuntu noble/main amd64 xz-utils amd64 5.6.1+really5.4.5-1 [267 kB] Get:154 http://ftpmaster.internal/ubuntu noble/main amd64 advancecomp amd64 2.5-1build1 [182 kB] Get:155 http://ftpmaster.internal/ubuntu noble/main amd64 libgprofng0 amd64 2.42-4ubuntu2 [851 kB] Get:156 http://ftpmaster.internal/ubuntu noble/main amd64 libctf0 amd64 2.42-4ubuntu2 [94.5 kB] Get:157 http://ftpmaster.internal/ubuntu noble/main amd64 libctf-nobfd0 amd64 2.42-4ubuntu2 [97.1 kB] Get:158 http://ftpmaster.internal/ubuntu noble/main amd64 binutils-x86-64-linux-gnu amd64 2.42-4ubuntu2 [2469 kB] Get:159 http://ftpmaster.internal/ubuntu noble/main amd64 libbinutils amd64 2.42-4ubuntu2 [572 kB] Get:160 http://ftpmaster.internal/ubuntu noble/main amd64 binutils amd64 2.42-4ubuntu2 [18.0 kB] Get:161 http://ftpmaster.internal/ubuntu noble/main amd64 binutils-common amd64 2.42-4ubuntu2 [239 kB] Get:162 http://ftpmaster.internal/ubuntu noble/main amd64 libsframe1 amd64 2.42-4ubuntu2 [14.8 kB] Get:163 http://ftpmaster.internal/ubuntu noble/main amd64 libubsan1 amd64 14-20240412-0ubuntu1 [1175 kB] Get:164 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13 amd64 13.2.0-23ubuntu4 [14.5 kB] Get:165 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++-13-dev amd64 13.2.0-23ubuntu4 [2399 kB] Get:166 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 14-20240412-0ubuntu1 [147 kB] Get:167 http://ftpmaster.internal/ubuntu noble/main amd64 libitm1 amd64 14-20240412-0ubuntu1 [28.9 kB] Get:168 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 14-20240412-0ubuntu1 [10.4 kB] Get:169 http://ftpmaster.internal/ubuntu noble/main amd64 libasan8 amd64 14-20240412-0ubuntu1 [3024 kB] Get:170 http://ftpmaster.internal/ubuntu noble/main amd64 liblsan0 amd64 14-20240412-0ubuntu1 [1313 kB] Get:171 http://ftpmaster.internal/ubuntu noble/main amd64 libhwasan0 amd64 14-20240412-0ubuntu1 [1632 kB] Get:172 http://ftpmaster.internal/ubuntu noble/main amd64 libquadmath0 amd64 14-20240412-0ubuntu1 [153 kB] Get:173 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13 amd64 13.2.0-23ubuntu4 [482 kB] Get:174 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-13-dev amd64 13.2.0-23ubuntu4 [2688 kB] Get:175 http://ftpmaster.internal/ubuntu noble/main amd64 libtsan2 amd64 14-20240412-0ubuntu1 [2736 kB] Get:176 http://ftpmaster.internal/ubuntu noble/main amd64 libcc1-0 amd64 14-20240412-0ubuntu1 [47.7 kB] Get:177 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13 amd64 13.2.0-23ubuntu4 [1032 B] Get:178 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-base amd64 13.2.0-23ubuntu4 [49.0 kB] Get:179 http://ftpmaster.internal/ubuntu noble/main amd64 libisl23 amd64 0.26-3build1 [680 kB] Get:180 http://ftpmaster.internal/ubuntu noble/main amd64 libmpfr6 amd64 4.2.1-1build1 [355 kB] Get:181 http://ftpmaster.internal/ubuntu noble/main amd64 libmpc3 amd64 1.3.1-1build1 [54.5 kB] Get:182 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-23ubuntu4 [21.9 MB] Get:183 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-23ubuntu4 [12.5 MB] Get:184 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-23ubuntu4 [11.2 MB] Get:185 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B] Get:186 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B] Get:187 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB] Get:188 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B] Get:189 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B] Get:190 http://ftpmaster.internal/ubuntu noble/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B] Get:191 http://ftpmaster.internal/ubuntu noble/main amd64 dpkg-dev all 1.22.6ubuntu6 [1074 kB] Get:192 http://ftpmaster.internal/ubuntu noble/main amd64 libdpkg-perl all 1.22.6ubuntu6 [268 kB] Get:193 http://ftpmaster.internal/ubuntu noble/main amd64 patch amd64 2.7.6-7build3 [104 kB] Get:194 http://ftpmaster.internal/ubuntu noble/main amd64 make amd64 4.3-4.1build2 [180 kB] Get:195 http://ftpmaster.internal/ubuntu noble/main amd64 lto-disabled-list all 47 [12.4 kB] Get:196 http://ftpmaster.internal/ubuntu noble/main amd64 libfakeroot amd64 1.33-1 [32.4 kB] Get:197 http://ftpmaster.internal/ubuntu noble/main amd64 fakeroot amd64 1.33-1 [67.2 kB] Get:198 http://ftpmaster.internal/ubuntu noble/main amd64 liblockfile-bin amd64 1.17-1build3 [11.2 kB] Get:199 http://ftpmaster.internal/ubuntu noble/main amd64 liblockfile1 amd64 1.17-1build3 [6840 B] Get:200 http://ftpmaster.internal/ubuntu noble/main amd64 lockfile-progs amd64 0.1.19build2 [8522 B] Preconfiguring packages ... 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Setting up libctf0:amd64 (2.42-4ubuntu2) ... Setting up pinentry-curses (1.2.1-3ubuntu5) ... Setting up apt-utils (2.7.14build2) ... Setting up cpp-13-x86-64-linux-gnu (13.2.0-23ubuntu4) ... Setting up debconf-i18n (1.5.86ubuntu1) ... Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu4) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 14 added, 5 removed; done. Setting up perl (5.38.2-3.2build2) ... Setting up libgprofng0:amd64 (2.42-4ubuntu2) ... Setting up optipng (0.7.8+ds-1build2) ... Setting up lockfile-progs (0.1.19build2) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6ubuntu2) ... Setting up libdpkg-perl (1.22.6ubuntu6) ... Setting up libreadline8t64:amd64 (8.2-4build1) ... Setting up libgcc-13-dev:amd64 (13.2.0-23ubuntu4) ... Setting up gpgconf (2.4.4-2ubuntu17) ... Setting up libc6-dev:amd64 (2.39-0ubuntu8) ... Setting up gpg (2.4.4-2ubuntu17) ... Setting up libstdc++-13-dev:amd64 (13.2.0-23ubuntu4) ... Setting up binutils-x86-64-linux-gnu (2.42-4ubuntu2) ... Setting up cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up gpg-agent (2.4.4-2ubuntu17) ... Setting up cpp-13 (13.2.0-23ubuntu4) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.1build1) ... Setting up gcc-13-x86-64-linux-gnu (13.2.0-23ubuntu4) ... Setting up binutils (2.42-4ubuntu2) ... Setting up dpkg-dev (1.22.6ubuntu6) ... Setting up libtirpc-dev:amd64 (1.3.4+ds-1.1build1) ... Setting up gcc-13 (13.2.0-23ubuntu4) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up libnsl2:amd64 (1.3.0-3build3) ... Setting up g++-13-x86-64-linux-gnu (13.2.0-23ubuntu4) ... Setting up gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libnss-nisplus:amd64 (1.3-5build1) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up libnss-nis:amd64 (3.1-0ubuntu7) ... Setting up libnsl-dev:amd64 (1.3.0-3build3) ... Setting up g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++-13 (13.2.0-23ubuntu4) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... Processing triggers for debianutils (5.17build1) ... (Reading database ... 15822 files and directories currently installed.) Purging configuration files for libssl3:amd64 (3.0.10-1ubuntu2) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-28269765 amd64 noble -c chroot:build-PACKAGEBUILD-28269765 --arch=amd64 --dist=noble --nolog -A t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc Initiating build PACKAGEBUILD-28269765 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-177-generic #197-Ubuntu SMP Thu Mar 28 22:45:47 UTC 2024 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-032.buildd +===============================================================================================+ | t-coffee 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 (amd64) Sun, 05 May 2024 22:30:59 +0000 | +===============================================================================================+ Package: t-coffee Version: 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 Source Version: 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 Distribution: noble Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-28269765/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/t-coffee-sbGhj5/resolver-rcweuk' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/t-coffee-sbGhj5/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/t-coffee-sbGhj5' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), 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 [370 B] Get:5 copy:/<>/apt_archive ./ Packages [452 B] Fetched 1779 B in 0s (135 kB/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 packages were automatically installed and are no longer required: apt-utils bash-completion ca-certificates debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libgssapi-krb5-2 libip4tc2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblocale-gettext-perl libnsl-dev libnsl2 libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libtirpc-common libtirpc-dev libtirpc3t64 libunistring2 openssl perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libdw1t64 libelf1t64 libfile-stripnondeterminism-perl libicu74 libmagic-mgc libmagic1t64 libpipeline1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf Suggested packages: autoconf-archive gnu-standards autoconf-doc 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 libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libdw1t64 libelf1t64 libfile-stripnondeterminism-perl libicu74 libmagic-mgc libmagic1t64 libpipeline1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 18.9 MB of archives. After this operation, 68.1 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [666 B] Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libelf1t64 amd64 0.190-1.1build4 [57.6 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libicu74 amd64 74.2-1ubuntu3 [10.9 MB] Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libxml2 amd64 2.9.14+dfsg-1.3ubuntu3 [762 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libmagic-mgc amd64 1:5.45-3build1 [307 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 libmagic1t64 amd64 1:5.45-3build1 [87.2 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 file amd64 1:5.45-3build1 [22.0 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 gettext-base amd64 0.21-14ubuntu2 [38.4 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libuchardet0 amd64 0.0.8-1build1 [75.3 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 groff-base amd64 1.23.0-3build2 [1020 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 libpipeline1 amd64 1.5.7-2 [23.6 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 man-db amd64 2.12.0-4build2 [1237 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 m4 amd64 1.4.19-4build1 [244 kB] Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 autoconf all 2.71-3 [339 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 autotools-dev all 20220109.1 [44.9 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 autopoint all 0.21-14ubuntu2 [422 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libdebhelper-perl all 13.14.1ubuntu5 [89.8 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libtool all 2.4.7-7build1 [166 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 dh-autoreconf all 20 [16.1 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libsub-override-perl all 0.10-1 [10.0 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 libdw1t64 amd64 0.190-1.1build4 [261 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 debugedit amd64 1:5.0-5build2 [46.1 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 dwz amd64 0.15-1build6 [115 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 gettext amd64 0.21-14ubuntu2 [864 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 debhelper all 13.14.1ubuntu5 [869 kB] Preconfiguring packages ... Fetched 18.9 MB in 0s (109 MB/s) Selecting previously unselected package libelf1t64:amd64. (Reading database ... 15822 files and directories currently installed.) Preparing to unpack .../00-libelf1t64_0.190-1.1build4_amd64.deb ... Unpacking libelf1t64:amd64 (0.190-1.1build4) ... Selecting previously unselected package libicu74:amd64. Preparing to unpack .../01-libicu74_74.2-1ubuntu3_amd64.deb ... Unpacking libicu74:amd64 (74.2-1ubuntu3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../02-libxml2_2.9.14+dfsg-1.3ubuntu3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3ubuntu3) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-3build1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3build1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../04-libmagic1t64_1%3a5.45-3build1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3build1) ... 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Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-177-generic #197-Ubuntu SMP Thu Mar 28 22:45:47 UTC 2024 amd64 (x86_64) Toolchain package versions: binutils_2.42-4ubuntu2 dpkg-dev_1.22.6ubuntu6 g++-13_13.2.0-23ubuntu4 gcc-13_13.2.0-23ubuntu4 libc6-dev_2.39-0ubuntu8 libstdc++-13-dev_13.2.0-23ubuntu4 libstdc++6_14-20240412-0ubuntu1 linux-libc-dev_6.8.0-31.31 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1build1 apt_2.7.14build2 apt-utils_2.7.14build2 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu2 autotools-dev_20220109.1 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gcc-13_13.2.0-23ubuntu4 gcc-13-base_13.2.0-23ubuntu4 gcc-13-x86-64-linux-gnu_13.2.0-23ubuntu4 gcc-14-base_14-20240412-0ubuntu1 gcc-x86-64-linux-gnu_4:13.2.0-7ubuntu1 gettext_0.21-14ubuntu2 gettext-base_0.21-14ubuntu2 gpg_2.4.4-2ubuntu17 gpg-agent_2.4.4-2ubuntu17 gpgconf_2.4.4-2ubuntu17 gpgv_2.4.4-2ubuntu17 grep_3.11-4build1 groff-base_1.23.0-3build2 gzip_1.12-1ubuntu3 hostname_3.23+nmu2ubuntu2 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-6ubuntu2 libacl1_2.3.2-1build1 libapparmor1_4.0.0-beta3-0ubuntu3 libapt-pkg6.0t64_2.7.14build2 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-4build1 libasan8_14-20240412-0ubuntu1 libassuan0_2.5.6-1build1 libatomic1_14-20240412-0ubuntu1 libattr1_1:2.5.2-1build1 libaudit-common_1:3.1.2-2.1build1 libaudit1_1:3.1.2-2.1build1 libbinutils_2.42-4ubuntu2 libblkid1_2.39.3-9ubuntu6 libbz2-1.0_1.0.8-5.1 libc-bin_2.39-0ubuntu8 libc-dev-bin_2.39-0ubuntu8 libc6_2.39-0ubuntu8 libc6-dev_2.39-0ubuntu8 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sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2build1 sensible-utils_0.0.22 systemd_255.4-1ubuntu8 systemd-dev_255.4-1ubuntu8 systemd-sysv_255.4-1ubuntu8 sysvinit-utils_3.08-6ubuntu3 tar_1.35+dfsg-3build1 tzdata_2024a-2ubuntu1 ubuntu-keyring_2023.11.28.1 util-linux_2.39.3-9ubuntu6 uuid-runtime_2.39.3-9ubuntu6 xz-utils_5.6.1+really5.4.5-1 zlib1g_1:1.3.dfsg-3.1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: t-coffee Binary: t-coffee, t-coffee-examples Architecture: any all Version: 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Étienne Mollier Homepage: https://www.tcoffee.org/Projects/tcoffee/index.html Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/t-coffee Vcs-Git: https://salsa.debian.org/med-team/t-coffee.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: t-coffee deb science optional arch=any t-coffee-examples deb science optional arch=all Checksums-Sha1: fab3dbecabca6c0248a8c8a0336f5995be3b4e3f 3229824 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg.orig.tar.xz dc1efbe2dfb5d379e2d04ce1a736f074322be181 18328 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.debian.tar.xz Checksums-Sha256: a1b37c67caba574ccf53c38279863dffa67d62232e017317754b5eb29db60746 3229824 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg.orig.tar.xz 3e83e95b016af77d28fc7d8315979dd397f12f333bcd4a45be5f471dbd9964ed 18328 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.debian.tar.xz Files: 74a867b32054875c3ce5f2a11767d610 3229824 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg.orig.tar.xz 13b9ba2309fb654eeb1c4c8017c4cdb7 18328 t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmOAlj0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtG4cw//Qlbaw6pe+7dbaQICdBzx3OMnMJidIS94 0hxonazxybmkqiXvFld5ETsDIyLhqlrCcz3/9pIFLfUyWuyuW7uc7CwFc041BnYY TxT7dRDR7tQ1enXZ3hLjtHLCVwKPHv1M0oVe/6+1JrcpiXIx+ZBQrtSTnmPtur+d Dl0vGvZAwIMjN3AifWvNPI5Noj7hD63bw0QTTVIAD/+sC97xl/TdkV6584b9XMy1 xW8MNaRgFEHWDcL+23X4IA9EfCIsz8wEv78mSA0Y/1fvP6xdKyKQ5ESJ2HwOw3dl S3WUobMn+wKeKbVBAwqTWiKVWIy93rwKIIX8hboX/0sCjAqN4qrtXNyP4k0Nuz6g 1zILk1lUUo21HRs803dCBtw9D3NKtV7ajZ9m1nO3ruzHmJUW7b598ifWPbYw4TEo iOgqNZ/S8O3Ev0idbD6ikfzMlMBfxuk8XUewSaPyOtgaw5BwrNdjEIV0XD0/hgio 6xI/VNkojvyL/3OO7PsIx/X5xQWOfFy5J4aziNNabGmO1KtuYNYHQpMlq0iPLEJI GveIU6JPk2KgUzdhPLo3DD5GsODHoyN83fa6eqV6vYR5x7lfzCZg3ewzcSR5gmYz z7Q6x0bPSenpQpCmcYhHjuPTKS+xD574zjOw/2w/umYCrsVYS4flr9ZJDX1+TQMo vXx4ah4rMEw= =bR2s -----END PGP SIGNATURE----- gpgv: Signature made Fri Nov 25 10:17:33 2022 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting t-coffee in /<> dpkg-source: info: unpacking t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg.orig.tar.xz dpkg-source: info: unpacking t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying probconsrna.patch dpkg-source: info: applying bypass_legacy_blast.patch dpkg-source: info: applying use_debian_packaged_TMalign.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying set_proper_dir_permissions.patch dpkg-source: info: applying mayhem.patch dpkg-source: info: applying stable-linking-inputs.patch dpkg-source: info: applying clustalw2.patch dpkg-source: info: applying verbose_build dpkg-source: info: applying increase_max_pid.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-28269765 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-28269765 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-28269765 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -b -rfakeroot dpkg-buildpackage: info: source package t-coffee dpkg-buildpackage: info: source version 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=t_coffee_source debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -rf t_coffee_source/*.o t_coffee_source/t_coffee bin/t_coffee example/ph_tree_scan.txt bin/t_coffee rm -rf t_coffee_source/TMalign find . -name "*.o" -delete find . -name "*.deps" -delete chmod 644 example/* make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--sourcedirectory=t_coffee_source dh_clean -O--sourcedirectory=t_coffee_source debian/rules binary dh binary --sourcedirectory=t_coffee_source dh_update_autotools_config -O--sourcedirectory=t_coffee_source dh_autoreconf -O--sourcedirectory=t_coffee_source dh_auto_configure -O--sourcedirectory=t_coffee_source debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- USER_BIN=../bin/ FCC="gfortran -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1" 'CC=$(CXX)' all cd t_coffee_source && make -j4 "INSTALL=install --strip-program=true" USER_BIN=../bin/ "FCC=gfortran -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1" CC=\$\(CXX\) all make[2]: Entering directory '/<>/t_coffee_source' CC dev_lib/dev1.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dev_lib/dev1.deps -c -o dev_lib/dev1.o dev_lib/dev1.c CC dp_lib/evaluate.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate.deps -c -o dp_lib/evaluate.o dp_lib/evaluate.c CC dp_lib/CUSTOM_evaluate_for_struc.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/CUSTOM_evaluate_for_struc.deps -c -o dp_lib/CUSTOM_evaluate_for_struc.o dp_lib/CUSTOM_evaluate_for_struc.c CC dp_lib/evaluate_dirichlet.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_dirichlet.deps -c -o dp_lib/evaluate_dirichlet.o dp_lib/evaluate_dirichlet.c In file included from ./io_lib_header.h:33, from dp_lib/evaluate_dirichlet.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, from dev_lib/dev1.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/CUSTOM_evaluate_for_struc.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ dev_lib/dev1.c: In function ‘void aln2hitMat(Alignment*, char*)’: dev_lib/dev1.c:89:26: warning: too many arguments for format [-Wformat-extra-args] 89 | fprintf (stdout, "Process positions\n", i); | ^~~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/evaluate.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/evaluate_dirichlet.c: In function ‘Mixture* read_dirichlet(char*)’: dp_lib/evaluate_dirichlet.c:317:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 317 | fscanf(fp, "%f\n", &f); | ~~~~~~^~~~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:319:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 319 | fscanf(fp, "%f", &f); | ~~~~~~^~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:323:31: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 323 | fscanf(fp, "%f", &f); | ~~~~~~^~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c:326:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 326 | fscanf(fp, "\n"); | ~~~~~~^~~~~~~~~~ CC dp_lib/evaluate_for_domain.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_domain.deps -c -o dp_lib/evaluate_for_domain.o dp_lib/evaluate_for_domain.c CC dp_lib/evaluate_for_struc.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_struc.deps -c -o dp_lib/evaluate_for_struc.o dp_lib/evaluate_for_struc.c dp_lib/evaluate.c: In function ‘Alignment* msa2distances(Alignment*, Constraint_list*, float, float, int)’: dp_lib/evaluate.c:3070:67: warning: format ‘%f’ expects argument of type ‘double’, but argument 4 has type ‘int’ [-Wformat=] 3070 | fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); | ~~~~^ ~~~ | | | | double int | %3.2d dp_lib/evaluate.c:3070:81: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘double’ [-Wformat=] 3070 | fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); | ~~^ ~~~~~~~ | | | | int double | %3f dp_lib/evaluate.c:3070:93: warning: format ‘%f’ expects argument of type ‘double’, but argument 6 has type ‘int’ [-Wformat=] 3070 | fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); | ~~~^ ~~~~~~~~ | | | | double int | %.3d dp_lib/evaluate.c:3070:109: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘double’ [-Wformat=] 3070 | fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); | ~~^ ~~~~~~ | | | | int double | %3f dp_lib/evaluate.c: In function ‘Alignment* fork_triplet_coffee_evaluate_output(Alignment*, Constraint_list*, int)’: dp_lib/evaluate.c:809:26: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 809 | fscanf (fp, "%d ", &res); | ~~~~~~~^~~~~~~~~~~~~~~~~ dp_lib/evaluate.c:814:26: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 814 | fscanf (fp, "%f %f", &sseq, &mseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate.c:819:18: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 819 | fscanf (fp, "%f %f", &sseq, &mseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate.c: In function ‘float** initialise_aa_physico_chemical_property_table(int*)’: dp_lib/evaluate.c:7626:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 7626 | fscanf (fp, "%f %c %*s",&v1, &c1 ); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/evaluate_for_domain.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/evaluate_for_struc.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/fsa_dp.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/fsa_dp.deps -c -o dp_lib/fsa_dp.o dp_lib/fsa_dp.c CC dp_lib/pavie_dp.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/pavie_dp.deps -c -o dp_lib/pavie_dp.o dp_lib/pavie_dp.c In file included from ./io_lib_header.h:33, from dp_lib/fsa_dp.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/pavie_dp.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/pavie_dp.c: In function ‘double** pavie_seq2pavie_aln(Sequence*, char*, char*)’: dp_lib/pavie_dp.c:127:18: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 127 | fscanf (fp, "%s\n",mat_list[nch++]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/pavie_dp.c: In function ‘char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)’: dp_lib/pavie_dp.c:1079:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1079 | system (command); | ~~~~~~~~^~~~~~~~~ dp_lib/pavie_dp.c:1081:14: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1081 | system (command); | ~~~~~~~^~~~~~~~~ dp_lib/pavie_dp.c: In function ‘Alignment* pavie_seq2pavie_msa(Sequence*, char*, char*)’: dp_lib/pavie_dp.c:1365:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1365 | fscanf (fp, "%s", mat); | ~~~~~~~^~~~~~~~~~~~~~~ dp_lib/pavie_dp.c: In function ‘output_pavie_mat_list(int***, double*, char**, int, char*, int, char**) [clone .constprop.0]’: dp_lib/pavie_dp.c:1078:33: warning: ‘%s’ directive writing up to 999 bytes into a region of size 996 [-Wformat-overflow=] 1078 | sprintf ( command, "cp %s %s", mat_name[a], latest); | ^~ ~~~~~~ In file included from /usr/include/stdio.h:980, from dp_lib/pavie_dp.c:27: In function ‘sprintf’, inlined from ‘output_pavie_mat_list(int***, double*, char**, int, char*, int, char**) [clone .constprop.0]’ at dp_lib/pavie_dp.c:1078:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output 5 or more bytes (assuming 1004) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dp_lib/pavie_dp.c: In function ‘output_pavie_mat_list(int***, double*, char**, int, char*, int, char**) [clone .constprop.0]’: dp_lib/pavie_dp.c:1080:30: warning: ‘%s’ directive writing up to 999 bytes into a region of size 997 [-Wformat-overflow=] 1080 | sprintf ( command, "cp %s %s", latest, current); | ^~ ~~~~~~ In function ‘sprintf’, inlined from ‘output_pavie_mat_list(int***, double*, char**, int, char*, int, char**) [clone .constprop.0]’ at dp_lib/pavie_dp.c:1080:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 5 and 2003 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC dp_lib/showpair.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/showpair.deps -c -o dp_lib/showpair.o dp_lib/showpair.c In file included from ./io_lib_header.h:33, from dp_lib/showpair.c:32: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_domain_dp.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp.deps -c -o dp_lib/util_domain_dp.o dp_lib/util_domain_dp.c In file included from ./io_lib_header.h:33, from dp_lib/util_domain_dp.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_domain_dp_drivers.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp_drivers.deps -c -o dp_lib/util_domain_dp_drivers.o dp_lib/util_domain_dp_drivers.c CC dp_lib/util_dp_cdna_fasta_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_cdna_fasta_nw.deps -c -o dp_lib/util_dp_cdna_fasta_nw.o dp_lib/util_dp_cdna_fasta_nw.c In file included from ./io_lib_header.h:33, from dp_lib/util_dp_cdna_fasta_nw.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_domain_dp_drivers.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_clean_maln.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_clean_maln.deps -c -o dp_lib/util_dp_clean_maln.o dp_lib/util_dp_clean_maln.c In file included from ./io_lib_header.h:33, from dp_lib/util_dp_clean_maln.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_drivers.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_drivers.deps -c -o dp_lib/util_dp_drivers.o dp_lib/util_dp_drivers.c CC dp_lib/util_dp_est.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_est.deps -c -o dp_lib/util_dp_est.o dp_lib/util_dp_est.c In file included from ./io_lib_header.h:33, from dp_lib/util_dp_drivers.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_fasta_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_nw.deps -c -o dp_lib/util_dp_fasta_nw.o dp_lib/util_dp_fasta_nw.c dp_lib/util_dp_drivers.c: In function ‘Constraint_list* sap_pair(char*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:2051:26: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 2051 | register int a; | ^ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_est.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/util_dp_drivers.c: In function ‘char* seq_file2msa_file(char*, char*, char*)’: dp_lib/util_dp_drivers.c:1014:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1014 | chdir (dir); | ~~~~~~^~~~~ dp_lib/util_dp_drivers.c:1028:16: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1028 | chdir (cdir); | ~~~~~~~~~^~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* align_pdb_pair_2(char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1080:17: warning: ignoring return value of ‘int atoi(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1080 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* align_pdb_pair(char*, char*, char*, char*, Constraint_list*, Job_TC*)’: dp_lib/util_dp_drivers.c:1108:17: warning: ignoring return value of ‘int atoi(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1108 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* hh_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1149:15: warning: ignoring return value of ‘int atoi(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1149 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1160:23: warning: ignoring return value of ‘char* tmpnam(char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1160 | tmpnam(aln1); | ~~~~~~^~~~~~ dp_lib/util_dp_drivers.c:1161:23: warning: ignoring return value of ‘char* tmpnam(char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1161 | tmpnam(aln2); | ~~~~~~^~~~~~ dp_lib/util_dp_drivers.c:1164:23: warning: ignoring return value of ‘char* tmpnam(char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1164 | tmpnam(hhfile); | ~~~~~~^~~~~~~~ dp_lib/util_dp_drivers.c:1211:17: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1211 | fgets (buf2, 10000, fp); | ~~~~~~^~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* profile_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1280:13: warning: ignoring return value of ‘int atoi(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1280 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:1363:28: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1363 | fscanf (fp, "%s", bufname); | ~~~~~~~^~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* profile_pair_decomposed(TC_method*, char*, Constraint_list*, char*)’: dp_lib/util_dp_drivers.c:1445:7: warning: ignoring return value of ‘int atoi(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1445 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* profile_subset_pair_old(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1581:7: warning: ignoring return value of ‘int atoi(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1581 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* pdbid_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1717:15: warning: ignoring return value of ‘int atoi(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1717 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* pdb_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1774:15: warning: ignoring return value of ‘int atoi(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1774 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* thread_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1906:15: warning: ignoring return value of ‘int atoi(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1906 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* lsqman_pair(char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1981:15: warning: ignoring return value of ‘int atoi(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1981 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* sap_pair(char*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:2073:17: warning: ignoring return value of ‘int atoi(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2073 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2121:24: warning: ignoring return value of ‘char* getcwd(char*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2121 | getcwd (cdir, sizeof(char)*1000); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2122:23: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2122 | chdir (get_cache_dir()); | ~~~~~~^~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c:2142:23: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2142 | chdir (cdir); | ~~~~~~^~~~~~ dp_lib/util_dp_drivers.c: In function ‘Constraint_list* rnapdb_pair(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:2256:13: warning: ignoring return value of ‘int atoi(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2256 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_fasta_nw.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/util_dp_fasta_nw.c: In function ‘int* makepointtable(int*, int*, int)’: dp_lib/util_dp_fasta_nw.c:157:17: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 157 | register int *p; | ^ CC dp_lib/util_dp_fasta_sw.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_sw.deps -c -o dp_lib/util_dp_fasta_sw.o dp_lib/util_dp_fasta_sw.c In file included from ./io_lib_header.h:33, from dp_lib/util_dp_fasta_sw.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_generic_fasta_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_generic_fasta_nw.deps -c -o dp_lib/util_dp_generic_fasta_nw.o dp_lib/util_dp_generic_fasta_nw.c dp_lib/util_dp_drivers.c: In function ‘method2pw_cl(TC_method*, Constraint_list*)’: dp_lib/util_dp_drivers.c:382:31: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 382 | sprintf ( mat, "%s", (strm(m, "default"))?"dna_idmat":m); | ^~ In file included from /usr/include/stdio.h:980, from dp_lib/util_dp_drivers.c:27: In function ‘sprintf’, inlined from ‘method2pw_cl(TC_method*, Constraint_list*)’ at dp_lib/util_dp_drivers.c:382:16: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘method2pw_cl(TC_method*, Constraint_list*)’: dp_lib/util_dp_drivers.c:373:30: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 373 | sprintf ( mat, "%s", (strm(m, "default"))?"blosum62mt":m); | ^~ In function ‘sprintf’, inlined from ‘method2pw_cl(TC_method*, Constraint_list*)’ at dp_lib/util_dp_drivers.c:373:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘method2pw_cl(TC_method*, Constraint_list*)’: dp_lib/util_dp_drivers.c:386:41: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 386 | if ( M->matrix[0])sprintf ( mat, "%s", M->matrix); | ^~ In function ‘sprintf’, inlined from ‘method2pw_cl(TC_method*, Constraint_list*)’ at dp_lib/util_dp_drivers.c:386:33: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ dp_lib/util_dp_drivers.c: In function ‘realign_block(Alignment*, int, int, char*)’: dp_lib/util_dp_drivers.c:921:25: warning: ‘ -infile=’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 921 | sprintf ( command, "%s -infile=%s -outfile=%s %s", script,seq_name, aln_name, TO_NULL_DEVICE); | ^~~~~~~~~ In function ‘sprintf’, inlined from ‘realign_block(Alignment*, int, int, char*)’ at dp_lib/util_dp_drivers.c:921:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output 38 or more bytes (assuming 1037) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_generic_fasta_nw.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/util_dp_drivers.c: In function ‘seq_msa(TC_method*, char*, Constraint_list*)’: dp_lib/util_dp_drivers.c:1854:80: warning: ‘%s’ directive writing up to 500 bytes into a region of size between 445 and 945 [-Wformat-overflow=] 1854 | sprintf ( command, "t_coffee -other_pg tc_generic_method.pl -mode=%s -method=%s %s %s%s %s %s%s -tmpdir=%s %s %s", M->executable, M->executable2, M->param1,M->in_flag,infile,M->param2,M->out_flag,outfile,get_tmp_4_tcoffee(),db,M->param); | ^~ In function ‘sprintf’, inlined from ‘seq_msa(TC_method*, char*, Constraint_list*)’ at dp_lib/util_dp_drivers.c:1854:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output 71 or more bytes (assuming 5068) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_gotoh_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_nw.deps -c -o dp_lib/util_dp_gotoh_nw.o dp_lib/util_dp_gotoh_nw.c In file included from ./io_lib_header.h:33, from dp_lib/util_dp_gotoh_nw.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_gotoh_sw.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_sw.deps -c -o dp_lib/util_dp_gotoh_sw.o dp_lib/util_dp_gotoh_sw.c In file included from ./io_lib_header.h:33, from dp_lib/util_dp_gotoh_sw.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/util_dp_gotoh_sw.c: In function ‘int gotoh_pair_wise_sw(Alignment*, int*, int**, Constraint_list*)’: dp_lib/util_dp_gotoh_sw.c:391:42: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 391 | fread ( &k, sizeof (TRACE_TYPE), 1, long_trace); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_mm_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_mm_nw.deps -c -o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_mm_nw.c CC dp_lib/util_dp_sim.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_sim.deps -c -o dp_lib/util_dp_sim.o dp_lib/util_dp_sim.c In file included from ./io_lib_header.h:33, from dp_lib/util_dp_mm_nw.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_sim.c:32: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ dp_lib/util_dp_sim.c: In function ‘int addnode(int, int, int, int, int, int, int)’: dp_lib/util_dp_sim.c:173:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 173 | register int d; | ^ dp_lib/util_dp_sim.c: In function ‘int sim_pair_wise_lalign(Alignment*, int*, int**, Constraint_list*)’: dp_lib/util_dp_sim.c:248:20: warning: empty parentheses were disambiguated as a function declaration [-Wvexing-parse] 248 | vertexptr findmax(); /* return the largest score node */ | ^~ dp_lib/util_dp_sim.c:248:20: note: remove parentheses to default-initialize a variable 248 | vertexptr findmax(); /* return the largest score node */ | ^~ | -- dp_lib/util_dp_sim.c:248:20: note: or replace parentheses with braces to value-initialize a variable dp_lib/util_dp_sim.c: In function ‘int big_pass(int*, int*, int, int, int, int)’: dp_lib/util_dp_sim.c:481:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 481 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:481:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 481 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:482:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 482 | register int c; /* best score at current point */ | ^ dp_lib/util_dp_sim.c:483:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 483 | register int f; /* best score ending with insertion */ | ^ dp_lib/util_dp_sim.c:484:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 484 | register int d; /* best score ending with deletion */ | ^ dp_lib/util_dp_sim.c:485:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 485 | register int p; /* best score at (i-1, j-1) */ | ^ dp_lib/util_dp_sim.c:486:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 486 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:486:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 486 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:487:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 487 | register int di, dj; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:487:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 487 | register int di, dj; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:488:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 488 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:488:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 488 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:489:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 489 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c:489:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 489 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c: In function ‘int locate(int*, int*, int)’: dp_lib/util_dp_sim.c:562:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 562 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:562:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 562 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:563:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 563 | register int c; /* best score at current point */ | ^ dp_lib/util_dp_sim.c:564:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 564 | register int f; /* best score ending with insertion */ | ^ dp_lib/util_dp_sim.c:565:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 565 | register int d; /* best score ending with deletion */ | ^ dp_lib/util_dp_sim.c:566:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 566 | register int p; /* best score at (i-1, j-1) */ | ^ dp_lib/util_dp_sim.c:567:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 567 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:567:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 567 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:568:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 568 | register int di=0, dj=0; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:568:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 568 | register int di=0, dj=0; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:569:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 569 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:569:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 569 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:570:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 570 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c:570:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 570 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c:572:16: warning: empty parentheses were disambiguated as a function declaration [-Wvexing-parse] 572 | int addnode(); /* function for inserting a node */ | ^~ dp_lib/util_dp_sim.c:572:16: note: remove parentheses to default-initialize a variable 572 | int addnode(); /* function for inserting a node */ | ^~ | -- dp_lib/util_dp_sim.c:572:16: note: or replace parentheses with braces to value-initialize a variable dp_lib/util_dp_sim.c: In function ‘int small_pass(int*, int*, int, int)’: dp_lib/util_dp_sim.c:786:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 786 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:786:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 786 | { register int i, j; /* row and column indices */ | ^ dp_lib/util_dp_sim.c:787:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 787 | register int c; /* best score at current point */ | ^ dp_lib/util_dp_sim.c:788:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 788 | register int f; /* best score ending with insertion */ | ^ dp_lib/util_dp_sim.c:789:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 789 | register int d; /* best score ending with deletion */ | ^ dp_lib/util_dp_sim.c:790:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 790 | register int p; /* best score at (i-1, j-1) */ | ^ dp_lib/util_dp_sim.c:791:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 791 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:791:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 791 | register int ci, cj; /* end-point associated with c */ | ^~ dp_lib/util_dp_sim.c:792:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 792 | register int di, dj; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:792:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 792 | register int di, dj; /* end-point associated with d */ | ^~ dp_lib/util_dp_sim.c:793:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 793 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:793:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 793 | register int fi, fj; /* end-point associated with f */ | ^~ dp_lib/util_dp_sim.c:794:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 794 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c:794:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 794 | register int pi, pj; /* end-point associated with p */ | ^~ dp_lib/util_dp_sim.c: In function ‘SIM_NODE* findmax()’: dp_lib/util_dp_sim.c:864:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 864 | register int i, j; | ^ dp_lib/util_dp_sim.c:864:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 864 | register int i, j; | ^ dp_lib/util_dp_sim.c: In function ‘int no_cross()’: dp_lib/util_dp_sim.c:883:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 883 | register int i; | ^ dp_lib/util_dp_sim.c: In function ‘int diff_sim(int*, int*, int, int, int, int)’: dp_lib/util_dp_sim.c:911:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 911 | register int i, j; | ^ dp_lib/util_dp_sim.c:911:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 911 | register int i, j; | ^ dp_lib/util_dp_sim.c:912:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ dp_lib/util_dp_sim.c:912:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ dp_lib/util_dp_sim.c:912:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ dp_lib/util_dp_sim.c:912:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ dp_lib/util_dp_drivers.c: In function ‘stack_progressive_aln(Alignment*, Constraint_list*, int, int)’: dp_lib/util_dp_drivers.c:3717:25: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 3717 | sprintf ( dp_mode, "%s", CL->dp_mode); | ^~ In function ‘sprintf’, inlined from ‘stack_progressive_aln(Alignment*, Constraint_list*, int, int)’ at dp_lib/util_dp_drivers.c:3717:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_ssec_pwaln.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_ssec_pwaln.deps -c -o dp_lib/util_dp_ssec_pwaln.o dp_lib/util_dp_ssec_pwaln.c In file included from ./io_lib_header.h:33, from dp_lib/util_dp_ssec_pwaln.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_suboptimal_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_suboptimal_nw.deps -c -o dp_lib/util_dp_suboptimal_nw.o dp_lib/util_dp_suboptimal_nw.c In file included from ./io_lib_header.h:33, from dp_lib/util_dp_suboptimal_nw.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_graph_maln.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_graph_maln.deps -c -o dp_lib/util_graph_maln.o dp_lib/util_graph_maln.c CC fastal/diagonal.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/diagonal.deps -c -o fastal/diagonal.o fastal/diagonal.c CC fastal/fastal.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal.deps -c -o fastal/fastal.o fastal/fastal.c In file included from ./io_lib_header.h:33, from fastal/diagonal.c:31: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ fastal/diagonal.c: In function ‘int seq_pair2blast_diagonal2(char*, char*, Diagonal**, int*, int, int, int)’: fastal/diagonal.c:434:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 434 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/diagonal.c:439:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 439 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/diagonal.c:440:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 440 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/diagonal.c:441:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 441 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_graph_maln.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, from fastal/fastal.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC fastal/fastal_opt_parsing.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal_opt_parsing.deps -c -o fastal/fastal_opt_parsing.o fastal/fastal_opt_parsing.c fastal/fastal.c: In function ‘int seq_pair2blast_diagonal(char*, char*, int**, int*, int, int, int)’: fastal/fastal.c:1924:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1924 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c:1929:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1929 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1930:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1930 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1931:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1931 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1976:23: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1976 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c:1980:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1980 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1981:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1981 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c:1982:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1982 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function ‘int seq_pair2blat_diagonal(char*, char*, int**, int*, int, int, int)’: fastal/fastal.c:2115:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2115 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c: In function ‘int seq_pair2blastz_diagonal(char*, char*, int**, int*, int, int, int)’: fastal/fastal.c:2262:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2262 | system(blast_command); | ~~~~~~^~~~~~~~~~~~~~~ fastal/fastal.c: In function ‘void file_pos2profile(FILE*, long int, Fastal_profile*, int, Fastal_param*)’: fastal/fastal.c:3201:15: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3201 | fgets (line, LINE_LENGTH , seq_file); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function ‘void profile_file2profile(Fastal_profile*, FILE*, long int, Fastal_param*)’: fastal/fastal.c:3323:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3323 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3326:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3326 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3329:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3329 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3331:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3331 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3333:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3333 | fgets(line, LINE_LENGTH, profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3352:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3352 | fgets(line, LINE_LENGTH , profile_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function ‘void edit_seq2aligned_seq(char*, FILE*, long int, FILE*)’: fastal/fastal.c:3502:15: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3502 | fgets (line, LINE_LENGTH , sequence_file); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c: In function ‘void edit2alignment(FILE*, long int*, FILE*, long int*, int, int, char*, int, FILE*, int, FILE*)’: fastal/fastal.c:3575:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3575 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3577:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3577 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3579:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3579 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3581:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3581 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/fastal.c:3643:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3643 | fgets(aligned_sequence, alignment_length+3, edit_seq_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC fastal/iteration.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/iteration.deps -c -o fastal/iteration.o fastal/iteration.c CC fastal/parttree.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/parttree.deps -c -o fastal/parttree.o fastal/parttree.c In file included from ./io_lib_header.h:33, from fastal/iteration.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, from fastal/parttree.c:36: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ fastal/parttree.c: In function ‘void makepointtable_fast(int*, int, int, int)’: fastal/parttree.c:757:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 757 | register int *p; | ^ fastal/iteration.c: In function ‘void split_set(FILE*, Fastal_profile*, Fastal_profile*, char*, int, int*, char*)’: fastal/iteration.c:185:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 185 | fgets(line, LINE_LENGTH , alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c: In function ‘void iterate(Fastal_param*, void*, char*, char*, int)’: fastal/iteration.c:310:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 310 | fgets(line, LINE_LENGTH , alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:435:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 435 | system(command); | ~~~~~~^~~~~~~~~ fastal/iteration.c: In function ‘void write_iterated_aln(char*, char*, char*, char*, int*, int, char*, int*, int)’: fastal/iteration.c:501:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 501 | fgets(alnline, ALNLINE_LENGTH , old_aln_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:504:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 504 | fgets(alnline, ALNLINE_LENGTH , old_aln_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:535:38: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 535 | fgets(alnline, ALNLINE_LENGTH, old_aln_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c: In function ‘void edit2seq_pattern(FILE*, char*, char*)’: fastal/iteration.c:563:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:565:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 565 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:567:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 567 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/iteration.c:569:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 569 | fgets(line, LINE_LENGTH , edit_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function ‘int** make_distance_matrix_sim(FILE*, long int*, int*, int, int**)’: fastal/parttree.c:695:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 695 | fgets(line, 500, aln_f); | ~~~~~^~~~~~~~~~~~~~~~~~ fastal/parttree.c:701:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 701 | fgets(line, 500, aln_f); | ~~~~~^~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function ‘void get_table(short int*, FILE*, long int)’: fastal/parttree.c:848:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 848 | fgets(line, LINE_LENGTH, tables_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:859:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 859 | fgets(line, LINE_LENGTH, tables_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function ‘int euclidean_dist(FILE*, long int, long int, short int*, short int*, int)’: fastal/parttree.c:891:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 891 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:903:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 903 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:906:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 906 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:912:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 912 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c: In function ‘int euclidean_dist_half(FILE*, long int, short int*, short int*, int)’: fastal/parttree.c:951:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 951 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/parttree.c:962:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 962 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ CC fastal/scoring.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/scoring.deps -c -o fastal/scoring.o fastal/scoring.c In file included from ./io_lib_header.h:33, from fastal/scoring.c:37: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ fastal/scoring.c: In function ‘double calculate_sum_of_pairs_score_affine(char*, int**, double, double)’: fastal/scoring.c:76:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 76 | fgets(line, LINE_LENGTH, alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:78:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 78 | fgets(line, LINE_LENGTH, alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:82:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 82 | fgets(line, LINE_LENGTH, alignment_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c: In function ‘void compute_ref_alignments(char*, char*, int, int)’: fastal/scoring.c:384:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 384 | fgets(line, LINE_LENGTH, seq_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:398:23: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 398 | system(aln_command); | ~~~~~~^~~~~~~~~~~~~ fastal/scoring.c: In function ‘void make_ref_alignment(char*, char*, char*, int)’: fastal/scoring.c:488:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 488 | fgets(line, LINE_LENGTH, seq_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:502:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 502 | system(command); | ~~~~~~^~~~~~~~~ fastal/scoring.c: In function ‘double agreement_score(char*, char*)’: fastal/scoring.c:583:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 583 | fgets(line, LINE_LENGTH, result); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:584:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 584 | fgets(line, LINE_LENGTH, result); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c:585:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 585 | fgets(line, LINE_LENGTH, result); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ fastal/scoring.c: In function ‘complete_agreement_score(char*, char const*)’: fastal/scoring.c:624:49: warning: ‘%s’ directive writing up to 499 bytes into a region of size 200 [-Wformat-overflow=] 624 | sprintf(ref_file_name, "%s/%s",directory, dp->d_name); | ^~ ~~~~~~~~~ In file included from /usr/include/stdio.h:980, from fastal/scoring.c:28: In function ‘sprintf’, inlined from ‘complete_agreement_score(char*, char const*)’ at fastal/scoring.c:624:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 2 and 756 bytes into a destination of size 200 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC fastal/tree.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/tree.deps -c -o fastal/tree.o fastal/tree.c CC io_lib/io_func.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/io_func.deps -c -o io_lib/io_func.o io_lib/io_func.c In file included from ./io_lib_header.h:33, from io_lib/io_func.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, from fastal/tree.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ io_lib/io_func.c: In function ‘int output_raw_score(Alignment*, Alignment*, char*)’: io_lib/io_func.c:1235:17: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 1235 | if (!A)return NULL; | ^~~~ io_lib/io_func.c: In function ‘int aln2compressed_ps(Alignment*, char*)’: io_lib/io_func.c:2076:1: warning: no return statement in function returning non-void [-Wreturn-type] 2076 | } | ^ io_lib/io_func.c: In function ‘int** read_matrice(char*)’: io_lib/io_func.c:511:30: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 511 | fscanf ( fp, "\n"); | ~~~~~~~^~~~~~~~~~~ io_lib/io_func.c: In function ‘void get_rgb_values(int, Color*)’: io_lib/io_func.c:971:29: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 971 | fscanf (fp, "%s %f %f %f", html_code[classC], &ps_code[classC][0], &ps_code[classC][1],&ps_code[classC][2]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC io_lib/pb_util_read_seq_util.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_seq_util.deps -c -o io_lib/pb_util_read_seq_util.o io_lib/pb_util_read_seq_util.c In file included from ./io_lib_header.h:33, from io_lib/pb_util_read_seq_util.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC io_lib/pb_util_read_sequence.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_sequence.deps -c -o io_lib/pb_util_read_sequence.o io_lib/pb_util_read_sequence.c io_lib/pb_util_read_seq_util.c: In function ‘void* ckalloc(size_t)’: io_lib/pb_util_read_seq_util.c:68:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 68 | register void *ret; | ^~~ io_lib/pb_util_read_seq_util.c: In function ‘void* ckvrealloc(void*, size_t)’: io_lib/pb_util_read_seq_util.c:91:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 91 | register void *ret; | ^~~ io_lib/pb_util_read_seq_util.c: In function ‘char* rtrim(char*)’: io_lib/pb_util_read_seq_util.c:191:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 191 | register int p; | ^ io_lib/pb_util_read_seq_util.c: In function ‘char* upstr(char*)’: io_lib/pb_util_read_seq_util.c:240:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 240 | register char *s = str; | ^ io_lib/pb_util_read_seq_util.c: In function ‘char* lowstr(char*)’: io_lib/pb_util_read_seq_util.c:258:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 258 | register char *s = str; | ^ io_lib/pb_util_read_seq_util.c: In function ‘void get_path(char*, char*)’: io_lib/pb_util_read_seq_util.c:356:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 356 | register int i; | ^ io_lib/pb_util_read_seq_util.c: In function ‘void getstr(char*, char*)’: io_lib/pb_util_read_seq_util.c:269:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 269 | fgets(outstr, 100, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_seq_util.c: In function ‘double getreal(char*, double, double, double)’: io_lib/pb_util_read_seq_util.c:280:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 280 | fgets(line, MAXLINE, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_seq_util.c: In function ‘int getint(char*, int, int, int)’: io_lib/pb_util_read_seq_util.c:305:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 305 | fgets(line, MAXLINE, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from io_lib/pb_util_read_sequence.c:35: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ io_lib/pb_util_read_sequence.c: In function ‘void fill_chartab()’: io_lib/pb_util_read_sequence.c:79:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 79 | register int i; | ^ io_lib/pb_util_read_sequence.c:80:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 80 | register int c; | ^ io_lib/pb_util_read_sequence.c: In function ‘void get_clustal_seq(char*, char*, int*, char*, int)’: io_lib/pb_util_read_sequence.c:144:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 144 | fgets(line,MAXLINE+1,fin); /* read the title line...ignore it */ | ~~~~~^~~~~~~~~~~~~~~~~~~~ io_lib/pb_util_read_sequence.c:149:51: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 149 | for(i=1;i>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/tree_util.deps -c -o io_lib/tree_util.o io_lib/tree_util.c In file included from ./io_lib_header.h:33, from io_lib/tree_util.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC km_coffee/Stack.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Stack.deps -c -o km_coffee/Stack.o km_coffee/Stack.c io_lib/tree_util.c: In function ‘tnode* tree_scan(Alignment*, NT_node, char*, char*)’: io_lib/tree_util.c:836:26: warning: too many arguments for format [-Wformat-extra-args] 836 | fprintf (stdout, "Process positions\n", i); | ^~~~~~~~~~~~~~~~~~~~~ io_lib/tree_util.c: In function ‘Alignment* phylotrim(Alignment*, NT_node, char*, char*, char*)’: io_lib/tree_util.c:1299:1: warning: no return statement in function returning non-void [-Wreturn-type] 1299 | } | ^ io_lib/tree_util.c: In function ‘tnode* no_rec_free_tree(NT_node)’: io_lib/tree_util.c:2317:1: warning: no return statement in function returning non-void [-Wreturn-type] 2317 | } | ^ io_lib/tree_util.c: In function ‘int node_sort(char*, NT_node)’: io_lib/tree_util.c:6273:1: warning: no return statement in function returning non-void [-Wreturn-type] 6273 | } | ^ io_lib/tree_util.c: In function ‘int treelist2leafgroup(Sequence*, Sequence*, char*)’: io_lib/tree_util.c:6566:1: warning: no return statement in function returning non-void [-Wreturn-type] 6566 | } | ^ io_lib/tree_util.c: In function ‘int count_tree_groups(Sequence*, char*)’: io_lib/tree_util.c:6669:1: warning: no return statement in function returning non-void [-Wreturn-type] 6669 | } | ^ io_lib/tree_util.c: In function ‘int treelist2splits(Sequence*, Sequence*)’: io_lib/tree_util.c:7047:1: warning: no return statement in function returning non-void [-Wreturn-type] 7047 | } | ^ io_lib/tree_util.c: In function ‘int treelist2splits_old(Sequence*, Sequence*)’: io_lib/tree_util.c:7131:1: warning: no return statement in function returning non-void [-Wreturn-type] 7131 | } | ^ io_lib/tree_util.c: In function ‘int treelist2frame(Sequence*, Sequence*)’: io_lib/tree_util.c:7204:1: warning: no return statement in function returning non-void [-Wreturn-type] 7204 | } | ^ io_lib/tree_util.c: In function ‘char* graph2cons_d(long unsigned int, int)’: io_lib/tree_util.c:10163:27: warning: NULL used in arithmetic [-Wpointer-arith] 10163 | while ((c=rn_c(s))!=NULL) | ^~~~ io_lib/tree_util.c: In function ‘long unsigned int insert_gap_in_graph_d(long unsigned int)’: io_lib/tree_util.c:10181:20: warning: converting to non-pointer type ‘long unsigned int’ from NULL [-Wconversion-null] 10181 | unsigned long pn=NULL; | ^~~~ io_lib/tree_util.c:10183:22: warning: converting to non-pointer type ‘long unsigned int’ from NULL [-Wconversion-null] 10183 | if (!start) return NULL; | ^~~~ io_lib/tree_util.c:10196:14: warning: passing NULL to non-pointer argument 2 of ‘void wn_c(long unsigned int, long unsigned int)’ [-Wconversion-null] 10196 | wn_c(n,NULL); | ^~~~ io_lib/tree_util.c:9947:46: note: declared here 9947 | void wn_c (unsigned long n, unsigned long t); | ~~~~~~~~~~~~~~^ io_lib/tree_util.c: In function ‘FILE* create_tree(NT_node, NT_node, int*, int*, int*, tnode***, FILE*)’: io_lib/tree_util.c:3973:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3973 | fscanf(fp,"%f",&dist); | ~~~~~~^~~~~~~~~~~~~~~ io_lib/tree_util.c:3981:19: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3981 | fscanf(fp,"%f",&bootstrap); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ CC km_coffee/Vector.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Vector.deps -c -o km_coffee/Vector.o km_coffee/Vector.c io_lib/tree_util.c: In function ‘int check_node(ALN_node, char*)’: io_lib/tree_util.c:9772:1: warning: control reaches end of non-void function [-Wreturn-type] 9772 | } | ^ CC km_coffee/classes.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/classes.deps -c -o km_coffee/classes.o km_coffee/classes.c CC km_coffee/km_coffee.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/km_coffee.deps -c -o km_coffee/km_coffee.o km_coffee/km_coffee.c km_coffee/Vector.c: In function ‘void print_vecs(VectorSet*, char*)’: km_coffee/Vector.c:869:34: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 869 | fprintf(out_F, "%i ", i); | ~^ ~ | | | | int size_t {aka long unsigned int} | %li In file included from ./io_lib_header.h:33, from km_coffee/km_coffee.c:43: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ km_coffee/km_coffee.c: In function ‘int km_coffee_align3(char*, int, int, char*, char*, int, int, int, char*)’: km_coffee/km_coffee.c:491:14: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 491 | chdir(km_tmp_dir); | ~~~~~^~~~~~~~~~~~ CC km_coffee/km_util.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/km_util.deps -c -o km_coffee/km_util.o km_coffee/km_util.c CC km_coffee/kmeans.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/kmeans.deps -c -o km_coffee/kmeans.o km_coffee/kmeans.c km_coffee/km_util.c: In function ‘char* my_make_temp_dir(char*, char*)’: km_coffee/km_util.c:96:69: warning: format ‘%s’ expects a matching ‘char*’ argument [-Wformat=] 96 | fprintf(stderr, "This error was caused by '%s' in '%s'\n", function); | ~^ | | | char* CC t_coffee_lib/t_coffee.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF t_coffee_lib/t_coffee.deps -c -o t_coffee_lib/t_coffee.o t_coffee_lib/t_coffee.c In file included from ./io_lib_header.h:33, from t_coffee_lib/t_coffee.c:35: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/aln_compare.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_compare.deps -c -o util_lib/aln_compare.o util_lib/aln_compare.c t_coffee_lib/t_coffee.c: In function ‘char** km_coffee(int, char**)’: t_coffee_lib/t_coffee.c:6577:1: warning: no return statement in function returning non-void [-Wreturn-type] 6577 | } | ^ t_coffee_lib/t_coffee.c: In function ‘Alignment* t_coffee_dpa(int, char**)’: t_coffee_lib/t_coffee.c:7172:57: warning: too many arguments for format [-Wformat-extra-args] 7172 | else { w=seq2dpa_weight (S, "longuest");fprintf ( le, "default longuest\n", dpa_weight);} | ^~~~~~~~~~~~~~~~~~~~ t_coffee_lib/t_coffee.c: In function ‘int run_other_pg(int, char**)’: t_coffee_lib/t_coffee.c:6139:30: warning: control reaches end of non-void function [-Wreturn-type] 6139 | unpack_all_perl_script (argv[0]+strlen ("unpack_")); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ t_coffee_lib/t_coffee.c: In function ‘Alignment* km_align_seq_slow(char*, Alignment*, int, char**, int, int)’: t_coffee_lib/t_coffee.c:6816:1: warning: control reaches end of non-void function [-Wreturn-type] 6816 | } | ^ In file included from ./io_lib_header.h:33, from util_lib/aln_compare.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/aln_convertion_util.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_convertion_util.deps -c -o util_lib/aln_convertion_util.o util_lib/aln_convertion_util.c In file included from /usr/include/string.h:548, from t_coffee_lib/t_coffee.c:32: In function ‘strcpy’, inlined from ‘km_coffee(int, char**)’ at t_coffee_lib/t_coffee.c:6543:14: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:79:33: warning: argument 1 null where non-null expected [-Wnonnull] 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/string_fortified.h:79:33: note: in a call to built-in function ‘memcpy’ In function ‘strcpy’, inlined from ‘km_coffee(int, char**)’ at t_coffee_lib/t_coffee.c:6545:14: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:79:33: warning: argument 1 null where non-null expected [-Wnonnull] 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/string_fortified.h:79:33: note: in a call to built-in function ‘memcpy’ In file included from ./io_lib_header.h:33, from util_lib/aln_convertion_util.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ util_lib/aln_convertion_util.c: In function ‘int trim_aln_file(char*, char*, char*, char*)’: util_lib/aln_convertion_util.c:3105:62: warning: NULL used in arithmetic [-Wpointer-arith] 3105 | while ((get_next_fasta_sequence(fp, &name, &comment,&seq)!=NULL)) | ^~~~ util_lib/aln_convertion_util.c: In function ‘Alignment* aln2conservation(Alignment*, int, char*)’: util_lib/aln_convertion_util.c:4511:1: warning: no return statement in function returning non-void [-Wreturn-type] 4511 | } | ^ util_lib/aln_convertion_util.c: In function ‘Alignment* aln2N_replicate(Alignment*, char*, char*)’: util_lib/aln_convertion_util.c:7762:1: warning: no return statement in function returning non-void [-Wreturn-type] 7762 | } | ^ t_coffee_lib/t_coffee.c: In function ‘batch_main(int, char**)’: t_coffee_lib/t_coffee.c:5662:66: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 981 and 991 [-Wformat-overflow=] 5662 | sprintf ( split_name, "%s.split.%d.%s", F->name, b,split_format); | ^~ ~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from t_coffee_lib/t_coffee.c:27: In function ‘sprintf’, inlined from ‘batch_main(int, char**)’ at t_coffee_lib/t_coffee.c:5662:18: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output 10 or more bytes (assuming 1019) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c: In function ‘Alignment* extract_aln3(Alignment*, char*)’: util_lib/aln_convertion_util.c:7524:16: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 7524 | fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7543:38: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 7543 | if ( c=='#' || c=='!')fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c:7547:20: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 7547 | fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/hsearch.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/hsearch.deps -c -o util_lib/hsearch.o util_lib/hsearch.c In file included from ./io_lib_header.h:33, from util_lib/hsearch.c:35: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/random.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/random.deps -c -o util_lib/random.o util_lib/random.c CC util_lib/reformat.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat.deps -c -o util_lib/reformat.o util_lib/reformat.c io_lib/tree_util.c: In function ‘get_nexus(char*)’: io_lib/tree_util.c:4597:40: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 4597 | sprintf (index, "%d", i); | ^~ io_lib/tree_util.c:4597:39: note: directive argument in the range [1, 2147483647] 4597 | sprintf (index, "%d", i); | ^~~~ In file included from /usr/include/stdio.h:980, from io_lib/tree_util.c:27: In function ‘sprintf’, inlined from ‘get_nexus(char*)’ at io_lib/tree_util.c:4597:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 2 and 11 bytes into a destination of size 5 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from util_lib/reformat.c:35: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ util_lib/reformat.c: In function ‘int output_suchard_aln(char*, Alignment*)’: util_lib/reformat.c:7551:1: warning: no return statement in function returning non-void [-Wreturn-type] 7551 | } | ^ util_lib/reformat.c: In function ‘int output_header_mat(int**, char*)’: util_lib/reformat.c:14453:1: warning: no return statement in function returning non-void [-Wreturn-type] 14453 | } | ^ util_lib/reformat.c: In function ‘Sequence* quick_read_seq(char*)’: util_lib/reformat.c:1332:1: warning: control reaches end of non-void function [-Wreturn-type] 1332 | } | ^ util_lib/reformat.c: In function ‘Alignment* quick_read_aln_static(char*)’: util_lib/reformat.c:1371:1: warning: control reaches end of non-void function [-Wreturn-type] 1371 | } | ^ util_lib/reformat.c: In function ‘Alignment* quick_read_aln(char*)’: util_lib/reformat.c:1413:1: warning: control reaches end of non-void function [-Wreturn-type] 1413 | } | ^ util_lib/reformat.c: In function ‘int read_nameseq(char*, char***, char***, char***)’: util_lib/reformat.c:1427:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1427 | fscanf (fp, "#NAMESEQ_01\n"); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1428:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1428 | fscanf (fp, "# %d\n", &nseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1438:22: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1438 | fscanf (fp, "%d %d ", &l1, &l2); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1441:22: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1441 | fscanf (fp, "%s %s\n", nam[0][nseq], seq[0][nseq]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1446:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1446 | fscanf (fp, "%d ", &l1); | ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c:1448:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1448 | fgets (com[0][nseq],l1, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int read_nameseq_old(char*, char***, char***, char***)’: util_lib/reformat.c:1472:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1472 | fscanf (fp, "#NAMESEQ_01\n"); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1473:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1473 | fscanf (fp, "# %d\n", &nseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1483:22: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1483 | fscanf (fp, "%d %d ", &l1, &l2); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1486:22: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1486 | fscanf (fp, "%s %s\n", nam[0][nseq], seq[0][nseq]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:1491:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1491 | fscanf (fp, "%d ", &l1); | ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c:1493:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1493 | fgets (com[0][nseq],l1, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int is_pdb_name(char*)’: util_lib/reformat.c:1788:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1788 | fscanf ( fp, "%d", &result); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘char* get_pdb_id(char*)’: util_lib/reformat.c:1826:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1826 | fscanf ( fp, "\n%s\n", buf); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int fast_format_determination(char*)’: util_lib/reformat.c:2507:1: warning: control reaches end of non-void function [-Wreturn-type] 2507 | } | ^ util_lib/reformat.c: In function ‘Weights* get_amps_sd_scores(char*)’: util_lib/reformat.c:3948:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3948 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3955:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3955 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3964:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3964 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3970:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3970 | fscanf ( fp, "%s",W->seq_name[a]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:3972:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3972 | fscanf ( fp, "%s", buf2); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:3983:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3983 | fscanf ( fp, "\n"); | ~~~~~~~^~~~~~~~~~~ util_lib/reformat.c: In function ‘Structure* read_rna_struc_number(Alignment*, char*)’: util_lib/reformat.c:4256:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4256 | fscanf ( fp, "%c\n%d\n",&x, &(ST)->tot_list); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4259:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4259 | fscanf ( fp, "%d %d %d %c %c %f\n", &(ST)->list[a][0],&(ST)->list[a][1],&(ST)->list[a][2], &x, &y, &f); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Sequence* get_struc_gor(char*)’: util_lib/reformat.c:4486:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4486 | fscanf ( fp, "%s %d", name, &len); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4507:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4507 | fscanf ( fp, "%s %d\n",S->name[S->nseq], &(S->len[S->nseq])); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:4512:28: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4512 | fscanf ( fp, " %*c %c %*f %*f %*f\n",&(S->seq[S->nseq][a])); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Sequence* get_sequence_dali(char*)’: util_lib/reformat.c:4549:32: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4549 | fscanf (fp, "%s",name); | ~~~~~~~^~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Sequence* get_dialign_sequence(char*)’: util_lib/reformat.c:4624:33: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4624 | {fscanf (fp, "%s",name); | ~~~~~~~^~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int get_next_fasta_sequence(FILE*, char**, char**, char**)’: util_lib/reformat.c:5264:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 5264 | fgets (line, ml,fp); | ~~~~~~^~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int fscanf_seq_name(FILE*, char*)’: util_lib/reformat.c:5724:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 5724 | fscanf (fp, "%s", name); | ~~~~~~~^~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int get_amps_seq_name(char**, char*)’: util_lib/reformat.c:6077:25: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 6077 | {fscanf (fp, "%*d >%s", name[nseq++]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Alignment* read_gotoh_aln(char*, Alignment*)’: util_lib/reformat.c:6126:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 6126 | fgets(buf, VERY_LONG_STRING, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:6148:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 6148 | fgets(buf, VERY_LONG_STRING, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘float output_maln_pval(char*, Alignment*)’: util_lib/reformat.c:6346:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 6346 | fscanf ( fp, "%s",string); | ~~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘Alignment* similarities_file2aln(char*)’: util_lib/reformat.c:6511:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 6511 | fscanf (fp, "%s %d", name,&i); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘int** read_blast_matrix(char*)’: util_lib/reformat.c:14294:20: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14294 | fscanf ( fp, "%s ", buf); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:14307:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14307 | fscanf ( fp, "%d ", &value); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14332:19: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14332 | fscanf(fp, "\n"); | ~~~~~~^~~~~~~~~~ util_lib/reformat.c: In function ‘int** read_blast_matrix_old(char*)’: util_lib/reformat.c:14357:19: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14357 | fgets ( sbuf, VERY_LONG_STRING, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14374:20: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14374 | fscanf ( fp, "%s ", buf); | ~~~~~~~^~~~~~~~~~~~~~~~~ util_lib/reformat.c:14387:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14387 | fscanf ( fp, "%d ", &value); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:14414:19: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14414 | fscanf(fp, "\n"); | ~~~~~~^~~~~~~~~~ util_lib/reformat.c: In function ‘int** read_pavie_matrix(char*)’: util_lib/reformat.c:14525:19: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14525 | fgets ( sbuf, VERY_LONG_STRING, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/reformat_struc.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat_struc.deps -c -o util_lib/reformat_struc.o util_lib/reformat_struc.c In file included from ./io_lib_header.h:33, from util_lib/reformat_struc.c:34: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ util_lib/reformat_struc.c: In function ‘void bfactor2x_in_pdb(char*, char*, float*)’: util_lib/reformat_struc.c:125:25: warning: too many arguments for format [-Wformat-extra-args] 125 | fprintf (out, "ATOM ", lw[1]);//ATOM | ^~~~~~~~ util_lib/reformat_struc.c: In function ‘Ca_trace* simple_read_ca_trace(char*)’: util_lib/reformat_struc.c:370:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 370 | fscanf ( fp, "%*s" ); | ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:372:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 372 | fscanf ( fp, "%*s" ); | ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:378:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 378 | fscanf (fp, "%*s %*s %c %*c %d %*f %*f %*f\n",&res,&res_num); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat_struc.c:405:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 405 | fscanf ( fp, "%*s" ); | ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:407:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 407 | fscanf ( fp, "%*s" ); | ~~~~~~~^~~~~~~~~~~~~ util_lib/reformat_struc.c:416:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 416 | fscanf (fp, "%*s %s %s %*c %d %f %f %f\n",A->type, A->res,&A->res_num, &A->x, &A->y, &A->z); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/util.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util.deps -c -o util_lib/util.o util_lib/util.c In file included from ./io_lib_header.h:33, from util_lib/util.c:52: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ util_lib/util.c: In function ‘int cherry(int, char**)’: util_lib/util.c:1009:1: warning: no return statement in function returning non-void [-Wreturn-type] 1009 | } | ^ util_lib/util.c: In function ‘int dump_nfc(char*, char*)’: util_lib/util.c:4456:1: warning: no return statement in function returning non-void [-Wreturn-type] 4456 | } | ^ util_lib/util.c: In function ‘int set_nproc(int)’: util_lib/util.c:5489:1: warning: no return statement in function returning non-void [-Wreturn-type] 5489 | } | ^ util_lib/util.c: In function ‘char* vremove3(char*, char*)’: util_lib/util.c:6938:1: warning: no return statement in function returning non-void [-Wreturn-type] 6938 | } | ^ util_lib/util.c: In function ‘FILE* hsort_file(FILE*, int, int, size_t, int, int, int (*)(const void*, const void*, int, int, size_t), void* (*)(void*, void*, size_t))’: util_lib/util.c:281:18: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 281 | fread( rra, size, len,fp); /*rra=ra[--l]*/ | ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c:286:18: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 286 | fread( rra, size, len,fp); /*rra=ra[ir]*/ | ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c:289:18: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 289 | fread( rrb, size, len,fp); /*rrb=ra[0]*/ | ~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c:306:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 306 | fread (ra_j, size, len, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:311:25: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 311 | fread (ra_j_1, size, len, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘void* bsearch_file(const void*, int*, int, int, FILE*, int, int, size_t, int (*)(const void*, const void*, int, int, size_t))’: util_lib/util.c:420:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fread ( key2, el_size, entry_len,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘FILE* get_number_list_in_file(FILE*, int*, int*, int*)’: util_lib/util.c:847:32: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 847 | fscanf ( fp, "%d",&list[n[0]++]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int quantile(int, char**)’: util_lib/util.c:1321:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1321 | fscanf ( fp, "%s %s\n", s1, s2); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int** input_array_int(char*)’: util_lib/util.c:1805:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1805 | fscanf (fp, "%d\n", &len); | ~~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/util.c:1809:13: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1809 | fscanf(fp, "%d ", &len2); | ~~~~~~^~~~~~~~~~~~~~~~~~ util_lib/util.c:1812:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1812 | fscanf(fp, "%d ", &array[a][b]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c:1813:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1813 | fscanf (fp, "\n"); | ~~~~~~~^~~~~~~~~~ util_lib/util.c: In function ‘int perl_strstr(char*, char*)’: util_lib/util.c:2468:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2468 | fscanf (fp, "%d", &r); | ~~~~~~~^~~~~~~~~~~~~~ util_lib/util.c: In function ‘int printf_system_direct_check(char*, ...)’: util_lib/util.c:4440:19: warning: control reaches end of non-void function [-Wreturn-type] 4440 | printf_exit ( EXIT_FAILURE, stderr, "ERROR: Could not run %s\n", buf); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* count_strings_in_file(char*, char*)’: util_lib/util.c:5761:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 5761 | fscanf (fp, "%s\n",list[n]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* redirect_stderr(char*)’: util_lib/util.c:6301:12: warning: ignoring return value of ‘FILE* freopen(const char*, const char*, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 6301 | freopen(stderr_file, "w", stderr); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘char* redirect_stdout(char*)’: util_lib/util.c:6344:12: warning: ignoring return value of ‘FILE* freopen(const char*, const char*, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 6344 | freopen(stdout_file, "w", stdout); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int get_cl_param(int, char**, FILE**, const char*, int*, const char*, int, int, const char*, ...)’: util_lib/util.c:7645:9: warning: second parameter of ‘va_start’ not last named argument [-Wvarargs] 7645 | va_start (ap, usage); | ^~~~~~~~ util_lib/util.c: In function ‘char** get_parameter(char*, int*, char*)’: util_lib/util.c:7912:15: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 7912 | fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘FILE* set_fp_id(FILE*, char*)’: util_lib/util.c:7932:32: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 7932 | fscanf ( fp, "%s", string); | ~~~~~~~^~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int** get_file_block_pattern(char*, int*, int)’: util_lib/util.c:8319:25: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 8319 | fgets ( line, lline,fp); | ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util.c:8349:25: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 8349 | fgets ( line, lline,fp); | ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int check_for_update(char*)’: util_lib/util.c:8436:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 8436 | fscanf ( fp, "Version_%f", &new_version); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int check_internet_connection(int)’: util_lib/util.c:8528:10: warning: control reaches end of non-void function [-Wreturn-type] 8528 | myexit (EXIT_FAILURE); | ~~~~~~~^~~~~~~~~~~~~~ util_lib/util.c: In function ‘int km_main(int, char**)’: util_lib/util.c:10533:1: warning: control reaches end of non-void function [-Wreturn-type] 10533 | } | ^ CC util_lib/util_aln_analyze.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_aln_analyze.deps -c -o util_lib/util_aln_analyze.o util_lib/util_aln_analyze.c In file included from ./io_lib_header.h:33, from util_lib/util_aln_analyze.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ util_lib/util_aln_analyze.c: In function ‘Alignment* sar_analyze(Alignment*, Alignment*, char*)’: util_lib/util_aln_analyze.c:713:1: warning: no return statement in function returning non-void [-Wreturn-type] 713 | } | ^ util_lib/util_aln_analyze.c: In function ‘Alignment* or_scan(Alignment*, Alignment*, char*)’: util_lib/util_aln_analyze.c:4480:1: warning: no return statement in function returning non-void [-Wreturn-type] 4480 | } | ^ util_lib/aln_convertion_util.c: In function ‘get_weight(Alignment*, Sequence*, char*)’: util_lib/aln_convertion_util.c:12147:32: warning: ‘ -w ’ directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 12147 | sprintf ( command, "%s %s -w %s", program, seq_name, weight_name); | ^~~~ In file included from /usr/include/stdio.h:980, from util_lib/aln_convertion_util.c:27: In function ‘sprintf’, inlined from ‘get_weight(Alignment*, Sequence*, char*)’ at util_lib/aln_convertion_util.c:12147:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output 6 or more bytes (assuming 1005) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/aln_convertion_util.c: In function ‘get_weight(Alignment*, Sequence*, char*)’: util_lib/aln_convertion_util.c:12141:32: warning: ‘ -i ’ directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 12141 | sprintf ( command, "%s %s -i %s -w %s", program, seq_name, aln_name, weight_name); | ^~~~ In function ‘sprintf’, inlined from ‘get_weight(Alignment*, Sequence*, char*)’ at util_lib/aln_convertion_util.c:12141:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output 10 or more bytes (assuming 1009) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘get_cache_4_tcoffee() [clone .part.0]’: util_lib/util.c:5385:42: warning: ‘/cache/’ directive writing 7 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5385 | else sprintf ( cache_4_tcoffee, "%s/cache/", get_dir_4_tcoffee()); | ^~~~~~~ In file included from /usr/include/stdio.h:980, from util_lib/util.c:32: In function ‘sprintf’, inlined from ‘get_cache_4_tcoffee() [clone .part.0]’ at util_lib/util.c:5385:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 8 and 1007 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘get_plugins_4_tcoffee()’: util_lib/util.c:5435:43: warning: ‘/plugins/’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5435 | else sprintf (plugins_4_tcoffee, "%s/plugins/%s/", get_dir_4_tcoffee(), get_os()); | ^~~~~~~~~ In function ‘sprintf’, inlined from ‘get_plugins_4_tcoffee()’ at util_lib/util.c:5435:20, inlined from ‘get_plugins_4_tcoffee()’ at util_lib/util.c:5419:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 11 and 1109 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)’: util_lib/reformat.c:13639:34: warning: ‘ -method ’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 13639 | sprintf ( command, "%s -method %s -aln %s -tree %s -dmatrix %s -weightfile %s %s",method_4_msa_weights, action_list[1],aln_name, tree_name, dist_matrix_name,weight_name, TO_NULL_DEVICE); | ^~~~~~~~~ In file included from /usr/include/stdio.h:980, from util_lib/reformat.c:27: In function ‘sprintf’, inlined from ‘modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)’ at util_lib/reformat.c:13639:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output 64 or more bytes (assuming 3059) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function ‘modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)’: util_lib/reformat.c:11638:32: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 11638 | sprintf (type, "%s", ACTION (2)); | ^~ util_lib/util.c: In function ‘get_mcoffee_4_tcoffee()’: util_lib/util.c:5400:44: warning: ‘/mcoffee/’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5400 | else sprintf ( mcoffee_4_tcoffee, "%s/mcoffee/", get_dir_4_tcoffee()); | ^~~~~~~~~ In function ‘sprintf’, inlined from ‘get_mcoffee_4_tcoffee()’ at util_lib/util.c:5400:20, inlined from ‘get_mcoffee_4_tcoffee()’ at util_lib/util.c:5392:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 10 and 1009 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘get_methods_4_tcoffee()’: util_lib/util.c:5413:44: warning: ‘/methods/’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5413 | else sprintf ( methods_4_tcoffee, "%s/methods/", get_dir_4_tcoffee()); | ^~~~~~~~~ In function ‘sprintf’, inlined from ‘get_methods_4_tcoffee()’ at util_lib/util.c:5413:20, inlined from ‘get_methods_4_tcoffee()’ at util_lib/util.c:5405:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 10 and 1009 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘get_cache_4_tcoffee()’: util_lib/util.c:5385:42: warning: ‘/cache/’ directive writing 7 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5385 | else sprintf ( cache_4_tcoffee, "%s/cache/", get_dir_4_tcoffee()); | ^~~~~~~ In function ‘sprintf’, inlined from ‘get_cache_4_tcoffee()’ at util_lib/util.c:5385:20, inlined from ‘get_cache_4_tcoffee()’ at util_lib/util.c:5376:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 8 and 1007 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC util_lib/util_analyse_constraints_list.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_analyse_constraints_list.deps -c -o util_lib/util_analyse_constraints_list.o util_lib/util_analyse_constraints_list.c In file included from ./io_lib_header.h:33, from util_lib/util_analyse_constraints_list.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/util_constraints_list.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_constraints_list.deps -c -o util_lib/util_constraints_list.o util_lib/util_constraints_list.c In file included from /usr/include/stdio.h:980, from util_lib/util_aln_analyze.c:27: In function ‘sprintf’, inlined from ‘combine_n_predictions(orp**, Alignment*, Alignment*)’ at util_lib/util_aln_analyze.c:4598:11, inlined from ‘or_sar(Alignment*, Alignment*, char*, int)’ at util_lib/util_aln_analyze.c:4560:29: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util_aln_analyze.c: In function ‘or_sar(Alignment*, Alignment*, char*, int)’: util_lib/util_aln_analyze.c:4599:23: warning: ‘COMBINED’ directive writing 8 bytes into a region of size 0 [-Wformat-overflow=] 4599 | sprintf ( N->mode, "COMBINED"); | ^~~~~~~~ In function ‘sprintf’, inlined from ‘combine_n_predictions(orp**, Alignment*, Alignment*)’ at util_lib/util_aln_analyze.c:4599:11, inlined from ‘or_sar(Alignment*, Alignment*, char*, int)’ at util_lib/util_aln_analyze.c:4560:29: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘sprintf’ output 9 bytes into a destination of size 0 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from util_lib/util_constraints_list.c:37: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ util_lib/util_constraints_list.c: In function ‘Constraint_list* unfreeze_constraint_list(Constraint_list*)’: util_lib/util_constraints_list.c:1311:1: warning: no return statement in function returning non-void [-Wreturn-type] 1311 | } | ^ util_lib/util_constraints_list.c: In function ‘Constraint_list* fork_read_n_constraint_list(char**, int, char*, char*, char*, char*, FILE*, Constraint_list*, char*, int)’: util_lib/util_constraints_list.c:2224:49: warning: too many arguments for format [-Wformat-extra-args] 2224 | fprintf ( local_stderr, "\n\t--- Process Method/Library/Aln %s", fname[a], ns); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘Constraint_list* read_constraint_list_file(Constraint_list*, char*)’: util_lib/util_constraints_list.c:2851:40: warning: too many arguments for format [-Wformat-extra-args] 2851 | x=sscanf (buf, "%s %d %d %d %d %d",arg, &length, &r1,&r2,&we,&cons,&misc); | ^~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘display_output_filename(_IO_FILE*, char*, char*, char*, int)’: util_lib/util.c:8658:68: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 8658 | fprintf ( io, "\n\t#### File Type= %-15s Format= %-15s Name= %s",type, format, name ); | ^~ util_lib/util_constraints_list.c: In function ‘Job_TC* submit_lib_job(Job_TC*)’: util_lib/util_constraints_list.c:582:19: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 582 | chdir (tdir); | ~~~~~~^~~~~~ util_lib/util_constraints_list.c:585:19: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 585 | chdir (cdir); | ~~~~~~^~~~~~ util_lib/util_constraints_list.c: In function ‘char* method_file_tag2value(char*, char*)’: util_lib/util_constraints_list.c:1150:23: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1150 | fgets ( line,LONG_STRING, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘TC_method* method_file2TC_method(char*)’: util_lib/util_constraints_list.c:1193:23: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1193 | fgets ( line,LONG_STRING, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘int read_cpu_in_list(char*)’: util_lib/util_constraints_list.c:2599:27: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2599 | if ( c=='C')fscanf( fp, "PU %d\n", &cpu); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘int read_seq_in_list(char*, int*, char***, char***, Genomic_info**)’: util_lib/util_constraints_list.c:2917:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2917 | fscanf (fp, "%d\n", &max_nseq); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2922:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2922 | fscanf (fp, "%*s %d %*s\n", &l); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2954:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2954 | fscanf ( fp, "%s %d %s\n", name, &seq_len, sequence); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c:2979:31: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2979 | fgets (line , 200 , fp); | ~~~~~~^~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘Constraint_list* nfork_relax_constraint_list_4gp(Constraint_list*)’: util_lib/util_constraints_list.c:4053:40: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4053 | fscanf (fp, "%d ", &CL->residue_index[s][r][a+WE]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/util_declare.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_declare.deps -c -o util_lib/util_declare.o util_lib/util_declare.c In file included from ./io_lib_header.h:33, from util_lib/util_declare.c:37: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/util_domain_constraints_list.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_domain_constraints_list.deps -c -o util_lib/util_domain_constraints_list.o util_lib/util_domain_constraints_list.c In file included from ./io_lib_header.h:33, from util_lib/util_domain_constraints_list.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ util_lib/util_constraints_list.c: In function ‘make_aln_command(TC_method*, char*, char*)’: util_lib/util_constraints_list.c:1286:28: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 499 and 999 [-Wformat-overflow=] 1286 | sprintf ( buf, "%s %s %s%s %s %s%s %s", m->executable, m->param1, m->in_flag, seq,m->param2, m->out_flag,aln, m->param); | ^~ In file included from /usr/include/stdio.h:980, from util_lib/util_constraints_list.c:29: In function ‘sprintf’, inlined from ‘make_aln_command(TC_method*, char*, char*)’ at util_lib/util_constraints_list.c:1286:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output 6 or more bytes (assuming 4503) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ CC util_lib/util_dps.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_dps.deps -c -o util_lib/util_dps.o util_lib/util_dps.c In file included from ./io_lib_header.h:33, from util_lib/util_dps.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/util_job_handling.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_job_handling.deps -c -o util_lib/util_job_handling.o util_lib/util_job_handling.c util_lib/util.c: In function ‘standard_initialisation(char**, int*) [clone .part.0]’: util_lib/util.c:5400:44: warning: ‘/mcoffee/’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5400 | else sprintf ( mcoffee_4_tcoffee, "%s/mcoffee/", get_dir_4_tcoffee()); | ^~~~~~~~~ In function ‘sprintf’, inlined from ‘get_mcoffee_4_tcoffee()’ at util_lib/util.c:5400:20, inlined from ‘get_mcoffee_4_tcoffee()’ at util_lib/util.c:5392:7, inlined from ‘standard_initialisation(char**, int*) [clone .part.0]’ at util_lib/util.c:10018:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 10 and 1009 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘standard_initialisation(char**, int*) [clone .part.0]’: util_lib/util.c:5413:44: warning: ‘/methods/’ directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5413 | else sprintf ( methods_4_tcoffee, "%s/methods/", get_dir_4_tcoffee()); | ^~~~~~~~~ In function ‘sprintf’, inlined from ‘get_methods_4_tcoffee()’ at util_lib/util.c:5413:20, inlined from ‘get_methods_4_tcoffee()’ at util_lib/util.c:5405:7, inlined from ‘standard_initialisation(char**, int*) [clone .part.0]’ at util_lib/util.c:10019:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 10 and 1009 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from util_lib/util_job_handling.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC util_lib/util_make_tree.c g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_make_tree.deps -c -o util_lib/util_make_tree.o util_lib/util_make_tree.c In file included from ./io_lib_header.h:33, from util_lib/util_make_tree.c:33: ./io_lib/tree_util.h:30:1: warning: ‘typedef’ was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ util_lib/util_make_tree.c: In function ‘tnode* redundate(Sequence*, NT_node, char*, char*)’: util_lib/util_make_tree.c:66:1: warning: no return statement in function returning non-void [-Wreturn-type] 66 | } | ^ util_lib/util_make_tree.c: In function ‘void fast_nj_tree(char**)’: util_lib/util_make_tree.c:853:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 853 | register int i; | ^ util_lib/util_make_tree.c: In function ‘char* seq2co_aln_file(char*, char*)’: util_lib/util_make_tree.c:124:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 124 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:127:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 127 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘char* seq2mafft_aln_file(char*, char*)’: util_lib/util_make_tree.c:157:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 157 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:160:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 160 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘char* seq2cw_aln_file(char*, char*)’: util_lib/util_make_tree.c:190:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 190 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:192:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 192 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘char* prf_pair2cw_aln_file(char*, char*, char*)’: util_lib/util_make_tree.c:223:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 223 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:226:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 226 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2fftns1_dnd(Sequence*)’: util_lib/util_make_tree.c:1855:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1855 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1868:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1868 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2fftns2_dnd(Sequence*)’: util_lib/util_make_tree.c:1884:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1884 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1897:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2mafft_dnd(Sequence*)’: util_lib/util_make_tree.c:1913:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1913 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1926:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1926 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2parttree_dnd(Sequence*)’: util_lib/util_make_tree.c:1943:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1943 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1956:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1956 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2dpparttree_dnd(Sequence*)’: util_lib/util_make_tree.c:1973:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1973 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:1988:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1988 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2fastparttree_dnd(Sequence*)’: util_lib/util_make_tree.c:2006:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2006 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2019:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2019 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2cwquick_dnd(Sequence*)’: util_lib/util_make_tree.c:2035:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2035 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2043:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2043 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2cw_dnd(Sequence*)’: util_lib/util_make_tree.c:2060:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2060 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2068:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2068 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* aln2cw_tree(Alignment*)’: util_lib/util_make_tree.c:2088:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2088 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2095:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2095 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_make_tree.c: In function ‘tnode* seq2cw_tree(Sequence*)’: util_lib/util_make_tree.c:2110:9: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2110 | chdir (dir); | ~~~~~~^~~~~ util_lib/util_make_tree.c:2119:12: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2119 | chdir (cdir); | ~~~~~~~~~^~~~~~ util_lib/util_constraints_list.c: In function ‘cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)’: util_lib/util_constraints_list.c:4922:26: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 4922 | sprintf ( mode, "%s", (CL && in_mode==NULL)?CL->distance_matrix_mode:in_mode); | ^~ In function ‘sprintf’, inlined from ‘cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)’ at util_lib/util_constraints_list.c:4922:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)’: util_lib/util_constraints_list.c:4923:30: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 4923 | sprintf ( sim_mode, "%s", (CL && in_sim_mode==NULL)?CL->distance_matrix_sim_mode:in_sim_mode); | ^~ In function ‘sprintf’, inlined from ‘cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)’ at util_lib/util_constraints_list.c:4923:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)’: util_lib/util_constraints_list.c:694:24: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 694 | sprintf ( aln_mode, "%s", method->aln_mode); | ^~ In function ‘sprintf’, inlined from ‘method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)’ at util_lib/util_constraints_list.c:694:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function ‘method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)’: util_lib/util_constraints_list.c:695:24: warning: ‘%s’ directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 695 | sprintf ( out_mode, "%s", method->out_mode); | ^~ In function ‘sprintf’, inlined from ‘method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)’ at util_lib/util_constraints_list.c:695:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 1 and 501 bytes into a destination of size 100 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ Linking... g++ dev_lib/dev1.o dp_lib/CUSTOM_evaluate_for_struc.o dp_lib/evaluate.o dp_lib/evaluate_dirichlet.o dp_lib/evaluate_for_domain.o dp_lib/evaluate_for_struc.o dp_lib/fsa_dp.o dp_lib/pavie_dp.o dp_lib/showpair.o dp_lib/util_domain_dp.o dp_lib/util_domain_dp_drivers.o dp_lib/util_dp_cdna_fasta_nw.o dp_lib/util_dp_clean_maln.o dp_lib/util_dp_drivers.o dp_lib/util_dp_est.o dp_lib/util_dp_fasta_nw.o dp_lib/util_dp_fasta_sw.o dp_lib/util_dp_generic_fasta_nw.o dp_lib/util_dp_gotoh_nw.o dp_lib/util_dp_gotoh_sw.o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_sim.o dp_lib/util_dp_ssec_pwaln.o dp_lib/util_dp_suboptimal_nw.o dp_lib/util_graph_maln.o fastal/diagonal.o fastal/fastal.o fastal/fastal_opt_parsing.o fastal/iteration.o fastal/parttree.o fastal/scoring.o fastal/tree.o io_lib/io_func.o io_lib/pb_util_read_seq_util.o io_lib/pb_util_read_sequence.o io_lib/tree_util.o km_coffee/Stack.o km_coffee/Vector.o km_coffee/classes.o km_coffee/km_coffee.o km_coffee/km_util.o km_coffee/kmeans.o t_coffee_lib/t_coffee.o util_lib/aln_compare.o util_lib/aln_convertion_util.o util_lib/hsearch.o util_lib/random.o util_lib/reformat.o util_lib/reformat_struc.o util_lib/util.o util_lib/util_aln_analyze.o util_lib/util_analyse_constraints_list.o util_lib/util_constraints_list.o util_lib/util_declare.o util_lib/util_domain_constraints_list.o util_lib/util_dps.o util_lib/util_job_handling.o util_lib/util_make_tree.o -o t_coffee -lm -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘memset’, inlined from ‘sub_vcalloc’ at util_lib/util_declare.c:1503:12, inlined from ‘sub_vcalloc’ at util_lib/util_declare.c:1480:7, inlined from ‘vcalloc’ at util_lib/util_declare.c:1474:22, inlined from ‘vcalloc’ at util_lib/util_declare.c:1472:7, inlined from ‘extract_N_diag’ at dp_lib/util_dp_fasta_nw.c:616:26: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:33: warning: ‘__builtin_memset’ specified bound 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 59 | return __builtin___memset_chk (__dest, __ch, __len, | ^ In function ‘vsnprintf’, inlined from ‘csprintf’ at util_lib/util.c:2582:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:36: warning: ‘__builtin___vsnprintf_chk’ specified bound 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overread] 68 | return __builtin___vsnprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^ In function ‘memset’, inlined from ‘sub_vcalloc’ at util_lib/util_declare.c:1503:12, inlined from ‘sub_vcalloc’ at util_lib/util_declare.c:1480:7, inlined from ‘vcalloc’ at util_lib/util_declare.c:1474:22, inlined from ‘vcalloc’ at util_lib/util_declare.c:1472:7, inlined from ‘extract_N_diag’ at dp_lib/util_dp_fasta_nw.c:616:26, inlined from ‘cfasta_cdna_pair_wise’ at dp_lib/util_dp_cdna_fasta_nw.c:82:22: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:33: warning: ‘__builtin_memset’ specified bound 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 59 | return __builtin___memset_chk (__dest, __ch, __len, | ^ In function ‘vsnprintf’, inlined from ‘fprintf_error’ at util_lib/util.c:5660:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:36: warning: ‘__builtin___vsnprintf_chk’ specified bound 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overread] 68 | return __builtin___vsnprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^ In function ‘memset’, inlined from ‘sub_vcalloc’ at util_lib/util_declare.c:1503:12, inlined from ‘sub_vcalloc’ at util_lib/util_declare.c:1480:7, inlined from ‘vcalloc’ at util_lib/util_declare.c:1474:22, inlined from ‘vcalloc’ at util_lib/util_declare.c:1472:7, inlined from ‘pair_wise_ms’ at dp_lib/util_dp_drivers.c:5517:31, inlined from ‘pair_wise’ at dp_lib/util_dp_drivers.c:5728:74: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:33: warning: ‘__builtin_memset’ specified bound 18446744073709551614 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 59 | return __builtin___memset_chk (__dest, __ch, __len, | ^ In function ‘memset’, inlined from ‘sub_vcalloc’ at util_lib/util_declare.c:1503:12, inlined from ‘sub_vcalloc’ at util_lib/util_declare.c:1480:7, inlined from ‘vcalloc’ at util_lib/util_declare.c:1474:22, inlined from ‘vcalloc’ at util_lib/util_declare.c:1472:7, inlined from ‘sorted_aln’ at dp_lib/util_dp_drivers.c:6234:19: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:33: warning: ‘__builtin_memset’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 59 | return __builtin___memset_chk (__dest, __ch, __len, | ^ In function ‘memset’, inlined from ‘sub_vcalloc’ at util_lib/util_declare.c:1503:12, inlined from ‘sub_vcalloc’ at util_lib/util_declare.c:1480:7, inlined from ‘vcalloc’ at util_lib/util_declare.c:1474:22, inlined from ‘vcalloc’ at util_lib/util_declare.c:1472:7, inlined from ‘extract_N_diag.constprop’ at dp_lib/util_dp_fasta_nw.c:616:26: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:33: warning: ‘__builtin_memset’ specified bound 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 59 | return __builtin___memset_chk (__dest, __ch, __len, | ^ /usr/bin/ld: /tmp/ccGM2I9b.ltrans4.ltrans.o: in function `profile_pair(TC_method*, char*, Constraint_list*)': /<>/t_coffee_source/dp_lib/util_dp_drivers.c:1160:(.text+0x2427): warning: the use of `tmpnam' is dangerous, better use `mkstemp' make[2]: Leaving directory '/<>/t_coffee_source' make[1]: Leaving directory '/<>' dh_auto_test -O--sourcedirectory=t_coffee_source create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=t_coffee_source dh_prep -O--sourcedirectory=t_coffee_source dh_auto_install -O--sourcedirectory=t_coffee_source dh_install -O--sourcedirectory=t_coffee_source dh_installdocs -O--sourcedirectory=t_coffee_source dh_installchangelogs -O--sourcedirectory=t_coffee_source debian/rules override_dh_installexamples make[1]: Entering directory '/<>' dh_installexamples for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/share/doc/*` ; do \ sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/<>' dh_installman -O--sourcedirectory=t_coffee_source dh_installsystemduser -O--sourcedirectory=t_coffee_source dh_perl -O--sourcedirectory=t_coffee_source dh_link -O--sourcedirectory=t_coffee_source dh_strip_nondeterminism -O--sourcedirectory=t_coffee_source debian/rules override_dh_compress make[1]: Entering directory '/<>' #Compressing most of the files in examples/ makes them unusable dh_compress -Xt-coffee-examples ( cd debian/t-coffee-examples/ && \ chmod 644 usr/share/doc/t-coffee-examples/changelog.Debian && \ gzip -9 -n usr/share/doc/t-coffee-examples/changelog.Debian ) || true make[1]: Leaving directory '/<>' dh_fixperms -O--sourcedirectory=t_coffee_source dh_missing -O--sourcedirectory=t_coffee_source dh_dwz -a -O--sourcedirectory=t_coffee_source dh_strip -a -O--sourcedirectory=t_coffee_source 26c4d37d690bdf993b9440f1a5cc22062b84de38 dh_makeshlibs -a -O--sourcedirectory=t_coffee_source dh_shlibdeps -a -O--sourcedirectory=t_coffee_source dh_installdeb -O--sourcedirectory=t_coffee_source dh_gencontrol -O--sourcedirectory=t_coffee_source dh_md5sums -O--sourcedirectory=t_coffee_source dh_builddeb -O--sourcedirectory=t_coffee_source INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing t-coffee (in debian/t-coffee); do_strip: , oemstrip: pkgstriptranslations: processing t-coffee-examples (in debian/t-coffee-examples); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/t-coffee-examples/DEBIAN/control, package t-coffee-examples, directory debian/t-coffee-examples pkgstripfiles: processing control file: debian/t-coffee/DEBIAN/control, package t-coffee, directory debian/t-coffee INFO: pkgstripfiles: waiting for lock (t-coffee-examples) ... pkgstripfiles: Running PNG optimization (using 4 cpus) for package t-coffee ... pkgstripfiles: No PNG files. dpkg-deb: building package 't-coffee' in '../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package t-coffee-examples ... pkgstripfiles: No PNG files. dpkg-deb: building package 't-coffee-examples' in '../t-coffee-examples_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-05-05T22:32:11Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.changes: -------------------------------------------------------------------- Format: 1.8 Date: Fri, 25 Nov 2022 11:13:19 +0100 Source: t-coffee Binary: t-coffee t-coffee-examples Built-For-Profiles: noudeb Architecture: all amd64 Version: 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 Distribution: noble Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: t-coffee - Multiple Sequence Alignment t-coffee-examples - annotated examples for the use of T-Coffee Closes: 1022570 1023230 Changes: t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) unstable; urgency=medium . [ Étienne Mollier ] * d/t/run-unit-test: don't meddle with user's home. * d/rules: build with -fsigned-char. This fixes infinite loops on CPU architectures defaulting to the char type being unsigned, such as on arm*, ppc* and s390*. (Closes: #1023230) * d/control: add myself to uploaders. . [ Andreas Tille ] * Revert version bump to latest upstream version until https://github.com/cbcrg/tcoffee/issues/56 is closed. 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6.8.0-31.31), login (= 1:4.13+dfsg1-4ubuntu3), lto-disabled-list (= 47), m4 (= 1.4.19-4build1), make (= 4.3-4.1build2), man-db (= 2.12.0-4build2), mawk (= 1.3.4.20240123-1build1), ncurses-base (= 6.4+20240113-1ubuntu2), ncurses-bin (= 6.4+20240113-1ubuntu2), patch (= 2.7.6-7build3), perl (= 5.38.2-3.2build2), perl-base (= 5.38.2-3.2build2), perl-modules-5.38 (= 5.38.2-3.2build2), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.2-0ubuntu7), sed (= 4.9-2build1), sensible-utils (= 0.0.22), sysvinit-utils (= 3.08-6ubuntu3), tar (= 1.35+dfsg-3build1), util-linux (= 2.39.3-9ubuntu6), xz-utils (= 5.6.1+really5.4.5-1), zlib1g (= 1:1.3.dfsg-3.1ubuntu2) Environment: DEB_BUILD_OPTIONS="noautodbgsym parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1669371199" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ t-coffee-examples_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_all.deb ---------------------------------------------------------------------- new Debian package, version 2.0. size 2652594 bytes: control archive=9049 bytes. 689 bytes, 18 lines control 30640 bytes, 360 lines md5sums Package: t-coffee-examples Source: t-coffee Version: 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 5681 Recommends: t-coffee Breaks: t-coffee (<< 13) Replaces: t-coffee (<< 13) Section: science Priority: optional Multi-Arch: foreign Homepage: https://www.tcoffee.org/Projects/tcoffee/index.html Description: annotated examples for the use of T-Coffee To help increasing the proficiency in the use of T-Coffee, this package provides examples for input sequences and their proper alignment. drwxr-xr-x root/root 0 2022-11-25 10:13 ./ drwxr-xr-x root/root 0 2022-11-25 10:13 ./usr/ drwxr-xr-x root/root 0 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Section: science Priority: optional Homepage: https://www.tcoffee.org/Projects/tcoffee/index.html Description: Multiple Sequence Alignment T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can mix sequences and structures. . T-Coffee allows the combination of a collection of multiple/pairwise, global or local alignments into a single model. It can also estimate the level of consistency of each position within the new alignment with the rest of the alignments. See the pre-print for more information . T-Coffee has a special called M-Coffee that makes it possible to combine the output of many multiple sequence alignment packages. In its published version, it uses MUSCLE, PROBCONS, POA, DiAlign-TS, MAFFT, Clustal W, PCMA and T-Coffee. A special version has been made for Debian, DM-Coffee, that uses only free software by replacing Clustal W by Kalign. Using the 8 Methods of M-Coffee can sometimes be a bit heavy. You can use a subset of your favorite methods if you prefer. drwxr-xr-x root/root 0 2022-11-25 10:13 ./ drwxr-xr-x root/root 0 2022-11-25 10:13 ./usr/ drwxr-xr-x root/root 0 2022-11-25 10:13 ./usr/bin/ -rwxr-xr-x root/root 2325456 2022-11-25 10:13 ./usr/bin/t_coffee drwxr-xr-x root/root 0 2022-11-25 10:13 ./usr/share/ drwxr-xr-x root/root 0 2022-11-25 10:13 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-11-25 10:13 ./usr/share/doc/t-coffee/ -rw-r--r-- root/root 1744 2022-11-25 10:13 ./usr/share/doc/t-coffee/README.Debian -rw-r--r-- root/root 261 2022-11-25 10:13 ./usr/share/doc/t-coffee/README.test -rw-r--r-- root/root 1240 2022-11-25 10:13 ./usr/share/doc/t-coffee/changelog.Debian.gz -rw-r--r-- root/root 1571 2022-11-25 10:13 ./usr/share/doc/t-coffee/copyright -rw-r--r-- root/root 3062 2022-11-25 10:13 ./usr/share/doc/t-coffee/run-unit-test drwxr-xr-x root/root 0 2022-11-25 10:13 ./usr/share/man/ drwxr-xr-x root/root 0 2022-11-25 10:13 ./usr/share/man/man1/ -rw-r--r-- root/root 1463 2022-11-25 10:13 ./usr/share/man/man1/t_coffee.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 81384 Build-Time: 66 Distribution: noble Host Architecture: amd64 Install-Time: 5 Job: t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc Machine Architecture: amd64 Package: t-coffee Package-Time: 72 Source-Version: 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 Space: 81384 Status: successful Version: 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 -------------------------------------------------------------------------------- Finished at 2024-05-05T22:32:11Z Build needed 00:01:12, 81384k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-28269765 Scanning for processes to kill in build PACKAGEBUILD-28269765