https://launchpad.net/ubuntu/+source/vienna-rna/2.5.1+dfsg-1build3/+build/27999130 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-009 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:37 UTC 2024 aarch64 Buildd toolchain package versions: launchpad-buildd_236~650~ubuntu20.04.1 python3-lpbuildd_236~650~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... 3 Apr 05:20:56 ntpdate[1845]: adjust time server 10.211.37.1 offset -0.000379 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27999130 --image-type chroot /home/buildd/filecache-default/59612f0fc5bae33f6226b6e60c2e882b82c04bd0 Creating target for build PACKAGEBUILD-27999130 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27999130 Starting target for build PACKAGEBUILD-27999130 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27999130 'deb http://ftpmaster.internal/ubuntu noble main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu noble-security main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu noble-updates main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu noble-proposed main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-27999130 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27999130 Updating target for build PACKAGEBUILD-27999130 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [89.7 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main armhf Packages [1336 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu noble/restricted armhf Packages [5188 B] Get:8 http://ftpmaster.internal/ubuntu noble/restricted Translation-en [14.3 kB] Get:9 http://ftpmaster.internal/ubuntu noble/universe armhf Packages [14.9 MB] Get:10 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6099 kB] Get:11 http://ftpmaster.internal/ubuntu noble/multiverse armhf Packages [172 kB] Get:12 http://ftpmaster.internal/ubuntu noble/multiverse Translation-en [108 kB] Get:13 http://ftpmaster.internal/ubuntu noble-updates/main armhf Packages [666 kB] Get:14 http://ftpmaster.internal/ubuntu noble-updates/main Translation-en [242 kB] Get:15 http://ftpmaster.internal/ubuntu noble-updates/restricted armhf Packages [2284 B] Get:16 http://ftpmaster.internal/ubuntu noble-updates/restricted Translation-en [13.3 kB] Get:17 http://ftpmaster.internal/ubuntu noble-updates/universe armhf Packages [4423 kB] Get:18 http://ftpmaster.internal/ubuntu noble-updates/universe Translation-en [1693 kB] Get:19 http://ftpmaster.internal/ubuntu noble-updates/multiverse armhf Packages [50.6 kB] Get:20 http://ftpmaster.internal/ubuntu noble-updates/multiverse Translation-en [38.2 kB] Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [610 kB] Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [228 kB] Get:23 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf Packages [1192 B] Get:24 http://ftpmaster.internal/ubuntu noble-proposed/restricted Translation-en [5056 B] Get:25 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [3778 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [1590 kB] Get:27 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf Packages [29.1 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Translation-en [41.0 kB] Fetched 37.1 MB in 21s (1732 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 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* libperl5.36* libpng16-16* libreadline8* libssl3* libtirpc3* usrmerge* The following NEW packages will be installed: cpp-13-arm-linux-gnueabihf cpp-arm-linux-gnueabihf g++-13-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-13-arm-linux-gnueabihf gcc-14-base gcc-arm-linux-gnueabihf 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: apt apt-utils base-files base-passwd bash bash-completion binutils binutils-arm-linux-gnueabihf binutils-common bsdextrautils bsdutils bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot 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 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 libgomp1 libgpg-error-l10n libgpg-error0 libgpm2 libgssapi-krb5-2 libidn2-0 libip4tc2 libjansson4 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblzma5 libmd0 libmount1 libncursesw6 libnsl-dev libnsl2 libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libproc2-0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libss2 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login logsave lto-disabled-list mawk mount ncurses-base ncurses-bin openssl optipng passwd perl perl-base pinentry-curses procps psmisc readline-common sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 154 upgraded, 23 newly installed, 15 to remove and 0 not upgraded. Need to get 96.8 MB of archives. After this operation, 24.8 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnsl-dev armhf 1.3.0-3build3 [66.2 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main armhf libcrypt-dev armhf 1:4.4.36-4 [136 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc6-dev armhf 2.39-0ubuntu8 [1352 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc-dev-bin armhf 2.39-0ubuntu8 [19.1 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtirpc-common all 1.3.4+ds-1.1build1 [8094 B] Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtirpc-dev armhf 1.3.4+ds-1.1build1 [184 kB] Get:7 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libnss-nisplus armhf 1.3-5build1 [20.1 kB] Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnsl2 armhf 1.3.0-3build3 [36.5 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgssapi-krb5-2 armhf 1.20.1-6ubuntu2 [119 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkrb5-3 armhf 1.20.1-6ubuntu2 [321 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libk5crypto3 armhf 1.20.1-6ubuntu2 [78.6 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkrb5support0 armhf 1.20.1-6ubuntu2 [31.4 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main armhf libacl1 armhf 2.3.2-1 [15.1 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libapparmor1 armhf 4.0.0-beta3-0ubuntu3 [45.1 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libaudit-common all 1:3.1.2-2.1build1 [5736 B] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcap-ng0 armhf 0.8.4-2build2 [13.6 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libaudit1 armhf 1:3.1.2-2.1build1 [44.4 kB] Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblkid1 armhf 2.39.3-9ubuntu4 [160 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main armhf libcap2 armhf 1:2.66-5ubuntu1 [25.8 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main armhf libcrypt1 armhf 1:4.4.36-4 [104 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main armhf libgpg-error-l10n all 1.47-3build1 [8024 B] Get:22 http://ftpmaster.internal/ubuntu noble/main armhf libgpg-error0 armhf 1.47-3build1 [61.6 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main armhf libgcrypt20 armhf 1.10.3-2 [454 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main armhf liblzma5 armhf 5.6.1+really5.4.5-1 [111 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main armhf libzstd1 armhf 1.5.5+dfsg2-2 [265 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkmod2 armhf 31+20240202-2ubuntu5 [45.0 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main armhf libpcre2-8-0 armhf 10.42-4ubuntu1 [198 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libselinux1 armhf 3.5-2ubuntu2 [70.9 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmount1 armhf 2.39.3-9ubuntu4 [171 kB] Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtext-iconv-perl armhf 1.7-8build3 [12.7 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main armhf libtext-charwidth-perl armhf 0.04-11build3 [8992 B] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl-modules-5.38 all 5.38.2-3.2build1 [3110 kB] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdb5.3t64 armhf 5.3.28+dfsg2-6build1 [661 kB] Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgdbm6t64 armhf 1.23-5.1build1 [30.3 kB] Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgdbm-compat4t64 armhf 1.23-5.1build1 [6216 B] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libperl5.38t64 armhf 5.38.2-3.2build1 [4109 kB] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl armhf 5.38.2-3.2build1 [231 kB] Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl-base armhf 5.38.2-3.2build1 [1671 kB] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblocale-gettext-perl armhf 1.07-6ubuntu5 [15.1 kB] Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc6 armhf 2.39-0ubuntu8 [2828 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc-bin armhf 2.39-0ubuntu8 [530 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssl armhf 3.0.13-0ubuntu3 [974 kB] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsystemd-shared armhf 255.4-1ubuntu6 [2010 kB] Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcryptsetup12 armhf 2:2.7.0-1ubuntu3 [238 kB] Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libssl3t64 armhf 3.0.13-0ubuntu3 [1558 kB] Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-dev all 255.4-1ubuntu6 [104 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-sysv armhf 255.4-1ubuntu6 [11.9 kB] Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd armhf 255.4-1ubuntu6 [3502 kB] Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsystemd0 armhf 255.4-1ubuntu6 [406 kB] Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-modules-bin armhf 1.5.3-5ubuntu4 [47.1 kB] Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-modules armhf 1.5.3-5ubuntu4 [260 kB] Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libapt-pkg6.0t64 armhf 2.7.14build2 [986 kB] Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnettle8t64 armhf 3.9.1-2.2build1 [187 kB] Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libhogweed6t64 armhf 3.9.1-2.2build1 [187 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main armhf libp11-kit0 armhf 0.25.3-4ubuntu1 [258 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main armhf libunistring5 armhf 1.1-2 [512 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgnutls30t64 armhf 3.8.3-1.1ubuntu3 [947 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apt armhf 2.7.14build2 [1368 kB] Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apt-utils armhf 2.7.14build2 [210 kB] Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bzip2 armhf 1.0.8-5.1 [33.5 kB] Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbz2-1.0 armhf 1.0.8-5.1 [31.1 kB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main armhf zlib1g armhf 1:1.3.dfsg-3.1ubuntu2 [49.2 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main armhf debconf-i18n all 1.5.86 [205 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main armhf debconf all 1.5.86 [124 kB] Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam0g armhf 1.5.3-5ubuntu4 [62.0 kB] Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libseccomp2 armhf 2.5.5-1ubuntu3 [49.5 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main armhf libargon2-1 armhf 0~20190702+dfsg-4 [22.3 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libudev1 armhf 255.4-1ubuntu6 [166 kB] Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdevmapper1.02.1 armhf 2:1.02.185-3ubuntu3 [135 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libuuid1 armhf 2.39.3-9ubuntu4 [34.6 kB] Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfdisk1 armhf 2.39.3-9ubuntu4 [196 kB] Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main armhf mount armhf 2.39.3-9ubuntu4 [134 kB] Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcom-err2 armhf 1.47.0-2.4~exp1ubuntu3 [21.9 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main armhf libkeyutils1 armhf 1.6.3-3 [8120 B] Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtirpc3t64 armhf 1.3.4+ds-1.1build1 [73.3 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main armhf linux-libc-dev armhf 6.8.0-20.20 [1555 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main armhf gcc-14-base armhf 14-20240330-1ubuntu2 [47.4 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main armhf libgcc-s1 armhf 14-20240330-1ubuntu2 [41.5 kB] Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main armhf base-files armhf 13ubuntu9 [73.4 kB] Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main armhf debianutils armhf 5.17build1 [89.0 kB] Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bash armhf 5.2.21-2ubuntu4 [668 kB] Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bsdutils armhf 1:2.39.3-9ubuntu4 [101 kB] Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main armhf coreutils armhf 9.4-3ubuntu5 [1280 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main armhf libstdc++6 armhf 14-20240330-1ubuntu2 [714 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main armhf libxxhash0 armhf 0.8.2-2 [31.3 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main armhf libffi8 armhf 3.4.6-1 [21.0 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main armhf libidn2-0 armhf 2.3.7-2 [96.1 kB] Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdebconfclient0 armhf 0.271ubuntu3 [10.9 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main armhf base-passwd armhf 3.6.3 [51.0 kB] Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsqlite3-0 armhf 3.45.1-1ubuntu2 [590 kB] Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg armhf 2.4.4-2ubuntu16 [524 kB] Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg-agent armhf 2.4.4-2ubuntu16 [235 kB] Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgconf armhf 2.4.4-2ubuntu16 [115 kB] Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main armhf readline-common all 8.2-4build1 [56.5 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main armhf libncursesw6 armhf 6.4+20240113-1ubuntu1 [118 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main armhf libtinfo6 armhf 6.4+20240113-1ubuntu1 [90.5 kB] Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libreadline8t64 armhf 8.2-4build1 [129 kB] Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main armhf pinentry-curses armhf 1.2.1-3ubuntu5 [36.7 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main armhf init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnpth0t64 armhf 1.6-3.1build1 [6998 B] Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgv armhf 2.4.4-2ubuntu16 [224 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main armhf ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main armhf tar armhf 1.35+dfsg-3 [236 kB] Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dpkg armhf 1.22.6ubuntu6 [1230 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main armhf dash armhf 0.5.12-6ubuntu5 [80.8 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main armhf diffutils armhf 1:3.10-1 [167 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main armhf grep armhf 3.11-4 [166 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main armhf gzip armhf 1.12-1ubuntu2 [95.8 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main armhf hostname armhf 3.23+nmu2ubuntu1 [10.3 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main armhf login armhf 1:4.13+dfsg1-4ubuntu1 [200 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main armhf ncurses-bin armhf 6.4+20240113-1ubuntu1 [178 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main armhf sed armhf 4.9-2 [198 kB] Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main armhf util-linux armhf 2.39.3-9ubuntu4 [1216 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main armhf ncurses-base all 6.4+20240113-1ubuntu1 [25.4 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main armhf sysvinit-utils armhf 3.08-6ubuntu2 [33.7 kB] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main armhf logsave armhf 1.47.0-2.4~exp1ubuntu3 [21.9 kB] Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libext2fs2t64 armhf 1.47.0-2.4~exp1ubuntu3 [201 kB] Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main armhf e2fsprogs armhf 1.47.0-2.4~exp1ubuntu3 [571 kB] Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main armhf optipng armhf 0.7.8+ds-1build2 [109 kB] Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpng16-16t64 armhf 1.6.43-5build1 [166 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main armhf init armhf 1.66ubuntu1 [6186 B] Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsmartcols1 armhf 2.39.3-9ubuntu4 [117 kB] Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main armhf uuid-runtime armhf 2.39.3-9ubuntu4 [41.7 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main armhf libattr1 armhf 1:2.5.2-1 [10.3 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main armhf libmd0 armhf 1.1.0-2 [23.1 kB] Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-runtime all 1.5.3-5ubuntu4 [40.8 kB] Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsemanage-common all 3.5-1build5 [10.1 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main armhf libsepol2 armhf 3.5-2 [262 kB] Get:129 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsemanage2 armhf 3.5-1build5 [84.5 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main armhf passwd armhf 1:4.13+dfsg1-4ubuntu1 [817 kB] Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libproc2-0 armhf 2:4.0.4-4ubuntu3 [49.0 kB] Get:132 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libss2 armhf 1.47.0-2.4~exp1ubuntu3 [14.7 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main armhf mawk armhf 1.3.4.20240123-1 [115 kB] Get:134 http://ftpmaster.internal/ubuntu noble-proposed/main armhf procps armhf 2:4.0.4-4ubuntu3 [700 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main armhf sensible-utils all 0.0.22 [22.5 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main armhf ca-certificates all 20240203 [159 kB] Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main armhf krb5-locales all 1.20.1-6ubuntu2 [13.8 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main armhf tzdata all 2024a-1ubuntu1 [273 kB] Get:139 http://ftpmaster.internal/ubuntu noble/main armhf bash-completion all 1:2.11-8 [180 kB] Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bsdextrautils armhf 2.39.3-9ubuntu4 [78.7 kB] Get:141 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgpm2 armhf 1.20.7-11 [13.6 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main armhf libip4tc2 armhf 1.8.10-3ubuntu1 [21.2 kB] Get:143 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjansson4 armhf 2.14-2build2 [28.2 kB] Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main armhf psmisc armhf 23.7-1build1 [176 kB] Get:145 http://ftpmaster.internal/ubuntu noble/main armhf xz-utils armhf 5.6.1+really5.4.5-1 [267 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main armhf libctf0 armhf 2.42-4ubuntu2 [87.7 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main armhf libctf-nobfd0 armhf 2.42-4ubuntu2 [88.0 kB] Get:148 http://ftpmaster.internal/ubuntu noble/main armhf binutils-arm-linux-gnueabihf armhf 2.42-4ubuntu2 [2925 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main armhf libbinutils armhf 2.42-4ubuntu2 [460 kB] Get:150 http://ftpmaster.internal/ubuntu noble/main armhf binutils armhf 2.42-4ubuntu2 [3072 B] Get:151 http://ftpmaster.internal/ubuntu noble/main armhf binutils-common armhf 2.42-4ubuntu2 [217 kB] Get:152 http://ftpmaster.internal/ubuntu noble/main armhf libsframe1 armhf 2.42-4ubuntu2 [13.1 kB] Get:153 http://ftpmaster.internal/ubuntu noble/main armhf libubsan1 armhf 14-20240330-1ubuntu2 [1153 kB] Get:154 http://ftpmaster.internal/ubuntu noble/main armhf libgomp1 armhf 14-20240330-1ubuntu2 [125 kB] Get:155 http://ftpmaster.internal/ubuntu noble/main armhf libatomic1 armhf 14-20240330-1ubuntu2 [7846 B] Get:156 http://ftpmaster.internal/ubuntu noble/main armhf libasan8 armhf 14-20240330-1ubuntu2 [2940 kB] Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main armhf g++-13 armhf 13.2.0-23ubuntu3 [14.5 kB] Get:158 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-13 armhf 13.2.0-23ubuntu3 [450 kB] Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libstdc++-13-dev armhf 13.2.0-23ubuntu3 [2455 kB] Get:160 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgcc-13-dev armhf 13.2.0-23ubuntu3 [899 kB] Get:161 http://ftpmaster.internal/ubuntu noble/main armhf libcc1-0 armhf 14-20240330-1ubuntu2 [39.1 kB] Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main armhf cpp-13 armhf 13.2.0-23ubuntu3 [1034 B] Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-13-base armhf 13.2.0-23ubuntu3 [48.6 kB] Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-13-arm-linux-gnueabihf armhf 13.2.0-23ubuntu3 [16.8 MB] Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main armhf g++-13-arm-linux-gnueabihf armhf 13.2.0-23ubuntu3 [9939 kB] Get:166 http://ftpmaster.internal/ubuntu noble-proposed/main armhf cpp-13-arm-linux-gnueabihf armhf 13.2.0-23ubuntu3 [8759 kB] Get:167 http://ftpmaster.internal/ubuntu noble/main armhf g++ armhf 4:13.2.0-7ubuntu1 [1090 B] Get:168 http://ftpmaster.internal/ubuntu noble/main armhf gcc armhf 4:13.2.0-7ubuntu1 [5022 B] Get:169 http://ftpmaster.internal/ubuntu noble/main armhf cpp armhf 4:13.2.0-7ubuntu1 [22.4 kB] Get:170 http://ftpmaster.internal/ubuntu noble/main armhf cpp-arm-linux-gnueabihf armhf 4:13.2.0-7ubuntu1 [5320 B] Get:171 http://ftpmaster.internal/ubuntu noble/main armhf gcc-arm-linux-gnueabihf armhf 4:13.2.0-7ubuntu1 [1220 B] Get:172 http://ftpmaster.internal/ubuntu noble/main armhf g++-arm-linux-gnueabihf armhf 4:13.2.0-7ubuntu1 [966 B] Get:173 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dpkg-dev all 1.22.6ubuntu6 [1074 kB] Get:174 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdpkg-perl all 1.22.6ubuntu6 [268 kB] Get:175 http://ftpmaster.internal/ubuntu noble/main armhf lto-disabled-list all 47 [12.4 kB] Get:176 http://ftpmaster.internal/ubuntu noble/main armhf libfakeroot armhf 1.33-1 [28.7 kB] Get:177 http://ftpmaster.internal/ubuntu noble/main armhf fakeroot armhf 1.33-1 [68.6 kB] Preconfiguring packages ... 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Installing new version of config file /etc/security/namespace.init ... dpkg: libnettle8:armhf: dependency problems, but removing anyway as you requested: libhogweed6:armhf depends on libnettle8. libgnutls30:armhf depends on libnettle8 (>= 3.7~). (Reading database ... 14943 files and directories currently installed.) Removing libnettle8:armhf (3.9.1-2) ... dpkg: libapt-pkg6.0:armhf: dependency problems, but removing anyway as you requested: apt-utils depends on libapt-pkg6.0 (>= 2.7.3). apt depends on libapt-pkg6.0 (>= 2.7.3). Removing libapt-pkg6.0:armhf (2.7.3) ... dpkg: libgnutls30:armhf: dependency problems, but removing anyway as you requested: apt depends on libgnutls30 (>= 3.7.5). Removing libgnutls30:armhf (3.8.1-4ubuntu1) ... Selecting previously unselected package libapt-pkg6.0t64:armhf. (Reading database ... 14877 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.7.14build2_armhf.deb ... Unpacking libapt-pkg6.0t64:armhf (2.7.14build2) ... 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(Reading database ... 14951 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.5-1ubuntu3_armhf.deb ... Unpacking libseccomp2:armhf (2.5.5-1ubuntu3) over (2.5.4-1ubuntu3) ... Setting up libseccomp2:armhf (2.5.5-1ubuntu3) ... (Reading database ... 14951 files and directories currently installed.) Preparing to unpack .../libargon2-1_0~20190702+dfsg-4_armhf.deb ... Unpacking libargon2-1:armhf (0~20190702+dfsg-4) over (0~20190702+dfsg-3) ... Preparing to unpack .../libudev1_255.4-1ubuntu6_armhf.deb ... Unpacking libudev1:armhf (255.4-1ubuntu6) over (253.5-1ubuntu6) ... Setting up libudev1:armhf (255.4-1ubuntu6) ... (Reading database ... 14951 files and directories currently installed.) Preparing to unpack .../libdevmapper1.02.1_2%3a1.02.185-3ubuntu3_armhf.deb ... Unpacking libdevmapper1.02.1:armhf (2:1.02.185-3ubuntu3) over (2:1.02.185-2ubuntu1) ... Preparing to unpack .../libuuid1_2.39.3-9ubuntu4_armhf.deb ... 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Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3 to /lib/arm-linux-gnueabihf/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0 to /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:armhf (1.3.4+ds-1.1build1) ... Preparing to unpack .../5-linux-libc-dev_6.8.0-20.20_armhf.deb ... Unpacking linux-libc-dev:armhf (6.8.0-20.20) over (6.5.0-9.9) ... Selecting previously unselected package gcc-14-base:armhf. Preparing to unpack .../6-gcc-14-base_14-20240330-1ubuntu2_armhf.deb ... Unpacking gcc-14-base:armhf (14-20240330-1ubuntu2) ... Setting up gcc-14-base:armhf (14-20240330-1ubuntu2) ... (Reading database ... 14977 files and directories currently installed.) Preparing to unpack .../libgcc-s1_14-20240330-1ubuntu2_armhf.deb ... Unpacking libgcc-s1:armhf (14-20240330-1ubuntu2) over (13.2.0-4ubuntu3) ... Setting up libgcc-s1:armhf (14-20240330-1ubuntu2) ... 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Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:armhf (8.2-4build1) ... Preparing to unpack .../pinentry-curses_1.2.1-3ubuntu5_armhf.deb ... Unpacking pinentry-curses (1.2.1-3ubuntu5) over (1.2.1-1ubuntu1) ... Preparing to unpack .../init-system-helpers_1.66ubuntu1_all.deb ... Unpacking init-system-helpers (1.66ubuntu1) over (1.65.2ubuntu1) ... Setting up init-system-helpers (1.66ubuntu1) ... 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Adding 'diversion of /lib/arm-linux-gnueabihf/libe2p.so.2 to /lib/arm-linux-gnueabihf/libe2p.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libe2p.so.2.3 to /lib/arm-linux-gnueabihf/libe2p.so.2.3.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libext2fs.so.2 to /lib/arm-linux-gnueabihf/libext2fs.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libext2fs.so.2.4 to /lib/arm-linux-gnueabihf/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' Unpacking libext2fs2t64:armhf (1.47.0-2.4~exp1ubuntu3) ... Setting up libcom-err2:armhf (1.47.0-2.4~exp1ubuntu3) ... Setting up libext2fs2t64:armhf (1.47.0-2.4~exp1ubuntu3) ... (Reading database ... 14978 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.47.0-2.4~exp1ubuntu3_armhf.deb ... 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Setting up libfdisk1:armhf (2.39.3-9ubuntu4) ... Setting up libkmod2:armhf (31+20240202-2ubuntu5) ... Setting up libsystemd-shared:armhf (255.4-1ubuntu6) ... Setting up systemd-dev (255.4-1ubuntu6) ... Setting up mount (2.39.3-9ubuntu4) ... Setting up systemd (255.4-1ubuntu6) ... Installing new version of config file /etc/systemd/journald.conf ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/pstore.conf ... Installing new version of config file /etc/systemd/sleep.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from random generator. Setting up systemd-sysv (255.4-1ubuntu6) ... (Reading database ... 14977 files and directories currently installed.) Preparing to unpack .../init_1.66ubuntu1_armhf.deb ... 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Setting up libc6-dev:armhf (2.39-0ubuntu8) ... Setting up binutils-arm-linux-gnueabihf (2.42-4ubuntu2) ... Setting up gpg (2.4.4-2ubuntu16) ... Setting up cpp-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ... Setting up libstdc++-13-dev:armhf (13.2.0-23ubuntu3) ... Setting up gpg-agent (2.4.4-2ubuntu16) ... Setting up cpp-13 (13.2.0-23ubuntu3) ... Setting up libtirpc3t64:armhf (1.3.4+ds-1.1build1) ... Setting up binutils (2.42-4ubuntu2) ... Setting up gcc-13-arm-linux-gnueabihf (13.2.0-23ubuntu3) ... Setting up dpkg-dev (1.22.6ubuntu6) ... Setting up libtirpc-dev:armhf (1.3.4+ds-1.1build1) ... Setting up gcc-13 (13.2.0-23ubuntu3) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up libnsl2:armhf (1.3.0-3build3) ... Setting up gcc-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ... Setting up g++-13-arm-linux-gnueabihf (13.2.0-23ubuntu3) ... Setting up g++-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ... Setting up g++-13 (13.2.0-23ubuntu3) ... Setting up libnss-nisplus:armhf (1.3-5build1) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Setting up libnsl-dev:armhf (1.3.0-3build3) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... Processing triggers for debianutils (5.17build1) ... (Reading database ... 15022 files and directories currently installed.) Purging configuration files for libssl3:armhf (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-27999130 armhf noble-proposed -c chroot:build-PACKAGEBUILD-27999130 --arch=armhf --dist=noble-proposed --nolog vienna-rna_2.5.1+dfsg-1build3.dsc Initiating build PACKAGEBUILD-27999130 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:37 UTC 2024 armv7l sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-arm64-009.buildd +==============================================================================+ | vienna-rna 2.5.1+dfsg-1build3 (armhf) Wed, 03 Apr 2024 05:25:00 +0000 | +==============================================================================+ Package: vienna-rna Version: 2.5.1+dfsg-1build3 Source Version: 2.5.1+dfsg-1build3 Distribution: noble-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27999130/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/vienna-rna-087pVg/resolver-FzgGMb' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- vienna-rna_2.5.1+dfsg-1build3.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/vienna-rna-087pVg/vienna-rna-2.5.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/vienna-rna-087pVg' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, python3-dev, pkg-config, libtool, gettext, swig (>= 4.0.2), perl-doc, perl, graphviz, libdlib-dev, libgsl-dev, liblapack-dev, libmpfr-dev, libsvm-dev, xxd, texlive-latex-extra, help2man, gengetopt, cthreadpool-dev, ghostscript, doxygen, texinfo, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3-dev, pkg-config, libtool, gettext, swig (>= 4.0.2), perl-doc, perl, graphviz, libdlib-dev, libgsl-dev, liblapack-dev, libmpfr-dev, libsvm-dev, xxd, texlive-latex-extra, help2man, gengetopt, cthreadpool-dev, ghostscript, doxygen, texinfo, 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 [511 B] Get:5 copy:/<>/apt_archive ./ Packages [590 B] Fetched 2058 B in 0s (21.8 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 libip4tc2 libnsl-dev libnsl2 libnss-nis libnss-nisplus 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 cthreadpool-dev debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism doxygen dwz file fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lmodern fonts-urw-base35 gengetopt gettext gettext-base ghostscript graphviz groff-base help2man intltool-debian libapache-pom-java libarchive-zip-perl libavahi-client3 libavahi-common-data libavahi-common3 libblas-dev libblas3 libbrotli1 libbsd0 libcairo2 libcdt5 libcgraph6 libclang-cpp18 libclang1-18 libcommons-logging-java libcommons-parent-java libcups2t64 libdatrie1 libdbus-1-3 libdebhelper-perl libdeflate0 libdlib-data libdlib-dev libdlib19.1t64 libdrm-amdgpu1 libdrm-common libdrm-nouveau2 libdrm-radeon1 libdrm2 libdw1t64 libedit2 libelf1t64 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfmt9 libfontbox-java libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgd3 libgfortran5 libgl1-mesa-dri libglapi-mesa libglib2.0-0t64 libglvnd0 libglx-mesa0 libglx0 libgmp-dev libgmpxx4ldbl libgraphite2-3 libgs-common libgs10 libgs10-common libgsl-dev libgsl27 libgslcblas0 libgts-0.7-5t64 libgvc6 libgvpr2 libharfbuzz0b libhwloc15 libice6 libicu74 libidn12 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore libkpathsea6 liblab-gamut1 liblapack-dev liblapack3 liblerc4 libllvm17t64 libllvm18 libltdl7 libmagic-mgc libmagic1t64 libmpfr-dev libopencv-core-dev libopencv-core406t64 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpathplan4 libpdfbox-java libpipeline1 libpixman-1-0 libpkgconf3 libpng-dev libpotrace0 libptexenc1 libpthread-stubs0-dev libpython3-dev libpython3-stdlib libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libsensors-config libsensors5 libsharpyuv0 libsm6 libsqlite3-dev libsub-override-perl libsvm-dev libsvm3 libsynctex2 libtbb-dev libtbb12 libtbbbind-2-5 libtbbmalloc2 libteckit0 libtexlua53-5 libtext-unidecode-perl libthai-data libthai0 libtiff6 libtool libuchardet0 libvulkan1 libwebp7 libx11-6 libx11-data libx11-dev libx11-xcb1 libxapian30 libxau-dev libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext6 libxfixes3 libxi6 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml2 libxmu6 libxpm4 libxrender1 libxshmfence1 libxt6t64 libxxf86vm1 libzzip-0-13t64 m4 man-db media-types netbase perl-doc pkg-config pkgconf pkgconf-bin po-debconf poppler-data preview-latex-style pybind11-dev python3 python3-dev python3-minimal python3-pkg-resources python3-setuptools python3.12 python3.12-dev python3.12-minimal swig t1utils tex-common texinfo texinfo-lib texlive-base texlive-binaries texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures ucf x11-common x11proto-dev xdg-utils xfonts-encodings xfonts-utils xorg-sgml-doctools xtrans-dev xxd zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make flit python3-build python3-installer python3-wheel doxygen-latex doxygen-doc doxygen-gui fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gettext-doc libasprintf-dev libgettextpo-dev gsfonts graphviz-doc groff liblapack-doc libavalon-framework-java libexcalibur-logkit-java liblog4j1.2-java cups-common libgd-tools low-memory-monitor gmp-doc libgmp10-doc gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libmpfr-doc lm-sensors sqlite3-doc libtbb-doc libtool-doc gfortran | fortran95-compiler gcj-jdk libx11-doc xapian-tools libxcb-doc m4-doc apparmor less www-browser libmail-box-perl poppler-utils fonts-japanese-mincho | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-nanum pybind11-doc python3-doc python3-tk python3-venv python-setuptools-doc python3.12-venv python3.12-doc binfmt-support swig-doc swig-examples texlive-plain-generic texlive-fonts-recommended perl-tk xpdf | pdf-viewer xzdec texlive-binaries-sse2 hintview texlive-latex-base-doc wp2latex python3-pygments icc-profiles libfile-which-perl texlive-latex-extra-doc texlive-science texlive-latex-recommended-doc texlive-luatex texlive-pstricks dot2tex prerex texlive-pictures-doc vprerex Recommended packages: curl | wget | lynx fonts-liberation2 dbus libarchive-cpio-perl libgl1-amber-dri libglib2.0-data shared-mime-info xdg-user-dirs fonts-droid-fallback libgts-bin libhwloc-plugins javascript-common libpng-tools libltdl-dev mesa-vulkan-drivers | vulkan-icd libwww-perl libxml-sax-expat-perl libmail-sendmail-perl libeigen3-dev lmodern dvisvgm default-jre libspreadsheet-parseexcel-perl texlive-fonts-recommended texlive-plain-generic ruby tk libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev cthreadpool-dev debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism doxygen dwz file fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lmodern fonts-urw-base35 gengetopt gettext gettext-base ghostscript graphviz groff-base help2man intltool-debian libapache-pom-java libarchive-zip-perl libavahi-client3 libavahi-common-data libavahi-common3 libblas-dev libblas3 libbrotli1 libbsd0 libcairo2 libcdt5 libcgraph6 libclang-cpp18 libclang1-18 libcommons-logging-java libcommons-parent-java libcups2t64 libdatrie1 libdbus-1-3 libdebhelper-perl libdeflate0 libdlib-data libdlib-dev libdlib19.1t64 libdrm-amdgpu1 libdrm-common libdrm-nouveau2 libdrm-radeon1 libdrm2 libdw1t64 libedit2 libelf1t64 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfmt9 libfontbox-java libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgd3 libgfortran5 libgl1-mesa-dri libglapi-mesa libglib2.0-0t64 libglvnd0 libglx-mesa0 libglx0 libgmp-dev libgmpxx4ldbl libgraphite2-3 libgs-common libgs10 libgs10-common libgsl-dev libgsl27 libgslcblas0 libgts-0.7-5t64 libgvc6 libgvpr2 libharfbuzz0b libhwloc15 libice6 libicu74 libidn12 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore libkpathsea6 liblab-gamut1 liblapack-dev liblapack3 liblerc4 libllvm17t64 libllvm18 libltdl7 libmagic-mgc libmagic1t64 libmpfr-dev libopencv-core-dev libopencv-core406t64 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpathplan4 libpdfbox-java libpipeline1 libpixman-1-0 libpkgconf3 libpng-dev libpotrace0 libptexenc1 libpthread-stubs0-dev libpython3-dev libpython3-stdlib libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libsensors-config libsensors5 libsharpyuv0 libsm6 libsqlite3-dev libsub-override-perl libsvm-dev libsvm3 libsynctex2 libtbb-dev libtbb12 libtbbbind-2-5 libtbbmalloc2 libteckit0 libtexlua53-5 libtext-unidecode-perl libthai-data libthai0 libtiff6 libtool libuchardet0 libvulkan1 libwebp7 libx11-6 libx11-data libx11-dev libx11-xcb1 libxapian30 libxau-dev libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext6 libxfixes3 libxi6 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml2 libxmu6 libxpm4 libxrender1 libxshmfence1 libxt6t64 libxxf86vm1 libzzip-0-13t64 m4 man-db media-types netbase perl-doc pkg-config pkgconf pkgconf-bin po-debconf poppler-data preview-latex-style pybind11-dev python3 python3-dev python3-minimal python3-pkg-resources python3-setuptools python3.12 python3.12-dev python3.12-minimal sbuild-build-depends-main-dummy swig t1utils tex-common texinfo texinfo-lib texlive-base texlive-binaries texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures ucf x11-common x11proto-dev xdg-utils xfonts-encodings xfonts-utils xorg-sgml-doctools xtrans-dev xxd zlib1g-dev 0 upgraded, 236 newly installed, 0 to remove and 0 not upgraded. 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http://ftpmaster.internal/ubuntu noble/main armhf python3-setuptools all 68.1.2-2ubuntu1 [396 kB] Get:61 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf dh-python all 6.20240401 [110 kB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libllvm18 armhf 1:18.1.2-1ubuntu3 [26.7 MB] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libclang-cpp18 armhf 1:18.1.2-1ubuntu3 [12.8 MB] Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libclang1-18 armhf 1:18.1.2-1ubuntu3 [7383 kB] Get:65 http://ftpmaster.internal/ubuntu noble/universe armhf libfmt9 armhf 9.1.0+ds1-2 [55.2 kB] Get:66 http://ftpmaster.internal/ubuntu noble/universe armhf libxapian30 armhf 1.4.22-1 [659 kB] Get:67 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf doxygen armhf 1.9.8+ds-2build5 [4881 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbrotli1 armhf 1.1.0-2build2 [319 kB] Get:69 http://ftpmaster.internal/ubuntu 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armhf 2.4.7-7 [37.9 kB] Get:117 http://ftpmaster.internal/ubuntu noble/main armhf libgraphite2-3 armhf 1.3.14-2 [72.7 kB] Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libharfbuzz0b armhf 8.3.0-2build2 [446 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main armhf libthai-data all 0.1.29-2 [158 kB] Get:120 http://ftpmaster.internal/ubuntu noble/main armhf libdatrie1 armhf 0.2.13-3 [16.9 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main armhf libthai0 armhf 0.1.29-2 [15.1 kB] Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpango-1.0-0 armhf 1.52.1+ds-1build1 [207 kB] Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpangoft2-1.0-0 armhf 1.52.1+ds-1build1 [36.5 kB] Get:124 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpangocairo-1.0-0 armhf 1.52.1+ds-1build1 [25.0 kB] Get:125 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libpathplan4 armhf 2.42.2-9build1 [21.6 kB] Get:126 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libblas-dev armhf 3.12.0-3 [132 kB] Get:136 http://ftpmaster.internal/ubuntu noble/universe armhf libcommons-parent-java all 56-1 [10.7 kB] Get:137 http://ftpmaster.internal/ubuntu noble/universe armhf libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] Get:138 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libdlib-data all 19.24+dfsg-1.1build1 [65.2 MB] Get:139 http://ftpmaster.internal/ubuntu noble/main armhf libgfortran5 armhf 14-20240330-1ubuntu2 [312 kB] Get:140 http://ftpmaster.internal/ubuntu noble/main armhf liblapack3 armhf 3.12.0-3 [2085 kB] Get:141 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libdlib19.1t64 armhf 19.24+dfsg-1.1build1 [3750 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main armhf libglvnd0 armhf 1.7.0-1 [83.7 kB] Get:143 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libglapi-mesa armhf 24.0.3-1ubuntu4 [47.8 kB] Get:144 http://ftpmaster.internal/ubuntu noble/main armhf libx11-xcb1 armhf 2:1.8.7-1 [7744 B] Get:145 http://ftpmaster.internal/ubuntu noble/main armhf libxcb-dri2-0 armhf 1.15-1 [6872 B] Get:146 http://ftpmaster.internal/ubuntu noble/main armhf libxcb-dri3-0 armhf 1.15-1 [6778 B] Get:147 http://ftpmaster.internal/ubuntu noble/main armhf libxcb-glx0 armhf 1.15-1 [22.6 kB] Get:148 http://ftpmaster.internal/ubuntu noble/main armhf libxcb-present0 armhf 1.15-1 [5526 B] Get:149 http://ftpmaster.internal/ubuntu noble/main armhf libxcb-randr0 armhf 1.15-1 [16.8 kB] Get:150 http://ftpmaster.internal/ubuntu noble/main armhf libxcb-sync1 armhf 1.15-1 [8794 B] Get:151 http://ftpmaster.internal/ubuntu noble/main armhf libxcb-xfixes0 armhf 1.15-1 [10.0 kB] Get:152 http://ftpmaster.internal/ubuntu noble/main armhf libxfixes3 armhf 1:6.0.0-2 [8966 B] Get:153 http://ftpmaster.internal/ubuntu noble/main armhf libxshmfence1 armhf 1.3-1build4 [5080 B] Get:154 http://ftpmaster.internal/ubuntu noble/main armhf libxxf86vm1 armhf 1:1.1.4-1build3 [9068 B] Get:155 http://ftpmaster.internal/ubuntu noble/main armhf libvulkan1 armhf 1.3.275.0-1 [122 kB] Get:156 http://ftpmaster.internal/ubuntu noble/main armhf libdrm-amdgpu1 armhf 2.4.120-2 [18.6 kB] Get:157 http://ftpmaster.internal/ubuntu noble/main armhf libdrm-nouveau2 armhf 2.4.120-2 [15.2 kB] Get:158 http://ftpmaster.internal/ubuntu noble/main armhf libdrm-radeon1 armhf 2.4.120-2 [18.2 kB] Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libllvm17t64 armhf 1:17.0.6-9build3 [25.3 MB] Get:160 http://ftpmaster.internal/ubuntu noble/main armhf libsensors-config all 1:3.6.0-9build1 [5546 B] Get:161 http://ftpmaster.internal/ubuntu noble/main armhf libsensors5 armhf 1:3.6.0-9build1 [24.6 kB] Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgl1-mesa-dri armhf 24.0.3-1ubuntu4 [7201 kB] Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libglx-mesa0 armhf 24.0.3-1ubuntu4 [132 kB] Get:164 http://ftpmaster.internal/ubuntu noble/main armhf libglx0 armhf 1.7.0-1 [37.0 kB] Get:165 http://ftpmaster.internal/ubuntu noble/universe armhf libtbbmalloc2 armhf 2021.11.0-2ubuntu2 [52.3 kB] Get:166 http://ftpmaster.internal/ubuntu noble/universe armhf libhwloc15 armhf 2.10.0-1 [145 kB] Get:167 http://ftpmaster.internal/ubuntu noble/universe armhf libtbbbind-2-5 armhf 2021.11.0-2ubuntu2 [14.6 kB] Get:168 http://ftpmaster.internal/ubuntu noble/universe armhf libtbb12 armhf 2021.11.0-2ubuntu2 [88.0 kB] Get:169 http://ftpmaster.internal/ubuntu noble/universe armhf libopencv-core406t64 armhf 4.6.0+dfsg-13.1build2 [973 kB] Get:170 http://ftpmaster.internal/ubuntu noble/universe armhf libtbb-dev armhf 2021.11.0-2ubuntu2 [253 kB] Get:171 http://ftpmaster.internal/ubuntu noble-proposed/main armhf zlib1g-dev armhf 1:1.3.dfsg-3.1ubuntu2 [880 kB] Get:172 http://ftpmaster.internal/ubuntu noble/universe armhf libopencv-core-dev armhf 4.6.0+dfsg-13.1build2 [1858 kB] Get:173 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpng-dev armhf 1.6.43-5build1 [248 kB] Get:174 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsqlite3-dev armhf 3.45.1-1ubuntu2 [816 kB] Get:175 http://ftpmaster.internal/ubuntu noble/main armhf xorg-sgml-doctools all 1:1.11-1.1 [10.9 kB] Get:176 http://ftpmaster.internal/ubuntu noble/main armhf x11proto-dev all 2023.2-1 [602 kB] Get:177 http://ftpmaster.internal/ubuntu noble/main armhf libxau-dev armhf 1:1.0.9-1build5 [8928 B] Get:178 http://ftpmaster.internal/ubuntu noble/main armhf libxdmcp-dev armhf 1:1.1.3-0ubuntu5 [25.0 kB] Get:179 http://ftpmaster.internal/ubuntu noble/main armhf xtrans-dev all 1.4.0-1 [68.9 kB] Get:180 http://ftpmaster.internal/ubuntu noble/main armhf libpthread-stubs0-dev armhf 0.4-1build2 [5504 B] Get:181 http://ftpmaster.internal/ubuntu noble/main armhf libxcb1-dev armhf 1.15-1 [84.6 kB] Get:182 http://ftpmaster.internal/ubuntu noble/main armhf libx11-dev armhf 2:1.8.7-1 [669 kB] Get:183 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.12t64 armhf 3.12.2-5ubuntu3 [2078 kB] Get:184 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libexpat1-dev armhf 2.6.1-2build1 [122 kB] Get:185 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3.12-dev armhf 3.12.2-5ubuntu3 [4317 kB] Get:186 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpython3-dev armhf 3.12.2-0ubuntu2 [10.1 kB] Get:187 http://ftpmaster.internal/ubuntu noble/universe armhf pybind11-dev all 2.11.1-2 [159 kB] Get:188 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libdlib-dev armhf 19.24+dfsg-1.1build1 [2155 kB] Get:189 http://ftpmaster.internal/ubuntu noble/main armhf libgmpxx4ldbl armhf 2:6.3.0+dfsg-2ubuntu4 [9040 B] Get:190 http://ftpmaster.internal/ubuntu noble/main armhf libgmp-dev armhf 2:6.3.0+dfsg-2ubuntu4 [289 kB] Get:191 http://ftpmaster.internal/ubuntu noble/universe armhf libgslcblas0 armhf 2.7.1+dfsg-6ubuntu1 [77.7 kB] Get:192 http://ftpmaster.internal/ubuntu noble/universe armhf libgsl27 armhf 2.7.1+dfsg-6ubuntu1 [827 kB] Get:193 http://ftpmaster.internal/ubuntu noble/universe armhf libgsl-dev armhf 2.7.1+dfsg-6ubuntu1 [1076 kB] Get:194 http://ftpmaster.internal/ubuntu noble/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] Get:195 http://ftpmaster.internal/ubuntu noble/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] Get:196 http://ftpmaster.internal/ubuntu noble/main armhf libjs-sphinxdoc all 7.2.6-6 [149 kB] Get:197 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkpathsea6 armhf 2023.20230311.66589-9build3 [57.6 kB] Get:198 http://ftpmaster.internal/ubuntu noble/main armhf liblapack-dev armhf 3.12.0-3 [2177 kB] Get:199 http://ftpmaster.internal/ubuntu noble/main armhf libmpfr-dev armhf 4.2.1-1 [249 kB] Get:200 http://ftpmaster.internal/ubuntu noble/main armhf libpaper-utils armhf 1.1.29 [8170 B] Get:201 http://ftpmaster.internal/ubuntu noble/main armhf libpkgconf3 armhf 1.8.1-2 [26.3 kB] Get:202 http://ftpmaster.internal/ubuntu noble/universe armhf libpotrace0 armhf 1.16-2 [14.6 kB] Get:203 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libptexenc1 armhf 2023.20230311.66589-9build3 [36.8 kB] Get:204 http://ftpmaster.internal/ubuntu noble/universe armhf libsvm3 armhf 3.24+ds-6ubuntu2 [38.0 kB] Get:205 http://ftpmaster.internal/ubuntu noble/universe armhf libsvm-dev armhf 3.24+ds-6ubuntu2 [49.8 kB] Get:206 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsynctex2 armhf 2023.20230311.66589-9build3 [47.6 kB] Get:207 http://ftpmaster.internal/ubuntu noble/universe armhf libteckit0 armhf 2.5.12+ds1-1 [323 kB] Get:208 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtexlua53-5 armhf 2023.20230311.66589-9build3 [97.6 kB] Get:209 http://ftpmaster.internal/ubuntu noble/universe armhf libtext-unidecode-perl all 1.30-3 [105 kB] Get:210 http://ftpmaster.internal/ubuntu noble/main armhf libxi6 armhf 2:1.8.1-1 [26.5 kB] Get:211 http://ftpmaster.internal/ubuntu noble/main armhf libxml-namespacesupport-perl all 1.12-2 [13.5 kB] Get:212 http://ftpmaster.internal/ubuntu noble/main armhf libxml-sax-base-perl all 1.09-3 [18.9 kB] Get:213 http://ftpmaster.internal/ubuntu noble/main armhf libxml-sax-perl all 1.02+dfsg-3 [57.0 kB] Get:214 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxml-libxml-perl armhf 2.0207+dfsg+really+2.0134-1build4 [291 kB] Get:215 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libzzip-0-13t64 armhf 0.13.72+dfsg.1-1.2build1 [24.4 kB] Get:216 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl-doc all 5.38.2-3.2build1 [7833 kB] Get:217 http://ftpmaster.internal/ubuntu noble/main armhf pkgconf-bin armhf 1.8.1-2 [20.6 kB] Get:218 http://ftpmaster.internal/ubuntu noble/main armhf pkgconf armhf 1.8.1-2 [16.7 kB] Get:219 http://ftpmaster.internal/ubuntu noble/main armhf pkg-config armhf 1.8.1-2 [7170 B] Get:220 http://ftpmaster.internal/ubuntu noble/universe armhf tex-common all 6.18 [32.8 kB] Get:221 http://ftpmaster.internal/ubuntu noble/universe armhf preview-latex-style all 13.2-1 [347 kB] Get:222 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3.12-dev armhf 3.12.2-5ubuntu3 [498 kB] Get:223 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-dev armhf 3.12.2-0ubuntu2 [26.7 kB] Get:224 http://ftpmaster.internal/ubuntu noble/universe armhf swig armhf 4.2.0-2ubuntu1 [1115 kB] Get:225 http://ftpmaster.internal/ubuntu noble/main armhf t1utils armhf 1.41-4build2 [53.1 kB] Get:226 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf texinfo-lib armhf 7.1-3build2 [114 kB] Get:227 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf texinfo all 7.1-3build2 [1273 kB] Get:228 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf texlive-binaries armhf 2023.20230311.66589-9build3 [7160 kB] Get:229 http://ftpmaster.internal/ubuntu noble/main armhf xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] Get:230 http://ftpmaster.internal/ubuntu noble/universe armhf texlive-base all 2023.20240207-1 [21.7 MB] Get:231 http://ftpmaster.internal/ubuntu noble/universe armhf texlive-latex-base all 2023.20240207-1 [1238 kB] Get:232 http://ftpmaster.internal/ubuntu noble/universe armhf libfontbox-java all 1:1.8.16-5 [208 kB] Get:233 http://ftpmaster.internal/ubuntu noble/universe armhf libpdfbox-java all 1:1.8.16-5 [5521 kB] Get:234 http://ftpmaster.internal/ubuntu noble/universe armhf texlive-latex-recommended all 2023.20240207-1 [8826 kB] Get:235 http://ftpmaster.internal/ubuntu noble/universe armhf texlive-pictures all 2023.20240207-1 [16.7 MB] Get:236 http://ftpmaster.internal/ubuntu noble/universe armhf texlive-latex-extra all 2023.20240207-1 [19.2 MB] Preconfiguring packages ... Fetched 332 MB in 23s (14.2 MB/s) Selecting previously unselected package libpython3.12-minimal:armhf. (Reading database ... 15022 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.2-5ubuntu3_armhf.deb ... Unpacking libpython3.12-minimal:armhf (3.12.2-5ubuntu3) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.6.1-2build1_armhf.deb ... Unpacking libexpat1:armhf (2.6.1-2build1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.2-5ubuntu3_armhf.deb ... Unpacking python3.12-minimal (3.12.2-5ubuntu3) ... Setting up libpython3.12-minimal:armhf (3.12.2-5ubuntu3) ... Setting up libexpat1:armhf (2.6.1-2build1) ... Setting up python3.12-minimal (3.12.2-5ubuntu3) ... Selecting previously unselected package python3-minimal. (Reading database ... 15340 files and directories currently installed.) 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Setting up libdbus-1-3:armhf (1.14.10-4ubuntu3) ... Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... Setting up libfribidi0:armhf (1.0.13-3) ... Setting up t1utils (1.41-4build2) ... Setting up libtexlua53-5:armhf (2023.20230311.66589-9build3) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libhwloc15:armhf (2.10.0-1) ... Setting up libidn12:armhf (1.42-1) ... Setting up autopoint (0.21-14ubuntu1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up ucf (3.0043+nmu1) ... Setting up pkgconf-bin (1.8.1-2) ... Setting up libsensors5:armhf (1:3.6.0-9build1) ... Setting up libjpeg-turbo8:armhf (2.1.5-2ubuntu1) ... Setting up libltdl7:armhf (2.4.7-7) ... Setting up libglapi-mesa:armhf (24.0.3-1ubuntu4) ... Setting up libkpathsea6:armhf (2023.20230311.66589-9build3) ... Setting up libgfortran5:armhf (14-20240330-1ubuntu2) ... Setting up libvulkan1:armhf (1.3.275.0-1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:armhf (1.3.2-0.4build3) ... Setting up libfmt9:armhf (9.1.0+ds1-2) ... Setting up libicu74:armhf (74.2-1ubuntu1) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg-3.1ubuntu2) ... Setting up dwz (0.15-1build6) ... Setting up libxshmfence1:armhf (1.3-1build4) ... Setting up libuchardet0:armhf (0.0.8-1) ... Setting up debugedit (1:5.0-5build1) ... Setting up fonts-lmodern (2.005-1) ... Setting up libopenjp2-7:armhf (2.5.0-2build3) ... Setting up libsub-override-perl (0.10-1) ... Setting up libharfbuzz0b:armhf (8.3.0-2build2) ... Setting up libthai-data (0.1.29-2) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up netbase (6.4) ... Setting up libgts-0.7-5t64:armhf (0.7.6+darcs121130-5.2build1) ... Setting up libcdt5:armhf (2.42.2-9build1) ... Setting up libcgraph6:armhf (2.42.2-9build1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libtext-unidecode-perl (1.30-3) ... Setting up libbsd0:armhf (0.12.1-1build1) ... Setting up libdrm-common (2.4.120-2) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3ubuntu3) ... Setting up libdlib-data (19.24+dfsg-1.1build1) ... Setting up xdg-utils (1.1.3-4.1ubuntu3) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libblas-dev:armhf (3.12.0-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode Setting up libsvm3:armhf (3.24+ds-6ubuntu2) ... Setting up libsynctex2:armhf (2023.20230311.66589-9build3) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libpotrace0:armhf (1.16-2) ... Setting up libjpeg8:armhf (8c-2ubuntu11) ... Setting up automake (1:1.16.5-1.3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up x11proto-dev (2023.2-1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libpaper1:armhf (1.1.29) ... Creating config file /etc/papersize with new version Setting up libice6:armhf (2:1.0.10-1build2) ... Setting up libxdmcp6:armhf (1:1.1.3-0ubuntu5) ... Setting up liblapack3:armhf (3.12.0-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up libxcb1:armhf (1.15-1) ... Setting up gettext (0.21-14ubuntu1) ... Setting up libgsl-dev (2.7.1+dfsg-6ubuntu1) ... Setting up libgmp-dev:armhf (2:6.3.0+dfsg-2ubuntu4) ... Setting up libxcb-xfixes0:armhf (1.15-1) ... Setting up libpdfbox-java (1:1.8.16-5) ... Setting up libxau-dev:armhf (1:1.0.9-1build5) ... Setting up libpython3.12-stdlib:armhf (3.12.2-5ubuntu3) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:armhf (1.15-1) ... Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... Setting up libxcb-glx0:armhf (1.15-1) ... Setting up python3.12 (3.12.2-5ubuntu3) ... Setting up libedit2:armhf (3.1-20230828-1) ... Setting up libpng-dev:armhf (1.6.43-5build1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:armhf (0.8-13ubuntu5) ... Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... Setting up libxcb-shm0:armhf (1.15-1) ... Setting up libpaper-utils (1.1.29) ... Setting up xfonts-utils (1:7.7+6build2) ... Setting up libmpfr-dev:armhf (4.2.1-1) ... Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up pkgconf:armhf (1.8.1-2) ... Setting up libtbbbind-2-5:armhf (2021.11.0-2ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libxcb-present0:armhf (1.15-1) ... Setting up libpython3.12t64:armhf (3.12.2-5ubuntu3) ... Setting up dh-autoreconf (20) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libthai0:armhf (0.1.29-2) ... Setting up libxdmcp-dev:armhf (1:1.1.3-0ubuntu5) ... Setting up libdlib19.1t64:armhf (19.24+dfsg-1.1build1) ... Setting up libptexenc1:armhf (2023.20230311.66589-9build3) ... Setting up libllvm17t64:armhf (1:17.0.6-9build3) ... Setting up libxcb-sync1:armhf (1.15-1) ... Setting up libsvm-dev:armhf (3.24+ds-6ubuntu2) ... Setting up liblapack-dev:armhf (3.12.0-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode Setting up pkg-config:armhf (1.8.1-2) ... Setting up libjs-sphinxdoc (7.2.6-6) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1build4) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libxcb-dri2-0:armhf (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libgvpr2:armhf (2.42.2-9build1) ... Setting up libdrm2:armhf (2.4.120-2) ... Setting up groff-base (1.23.0-3build2) ... Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu2) ... Setting up libxcb-randr0:armhf (1.15-1) ... Setting up libx11-6:armhf (2:1.8.7-1) ... Setting up libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... Setting up libsm6:armhf (2:1.2.3-1build2) ... Setting up libavahi-client3:armhf (0.8-13ubuntu5) ... Setting up libpython3-stdlib:armhf (3.12.2-0ubuntu2) ... Setting up libllvm18:armhf (1:18.1.2-1ubuntu3) ... Setting up libdrm-amdgpu1:armhf (2.4.120-2) ... Setting up libxcb-dri3-0:armhf (1.15-1) ... Setting up libclang1-18 (1:18.1.2-1ubuntu3) ... Setting up libx11-xcb1:armhf (2:1.8.7-1) ... Setting up fontconfig (2.15.0-1.1ubuntu2) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:armhf (2.4.120-2) ... Setting up libxcb1-dev:armhf (1.15-1) ... Setting up libxpm4:armhf (1:3.5.17-1build2) ... Setting up libxrender1:armhf (1:0.9.10-1.1) ... Setting up libdrm-radeon1:armhf (2.4.120-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up preview-latex-style (13.2-1) ... Setting up libpango-1.0-0:armhf (1.52.1+ds-1build1) ... Setting up libgl1-mesa-dri:armhf (24.0.3-1ubuntu4) ... Setting up libx11-dev:armhf (2:1.8.7-1) ... Setting up libxext6:armhf (2:1.3.4-1build1) ... Setting up python3 (3.12.2-0ubuntu2) ... Setting up libpython3.12-dev:armhf (3.12.2-5ubuntu3) ... Setting up libtbb12:armhf (2021.11.0-2ubuntu2) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up man-db (2.12.0-4build1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /usr/lib/systemd/system/man-db.timer. Setting up libcairo2:armhf (1.18.0-3) ... Setting up libxxf86vm1:armhf (1:1.1.4-1build3) ... Setting up libxfixes3:armhf (1:6.0.0-2) ... Setting up libxt6t64:armhf (1:1.2.1-1.2build1) ... Setting up libgd3:armhf (2.3.3-9ubuntu4) ... Setting up python3.12-dev (3.12.2-5ubuntu3) ... Setting up texinfo (7.1-3build2) ... Running mktexlsr. This may take some time. ... done. Setting up libtbb-dev:armhf (2021.11.0-2ubuntu2) ... Setting up libpangoft2-1.0-0:armhf (1.52.1+ds-1build1) ... Setting up libclang-cpp18 (1:18.1.2-1ubuntu3) ... Setting up libcups2t64:armhf (2.4.7-1.2ubuntu3) ... Setting up libpangocairo-1.0-0:armhf (1.52.1+ds-1build1) ... Setting up python3-pkg-resources (68.1.2-2ubuntu1) ... Setting up libgs10-common (10.02.1~dfsg1-0ubuntu6) ... Setting up libxmu6:armhf (2:1.1.3-3build2) ... Setting up libglx-mesa0:armhf (24.0.3-1ubuntu4) ... Setting up libpython3-dev:armhf (3.12.2-0ubuntu2) ... Setting up python3-setuptools (68.1.2-2ubuntu1) ... Setting up libxi6:armhf (2:1.8.1-1) ... Setting up libglx0:armhf (1.7.0-1) ... Setting up debhelper (13.14.1ubuntu5) ... Setting up libxaw7:armhf (2:1.0.14-1build2) ... Setting up pybind11-dev (2.11.1-2) ... Setting up doxygen (1.9.8+ds-2build5) ... Setting up python3-dev (3.12.2-0ubuntu2) ... Setting up libgvc6 (2.42.2-9build1) ... Setting up texlive-binaries (2023.20230311.66589-9build3) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up texlive-base (2023.20240207-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up libopencv-core406t64:armhf (4.6.0+dfsg-13.1build2) ... Setting up libgs10:armhf (10.02.1~dfsg1-0ubuntu6) ... Setting up dh-python (6.20240401) ... Setting up graphviz (2.42.2-9build1) ... Setting up ghostscript (10.02.1~dfsg1-0ubuntu6) ... Setting up texlive-latex-base (2023.20240207-1) ... Setting up texlive-latex-recommended (2023.20240207-1) ... Setting up texlive-pictures (2023.20240207-1) ... Setting up libopencv-core-dev:armhf (4.6.0+dfsg-13.1build2) ... Setting up texlive-latex-extra (2023.20240207-1) ... Setting up libdlib-dev:armhf (19.24+dfsg-1.1build1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for systemd (255.4-1ubuntu6) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:37 UTC 2024 arm64 (armv7l) Toolchain package versions: binutils_2.42-4ubuntu2 dpkg-dev_1.22.6ubuntu6 g++-13_13.2.0-23ubuntu3 gcc-13_13.2.0-23ubuntu3 libc6-dev_2.39-0ubuntu8 libstdc++-13-dev_13.2.0-23ubuntu3 libstdc++6_14-20240330-1ubuntu2 linux-libc-dev_6.8.0-20.20 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.14build2 apt-utils_2.7.14build2 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu1 autotools-dev_20220109.1 base-files_13ubuntu9 base-passwd_3.6.3 bash_5.2.21-2ubuntu4 bash-completion_1:2.11-8 binutils_2.42-4ubuntu2 binutils-arm-linux-gnueabihf_2.42-4ubuntu2 binutils-common_2.42-4ubuntu2 bsdextrautils_2.39.3-9ubuntu4 bsdutils_1:2.39.3-9ubuntu4 build-essential_12.10ubuntu1 bzip2_1.0.8-5.1 ca-certificates_20240203 coreutils_9.4-3ubuntu5 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-23ubuntu3 cpp-13-arm-linux-gnueabihf_13.2.0-23ubuntu3 cpp-arm-linux-gnueabihf_4:13.2.0-7ubuntu1 cthreadpool-dev_0.0+git20231218.4eb5a69-1build1 dash_0.5.12-6ubuntu5 debconf_1.5.86 debconf-i18n_1.5.86 debhelper_13.14.1ubuntu5 debianutils_5.17build1 debugedit_1:5.0-5build1 dh-autoreconf_20 dh-python_6.20240401 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 doxygen_1.9.8+ds-2build5 dpkg_1.22.6ubuntu6 dpkg-dev_1.22.6ubuntu6 dwz_0.15-1build6 e2fsprogs_1.47.0-2.4~exp1ubuntu3 fakeroot_1.33-1 file_1:5.45-3build1 findutils_4.9.0-5 fontconfig_2.15.0-1.1ubuntu2 fontconfig-config_2.15.0-1.1ubuntu2 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 fonts-lmodern_2.005-1 fonts-urw-base35_20200910-8 g++_4:13.2.0-7ubuntu1 g++-13_13.2.0-23ubuntu3 g++-13-arm-linux-gnueabihf_13.2.0-23ubuntu3 g++-arm-linux-gnueabihf_4:13.2.0-7ubuntu1 gcc_4:13.2.0-7ubuntu1 gcc-13_13.2.0-23ubuntu3 gcc-13-arm-linux-gnueabihf_13.2.0-23ubuntu3 gcc-13-base_13.2.0-23ubuntu3 gcc-14-base_14-20240330-1ubuntu2 gcc-arm-linux-gnueabihf_4:13.2.0-7ubuntu1 gengetopt_2.23+dfsg1-1 gettext_0.21-14ubuntu1 gettext-base_0.21-14ubuntu1 ghostscript_10.02.1~dfsg1-0ubuntu6 gpg_2.4.4-2ubuntu16 gpg-agent_2.4.4-2ubuntu16 gpgconf_2.4.4-2ubuntu16 gpgv_2.4.4-2ubuntu16 graphviz_2.42.2-9build1 grep_3.11-4 groff-base_1.23.0-3build2 gzip_1.12-1ubuntu2 help2man_1.49.3 hostname_3.23+nmu2ubuntu1 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-6ubuntu2 libacl1_2.3.2-1 libapache-pom-java_29-2 libapparmor1_4.0.0-beta3-0ubuntu3 libapt-pkg6.0t64_2.7.14build2 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-4 libasan8_14-20240330-1ubuntu2 libassuan0_2.5.6-1 libatomic1_14-20240330-1ubuntu2 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2.1build1 libaudit1_1:3.1.2-2.1build1 libavahi-client3_0.8-13ubuntu5 libavahi-common-data_0.8-13ubuntu5 libavahi-common3_0.8-13ubuntu5 libbinutils_2.42-4ubuntu2 libblas-dev_3.12.0-3 libblas3_3.12.0-3 libblkid1_2.39.3-9ubuntu4 libbrotli1_1.1.0-2build2 libbsd0_0.12.1-1build1 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 libcairo2_1.18.0-3 libcap-ng0_0.8.4-2build2 libcap2_1:2.66-5ubuntu1 libcc1-0_14-20240330-1ubuntu2 libcdt5_2.42.2-9build1 libcgraph6_2.42.2-9build1 libclang-cpp18_1:18.1.2-1ubuntu3 libclang1-18_1:18.1.2-1ubuntu3 libcom-err2_1.47.0-2.4~exp1ubuntu3 libcommons-logging-java_1.3.0-1ubuntu1 libcommons-parent-java_56-1 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libcryptsetup12_2:2.7.0-1ubuntu3 libctf-nobfd0_2.42-4ubuntu2 libctf0_2.42-4ubuntu2 libcups2t64_2.4.7-1.2ubuntu3 libdatrie1_0.2.13-3 libdb5.3t64_5.3.28+dfsg2-6build1 libdbus-1-3_1.14.10-4ubuntu3 libdebconfclient0_0.271ubuntu3 libdebhelper-perl_13.14.1ubuntu5 libdeflate0_1.19-1 libdevmapper1.02.1_2:1.02.185-3ubuntu3 libdlib-data_19.24+dfsg-1.1build1 libdlib-dev_19.24+dfsg-1.1build1 libdlib19.1t64_19.24+dfsg-1.1build1 libdpkg-perl_1.22.6ubuntu6 libdrm-amdgpu1_2.4.120-2 libdrm-common_2.4.120-2 libdrm-nouveau2_2.4.120-2 libdrm-radeon1_2.4.120-2 libdrm2_2.4.120-2 libdw1t64_0.190-1.1build3 libedit2_3.1-20230828-1 libelf1t64_0.190-1.1build3 libexpat1_2.6.1-2build1 libexpat1-dev_2.6.1-2build1 libext2fs2t64_1.47.0-2.4~exp1ubuntu3 libfakeroot_1.33-1 libfdisk1_2.39.3-9ubuntu4 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.13.1-1 libfmt9_9.1.0+ds1-2 libfontbox-java_1:1.8.16-5 libfontconfig1_2.15.0-1.1ubuntu2 libfontenc1_1:1.1.8-1build1 libfreetype6_2.13.2+dfsg-1build3 libfribidi0_1.0.13-3 libgcc-13-dev_13.2.0-23ubuntu3 libgcc-s1_14-20240330-1ubuntu2 libgcrypt20_1.10.3-2 libgd3_2.3.3-9ubuntu4 libgdbm-compat4t64_1.23-5.1build1 libgdbm6t64_1.23-5.1build1 libgfortran5_14-20240330-1ubuntu2 libgl1-mesa-dri_24.0.3-1ubuntu4 libglapi-mesa_24.0.3-1ubuntu4 libglib2.0-0t64_2.80.0-6ubuntu1 libglvnd0_1.7.0-1 libglx-mesa0_24.0.3-1ubuntu4 libglx0_1.7.0-1 libgmp-dev_2:6.3.0+dfsg-2ubuntu4 libgmp10_2:6.3.0+dfsg-2ubuntu4 libgmpxx4ldbl_2:6.3.0+dfsg-2ubuntu4 libgnutls30t64_3.8.3-1.1ubuntu3 libgomp1_14-20240330-1ubuntu2 libgpg-error-l10n_1.47-3build1 libgpg-error0_1.47-3build1 libgpm2_1.20.7-11 libgraphite2-3_1.3.14-2 libgs-common_10.02.1~dfsg1-0ubuntu6 libgs10_10.02.1~dfsg1-0ubuntu6 libgs10-common_10.02.1~dfsg1-0ubuntu6 libgsl-dev_2.7.1+dfsg-6ubuntu1 libgsl27_2.7.1+dfsg-6ubuntu1 libgslcblas0_2.7.1+dfsg-6ubuntu1 libgssapi-krb5-2_1.20.1-6ubuntu2 libgts-0.7-5t64_0.7.6+darcs121130-5.2build1 libgvc6_2.42.2-9build1 libgvpr2_2.42.2-9build1 libharfbuzz0b_8.3.0-2build2 libhogweed6t64_3.9.1-2.2build1 libhwloc15_2.10.0-1 libice6_2:1.0.10-1build2 libicu74_74.2-1ubuntu1 libidn12_1.42-1 libidn2-0_2.3.7-2 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libtexlua53-5_2023.20230311.66589-9build3 libtext-charwidth-perl_0.04-11build3 libtext-iconv-perl_1.7-8build3 libtext-unidecode-perl_1.30-3 libtext-wrapi18n-perl_0.06-10 libthai-data_0.1.29-2 libthai0_0.1.29-2 libtiff6_4.5.1+git230720-4ubuntu2 libtinfo6_6.4+20240113-1ubuntu1 libtirpc-common_1.3.4+ds-1.1build1 libtirpc-dev_1.3.4+ds-1.1build1 libtirpc3t64_1.3.4+ds-1.1build1 libtool_2.4.7-7 libubsan1_14-20240330-1ubuntu2 libuchardet0_0.0.8-1 libudev1_255.4-1ubuntu6 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.3-9ubuntu4 libvulkan1_1.3.275.0-1 libwebp7_1.3.2-0.4build3 libx11-6_2:1.8.7-1 libx11-data_2:1.8.7-1 libx11-dev_2:1.8.7-1 libx11-xcb1_2:1.8.7-1 libxapian30_1.4.22-1 libxau-dev_1:1.0.9-1build5 libxau6_1:1.0.9-1build5 libxaw7_2:1.0.14-1build2 libxcb-dri2-0_1.15-1 libxcb-dri3-0_1.15-1 libxcb-glx0_1.15-1 libxcb-present0_1.15-1 libxcb-randr0_1.15-1 libxcb-render0_1.15-1 libxcb-shm0_1.15-1 libxcb-sync1_1.15-1 libxcb-xfixes0_1.15-1 libxcb1_1.15-1 libxcb1-dev_1.15-1 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perl-base_5.38.2-3.2build1 perl-doc_5.38.2-3.2build1 perl-modules-5.36_5.36.0-9ubuntu1 perl-modules-5.38_5.38.2-3.2build1 pinentry-curses_1.2.1-3ubuntu5 pkg-config_1.8.1-2 pkgbinarymangler_154 pkgconf_1.8.1-2 pkgconf-bin_1.8.1-2 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 poppler-data_0.4.12-1 preview-latex-style_13.2-1 procps_2:4.0.4-4ubuntu3 psmisc_23.7-1build1 pybind11-dev_2.11.1-2 python3_3.12.2-0ubuntu2 python3-dev_3.12.2-0ubuntu2 python3-minimal_3.12.2-0ubuntu2 python3-pkg-resources_68.1.2-2ubuntu1 python3-setuptools_68.1.2-2ubuntu1 python3.12_3.12.2-5ubuntu3 python3.12-dev_3.12.2-5ubuntu3 python3.12-minimal_3.12.2-5ubuntu3 readline-common_8.2-4build1 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 swig_4.2.0-2ubuntu1 systemd_255.4-1ubuntu6 systemd-dev_255.4-1ubuntu6 systemd-sysv_255.4-1ubuntu6 sysvinit-utils_3.08-6ubuntu2 t1utils_1.41-4build2 tar_1.35+dfsg-3 tex-common_6.18 texinfo_7.1-3build2 texinfo-lib_7.1-3build2 texlive-base_2023.20240207-1 texlive-binaries_2023.20230311.66589-9build3 texlive-latex-base_2023.20240207-1 texlive-latex-extra_2023.20240207-1 texlive-latex-recommended_2023.20240207-1 texlive-pictures_2023.20240207-1 tzdata_2024a-1ubuntu1 ubuntu-keyring_2023.11.28.1 ucf_3.0043+nmu1 util-linux_2.39.3-9ubuntu4 uuid-runtime_2.39.3-9ubuntu4 x11-common_1:7.7+23ubuntu2 x11proto-dev_2023.2-1 xdg-utils_1.1.3-4.1ubuntu3 xfonts-encodings_1:1.0.5-0ubuntu2 xfonts-utils_1:7.7+6build2 xorg-sgml-doctools_1:1.11-1.1 xtrans-dev_1.4.0-1 xxd_2:9.1.0016-1ubuntu7 xz-utils_5.6.1+really5.4.5-1 zlib1g_1:1.3.dfsg-3.1ubuntu2 zlib1g-dev_1:1.3.dfsg-3.1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: vienna-rna Binary: vienna-rna, python3-rna, librna-perl Architecture: any Version: 2.5.1+dfsg-1build3 Maintainer: Ubuntu Developers Uploaders: Olivier Sallou , Steffen Moeller Homepage: https://www.tbi.univie.ac.at/RNA/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/vienna-rna Vcs-Git: https://salsa.debian.org/med-team/vienna-rna.git Build-Depends: debhelper-compat (= 13), dh-python, python3-dev, pkg-config, libtool, gettext, swig (>= 4.0.2), perl-doc, perl, graphviz, libdlib-dev, libgsl-dev, liblapack-dev, libmpfr-dev, libsvm-dev, xxd, texlive-latex-extra, help2man, gengetopt, cthreadpool-dev, ghostscript, doxygen, texinfo Package-List: librna-perl deb non-free/perl optional arch=any python3-rna deb non-free/python optional arch=any vienna-rna deb non-free/science optional arch=any Checksums-Sha1: 3a4f05befe16b0cfbd319e122311cb9ff2fcaadb 20223836 vienna-rna_2.5.1+dfsg.orig.tar.xz 9a860c2d2f58cfc04613d867b70dbb1745f598c1 11888 vienna-rna_2.5.1+dfsg-1build3.debian.tar.xz Checksums-Sha256: 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space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-27999130 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27999130 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27999130 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 vienna-rna dpkg-buildpackage: info: source version 2.5.1+dfsg-1build3 dpkg-buildpackage: info: source distribution noble dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean rm -f doc/RNAlib* rm -f doc/*.db rm -f interfaces/Perl/Makefile.perl.old rm -f interfaces/Python/install.record rm -rf doc/html rm -rf doc/latex rm -rf src/cthreadpool #find . \( -type f -a \( -name config.status -o -name config.sub -o -name config.guess \) \) -delete find src/ViennaRNA -name "*.hex" -delete find . -name "*eps-converted-to.pdf" -delete rm -f src/bin/RNAfold_cmdl.[ch] rm -f aclocal.m4 src/Kinfold/aclocal.m4 grep -rl "DO NOT MODIFY THIS FILE! It was generated by help2man" man | xargs -r rm -f grep -lri "DO NOT EDIT THIS FILE." src | grep -v debian | xargs -r rm grep -lri "File autogenerated by gengetopt" src | grep -v debian | xargs -r rm grep -lri "Generated from configure.ac" . | grep -v debian | xargs -r rm grep -lri "generated by GNU Gengetopt" . | grep -v debian | xargs -r rm grep -lri "DO NOT MODIFY THIS FILE" man | grep -v debian | xargs -r rm grep -lri "made by GNU Bison" src | grep -v debian | xargs -r rm grep -lri "produced by makeinfo version" man | grep -v debian | xargs -r rm #rm -f src/Kinfold/INSTALL src/RNAforester/INSTALL src/RNAlocmin/RNAlocmin # removal of self-added symbolic links rm -rf src/cthreadpool/ find . -name Makefile.in -delete #rm -f config/ar-lib config/compile config/depcomp config/install-sh config/ltmain.sh config/missing config/test-driver config/texinfo.tex rm -f configure rm -f m4/libtool.m4 rm -f src/{RNAforester,RNAlocmin,Kinfold,Kinwalker}/{compile,depcomp,install-sh,missing,aclocal.m4,ylwrap} rm -f src/{Kinwalker,RNAforester}/{aclocal.m4,ylwrap,install-sh rm -f src/Kinfold/config.guess src/Kinfold/config.sub src/Kinfold/configure rm -f src/Kinwalker/configure rm -f src/RNAforester/configure src/RNAforester/g2-0.72/configure rm -f src/RNAlocmin/config.guess src/RNAlocmin/config.sub src/RNAlocmin/configure rm -f config/ltmain.sh src/Kinfold/INSTALL src/RNAforester/INSTALL # removing self-created man pages find man/ -name "*.1" -delete make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-arch --with python3 dh_update_autotools_config -a dh_autoreconf -a configure.ac:17: installing './compile' configure.ac:28: installing './config.guess' configure.ac:28: installing './config.sub' configure.ac:11: installing './install-sh' configure.ac:11: installing './missing' Makefile.am: installing './depcomp' configure.ac:14: installing './compile' configure.ac:7: installing './install-sh' configure.ac:7: installing './missing' Makefile.am: installing './INSTALL' src/Makefile.am: installing './depcomp' configure.ac: installing './ylwrap' configure.ac:14: installing './compile' configure.ac:4: installing './install-sh' configure.ac:4: installing './missing' Makefile.am: installing './depcomp' configure.ac:11: installing './compile' configure.ac:19: installing './config.guess' configure.ac:19: installing './config.sub' configure.ac:14: installing './install-sh' configure.ac:14: installing './missing' Makefile.am: installing './depcomp' libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'. libtoolize: copying file 'config/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:39: warning: The macro `AC_PROG_CC_C99' is obsolete. configure.ac:39: You should run autoupdate. ./lib/autoconf/c.m4:1659: AC_PROG_CC_C99 is expanded from... configure.ac:39: the top level configure.ac:48: installing 'config/ar-lib' configure.ac:15: installing 'config/compile' configure.ac:32: installing 'config/config.guess' configure.ac:32: installing 'config/config.sub' configure.ac:21: installing 'config/install-sh' configure.ac:21: installing 'config/missing' configure.ac:82: installing 'config/tap-driver.sh' interfaces/Perl/Makefile.am: installing 'config/depcomp' man/Makefile.am:5: installing 'config/texinfo.tex' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' CFLAGS="-I/usr/include/json-c/ -I/usr/include/libsvm/" \ CXXFLAGS="-I/usr/include/json-c/ -I/usr/include/libsvm/" \ dh_auto_configure -- \ --with-cluster \ --without-python2 \ --with-python \ --without-forester \ --without-doc \ --without-tutorial ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-cluster --without-python2 --with-python --without-forester --without-doc --without-tutorial checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for wchar.h... yes checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking whether _XOPEN_SOURCE should be defined... no checking whether make supports nested variables... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether UID '2001' is supported by ustar format... yes checking whether GID '2501' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking dependency style of gcc... none checking if malloc debugging is wanted... no checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for gcc... 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(cached) yes checking for asprintf... yes checking for vasprintf... yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking for inline... inline checking for pdflatex... /usr/bin/pdflatex checking for bibtex... /usr/bin/bibtex checking for makeindex... /usr/bin/makeindex checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for C compiler vendor... gnu checking for perl... /usr/bin/perl checking whether C compiler accepts -fno-strict-aliasing... yes checking whether C++ compiler accepts -fno-strict-aliasing... yes checking whether the linker accepts -fno-strict-aliasing... yes checking whether the C compiler allows unnamed unions of unnamed structs... yes checking whether the C++ compiler allows unnamed unions of unnamed structs... yes checking whether C compiler accepts -flto... yes checking whether C++ compiler accepts -flto... yes checking whether C compiler accepts -ffat-lto-objects... yes checking whether C++ compiler accepts -ffat-lto-objects... yes configure: WARNING: Trying to re-set ar/ranlib/nm to compiler specific wrappers checking for gcc-ar... gcc-ar checking for gcc-ranlib... gcc-ranlib checking for gcc-nm... gcc-nm checking whether the linker supports Link time Optimization (LTO)... yes checking for ./src/libsvm-3.25/svm.cpp... no checking for ./src/libsvm-3.25/svm.h... no checking for ./src/json/json.c... no checking for ./src/json/json.h... no checking for cblas_dgemm in -lgslcblas... yes checking for gsl_blas_dgemm in -lgsl... yes checking for OpenMP flag of C compiler... -fopenmp checking for OpenMP flag of C++ compiler... -fopenmp checking whether gcc is Clang... no checking whether pthreads work with "-pthread" and "-lpthread"... yes checking for joinable pthread attribute... 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/usr/bin/egrep checking for perl... /usr/bin/perl checking for htlatex... no checking for LaTeX package(s) babel fancyhdr geometry hyperref inputenc lastpage xcolor... yes checking for check >= 0.9.4... no configure: WARNING: check not found -- will not build C-library Unit tests checking for diff... /usr/bin/diff checking for xxd... /usr/bin/xxd checking for gengetopt... /usr/bin/gengetopt checking for help2man... /usr/bin/help2man checking whether g++ supports C++11 features with -std=c++11... yes checking for ./src/Kinfold/Makefile.am... yes checking for ./src/Cluster/Makefile.am... yes checking for ./src/RNAlocmin/Makefile.am... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating packaging/macosx/Makefile config.status: creating packaging/macosx/Distribution.xml config.status: creating packaging/macosx/resources/welcome.txt config.status: creating src/ViennaRNA/plotting/naview/Makefile config.status: creating interfaces/Perl/Makefile config.status: creating interfaces/Perl/version.i config.status: creating interfaces/Python/Makefile config.status: creating interfaces/Python/version.i config.status: creating tests/Makefile config.status: creating tests/RNApath.py config.status: creating tests/RNAHelpers.pm config.status: creating tests/test-env.sh config.status: creating src/ViennaRNA/static/templates_postscript.h config.status: creating src/ViennaRNA/static/templates_svg.h config.status: creating src/ViennaRNA/static/energy_parameter_sets.h config.status: creating src/Cluster/Makefile config.status: creating src/ViennaRNA/vrna_config.h config.status: creating misc/Makefile config.status: creating interfaces/Makefile config.status: creating Makefile config.status: creating RNAlib2.pc config.status: creating src/Utils/Makefile config.status: creating src/bin/Makefile config.status: creating src/Makefile config.status: creating src/ViennaRNA/Makefile config.status: creating src/ViennaRNA/static/Makefile config.status: creating man/Makefile config.status: creating doc/Makefile config.status: creating doc/CLA/Makefile config.status: creating RNA-Tutorial/Makefile config.status: creating man/cmdlopt.sh config.status: creating examples/Makefile config.status: creating packaging/viennarna.spec config.status: creating packaging/PKGBUILD config.status: creating packaging/win_installer_archlinux_i686.nsi config.status: creating packaging/win_installer_archlinux_x86_64.nsi config.status: creating packaging/win_installer_fedora_i686.nsi config.status: creating packaging/win_installer_fedora_x86_64.nsi config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands === configuring in src/Kinfold (/<>/src/Kinfold) configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr' '--build=arm-linux-gnueabihf' '--includedir=${prefix}/include' '--mandir=${prefix}/share/man' '--infodir=${prefix}/share/info' '--sysconfdir=/etc' '--localstatedir=/var' '--disable-silent-rules' '--libdir=${prefix}/lib/arm-linux-gnueabihf' '--runstatedir=/run' '--disable-maintainer-mode' '--disable-dependency-tracking' '--with-cluster' '--without-python2' '--with-python' '--without-forester' '--without-doc' '--without-tutorial' 'build_alias=arm-linux-gnueabihf' 'CFLAGS=-I/usr/include/json-c/ -I/usr/include/libsvm/' 'LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro' 'CPPFLAGS=-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3' 'CXXFLAGS=-I/usr/include/json-c/ -I/usr/include/libsvm/' 'CC=gcc' 'CXX=g++' 'AR=gcc-ar' 'RANLIB=gcc-ranlib' 'NM=gcc-nm' 'VRNA_CFLAGS=-I$(top_srcdir)/../../src/ViennaRNA -I$(top_srcdir)/../../src -DVRNA_WITH_NAVIEW_LAYOUT' 'VRNA_LIBS=-fno-strict-aliasing -flto -L$(top_builddir)/../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp' --cache-file=/dev/null --srcdir=. checking whether make supports nested variables... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking if malloc debugging is wanted... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking for strdup... yes checking for memset... yes checking for strchr... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for RNAlib2 >= 2.2.0... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes ./configure: line 4958: #include: command not found checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for exp in -lm... yes checking for an ANSI C-conforming const... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Example/Makefile config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands === configuring in src/RNAlocmin (/<>/src/RNAlocmin) configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr' '--build=arm-linux-gnueabihf' '--includedir=${prefix}/include' '--mandir=${prefix}/share/man' '--infodir=${prefix}/share/info' '--sysconfdir=/etc' '--localstatedir=/var' '--disable-silent-rules' '--libdir=${prefix}/lib/arm-linux-gnueabihf' '--runstatedir=/run' '--disable-maintainer-mode' '--disable-dependency-tracking' '--with-cluster' '--without-python2' '--with-python' '--without-forester' '--without-doc' '--without-tutorial' 'build_alias=arm-linux-gnueabihf' 'CFLAGS=-I/usr/include/json-c/ -I/usr/include/libsvm/' 'LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro' 'CPPFLAGS=-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3' 'CXXFLAGS=-I/usr/include/json-c/ -I/usr/include/libsvm/' 'CC=gcc' 'CXX=g++' 'AR=gcc-ar' 'RANLIB=gcc-ranlib' 'NM=gcc-nm' 'VRNA_CFLAGS=-I$(top_srcdir)/../../src/ViennaRNA -I$(top_srcdir)/../../src -DVRNA_WITH_NAVIEW_LAYOUT' 'VRNA_LIBS=-fno-strict-aliasing -flto -L$(top_builddir)/../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp' --cache-file=/dev/null --srcdir=. checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for wchar.h... yes checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking whether _XOPEN_SOURCE should be defined... no checking whether make supports nested variables... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking how to run the C preprocessor... gcc -E checking whether g++ supports C++11 features by default... yes checking for strchr... yes checking for strdup... yes checking for strtol... yes checking for limits.h... yes checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for inline... inline checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking for working strtod... yes checking for size_t... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for RNAlib2... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands configure: ====================================== ViennaRNA Package 2.5.1 ====================================== Successfully configured with the following options: Sub Packages ------------ * Kinfold : yes * RNAforester : no * Analyse{Dists,Seqs} : yes * RNAlocmin : yes * Kinwalker : no Extra Libraries --------------- * Support Vector Machine : no * GNU Scientific Library : yes * GNU MPFR : yes * JSON : no Features -------- * Use hash for NR Sampling : no * C11 features : yes * TTY colors : yes * Float Precision(PF} : no * Deprecation Warnings : no Optimizations ------------- * Auto Vectorization : yes * Explicit SIMD Extension : yes * Link Time Optimization : yes * POSIX Threads : yes * OpenMP : yes Scripting Language Interfaces ----------------------------- * Perl 5 : yes * Python 3.x : yes * Python 2.x : no Documentation ------------- * Reference Manual (PDF) : no * Reference Manual (HTML) : no * Tutorial (PDF) : no * Tutorial (HTML) : no * CLA (PDF) : yes Unit Tests ---------- * Executable Programs : yes * C-Library : no * Perl 5 Interface : yes * Python 3.x Interface : yes * Python 2.x Interface : no MacOS X ------- * Universal Binary : no * Installer : no * SDK : no Install Directories ------------------- * Executables : /usr/bin * Libraries : /usr/lib/arm-linux-gnueabihf * Header files : /usr/include * Extra Data : /usr/share * Man pages : /usr/share/man * Documentation : Not to be installed (HTML) : (PDF) : * Perl5 Interface : (binaries) : /usr/lib/arm-linux-gnueabihf/perl/5.38.2 (scripts) : /usr/share/perl/5.38.2 * Python 3.x Interface : (binaries) : /usr/lib/python3.12/site-packages (scripts) : /usr/lib/python3.12/site-packages * Python 2.x Interface : Not to be installed (binaries) : (scripts) : You can run 'make', 'make check', and 'make install' now! if [ -r man/help2manWrapper.sh ] \ ; then chmod +x man/help2manWrapper.sh \ ; fi make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' if [ ! -d src/cthreadpool ]; then \ mkdir -p src/cthreadpool && \ cd src/cthreadpool && \ ln -s /usr/include/cthreadpool/thpool.h . && \ ln -s /usr/share/cthreadpool/thpool.c . ; \ fi dh_auto_build make -j4 make[2]: Entering directory '/<>' make all-recursive make[3]: Entering directory '/<>' Making all in src make[4]: Entering directory '/<>/src' Making all in ViennaRNA make[5]: Entering directory '/<>/src/ViennaRNA' Making all in static make[6]: Entering directory '/<>/src/ViennaRNA/static' /usr/bin/xxd -i < postscript/structure_plot_macro_base.ps > postscript/structure_plot_macro_base.hex && echo ',0x00' >> postscript/structure_plot_macro_base.hex /usr/bin/xxd -i < postscript/structure_plot_macro_extras.ps > postscript/structure_plot_macro_extras.hex && echo ',0x00' >> postscript/structure_plot_macro_extras.hex /usr/bin/xxd -i < postscript/dot_plot_macro_base.ps > postscript/dot_plot_macro_base.hex && echo ',0x00' >> postscript/dot_plot_macro_base.hex /usr/bin/xxd -i < postscript/dot_plot_macro_turn.ps > postscript/dot_plot_macro_turn.hex && echo ',0x00' >> postscript/dot_plot_macro_turn.hex /usr/bin/xxd -i < postscript/dot_plot_macro_sd.ps > postscript/dot_plot_macro_sd.hex && echo ',0x00' >> postscript/dot_plot_macro_sd.hex /usr/bin/xxd -i < postscript/dot_plot_macro_ud.ps > postscript/dot_plot_macro_ud.hex && echo ',0x00' >> postscript/dot_plot_macro_ud.hex /usr/bin/xxd -i < postscript/dot_plot_macro_sc_motifs.ps > postscript/dot_plot_macro_sc_motifs.hex && echo ',0x00' >> postscript/dot_plot_macro_sc_motifs.hex /usr/bin/xxd -i < postscript/dot_plot_macro_linear_data.ps > postscript/dot_plot_macro_linear_data.hex && echo ',0x00' >> postscript/dot_plot_macro_linear_data.hex /usr/bin/xxd -i < postscript/aln_macro_base.ps > postscript/aln_macro_base.hex && echo ',0x00' >> postscript/aln_macro_base.hex /usr/bin/xxd -i < svg/structure_plot_header.svg > svg/structure_plot_header.hex && echo ',0x00' >> svg/structure_plot_header.hex /usr/bin/xxd -i < svg/structure_plot_footer.svg > svg/structure_plot_footer.hex && echo ',0x00' >> svg/structure_plot_footer.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/dna_mathews1999.par > misc/dna_mathews1999.hex && echo ',0x00' >> misc/dna_mathews1999.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/dna_mathews2004.par > misc/dna_mathews2004.hex && echo ',0x00' >> misc/dna_mathews2004.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/rna_andronescu2007.par > misc/rna_andronescu2007.hex && echo ',0x00' >> misc/rna_andronescu2007.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/rna_langdon2018.par > misc/rna_langdon2018.hex && echo ',0x00' >> misc/rna_langdon2018.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/rna_misc_special_hairpins.par > misc/rna_misc_special_hairpins.hex && echo ',0x00' >> misc/rna_misc_special_hairpins.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/rna_turner1999.par > misc/rna_turner1999.hex && echo ',0x00' >> misc/rna_turner1999.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/rna_turner2004.par > misc/rna_turner2004.hex && echo ',0x00' >> misc/rna_turner2004.hex make all-am make[7]: Entering directory '/<>/src/ViennaRNA/static' make[7]: Nothing to be done for 'all-am'. make[7]: Leaving directory '/<>/src/ViennaRNA/static' make[6]: Leaving directory '/<>/src/ViennaRNA/static' Making all in plotting/naview make[6]: Entering directory '/<>/src/ViennaRNA/plotting/naview' /bin/bash ../../../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o naview.lo naview.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c naview.c -fPIC -DPIC -o .libs/naview.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c naview.c -fPIC -DPIC -o naview.o >/dev/null 2>&1 /bin/bash ../../../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o libRNA_naview.la naview.lo -lgsl -lgslcblas -lm libtool: link: gcc-ar cr .libs/libRNA_naview.a .libs/naview.o libtool: link: gcc-ranlib .libs/libRNA_naview.a libtool: link: ( cd ".libs" && rm -f "libRNA_naview.la" && ln -s "../libRNA_naview.la" "libRNA_naview.la" ) make[6]: Leaving directory '/<>/src/ViennaRNA/plotting/naview' make[6]: Entering directory '/<>/src/ViennaRNA' /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o fold_compound.lo fold_compound.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o dist_vars.lo dist_vars.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o part_func.lo part_func.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o part_func_wrappers.lo part_func_wrappers.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c part_func.c -fPIC -DPIC -o .libs/part_func.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c part_func_wrappers.c -fPIC -DPIC -o .libs/part_func_wrappers.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c fold_compound.c -fPIC -DPIC -o .libs/fold_compound.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c dist_vars.c -fPIC -DPIC -o .libs/dist_vars.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c dist_vars.c -fPIC -DPIC -o dist_vars.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c part_func_wrappers.c -fPIC -DPIC -o part_func_wrappers.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o pf_fold.lo pf_fold.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o pf_multifold.lo pf_multifold.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c pf_fold.c -fPIC -DPIC -o .libs/pf_fold.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c fold_compound.c -fPIC -DPIC -o fold_compound.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c part_func.c -fPIC -DPIC -o part_func.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c pf_multifold.c -fPIC -DPIC -o .libs/pf_multifold.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o treedist.lo treedist.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c pf_multifold.c -fPIC -DPIC -o pf_multifold.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c pf_fold.c -fPIC -DPIC -o pf_fold.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o inverse.lo inverse.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o ProfileDist.lo ProfileDist.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c treedist.c -fPIC -DPIC -o .libs/treedist.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAstruct.lo RNAstruct.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c inverse.c -fPIC -DPIC -o .libs/inverse.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c ProfileDist.c -fPIC -DPIC -o .libs/ProfileDist.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c treedist.c -fPIC -DPIC -o treedist.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c RNAstruct.c -fPIC -DPIC -o .libs/RNAstruct.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c ProfileDist.c -fPIC -DPIC -o ProfileDist.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o mfe.lo mfe.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c inverse.c -fPIC -DPIC -o inverse.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c RNAstruct.c -fPIC -DPIC -o RNAstruct.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c mfe.c -fPIC -DPIC -o .libs/mfe.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o mfe_window.lo mfe_window.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o mfe_wrappers.lo mfe_wrappers.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o mfe_window_wrappers.lo mfe_window_wrappers.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c mfe_window.c -fPIC -DPIC -o .libs/mfe_window.o mfe_window.c: In function ‘print_block_list’: mfe_window.c:1608:21: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 1608 | printf("block %lu: en=%d, start: %lu, end: %lu, shift: %lu\n", | ~~^ | | | long unsigned int | %u 1609 | cnt, | ~~~ | | | size_t {aka unsigned int} mfe_window.c:1614:13: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 1614 | printf("%lu blocks remaining\n", cnt); | ~~^ ~~~ | | | | long unsigned int size_t {aka unsigned int} | %u libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c mfe_wrappers.c -fPIC -DPIC -o .libs/mfe_wrappers.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c mfe_window_wrappers.c -fPIC -DPIC -o .libs/mfe_window_wrappers.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c mfe_window_wrappers.c -fPIC -DPIC -o mfe_window_wrappers.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c mfe_window.c -fPIC -DPIC -o mfe_window.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c mfe_wrappers.c -fPIC -DPIC -o mfe_wrappers.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c mfe.c -fPIC -DPIC -o mfe.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o fold.lo fold.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o stringdist.lo stringdist.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c fold.c -fPIC -DPIC -o .libs/fold.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c stringdist.c -fPIC -DPIC -o .libs/stringdist.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o subopt.lo subopt.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c fold.c -fPIC -DPIC -o fold.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c stringdist.c -fPIC -DPIC -o stringdist.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c subopt.c -fPIC -DPIC -o .libs/subopt.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o subopt_zuker.lo subopt_zuker.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o Lfold.lo Lfold.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o cofold.lo cofold.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c subopt_zuker.c -fPIC -DPIC -o .libs/subopt_zuker.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c Lfold.c -fPIC -DPIC -o .libs/Lfold.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c Lfold.c -fPIC -DPIC -o Lfold.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c cofold.c -fPIC -DPIC -o .libs/cofold.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c cofold.c -fPIC -DPIC -o cofold.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c subopt_zuker.c -fPIC -DPIC -o subopt_zuker.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o part_func_co.lo part_func_co.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c part_func_co.c -fPIC -DPIC -o .libs/part_func_co.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o ProfileAln.lo ProfileAln.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c subopt.c -fPIC -DPIC -o subopt.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o duplex.lo duplex.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c part_func_co.c -fPIC -DPIC -o part_func_co.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c ProfileAln.c -fPIC -DPIC -o .libs/ProfileAln.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c duplex.c -fPIC -DPIC -o .libs/duplex.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o alifold.lo alifold.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c ProfileAln.c -fPIC -DPIC -o ProfileAln.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c alifold.c -fPIC -DPIC -o .libs/alifold.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o alipfold.lo alipfold.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c alipfold.c -fPIC -DPIC -o .libs/alipfold.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c duplex.c -fPIC -DPIC -o duplex.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c alifold.c -fPIC -DPIC -o alifold.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c alipfold.c -fPIC -DPIC -o alipfold.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o LPfold.lo LPfold.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o part_func_up.lo part_func_up.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp 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-ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c part_func_up.c -fPIC -DPIC -o .libs/part_func_up.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c MEA.c -fPIC -DPIC -o .libs/MEA.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c ribo.c -fPIC -DPIC -o .libs/ribo.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c MEA.c -fPIC -DPIC -o MEA.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c LPfold.c -fPIC -DPIC -o LPfold.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c part_func_up.c -fPIC -DPIC -o part_func_up.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c ribo.c -fPIC -DPIC -o ribo.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o mm.lo mm.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c mm.c -fPIC -DPIC -o .libs/mm.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o 2Dfold.lo 2Dfold.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o 2Dpfold.lo 2Dpfold.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o plex_functions.lo plex_functions.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c 2Dfold.c -fPIC -DPIC -o .libs/2Dfold.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c mm.c -fPIC -DPIC -o mm.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c 2Dpfold.c -fPIC -DPIC -o .libs/2Dpfold.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c plex_functions.c -fPIC -DPIC -o .libs/plex_functions.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o ali_plex.lo ali_plex.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c ali_plex.c -fPIC -DPIC -o .libs/ali_plex.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c plex_functions.c -fPIC -DPIC -o plex_functions.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o c_plex.lo c_plex.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c c_plex.c -fPIC -DPIC -o .libs/c_plex.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c 2Dfold.c -fPIC -DPIC -o 2Dfold.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c 2Dpfold.c -fPIC -DPIC -o 2Dpfold.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c c_plex.c -fPIC -DPIC -o c_plex.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o plex.lo plex.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o snofold.lo snofold.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c plex.c -fPIC -DPIC -o .libs/plex.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c snofold.c -fPIC -DPIC -o .libs/snofold.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o snoop.lo snoop.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c snoop.c -fPIC -DPIC -o .libs/snoop.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c ali_plex.c -fPIC -DPIC -o ali_plex.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 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-DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c plex.c -fPIC -DPIC -o plex.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c snoop.c -fPIC -DPIC -o snoop.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c gquad.c -fPIC -DPIC -o gquad.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o perturbation_fold.lo perturbation_fold.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c perturbation_fold.c -fPIC -DPIC -o .libs/perturbation_fold.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp 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special_const.lo special_const.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o constraints/constraints.lo constraints/constraints.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c special_const.c -fPIC -DPIC -o .libs/special_const.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c move_set.c -fPIC -DPIC -o move_set.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c special_const.c -fPIC -DPIC -o special_const.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o constraints/SHAPE.lo constraints/SHAPE.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src 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-fPIC -DPIC -o constraints/.libs/SHAPE.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c constraints/constraints.c -fPIC -DPIC -o constraints/constraints.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c constraints/hard.c -fPIC -DPIC -o constraints/.libs/hard.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o constraints/soft.lo constraints/soft.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c constraints/soft.c -fPIC -DPIC -o constraints/.libs/soft.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c constraints/SHAPE.c -fPIC -DPIC -o constraints/SHAPE.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o constraints/ligand.lo constraints/ligand.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c constraints/hard.c -fPIC -DPIC -o constraints/hard.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c constraints/soft.c -fPIC -DPIC -o constraints/soft.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c constraints/ligand.c -fPIC -DPIC -o constraints/.libs/ligand.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c constraints/ligand.c -fPIC -DPIC -o constraints/ligand.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o datastructures/basic_datastructures.lo datastructures/basic_datastructures.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o datastructures/lists.lo datastructures/lists.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o datastructures/char_stream.lo datastructures/char_stream.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c datastructures/basic_datastructures.c -fPIC -DPIC -o datastructures/.libs/basic_datastructures.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c datastructures/lists.c -fPIC -DPIC -o datastructures/.libs/lists.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c datastructures/basic_datastructures.c -fPIC -DPIC -o datastructures/basic_datastructures.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c datastructures/lists.c -fPIC -DPIC -o datastructures/lists.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o datastructures/stream_output.lo datastructures/stream_output.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c datastructures/char_stream.c -fPIC -DPIC -o datastructures/.libs/char_stream.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o datastructures/hash_tables.lo datastructures/hash_tables.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE 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datastructures/.libs/heap.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c utils/utils.c -fPIC -DPIC -o utils/.libs/utils.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o utils/string_utils.lo utils/string_utils.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c datastructures/heap.c -fPIC -DPIC -o datastructures/heap.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c utils/string_utils.c -fPIC -DPIC -o utils/.libs/string_utils.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c utils/utils.c -fPIC -DPIC -o utils/utils.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. 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-I/usr/include/libsvm/ -c utils/string_utils.c -fPIC -DPIC -o utils/string_utils.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c utils/structure_utils.c -fPIC -DPIC -o utils/.libs/structure_utils.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c utils/structure_tree.c -fPIC -DPIC -o utils/.libs/structure_tree.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o utils/msa_utils.lo utils/msa_utils.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c utils/structure_tree.c -fPIC -DPIC -o utils/structure_tree.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c utils/msa_utils.c -fPIC -DPIC -o utils/.libs/msa_utils.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o utils/higher_order_functions.lo utils/higher_order_functions.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c utils/higher_order_functions.c -fPIC -DPIC -o utils/.libs/higher_order_functions.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c utils/structure_utils.c -fPIC -DPIC -o utils/structure_utils.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c utils/higher_order_functions.c -fPIC -DPIC -o utils/higher_order_functions.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c utils/msa_utils.c -fPIC -DPIC -o utils/msa_utils.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o utils/cpu.lo utils/cpu.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c utils/cpu.c -fPIC -DPIC -o utils/.libs/cpu.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o utils/units.lo utils/units.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c utils/cpu.c -fPIC -DPIC -o utils/cpu.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c utils/units.c -fPIC -DPIC -o utils/.libs/units.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o io/io_utils.lo io/io_utils.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o io/file_formats.lo io/file_formats.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c utils/units.c -fPIC -DPIC -o utils/units.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c io/io_utils.c -fPIC -DPIC -o io/.libs/io_utils.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c io/file_formats.c -fPIC -DPIC -o io/.libs/file_formats.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o io/file_formats_msa.lo io/file_formats_msa.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c io/io_utils.c -fPIC -DPIC -o io/io_utils.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c io/file_formats_msa.c -fPIC -DPIC -o io/.libs/file_formats_msa.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o search/BoyerMoore.lo search/BoyerMoore.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c io/file_formats.c -fPIC -DPIC -o io/file_formats.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c search/BoyerMoore.c -fPIC -DPIC -o search/.libs/BoyerMoore.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c io/file_formats_msa.c -fPIC -DPIC -o io/file_formats_msa.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c search/BoyerMoore.c -fPIC -DPIC -o search/BoyerMoore.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o plotting/alignments.lo plotting/alignments.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o plotting/layouts.lo plotting/layouts.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o plotting/probabilities.lo plotting/probabilities.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 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plotting/RNApuzzler/.libs/RNAturtle.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o params/io.lo params/io.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c plotting/RNApuzzler/RNAturtle.c -fPIC -DPIC -o plotting/RNApuzzler/RNAturtle.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c params/io.c -fPIC -DPIC -o params/.libs/io.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c plotting/RNApuzzler/RNApuzzler.c -fPIC -DPIC -o plotting/RNApuzzler/RNApuzzler.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o params/default.lo params/default.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c params/default.c -fPIC -DPIC -o params/.libs/default.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c params/default.c -fPIC -DPIC -o params/default.o >/dev/null 2>&1 libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -DDLIB_NO_GUI_SUPPORT -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c wrap_dlib.cpp -fPIC -DPIC -o libRNA_concentrations_la-wrap_dlib.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o params/params.lo params/params.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o params/convert.lo params/convert.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c params/params.c -fPIC -DPIC -o params/.libs/params.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c params/convert.c -fPIC -DPIC -o params/.libs/convert.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c params/params.c -fPIC -DPIC -o params/params.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c params/convert.c -fPIC -DPIC -o params/convert.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o libRNA_eval.la eval.lo eval_covariance.lo eval_wrappers.lo -lgsl -lgslcblas -lm /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o loops/external.lo loops/external.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c loops/external.c -fPIC -DPIC -o loops/.libs/external.o libtool: link: gcc-ar cr .libs/libRNA_eval.a .libs/eval.o .libs/eval_covariance.o .libs/eval_wrappers.o libtool: link: gcc-ranlib .libs/libRNA_eval.a libtool: link: ( cd ".libs" && rm -f "libRNA_eval.la" && ln -s "../libRNA_eval.la" "libRNA_eval.la" ) /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o loops/external_bt.lo loops/external_bt.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c loops/external_bt.c -fPIC -DPIC -o loops/.libs/external_bt.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c loops/external.c -fPIC -DPIC -o loops/external.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c loops/external_bt.c -fPIC -DPIC -o loops/external_bt.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o loops/external_pf.lo loops/external_pf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c loops/external_pf.c -fPIC -DPIC -o loops/.libs/external_pf.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o loops/hairpin.lo loops/hairpin.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c loops/hairpin.c -fPIC -DPIC -o loops/.libs/hairpin.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c params/io.c -fPIC -DPIC -o params/io.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c loops/hairpin.c -fPIC -DPIC -o loops/hairpin.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c loops/external_pf.c -fPIC -DPIC -o loops/external_pf.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time 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-DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o landscape/move.lo landscape/move.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c landscape/move.c -fPIC -DPIC -o landscape/.libs/move.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c landscape/move.c -fPIC -DPIC -o landscape/move.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o landscape/findpath.lo landscape/findpath.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o landscape/neighbor.lo landscape/neighbor.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing 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-I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o landscape/walk.lo landscape/walk.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c landscape/walk.c -fPIC -DPIC -o landscape/.libs/walk.o /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o libRNA_special_const.la special_const.lo -lgsl -lgslcblas -lm libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c landscape/walk.c -fPIC -DPIC -o landscape/walk.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CXX --mode=link g++ -std=c++11 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o libRNA_concentrations.la libRNA_concentrations_la-concentrations.lo libRNA_concentrations_la-wrap_dlib.lo -lgsl -lgslcblas -lm libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c landscape/neighbor.c -fPIC -DPIC -o landscape/neighbor.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o libRNA_constraints.la constraints/constraints.lo constraints/SHAPE.lo constraints/hard.lo constraints/soft.lo constraints/ligand.lo -lgsl -lgslcblas -lm libtool: link: gcc-ar cr .libs/libRNA_special_const.a .libs/special_const.o /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o libRNA_datastructures.la datastructures/basic_datastructures.lo datastructures/lists.lo datastructures/char_stream.lo datastructures/stream_output.lo datastructures/hash_tables.lo datastructures/heap.lo -lgsl -lgslcblas -lm libtool: link: gcc-ranlib .libs/libRNA_special_const.a libtool: link: ( cd ".libs" && rm -f "libRNA_special_const.la" && ln -s "../libRNA_special_const.la" "libRNA_special_const.la" ) /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o libRNA_utils.la utils/utils.lo utils/string_utils.lo utils/structure_utils.lo utils/structure_tree.lo utils/msa_utils.lo utils/higher_order_functions.lo utils/cpu.lo utils/units.lo io/io_utils.lo io/file_formats.lo io/file_formats_msa.lo search/BoyerMoore.lo commands.lo combinatorics.lo -lgsl -lgslcblas -lm libtool: link: gcc-ar cr .libs/libRNA_concentrations.a .libs/libRNA_concentrations_la-concentrations.o .libs/libRNA_concentrations_la-wrap_dlib.o libtool: link: gcc-ranlib .libs/libRNA_concentrations.a libtool: link: gcc-ar cr .libs/libRNA_constraints.a constraints/.libs/constraints.o constraints/.libs/SHAPE.o constraints/.libs/hard.o constraints/.libs/soft.o constraints/.libs/ligand.o libtool: link: ( cd ".libs" && rm -f "libRNA_concentrations.la" && ln -s "../libRNA_concentrations.la" "libRNA_concentrations.la" ) /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o libRNA_plotting.la plotting/alignments.lo plotting/layouts.lo plotting/probabilities.lo plotting/structures.lo plotting/plot_utils.lo plotting/RNApuzzler/RNApuzzler.lo plotting/RNApuzzler/RNAturtle.lo plotting/naview/libRNA_naview.la -lgsl -lgslcblas -lm libtool: link: gcc-ranlib .libs/libRNA_constraints.a libtool: link: ( cd ".libs" && rm -f "libRNA_constraints.la" && ln -s "../libRNA_constraints.la" "libRNA_constraints.la" ) /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o libRNA_params.la params/io.lo params/default.lo params/params.lo params/convert.lo -lgsl -lgslcblas -lm libtool: link: gcc-ar cr .libs/libRNA_datastructures.a datastructures/.libs/basic_datastructures.o datastructures/.libs/lists.o datastructures/.libs/char_stream.o datastructures/.libs/stream_output.o datastructures/.libs/hash_tables.o datastructures/.libs/heap.o libtool: link: gcc-ranlib .libs/libRNA_datastructures.a libtool: link: ( cd ".libs" && rm -f "libRNA_datastructures.la" && ln -s "../libRNA_datastructures.la" "libRNA_datastructures.la" ) /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o libRNA_loops.la loops/external.lo loops/external_bt.lo loops/external_pf.lo loops/hairpin.lo loops/hairpin_bt.lo loops/hairpin_pf.lo loops/internal.lo loops/internal_bt.lo loops/internal_pf.lo loops/multibranch.lo loops/multibranch_bt.lo loops/multibranch_pf.lo -lgsl -lgslcblas -lm libtool: link: gcc-ar cr .libs/libRNA_utils.a utils/.libs/utils.o utils/.libs/string_utils.o utils/.libs/structure_utils.o utils/.libs/structure_tree.o utils/.libs/msa_utils.o utils/.libs/higher_order_functions.o utils/.libs/cpu.o utils/.libs/units.o io/.libs/io_utils.o io/.libs/file_formats.o io/.libs/file_formats_msa.o search/.libs/BoyerMoore.o .libs/commands.o .libs/combinatorics.o libtool: link: gcc-ar cr .libs/libRNA_params.a params/.libs/io.o params/.libs/default.o params/.libs/params.o params/.libs/convert.o libtool: link: (cd .libs/libRNA_plotting.lax/libRNA_naview.a && gcc-ar x "/<>/src/ViennaRNA/plotting/naview/.libs/libRNA_naview.a") libtool: link: gcc-ranlib .libs/libRNA_utils.a libtool: link: gcc-ranlib .libs/libRNA_params.a libtool: link: ( cd ".libs" && rm -f "libRNA_utils.la" && ln -s "../libRNA_utils.la" "libRNA_utils.la" ) /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o libRNA_landscape.la move_set.lo landscape/move.lo landscape/findpath.lo landscape/neighbor.lo landscape/walk.lo -lgsl -lgslcblas -lm libtool: link: ( cd ".libs" && rm -f "libRNA_params.la" && ln -s "../libRNA_params.la" "libRNA_params.la" ) libtool: link: gcc-ar cr .libs/libRNA_plotting.a plotting/.libs/alignments.o plotting/.libs/layouts.o plotting/.libs/probabilities.o plotting/.libs/structures.o plotting/.libs/plot_utils.o plotting/RNApuzzler/.libs/RNApuzzler.o plotting/RNApuzzler/.libs/RNAturtle.o .libs/libRNA_plotting.lax/libRNA_naview.a/naview.o libtool: link: gcc-ranlib .libs/libRNA_plotting.a libtool: link: gcc-ar cr .libs/libRNA_loops.a loops/.libs/external.o loops/.libs/external_bt.o loops/.libs/external_pf.o loops/.libs/hairpin.o loops/.libs/hairpin_bt.o loops/.libs/hairpin_pf.o loops/.libs/internal.o loops/.libs/internal_bt.o loops/.libs/internal_pf.o loops/.libs/multibranch.o loops/.libs/multibranch_bt.o loops/.libs/multibranch_pf.o libtool: link: rm -fr .libs/libRNA_plotting.lax libtool: link: ( cd ".libs" && rm -f "libRNA_plotting.la" && ln -s "../libRNA_plotting.la" "libRNA_plotting.la" ) libtool: link: gcc-ranlib .libs/libRNA_loops.a libtool: link: ( cd ".libs" && rm -f "libRNA_loops.la" && ln -s "../libRNA_loops.la" "libRNA_loops.la" ) libtool: link: gcc-ar cr .libs/libRNA_landscape.a .libs/move_set.o landscape/.libs/move.o landscape/.libs/findpath.o landscape/.libs/neighbor.o landscape/.libs/walk.o libtool: link: gcc-ranlib .libs/libRNA_landscape.a libtool: link: ( cd ".libs" && rm -f "libRNA_landscape.la" && ln -s "../libRNA_landscape.la" "libRNA_landscape.la" ) /bin/bash ../../libtool --tag=CXX --mode=link g++ -std=c++11 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o libRNA_conv.la fold_compound.lo dist_vars.lo part_func.lo part_func_wrappers.lo pf_fold.lo pf_multifold.lo treedist.lo inverse.lo ProfileDist.lo RNAstruct.lo mfe.lo mfe_window.lo mfe_wrappers.lo mfe_window_wrappers.lo fold.lo stringdist.lo subopt.lo subopt_zuker.lo Lfold.lo cofold.lo part_func_co.lo ProfileAln.lo duplex.lo alifold.lo alipfold.lo LPfold.lo part_func_up.lo ribo.lo MEA.lo mm.lo 2Dfold.lo 2Dpfold.lo plex_functions.lo ali_plex.lo c_plex.lo plex.lo snofold.lo snoop.lo gquad.lo perturbation_fold.lo centroid.lo model.lo dp_matrices.lo boltzmann_sampling.lo bs_wrappers.lo equilibrium_probs.lo alphabet.lo sequence.lo unstructured_domains.lo grammar.lo heat_capacity.lo libRNA_concentrations.la libRNA_constraints.la libRNA_datastructures.la libRNA_utils.la libRNA_plotting.la libRNA_params.la libRNA_eval.la libRNA_loops.la libRNA_landscape.la -lgsl -lgslcblas -lm libtool: link: (cd .libs/libRNA_conv.lax/libRNA_concentrations.a && gcc-ar x "/<>/src/ViennaRNA/./.libs/libRNA_concentrations.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_constraints.a && gcc-ar x "/<>/src/ViennaRNA/./.libs/libRNA_constraints.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_datastructures.a && gcc-ar x "/<>/src/ViennaRNA/./.libs/libRNA_datastructures.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_utils.a && gcc-ar x "/<>/src/ViennaRNA/./.libs/libRNA_utils.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_plotting.a && gcc-ar x "/<>/src/ViennaRNA/./.libs/libRNA_plotting.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_params.a && gcc-ar x "/<>/src/ViennaRNA/./.libs/libRNA_params.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_eval.a && gcc-ar x "/<>/src/ViennaRNA/./.libs/libRNA_eval.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_loops.a && gcc-ar x "/<>/src/ViennaRNA/./.libs/libRNA_loops.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_landscape.a && gcc-ar x "/<>/src/ViennaRNA/./.libs/libRNA_landscape.a") libtool: link: gcc-ar cr .libs/libRNA_conv.a .libs/fold_compound.o .libs/dist_vars.o .libs/part_func.o .libs/part_func_wrappers.o .libs/pf_fold.o .libs/pf_multifold.o .libs/treedist.o .libs/inverse.o .libs/ProfileDist.o .libs/RNAstruct.o .libs/mfe.o .libs/mfe_window.o .libs/mfe_wrappers.o .libs/mfe_window_wrappers.o .libs/fold.o .libs/stringdist.o .libs/subopt.o .libs/subopt_zuker.o .libs/Lfold.o .libs/cofold.o .libs/part_func_co.o .libs/ProfileAln.o .libs/duplex.o .libs/alifold.o .libs/alipfold.o .libs/LPfold.o .libs/part_func_up.o .libs/ribo.o .libs/MEA.o .libs/mm.o .libs/2Dfold.o .libs/2Dpfold.o .libs/plex_functions.o .libs/ali_plex.o .libs/c_plex.o .libs/plex.o .libs/snofold.o .libs/snoop.o .libs/gquad.o .libs/perturbation_fold.o .libs/centroid.o .libs/model.o .libs/dp_matrices.o .libs/boltzmann_sampling.o .libs/bs_wrappers.o .libs/equilibrium_probs.o .libs/alphabet.o .libs/sequence.o .libs/unstructured_domains.o .libs/grammar.o .libs/heat_capacity.o .libs/libRNA_conv.lax/libRNA_concentrations.a/libRNA_concentrations_la-concentrations.o .libs/libRNA_conv.lax/libRNA_concentrations.a/libRNA_concentrations_la-wrap_dlib.o .libs/libRNA_conv.lax/libRNA_constraints.a/SHAPE.o .libs/libRNA_conv.lax/libRNA_constraints.a/constraints.o .libs/libRNA_conv.lax/libRNA_constraints.a/hard.o .libs/libRNA_conv.lax/libRNA_constraints.a/ligand.o .libs/libRNA_conv.lax/libRNA_constraints.a/soft.o .libs/libRNA_conv.lax/libRNA_datastructures.a/basic_datastructures.o .libs/libRNA_conv.lax/libRNA_datastructures.a/char_stream.o .libs/libRNA_conv.lax/libRNA_datastructures.a/hash_tables.o .libs/libRNA_conv.lax/libRNA_datastructures.a/heap.o .libs/libRNA_conv.lax/libRNA_datastructures.a/lists.o .libs/libRNA_conv.lax/libRNA_datastructures.a/stream_output.o .libs/libRNA_conv.lax/libRNA_utils.a/BoyerMoore.o .libs/libRNA_conv.lax/libRNA_utils.a/combinatorics.o .libs/libRNA_conv.lax/libRNA_utils.a/commands.o .libs/libRNA_conv.lax/libRNA_utils.a/cpu.o .libs/libRNA_conv.lax/libRNA_utils.a/file_formats.o .libs/libRNA_conv.lax/libRNA_utils.a/file_formats_msa.o .libs/libRNA_conv.lax/libRNA_utils.a/higher_order_functions.o .libs/libRNA_conv.lax/libRNA_utils.a/io_utils.o .libs/libRNA_conv.lax/libRNA_utils.a/msa_utils.o .libs/libRNA_conv.lax/libRNA_utils.a/string_utils.o .libs/libRNA_conv.lax/libRNA_utils.a/structure_tree.o .libs/libRNA_conv.lax/libRNA_utils.a/structure_utils.o .libs/libRNA_conv.lax/libRNA_utils.a/units.o .libs/libRNA_conv.lax/libRNA_utils.a/utils.o .libs/libRNA_conv.lax/libRNA_plotting.a/RNApuzzler.o .libs/libRNA_conv.lax/libRNA_plotting.a/RNAturtle.o .libs/libRNA_conv.lax/libRNA_plotting.a/alignments.o .libs/libRNA_conv.lax/libRNA_plotting.a/layouts.o .libs/libRNA_conv.lax/libRNA_plotting.a/naview.o .libs/libRNA_conv.lax/libRNA_plotting.a/plot_utils.o .libs/libRNA_conv.lax/libRNA_plotting.a/probabilities.o .libs/libRNA_conv.lax/libRNA_plotting.a/structures.o .libs/libRNA_conv.lax/libRNA_params.a/convert.o .libs/libRNA_conv.lax/libRNA_params.a/default.o .libs/libRNA_conv.lax/libRNA_params.a/io.o .libs/libRNA_conv.lax/libRNA_params.a/params.o .libs/libRNA_conv.lax/libRNA_eval.a/eval.o .libs/libRNA_conv.lax/libRNA_eval.a/eval_covariance.o .libs/libRNA_conv.lax/libRNA_eval.a/eval_wrappers.o .libs/libRNA_conv.lax/libRNA_loops.a/external.o .libs/libRNA_conv.lax/libRNA_loops.a/external_bt.o .libs/libRNA_conv.lax/libRNA_loops.a/external_pf.o .libs/libRNA_conv.lax/libRNA_loops.a/hairpin.o .libs/libRNA_conv.lax/libRNA_loops.a/hairpin_bt.o .libs/libRNA_conv.lax/libRNA_loops.a/hairpin_pf.o .libs/libRNA_conv.lax/libRNA_loops.a/internal.o .libs/libRNA_conv.lax/libRNA_loops.a/internal_bt.o .libs/libRNA_conv.lax/libRNA_loops.a/internal_pf.o .libs/libRNA_conv.lax/libRNA_loops.a/multibranch.o .libs/libRNA_conv.lax/libRNA_loops.a/multibranch_bt.o .libs/libRNA_conv.lax/libRNA_loops.a/multibranch_pf.o .libs/libRNA_conv.lax/libRNA_landscape.a/findpath.o .libs/libRNA_conv.lax/libRNA_landscape.a/move.o .libs/libRNA_conv.lax/libRNA_landscape.a/move_set.o .libs/libRNA_conv.lax/libRNA_landscape.a/neighbor.o .libs/libRNA_conv.lax/libRNA_landscape.a/walk.o libtool: link: gcc-ranlib .libs/libRNA_conv.a libtool: link: rm -fr .libs/libRNA_conv.lax libtool: link: ( cd ".libs" && rm -f "libRNA_conv.la" && ln -s "../libRNA_conv.la" "libRNA_conv.la" ) /bin/bash ../../libtool --tag=CXX --mode=link g++ -std=c++11 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -avoid-version -static -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o libRNA.la -rpath /usr/lib/arm-linux-gnueabihf libRNA_conv.la -lgsl -lgslcblas -lm libtool: link: (cd .libs/libRNA.lax/libRNA_conv.a && gcc-ar x "/<>/src/ViennaRNA/./.libs/libRNA_conv.a") libtool: link: gcc-ar cr .libs/libRNA.a .libs/libRNA.lax/libRNA_conv.a/2Dfold.o .libs/libRNA.lax/libRNA_conv.a/2Dpfold.o .libs/libRNA.lax/libRNA_conv.a/BoyerMoore.o .libs/libRNA.lax/libRNA_conv.a/LPfold.o .libs/libRNA.lax/libRNA_conv.a/Lfold.o .libs/libRNA.lax/libRNA_conv.a/MEA.o .libs/libRNA.lax/libRNA_conv.a/ProfileAln.o .libs/libRNA.lax/libRNA_conv.a/ProfileDist.o .libs/libRNA.lax/libRNA_conv.a/RNApuzzler.o .libs/libRNA.lax/libRNA_conv.a/RNAstruct.o .libs/libRNA.lax/libRNA_conv.a/RNAturtle.o .libs/libRNA.lax/libRNA_conv.a/SHAPE.o .libs/libRNA.lax/libRNA_conv.a/ali_plex.o .libs/libRNA.lax/libRNA_conv.a/alifold.o .libs/libRNA.lax/libRNA_conv.a/alignments.o .libs/libRNA.lax/libRNA_conv.a/alipfold.o .libs/libRNA.lax/libRNA_conv.a/alphabet.o .libs/libRNA.lax/libRNA_conv.a/basic_datastructures.o .libs/libRNA.lax/libRNA_conv.a/boltzmann_sampling.o .libs/libRNA.lax/libRNA_conv.a/bs_wrappers.o .libs/libRNA.lax/libRNA_conv.a/c_plex.o .libs/libRNA.lax/libRNA_conv.a/centroid.o .libs/libRNA.lax/libRNA_conv.a/char_stream.o .libs/libRNA.lax/libRNA_conv.a/cofold.o .libs/libRNA.lax/libRNA_conv.a/combinatorics.o .libs/libRNA.lax/libRNA_conv.a/commands.o .libs/libRNA.lax/libRNA_conv.a/constraints.o .libs/libRNA.lax/libRNA_conv.a/convert.o .libs/libRNA.lax/libRNA_conv.a/cpu.o .libs/libRNA.lax/libRNA_conv.a/default.o .libs/libRNA.lax/libRNA_conv.a/dist_vars.o .libs/libRNA.lax/libRNA_conv.a/dp_matrices.o .libs/libRNA.lax/libRNA_conv.a/duplex.o .libs/libRNA.lax/libRNA_conv.a/equilibrium_probs.o .libs/libRNA.lax/libRNA_conv.a/eval.o .libs/libRNA.lax/libRNA_conv.a/eval_covariance.o .libs/libRNA.lax/libRNA_conv.a/eval_wrappers.o .libs/libRNA.lax/libRNA_conv.a/external.o .libs/libRNA.lax/libRNA_conv.a/external_bt.o .libs/libRNA.lax/libRNA_conv.a/external_pf.o .libs/libRNA.lax/libRNA_conv.a/file_formats.o .libs/libRNA.lax/libRNA_conv.a/file_formats_msa.o .libs/libRNA.lax/libRNA_conv.a/findpath.o .libs/libRNA.lax/libRNA_conv.a/fold.o .libs/libRNA.lax/libRNA_conv.a/fold_compound.o .libs/libRNA.lax/libRNA_conv.a/gquad.o .libs/libRNA.lax/libRNA_conv.a/grammar.o .libs/libRNA.lax/libRNA_conv.a/hairpin.o .libs/libRNA.lax/libRNA_conv.a/hairpin_bt.o .libs/libRNA.lax/libRNA_conv.a/hairpin_pf.o .libs/libRNA.lax/libRNA_conv.a/hard.o .libs/libRNA.lax/libRNA_conv.a/hash_tables.o .libs/libRNA.lax/libRNA_conv.a/heap.o .libs/libRNA.lax/libRNA_conv.a/heat_capacity.o .libs/libRNA.lax/libRNA_conv.a/higher_order_functions.o .libs/libRNA.lax/libRNA_conv.a/internal.o .libs/libRNA.lax/libRNA_conv.a/internal_bt.o .libs/libRNA.lax/libRNA_conv.a/internal_pf.o .libs/libRNA.lax/libRNA_conv.a/inverse.o .libs/libRNA.lax/libRNA_conv.a/io.o .libs/libRNA.lax/libRNA_conv.a/io_utils.o .libs/libRNA.lax/libRNA_conv.a/layouts.o .libs/libRNA.lax/libRNA_conv.a/libRNA_concentrations_la-concentrations.o .libs/libRNA.lax/libRNA_conv.a/libRNA_concentrations_la-wrap_dlib.o .libs/libRNA.lax/libRNA_conv.a/ligand.o .libs/libRNA.lax/libRNA_conv.a/lists.o .libs/libRNA.lax/libRNA_conv.a/mfe.o .libs/libRNA.lax/libRNA_conv.a/mfe_window.o .libs/libRNA.lax/libRNA_conv.a/mfe_window_wrappers.o .libs/libRNA.lax/libRNA_conv.a/mfe_wrappers.o .libs/libRNA.lax/libRNA_conv.a/mm.o .libs/libRNA.lax/libRNA_conv.a/model.o .libs/libRNA.lax/libRNA_conv.a/move.o .libs/libRNA.lax/libRNA_conv.a/move_set.o .libs/libRNA.lax/libRNA_conv.a/msa_utils.o .libs/libRNA.lax/libRNA_conv.a/multibranch.o .libs/libRNA.lax/libRNA_conv.a/multibranch_bt.o .libs/libRNA.lax/libRNA_conv.a/multibranch_pf.o .libs/libRNA.lax/libRNA_conv.a/naview.o .libs/libRNA.lax/libRNA_conv.a/neighbor.o .libs/libRNA.lax/libRNA_conv.a/params.o .libs/libRNA.lax/libRNA_conv.a/part_func.o .libs/libRNA.lax/libRNA_conv.a/part_func_co.o .libs/libRNA.lax/libRNA_conv.a/part_func_up.o .libs/libRNA.lax/libRNA_conv.a/part_func_wrappers.o .libs/libRNA.lax/libRNA_conv.a/perturbation_fold.o .libs/libRNA.lax/libRNA_conv.a/pf_fold.o .libs/libRNA.lax/libRNA_conv.a/pf_multifold.o .libs/libRNA.lax/libRNA_conv.a/plex.o .libs/libRNA.lax/libRNA_conv.a/plex_functions.o .libs/libRNA.lax/libRNA_conv.a/plot_utils.o .libs/libRNA.lax/libRNA_conv.a/probabilities.o .libs/libRNA.lax/libRNA_conv.a/ribo.o .libs/libRNA.lax/libRNA_conv.a/sequence.o .libs/libRNA.lax/libRNA_conv.a/snofold.o .libs/libRNA.lax/libRNA_conv.a/snoop.o .libs/libRNA.lax/libRNA_conv.a/soft.o .libs/libRNA.lax/libRNA_conv.a/stream_output.o .libs/libRNA.lax/libRNA_conv.a/string_utils.o .libs/libRNA.lax/libRNA_conv.a/stringdist.o .libs/libRNA.lax/libRNA_conv.a/structure_tree.o .libs/libRNA.lax/libRNA_conv.a/structure_utils.o .libs/libRNA.lax/libRNA_conv.a/structures.o .libs/libRNA.lax/libRNA_conv.a/subopt.o .libs/libRNA.lax/libRNA_conv.a/subopt_zuker.o .libs/libRNA.lax/libRNA_conv.a/treedist.o .libs/libRNA.lax/libRNA_conv.a/units.o .libs/libRNA.lax/libRNA_conv.a/unstructured_domains.o .libs/libRNA.lax/libRNA_conv.a/utils.o .libs/libRNA.lax/libRNA_conv.a/walk.o libtool: link: gcc-ranlib .libs/libRNA.a libtool: link: rm -fr .libs/libRNA.lax libtool: link: ( cd ".libs" && rm -f "libRNA.la" && ln -s "../libRNA.la" "libRNA.la" ) ( \ /bin/bash ../../libtool --config > libtoolconfig.tmp && \ ( \. ./libtoolconfig.tmp; cp "$objdir/libRNA.a" ./ ) && \ rm -f libtoolconfig.tmp \ ) make[6]: Leaving directory '/<>/src/ViennaRNA' make[5]: Leaving directory '/<>/src/ViennaRNA' Making all in bin make[5]: Entering directory '/<>/src/bin' /usr/bin/gengetopt -i RNAfold.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAfold.o RNAfold.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o input_id_helpers.lo input_id_helpers.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o parallel_helpers.lo parallel_helpers.c /usr/bin/gengetopt -i RNAeval.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAeval.o RNAeval.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c input_id_helpers.c -fPIC -DPIC -o .libs/input_id_helpers.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c parallel_helpers.c -fPIC -DPIC -o .libs/parallel_helpers.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c input_id_helpers.c -fPIC -DPIC -o input_id_helpers.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c parallel_helpers.c -fPIC -DPIC -o parallel_helpers.o >/dev/null 2>&1 /usr/bin/gengetopt -i RNAheat.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAheat.o RNAheat.c /usr/bin/gengetopt -i RNApdist.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNApdist.o RNApdist.c /usr/bin/gengetopt -i RNAdistance.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAdistance.o RNAdistance.c /usr/bin/gengetopt -i RNAinverse.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAinverse.o RNAinverse.c /usr/bin/gengetopt -i RNAplot.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAplot.o RNAplot.c /usr/bin/gengetopt -i RNAsubopt.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAsubopt.o RNAsubopt.c /usr/bin/gengetopt -i RNALfold.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNALfold.o RNALfold.c /usr/bin/gengetopt -i RNAcofold.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAcofold.o RNAcofold.c /usr/bin/gengetopt -i RNApaln.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNApaln.o RNApaln.c /usr/bin/gengetopt -i RNAduplex.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAduplex.o RNAduplex.c /usr/bin/gengetopt -i RNAalifold.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAalifold.o RNAalifold.c /usr/bin/gengetopt -i RNAplfold.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAplfold.o RNAplfold.c /usr/bin/gengetopt -i RNAup.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAup.o RNAup.c /usr/bin/gengetopt -i RNAaliduplex.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAaliduplex.o RNAaliduplex.c /usr/bin/gengetopt -i RNALalifold.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNALalifold.o RNALalifold.c /usr/bin/gengetopt -i RNA2Dfold.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNA2Dfold.o RNA2Dfold.c /usr/bin/gengetopt -i RNAparconv.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAparconv.o RNAparconv.c /usr/bin/gengetopt -i RNAPKplex.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAPKplex.o RNAPKplex.c /usr/bin/gengetopt -i RNAplex.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAplex.o RNAplex.c /usr/bin/gengetopt -i RNAsnoop.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAsnoop.o RNAsnoop.c /usr/bin/gengetopt -i RNApvmin.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNApvmin.o RNApvmin.c /usr/bin/gengetopt -i RNAdos.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAdos.o RNAdos.c RNAsnoop.c: In function ‘redraw_output’: RNAsnoop.c:1357:25: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 1357 | sprintf(str, "%d", count); | ^~ RNAsnoop.c:1357:24: note: directive argument in the range [1, 2147483647] 1357 | sprintf(str, "%d", count); | ^~~~ RNAsnoop.c:1357:11: note: ‘sprintf’ output between 2 and 11 bytes into a destination of size 9 1357 | sprintf(str, "%d", count); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/gengetopt -i RNAmultifold.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAmultifold.o RNAmultifold.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAfold_cmdl.o RNAfold_cmdl.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o ../cthreadpool/thpool.lo ../cthreadpool/thpool.c RNAmultifold.c: In function ‘process_record’: RNAmultifold.c:846:59: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 846 | fprintf(stderr, "Processing complexes of size %lu\n", k); | ~~^ ~ | | | | | size_t {aka unsigned int} | long unsigned int | %u RNAmultifold.c:899:52: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 899 | fprintf(stderr, "\r%s, permutation %lu/%lu ", | ~~^ | | | long unsigned int | %u 900 | verbose_line, 901 | i + 1, num_perm); | ~~~~~ | | | size_t {aka unsigned int} RNAmultifold.c:899:56: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 899 | fprintf(stderr, "\r%s, permutation %lu/%lu ", | ~~^ | | | long unsigned int | %u 900 | verbose_line, 901 | i + 1, num_perm); | ~~~~~~~~ | | | size_t {aka unsigned int} libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c ../cthreadpool/thpool.c -fPIC -DPIC -o ../cthreadpool/.libs/thpool.o gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAeval_cmdl.o RNAeval_cmdl.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c ../cthreadpool/thpool.c -fPIC -DPIC -o ../cthreadpool/thpool.o >/dev/null 2>&1 gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAheat_cmdl.o RNAheat_cmdl.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNApdist_cmdl.o RNApdist_cmdl.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAdistance_cmdl.o RNAdistance_cmdl.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAinverse_cmdl.o RNAinverse_cmdl.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAplot_cmdl.o RNAplot_cmdl.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAsubopt_cmdl.o RNAsubopt_cmdl.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNALfold_cmdl.o RNALfold_cmdl.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAcofold_cmdl.o RNAcofold_cmdl.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNApaln_cmdl.o RNApaln_cmdl.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAduplex_cmdl.o RNAduplex_cmdl.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAalifold_cmdl.o RNAalifold_cmdl.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAplfold_cmdl.o RNAplfold_cmdl.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAup_cmdl.o RNAup_cmdl.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAaliduplex_cmdl.o RNAaliduplex_cmdl.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNALalifold_cmdl.o RNALalifold_cmdl.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNA2Dfold_cmdl.o RNA2Dfold_cmdl.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAparconv_cmdl.o RNAparconv_cmdl.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAPKplex_cmdl.o RNAPKplex_cmdl.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAplex_cmdl.o RNAplex_cmdl.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAsnoop_cmdl.o RNAsnoop_cmdl.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNApvmin_cmdl.o RNApvmin_cmdl.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAdos_cmdl.o RNAdos_cmdl.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/cthreadpool -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAmultifold_cmdl.o RNAmultifold_cmdl.c /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp 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-lpthread ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAfold RNAfold_cmdl.o RNAfold.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o RNAdistance RNAdistance_cmdl.o RNAdistance.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAdistance RNAdistance_cmdl.o RNAdistance.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o RNAinverse RNAinverse_cmdl.o RNAinverse.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAinverse RNAinverse_cmdl.o RNAinverse.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o RNAplot RNAplot_cmdl.o RNAplot.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAplot RNAplot_cmdl.o RNAplot.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o RNAsubopt RNAsubopt_cmdl.o RNAsubopt.o 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-Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNALfold RNALfold_cmdl.o RNALfold.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o RNAcofold RNAcofold_cmdl.o RNAcofold.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAcofold RNAcofold_cmdl.o RNAcofold.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o RNApaln RNApaln_cmdl.o RNApaln.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNApaln RNApaln_cmdl.o RNApaln.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o RNAduplex RNAduplex_cmdl.o RNAduplex.o 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-Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAalifold RNAalifold_cmdl.o RNAalifold.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o RNAplfold RNAplfold_cmdl.o RNAplfold.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAplfold RNAplfold_cmdl.o RNAplfold.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o RNAup RNAup_cmdl.o RNAup.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAup RNAup_cmdl.o RNAup.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o RNAaliduplex RNAaliduplex_cmdl.o RNAaliduplex.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAaliduplex RNAaliduplex_cmdl.o RNAaliduplex.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o RNALalifold RNALalifold_cmdl.o RNALalifold.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNALalifold RNALalifold_cmdl.o RNALalifold.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o RNA2Dfold RNA2Dfold_cmdl.o RNA2Dfold.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o RNAparconv RNAparconv_cmdl.o RNAparconv.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNA2Dfold RNA2Dfold_cmdl.o RNA2Dfold.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAparconv RNAparconv_cmdl.o RNAparconv.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o RNAPKplex RNAPKplex_cmdl.o RNAPKplex.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAPKplex RNAPKplex_cmdl.o RNAPKplex.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o RNAplex RNAplex_cmdl.o RNAplex.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAplex RNAplex_cmdl.o RNAplex.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o RNAsnoop RNAsnoop_cmdl.o RNAsnoop.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAsnoop RNAsnoop_cmdl.o RNAsnoop.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o RNApvmin RNApvmin_cmdl.o RNApvmin.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNApvmin RNApvmin_cmdl.o RNApvmin.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o RNAdos RNAdos_cmdl.o RNAdos.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAdos RNAdos_cmdl.o RNAdos.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o RNAmultifold RNAmultifold_cmdl.o RNAmultifold.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lstdc++ -ldlib -llapack -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAmultifold RNAmultifold_cmdl.o RNAmultifold.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread ./.libs/libhelpers.a -lmpfr -lgmp -lstdc++ -ldlib -llapack -lgsl -lgslcblas -lm -pthread -fopenmp make[5]: Leaving directory '/<>/src/bin' Making all in Utils make[5]: Entering directory '/<>/src/Utils' gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o b2ct.o b2ct.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o popt.o popt.c gengetopt -i ct2db.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o ct2db.o ct2db.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o ct2db_cmdl.o ct2db_cmdl.c /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o b2ct b2ct.o ../../src/ViennaRNA/libRNA_conv.la -lm -lgsl -lgslcblas -lm /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o popt popt.o ../../src/ViennaRNA/libRNA_conv.la -lm -lgsl -lgslcblas -lm /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o ct2db ct2db_cmdl.o ct2db.o ../../src/ViennaRNA/libRNA_conv.la -lm -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o b2ct b2ct.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o ct2db ct2db_cmdl.o ct2db.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o popt popt.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread -lgsl -lgslcblas -lm -pthread -fopenmp make[5]: Leaving directory '/<>/src/Utils' Making all in Cluster make[5]: Entering directory '/<>/src/Cluster' gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../.. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o split.o split.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../.. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o distance_matrix.o distance_matrix.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../.. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o cluster.o cluster.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../.. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o treeplot.o treeplot.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../.. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o AD_main.o AD_main.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../.. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o statgeom.o statgeom.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../.. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o AS_main.o AS_main.c gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../.. -I../.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o PS3D.o PS3D.c /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -ldlib -Wl,-Bsymbolic-functions -Wl,-z,relro -o AnalyseDists split.o distance_matrix.o cluster.o treeplot.o AD_main.o ../../src/ViennaRNA/libRNA_conv.la -lgsl -lgslcblas -lm /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -lpthread -ldlib -Wl,-Bsymbolic-functions -Wl,-z,relro -o AnalyseSeqs statgeom.o distance_matrix.o cluster.o AS_main.o split.o treeplot.o PS3D.o ../../src/ViennaRNA/libRNA_conv.la -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o AnalyseDists split.o distance_matrix.o cluster.o treeplot.o AD_main.o -ldlib ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o AnalyseSeqs statgeom.o distance_matrix.o cluster.o AS_main.o split.o treeplot.o PS3D.o -ldlib ../../src/ViennaRNA/.libs/libRNA_conv.a -lpthread -lgsl -lgslcblas -lm -pthread -fopenmp make[5]: Leaving directory '/<>/src/Cluster' make[5]: Entering directory '/<>/src' make[5]: Nothing to be done for 'all-am'. make[5]: Leaving directory '/<>/src' make[4]: Leaving directory '/<>/src' Making all in man make[4]: Entering directory '/<>/man' restore=: && backupdir=".am$$" && \ am__cwd=`pwd` && CDPATH="${ZSH_VERSION+.}:" && cd . && \ rm -rf $backupdir && mkdir $backupdir && \ if (/bin/bash '/<>/config/missing' makeinfo --version) >/dev/null 2>&1; then \ for f in RNAlib.info RNAlib.info-[0-9] RNAlib.info-[0-9][0-9] RNAlib.i[0-9] RNAlib.i[0-9][0-9]; do \ if test -f $f; then mv $f $backupdir; restore=mv; else :; fi; \ done; \ else :; fi && \ cd "$am__cwd"; \ if /bin/bash '/<>/config/missing' makeinfo -I . \ -o RNAlib.info RNAlib.texi; \ then \ rc=0; \ CDPATH="${ZSH_VERSION+.}:" && cd .; \ else \ rc=$?; \ CDPATH="${ZSH_VERSION+.}:" && cd . && \ $restore $backupdir/* `echo "./RNAlib.info" | sed 's|[^/]*$||'`; \ fi; \ rm -rf $backupdir; exit $rc ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNA2Dfold.ggo | perl -pe 's/\\e\\e/\\e/g' > RNA2Dfold.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAaliduplex.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAaliduplex.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAalifold.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAalifold.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAcofold.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAcofold.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAduplex.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAduplex.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAeval.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAeval.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAfold.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAfold.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAheat.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAheat.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAinverse.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAinverse.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNALalifold.ggo | perl -pe 's/\\e\\e/\\e/g' > RNALalifold.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNALfold.ggo | perl -pe 's/\\e\\e/\\e/g' > RNALfold.1 RNAlib.texi:803: warning: @noindent is useless inside of a paragraph ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAmultifold.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAmultifold.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNApaln.ggo | perl -pe 's/\\e\\e/\\e/g' > RNApaln.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAparconv.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAparconv.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAplfold.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAplfold.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAplot.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAplot.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNApvmin.ggo | perl -pe 's/\\e\\e/\\e/g' > RNApvmin.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAsubopt.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAsubopt.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAup.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAup.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAPKplex.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAPKplex.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAsnoop.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAsnoop.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAplex.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAplex.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAdistance.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAdistance.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNApdist.ggo | perl -pe 's/\\e\\e/\\e/g' > RNApdist.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAdos.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAdos.1 /usr/bin/help2man \ -N \ --help-option=--detailed-help \ --opt-include=./include/ref_package.inc \ "./cmdlopt.sh ../src/Utils/ct2db" > ct2db.1 make[4]: Leaving directory '/<>/man' Making all in misc make[4]: Entering directory '/<>/misc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/misc' Making all in doc make[4]: Entering directory '/<>/doc' Making all in CLA make[5]: Entering directory '/<>/doc/CLA' rm -f *.dvi *.idv *.aux *.toc *.idx *.ind *.ilg *.log *.out *.brf *.blg *.bbl CLA-*.pdf && \ /usr/bin/pdflatex -interaction=nonstopmode -halt-on-error CLA-Individual >/dev/null 2>&1 && \ /usr/bin/pdflatex -interaction=nonstopmode -halt-on-error CLA-Individual >/dev/null 2>&1 && \ /usr/bin/pdflatex -interaction=nonstopmode -halt-on-error CLA-Individual >/dev/null 2>&1 && \ mv CLA-Individual.pdf ViennaRNA-CLA-Individual.pdf ; rm -f *.dvi *.idv *.aux *.toc *.idx *.ind *.ilg *.log *.out *.brf *.blg *.bbl CLA-*.pdf && \ /usr/bin/pdflatex -interaction=nonstopmode -halt-on-error CLA-Entity >/dev/null 2>&1 && \ /usr/bin/pdflatex -interaction=nonstopmode -halt-on-error CLA-Entity >/dev/null 2>&1 && \ /usr/bin/pdflatex -interaction=nonstopmode -halt-on-error CLA-Entity >/dev/null 2>&1 && \ mv CLA-Entity.pdf ViennaRNA-CLA-Entity.pdf ; make[5]: Leaving directory '/<>/doc/CLA' make[5]: Entering directory '/<>/doc' make[5]: Nothing to be done for 'all-am'. make[5]: Leaving directory '/<>/doc' make[4]: Leaving directory '/<>/doc' Making all in RNA-Tutorial make[4]: Entering directory '/<>/RNA-Tutorial' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/RNA-Tutorial' Making all in interfaces make[4]: Entering directory '/<>/interfaces' Making all in Perl make[5]: Entering directory '/<>/interfaces/Perl' /usr/bin/swig \ -I../../src \ -I. \ -I. \ -DVRNA_WITH_NAVIEW_LAYOUT \ -perl5 \ -proxy \ -const \ -c++ \ -w509 \ -module RNA \ -o RNA_wrap.cpp \ ./../RNA.i /usr/bin/swig \ -I../../src \ -I. \ -I. \ -DVRNA_WITH_NAVIEW_LAYOUT \ -perl5 \ -proxy \ -const \ -c++ \ -w509 \ -module RNA \ -o RNA_wrap.cpp \ ./../RNA.i /bin/bash ../../libtool --tag=CXX --mode=compile g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I/usr/lib/arm-linux-gnueabihf/perl/5.38/CORE -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -pthread -Wno-unused-label -Wno-unused-variable -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNA_la-RNA_wrap.lo `test -f 'RNA_wrap.cpp' || echo './'`RNA_wrap.cpp libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I/usr/lib/arm-linux-gnueabihf/perl/5.38/CORE -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -pthread -Wno-unused-label -Wno-unused-variable -I/usr/include/json-c/ -I/usr/include/libsvm/ -c RNA_wrap.cpp -fPIC -DPIC -o .libs/RNA_la-RNA_wrap.o libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I/usr/lib/arm-linux-gnueabihf/perl/5.38/CORE -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -pthread -Wno-unused-label -Wno-unused-variable -I/usr/include/json-c/ -I/usr/include/libsvm/ -c RNA_wrap.cpp -fPIC -DPIC -o RNA_la-RNA_wrap.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CXX --mode=link g++ -std=c++11 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -pthread -Wno-unused-label -Wno-unused-variable -I/usr/include/json-c/ -I/usr/include/libsvm/ -Xcompiler -pthread -lpthread -avoid-version -module -shared -export-dynamic -shrext .so -Wl,-Bsymbolic-functions -Wl,-z,relro -o RNA.la -rpath /usr/lib/arm-linux-gnueabihf/perl/5.38.2/auto/RNA RNA_la-RNA_wrap.lo -ldlib ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/13/crtbeginS.o .libs/RNA_la-RNA_wrap.o -Wl,--whole-archive ../../src/ViennaRNA/.libs/libRNA_conv.a -Wl,--no-whole-archive -ldlib -lpthread -lmpfr -lgmp -lgsl -lgslcblas -L/usr/lib/gcc/arm-linux-gnueabihf/13 -L/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/13/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/13/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/crtn.o -flto -fopenmp -pthread -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -fopenmp -pthread -Wl,-soname -Wl,RNA.so -o .libs/RNA.so libtool: link: ( cd ".libs" && rm -f "RNA.la" && ln -s "../RNA.la" "RNA.la" ) ( /usr/bin/mkdir -p auto/RNA ) && \ ( \ /bin/bash ../../libtool --config > libtoolconfig.tmp && \ ( . ./libtoolconfig.tmp; cp "$objdir/RNA.so" auto/RNA ) && \ rm -f libtoolconfig.tmp \ ) make[5]: Leaving directory '/<>/interfaces/Perl' Making all in Python make[5]: Entering directory '/<>/interfaces/Python' /usr/bin/swig \ -I../../src \ -I. \ -I. \ -DPY3 \ -DVRNA_WITH_NAVIEW_LAYOUT \ -python \ -py3 \ -c++ \ -keyword \ -w511,509 \ -o RNA_wrap.cpp \ ./../RNA.i Deprecated command 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Ignored, this option is no longer supported. /bin/bash ../../libtool --tag=CXX --mode=compile g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I/usr/include/python3.12 -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -pthread -Wno-unused-label -Wno-unused-variable -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o _RNA_la-RNA_wrap.lo `test -f 'RNA_wrap.cpp' || echo './'`RNA_wrap.cpp ( test -d RNA || /usr/bin/mkdir -p RNA ) && \ cp `test -f RNA.py || echo './'`RNA.py RNA/__init__.py libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I/usr/include/python3.12 -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -pthread -Wno-unused-label -Wno-unused-variable -I/usr/include/json-c/ -I/usr/include/libsvm/ -c RNA_wrap.cpp -fPIC -DPIC -o .libs/_RNA_la-RNA_wrap.o libtool: compile: g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I/usr/include/python3.12 -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -pthread -Wno-unused-label -Wno-unused-variable -I/usr/include/json-c/ -I/usr/include/libsvm/ -c RNA_wrap.cpp -fPIC -DPIC -o _RNA_la-RNA_wrap.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CXX --mode=link g++ -std=c++11 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -pthread -Wno-unused-label -Wno-unused-variable -I/usr/include/json-c/ -I/usr/include/libsvm/ -Xcompiler -pthread -lpthread -avoid-version -module -shared -export-dynamic -shrext .so -Wl,-Bsymbolic-functions -Wl,-z,relro -o _RNA.la -rpath /usr/lib/python3.12/site-packages/RNA _RNA_la-RNA_wrap.lo -ldlib ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/13/crtbeginS.o .libs/_RNA_la-RNA_wrap.o -Wl,--whole-archive ../../src/ViennaRNA/.libs/libRNA_conv.a -Wl,--no-whole-archive -ldlib -lpthread -lmpfr -lgmp -lgsl -lgslcblas -L/usr/lib/gcc/arm-linux-gnueabihf/13 -L/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/13/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/13/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/crtn.o -flto -fopenmp -pthread -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -fopenmp -pthread -Wl,-soname -Wl,_RNA.so -o .libs/_RNA.so libtool: link: ( cd ".libs" && rm -f "_RNA.la" && ln -s "../_RNA.la" "_RNA.la" ) ( test -d RNA || /usr/bin/mkdir -p RNA ) && \ ( /bin/bash ../../libtool --config > libtoolconfig.tmp ) && \ ( . ./libtoolconfig.tmp; cp $objdir/_RNA.so RNA ) && \ rm -f libtoolconfig.tmp ( PYTHONPATH="RNA:$PYTHONPATH" /usr/bin/python3 -c "import _RNA" ; \ PYTHONPATH=".:$PYTHONPATH" /usr/bin/python3 -c "import RNA" ) ( PYTHONPATH="RNA:$PYTHONPATH" /usr/bin/python3 -O -c "import _RNA" ; \ PYTHONPATH=".:$PYTHONPATH" /usr/bin/python3 -O -c "import RNA" ) make[5]: Leaving directory '/<>/interfaces/Python' make[5]: Entering directory '/<>/interfaces' make[5]: Nothing to be done for 'all-am'. make[5]: Leaving directory '/<>/interfaces' make[4]: Leaving directory '/<>/interfaces' Making all in src/Kinfold make[4]: Entering directory '/<>/src/Kinfold' make all-recursive make[5]: Entering directory '/<>/src/Kinfold' Making all in Example make[6]: Entering directory '/<>/src/Kinfold/Example' make[6]: Nothing to be done for 'all'. make[6]: Leaving directory '/<>/src/Kinfold/Example' make[6]: Entering directory '/<>/src/Kinfold' gcc -DHAVE_CONFIG_H -I. -I./src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o baum.o baum.c gcc -DHAVE_CONFIG_H -I. -I./src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o cache.o cache.c gengetopt -i kinfold.ggo gcc -DHAVE_CONFIG_H -I. -I./src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o main.o main.c gcc -DHAVE_CONFIG_H -I. -I./src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o nachbar.o nachbar.c gcc -DHAVE_CONFIG_H -I. -I./src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o cmdline.o cmdline.c gcc -DHAVE_CONFIG_H -I. -I./src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o globals.o globals.c globals.c: In function ‘process_options_gg’: globals.c:358:41: warning: format ‘%g’ expects argument of type ‘float *’, but argument 3 has type ‘double *’ [-Wformat=] 358 | if (sscanf(args_info.pbounds_arg, "%g=%g=%g", | ~^ | | | float * | %lg 359 | &GAV.phi_bounds[0], | ~~~~~~~~~~~~~~~~~~ | | | double * globals.c:358:44: warning: format ‘%g’ expects argument of type ‘float *’, but argument 4 has type ‘double *’ [-Wformat=] 358 | if (sscanf(args_info.pbounds_arg, "%g=%g=%g", | ~^ | | | float * | %lg 359 | &GAV.phi_bounds[0], 360 | &GAV.phi_bounds[1], | ~~~~~~~~~~~~~~~~~~ | | | double * globals.c:358:47: warning: format ‘%g’ expects argument of type ‘float *’, but argument 5 has type ‘double *’ [-Wformat=] 358 | if (sscanf(args_info.pbounds_arg, "%g=%g=%g", | ~^ | | | float * | %lg ...... 361 | &GAV.phi_bounds[2]) == 0) | ~~~~~~~~~~~~~~~~~~ | | | double * globals.c: In function ‘process_options’: globals.c:448:32: warning: format ‘%g’ expects argument of type ‘float *’, but argument 3 has type ‘double *’ [-Wformat=] 448 | if (sscanf(optarg, "%g=%g=%g", | ~^ | | | float * | %lg 449 | &GAV.phi_bounds[0], | ~~~~~~~~~~~~~~~~~~ | | | double * globals.c:448:35: warning: format ‘%g’ expects argument of type ‘float *’, but argument 4 has type ‘double *’ [-Wformat=] 448 | if (sscanf(optarg, "%g=%g=%g", | ~^ | | | float * | %lg 449 | &GAV.phi_bounds[0], 450 | &GAV.phi_bounds[1], | ~~~~~~~~~~~~~~~~~~ | | | double * globals.c:448:38: warning: format ‘%g’ expects argument of type ‘float *’, but argument 5 has type ‘double *’ [-Wformat=] 448 | if (sscanf(optarg, "%g=%g=%g", | ~^ | | | float * | %lg ...... 451 | &GAV.phi_bounds[2]) == 0) | ~~~~~~~~~~~~~~~~~~ | | | double * gcc -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -I/usr/include/json-c/ -I/usr/include/libsvm/ -Wl,-Bsymbolic-functions -Wl,-z,relro -o Kinfold baum.o cache.o globals.o main.o nachbar.o cmdline.o -fno-strict-aliasing -flto -L./../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lm make[6]: Leaving directory '/<>/src/Kinfold' make[5]: Leaving directory '/<>/src/Kinfold' make[4]: Leaving directory '/<>/src/Kinfold' Making all in src/RNAlocmin make[4]: Entering directory '/<>/src/RNAlocmin' make all-am make[5]: Entering directory '/<>/src/RNAlocmin' gengetopt -i RNAlocmin.ggo g++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -Wno-write-strings -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o barrier_tree.o barrier_tree.cpp g++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -Wno-write-strings -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o findpath_pk.o findpath_pk.cpp g++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -Wno-write-strings -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o flood.o flood.cpp g++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -Wno-write-strings -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o globals.o globals.cpp In file included from flood.h:4, from flood.cpp:12: hash_util.h: In member function ‘size_t hash_fncts::operator()(const Structure&) const’: hash_util.h:82:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 82 | register short *k; /* the key */ | ^ hash_util.h:83:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 83 | register unsigned length; /* the length of the key */ | ^~~~~~ hash_util.h:84:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 84 | register unsigned initval=0; /* the previous hash, or an arbitrary value */ | ^~~~~~~ hash_util.h:85:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 85 | register unsigned a,b,c,len; | ^ hash_util.h:85:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 85 | register unsigned a,b,c,len; | ^ hash_util.h:85:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 85 | register unsigned a,b,c,len; | ^ hash_util.h:85:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 85 | register unsigned a,b,c,len; | ^~~ hash_util.h: In member function ‘size_t hash_fncts::operator()(const struct_en&) const’: hash_util.h:126:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 126 | register short *k; /* the key */ | ^ hash_util.h:127:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 127 | register unsigned length; /* the length of the key */ | ^~~~~~ hash_util.h:128:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 128 | register unsigned initval=0; /* the previous hash, or an arbitrary value */ | ^~~~~~~ hash_util.h:129:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 129 | register unsigned a,b,c,len; | ^ hash_util.h:129:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 129 | register unsigned a,b,c,len; | ^ hash_util.h:129:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 129 | register unsigned a,b,c,len; | ^ hash_util.h:129:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 129 | register unsigned a,b,c,len; | ^~~ hash_util.h: In member function ‘size_t hash_fncts::operator()(const Structure*) const’: hash_util.h:168:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register short *k; /* the key */ | ^ hash_util.h:169:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 169 | register unsigned length; /* the length of the key */ | ^~~~~~ hash_util.h:170:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 170 | register unsigned initval=0; /* the previous hash, or an arbitrary value */ | ^~~~~~~ hash_util.h:171:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 171 | register unsigned a,b,c,len; | ^ hash_util.h:171:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 171 | register unsigned a,b,c,len; | ^ hash_util.h:171:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 171 | register unsigned a,b,c,len; | ^ hash_util.h:171:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 171 | register unsigned a,b,c,len; | ^~~ hash_util.h: In member function ‘size_t hash_fncts::operator()(const struct_en*) const’: hash_util.h:212:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 212 | register short *k; /* the key */ | ^ hash_util.h:213:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 213 | register unsigned length; /* the length of the key */ | ^~~~~~ hash_util.h:214:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 214 | register unsigned initval=0; /* the previous hash, or an arbitrary value */ | ^~~~~~~ hash_util.h:215:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 215 | register unsigned a,b,c,len; | ^ hash_util.h:215:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 215 | register unsigned a,b,c,len; | ^ hash_util.h:215:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 215 | register unsigned a,b,c,len; | ^ hash_util.h:215:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 215 | register unsigned a,b,c,len; | ^~~ In file included from globals.h:10, from globals.cpp:15: hash_util.h: In member function ‘size_t hash_fncts::operator()(const Structure&) const’: hash_util.h:82:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 82 | register short *k; /* the key */ | ^ hash_util.h:83:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 83 | register unsigned length; /* the length of the key */ | ^~~~~~ hash_util.h:84:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 84 | register unsigned initval=0; /* the previous hash, or an arbitrary value */ | ^~~~~~~ hash_util.h:85:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 85 | register unsigned a,b,c,len; | ^ hash_util.h:85:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 85 | register unsigned a,b,c,len; | ^ hash_util.h:85:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 85 | register unsigned a,b,c,len; | ^ hash_util.h:85:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 85 | register unsigned a,b,c,len; | ^~~ hash_util.h: In member function ‘size_t hash_fncts::operator()(const struct_en&) const’: hash_util.h:126:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 126 | register short *k; /* the key */ | ^ hash_util.h:127:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 127 | register unsigned length; /* the length of the key */ | ^~~~~~ hash_util.h:128:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 128 | register unsigned initval=0; /* the previous hash, or an arbitrary value */ | ^~~~~~~ hash_util.h:129:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 129 | register unsigned a,b,c,len; | ^ hash_util.h:129:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 129 | register unsigned a,b,c,len; | ^ hash_util.h:129:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 129 | register unsigned a,b,c,len; | ^ hash_util.h:129:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 129 | register unsigned a,b,c,len; | ^~~ hash_util.h: In member function ‘size_t hash_fncts::operator()(const Structure*) const’: hash_util.h:168:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register short *k; /* the key */ | ^ hash_util.h:169:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 169 | register unsigned length; /* the length of the key */ | ^~~~~~ hash_util.h:170:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 170 | register unsigned initval=0; /* the previous hash, or an arbitrary value */ | ^~~~~~~ hash_util.h:171:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 171 | register unsigned a,b,c,len; | ^ hash_util.h:171:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 171 | register unsigned a,b,c,len; | ^ hash_util.h:171:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 171 | register unsigned a,b,c,len; | ^ hash_util.h:171:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 171 | register unsigned a,b,c,len; | ^~~ g++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -Wno-write-strings -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o hash_util.o hash_util.cpp hash_util.h: In member function ‘size_t hash_fncts::operator()(const struct_en*) const’: hash_util.h:212:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 212 | register short *k; /* the key */ | ^ hash_util.h:213:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 213 | register unsigned length; /* the length of the key */ | ^~~~~~ hash_util.h:214:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 214 | register unsigned initval=0; /* the previous hash, or an arbitrary value */ | ^~~~~~~ hash_util.h:215:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 215 | register unsigned a,b,c,len; | ^ hash_util.h:215:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 215 | register unsigned a,b,c,len; | ^ hash_util.h:215:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 215 | register unsigned a,b,c,len; | ^ hash_util.h:215:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 215 | register unsigned a,b,c,len; | ^~~ g++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -Wno-write-strings -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o main.o main.cpp gcc -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -Wno-write-strings -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fexceptions -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o move_set_inside.o move_set_inside.c g++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -Wno-write-strings -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o move_set_pk.o move_set_pk.cpp g++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -Wno-write-strings -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o neighbourhood.o neighbourhood.cpp In file included from hash_util.cpp:5: hash_util.h: In member function ‘size_t hash_fncts::operator()(const Structure&) const’: hash_util.h:82:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 82 | register short *k; /* the key */ | ^ hash_util.h:83:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 83 | register unsigned length; /* the length of the key */ | ^~~~~~ hash_util.h:84:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 84 | register unsigned initval=0; /* the previous hash, or an arbitrary value */ | ^~~~~~~ hash_util.h:85:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 85 | register unsigned a,b,c,len; | ^ hash_util.h:85:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 85 | register unsigned a,b,c,len; | ^ hash_util.h:85:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 85 | register unsigned a,b,c,len; | ^ hash_util.h:85:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 85 | register unsigned a,b,c,len; | ^~~ hash_util.h: In member function ‘size_t hash_fncts::operator()(const struct_en&) const’: hash_util.h:126:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 126 | register short *k; /* the key */ | ^ hash_util.h:127:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 127 | register unsigned length; /* the length of the key */ | ^~~~~~ hash_util.h:128:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 128 | register unsigned initval=0; /* the previous hash, or an arbitrary value */ | ^~~~~~~ hash_util.h:129:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 129 | register unsigned a,b,c,len; | ^ hash_util.h:129:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 129 | register unsigned a,b,c,len; | ^ hash_util.h:129:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 129 | register unsigned a,b,c,len; | ^ hash_util.h:129:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 129 | register unsigned a,b,c,len; | ^~~ hash_util.h: In member function ‘size_t hash_fncts::operator()(const Structure*) const’: hash_util.h:168:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register short *k; /* the key */ | ^ hash_util.h:169:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 169 | register unsigned length; /* the length of the key */ | ^~~~~~ hash_util.h:170:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 170 | register unsigned initval=0; /* the previous hash, or an arbitrary value */ | ^~~~~~~ hash_util.h:171:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 171 | register unsigned a,b,c,len; | ^ hash_util.h:171:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 171 | register unsigned a,b,c,len; | ^ hash_util.h:171:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 171 | register unsigned a,b,c,len; | ^ hash_util.h:171:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 171 | register unsigned a,b,c,len; | ^~~ hash_util.h: In member function ‘size_t hash_fncts::operator()(const struct_en*) const’: hash_util.h:212:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 212 | register short *k; /* the key */ | ^ hash_util.h:213:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 213 | register unsigned length; /* the length of the key */ | ^~~~~~ hash_util.h:214:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 214 | register unsigned initval=0; /* the previous hash, or an arbitrary value */ | ^~~~~~~ hash_util.h:215:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 215 | register unsigned a,b,c,len; | ^ hash_util.h:215:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 215 | register unsigned a,b,c,len; | ^ hash_util.h:215:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 215 | register unsigned a,b,c,len; | ^ hash_util.h:215:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 215 | register unsigned a,b,c,len; | ^~~ In file included from main.cpp:28: hash_util.h: In member function ‘size_t hash_fncts::operator()(const Structure&) const’: hash_util.h:82:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 82 | register short *k; /* the key */ | ^ hash_util.h:83:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 83 | register unsigned length; /* the length of the key */ | ^~~~~~ hash_util.h:84:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 84 | register unsigned initval=0; /* the previous hash, or an arbitrary value */ | ^~~~~~~ hash_util.h:85:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 85 | register unsigned a,b,c,len; | ^ hash_util.h:85:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 85 | register unsigned a,b,c,len; | ^ hash_util.h:85:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 85 | register unsigned a,b,c,len; | ^ hash_util.h:85:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 85 | register unsigned a,b,c,len; | ^~~ hash_util.h: In member function ‘size_t hash_fncts::operator()(const struct_en&) const’: hash_util.h:126:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 126 | register short *k; /* the key */ | ^ hash_util.h:127:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 127 | register unsigned length; /* the length of the key */ | ^~~~~~ hash_util.h:128:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 128 | register unsigned initval=0; /* the previous hash, or an arbitrary value */ | ^~~~~~~ hash_util.h:129:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 129 | register unsigned a,b,c,len; | ^ hash_util.h:129:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 129 | register unsigned a,b,c,len; | ^ hash_util.h:129:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 129 | register unsigned a,b,c,len; | ^ hash_util.h:129:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 129 | register unsigned a,b,c,len; | ^~~ hash_util.h: In member function ‘size_t hash_fncts::operator()(const Structure*) const’: hash_util.h:168:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register short *k; /* the key */ | ^ hash_util.h:169:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 169 | register unsigned length; /* the length of the key */ | ^~~~~~ hash_util.h:170:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 170 | register unsigned initval=0; /* the previous hash, or an arbitrary value */ | ^~~~~~~ hash_util.h:171:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 171 | register unsigned a,b,c,len; | ^ hash_util.h:171:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 171 | register unsigned a,b,c,len; | ^ hash_util.h:171:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 171 | register unsigned a,b,c,len; | ^ hash_util.h:171:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 171 | register unsigned a,b,c,len; | ^~~ hash_util.h: In member function ‘size_t hash_fncts::operator()(const struct_en*) const’: hash_util.h:212:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 212 | register short *k; /* the key */ | ^ hash_util.h:213:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 213 | register unsigned length; /* the length of the key */ | ^~~~~~ hash_util.h:214:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 214 | register unsigned initval=0; /* the previous hash, or an arbitrary value */ | ^~~~~~~ hash_util.h:215:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 215 | register unsigned a,b,c,len; | ^ hash_util.h:215:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 215 | register unsigned a,b,c,len; | ^ hash_util.h:215:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 215 | register unsigned a,b,c,len; | ^ hash_util.h:215:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 215 | register unsigned a,b,c,len; | ^~~ In file included from globals.h:10, from RNAlocmin.h:7, from neighbourhood.cpp:8: hash_util.h: In member function ‘size_t hash_fncts::operator()(const Structure&) const’: hash_util.h:82:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 82 | register short *k; /* the key */ | ^ hash_util.h:83:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 83 | register unsigned length; /* the length of the key */ | ^~~~~~ hash_util.h:84:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 84 | register unsigned initval=0; /* the previous hash, or an arbitrary value */ | ^~~~~~~ hash_util.h:85:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 85 | register unsigned a,b,c,len; | ^ hash_util.h:85:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 85 | register unsigned a,b,c,len; | ^ hash_util.h:85:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 85 | register unsigned a,b,c,len; | ^ hash_util.h:85:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 85 | register unsigned a,b,c,len; | ^~~ hash_util.h: In member function ‘size_t hash_fncts::operator()(const struct_en&) const’: hash_util.h:126:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 126 | register short *k; /* the key */ | ^ hash_util.h:127:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 127 | register unsigned length; /* the length of the key */ | ^~~~~~ hash_util.h:128:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 128 | register unsigned initval=0; /* the previous hash, or an arbitrary value */ | ^~~~~~~ hash_util.h:129:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 129 | register unsigned a,b,c,len; | ^ hash_util.h:129:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 129 | register unsigned a,b,c,len; | ^ hash_util.h:129:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 129 | register unsigned a,b,c,len; | ^ hash_util.h:129:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 129 | register unsigned a,b,c,len; | ^~~ hash_util.h: In member function ‘size_t hash_fncts::operator()(const Structure*) const’: hash_util.h:168:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register short *k; /* the key */ | ^ hash_util.h:169:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 169 | register unsigned length; /* the length of the key */ | ^~~~~~ hash_util.h:170:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 170 | register unsigned initval=0; /* the previous hash, or an arbitrary value */ | ^~~~~~~ hash_util.h:171:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 171 | register unsigned a,b,c,len; | ^ hash_util.h:171:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 171 | register unsigned a,b,c,len; | ^ hash_util.h:171:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 171 | register unsigned a,b,c,len; | ^ hash_util.h:171:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 171 | register unsigned a,b,c,len; | ^~~ hash_util.h: In member function ‘size_t hash_fncts::operator()(const struct_en*) const’: hash_util.h:212:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 212 | register short *k; /* the key */ | ^ hash_util.h:213:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 213 | register unsigned length; /* the length of the key */ | ^~~~~~ hash_util.h:214:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 214 | register unsigned initval=0; /* the previous hash, or an arbitrary value */ | ^~~~~~~ hash_util.h:215:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 215 | register unsigned a,b,c,len; | ^ hash_util.h:215:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 215 | register unsigned a,b,c,len; | ^ hash_util.h:215:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 215 | register unsigned a,b,c,len; | ^ hash_util.h:215:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 215 | register unsigned a,b,c,len; | ^~~ g++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -Wno-write-strings -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o pknots.o pknots.cpp g++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -Wno-write-strings -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAlocmin.o RNAlocmin.cpp g++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -Wno-write-strings -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o treeplot.o treeplot.cpp gcc -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -Wno-write-strings -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fexceptions -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAlocmin_cmdline.o RNAlocmin_cmdline.c In file included from globals.h:10, from RNAlocmin.h:7, from RNAlocmin.cpp:16: hash_util.h: In member function ‘size_t hash_fncts::operator()(const Structure&) const’: hash_util.h:82:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 82 | register short *k; /* the key */ | ^ hash_util.h:83:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 83 | register unsigned length; /* the length of the key */ | ^~~~~~ hash_util.h:84:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 84 | register unsigned initval=0; /* the previous hash, or an arbitrary value */ | ^~~~~~~ hash_util.h:85:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 85 | register unsigned a,b,c,len; | ^ hash_util.h:85:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 85 | register unsigned a,b,c,len; | ^ hash_util.h:85:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 85 | register unsigned a,b,c,len; | ^ hash_util.h:85:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 85 | register unsigned a,b,c,len; | ^~~ hash_util.h: In member function ‘size_t hash_fncts::operator()(const struct_en&) const’: hash_util.h:126:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 126 | register short *k; /* the key */ | ^ hash_util.h:127:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 127 | register unsigned length; /* the length of the key */ | ^~~~~~ hash_util.h:128:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 128 | register unsigned initval=0; /* the previous hash, or an arbitrary value */ | ^~~~~~~ hash_util.h:129:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 129 | register unsigned a,b,c,len; | ^ hash_util.h:129:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 129 | register unsigned a,b,c,len; | ^ hash_util.h:129:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 129 | register unsigned a,b,c,len; | ^ hash_util.h:129:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 129 | register unsigned a,b,c,len; | ^~~ hash_util.h: In member function ‘size_t hash_fncts::operator()(const Structure*) const’: hash_util.h:168:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register short *k; /* the key */ | ^ hash_util.h:169:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 169 | register unsigned length; /* the length of the key */ | ^~~~~~ hash_util.h:170:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 170 | register unsigned initval=0; /* the previous hash, or an arbitrary value */ | ^~~~~~~ hash_util.h:171:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 171 | register unsigned a,b,c,len; | ^ hash_util.h:171:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 171 | register unsigned a,b,c,len; | ^ hash_util.h:171:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 171 | register unsigned a,b,c,len; | ^ hash_util.h:171:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 171 | register unsigned a,b,c,len; | ^~~ hash_util.h: In member function ‘size_t hash_fncts::operator()(const struct_en*) const’: hash_util.h:212:19: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 212 | register short *k; /* the key */ | ^ hash_util.h:213:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 213 | register unsigned length; /* the length of the key */ | ^~~~~~ hash_util.h:214:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 214 | register unsigned initval=0; /* the previous hash, or an arbitrary value */ | ^~~~~~~ hash_util.h:215:21: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 215 | register unsigned a,b,c,len; | ^ hash_util.h:215:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 215 | register unsigned a,b,c,len; | ^ hash_util.h:215:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 215 | register unsigned a,b,c,len; | ^ hash_util.h:215:27: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 215 | register unsigned a,b,c,len; | ^~~ g++ -I/usr/include/json-c/ -I/usr/include/libsvm/ -Wl,-Bsymbolic-functions -Wl,-z,relro -o RNAlocmin RNAlocmin_cmdline.o barrier_tree.o findpath_pk.o flood.o globals.o hash_util.o main.o move_set_inside.o move_set_pk.o neighbourhood.o pknots.o RNAlocmin.o treeplot.o -fno-strict-aliasing -flto -L./../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp make[5]: Leaving directory '/<>/src/RNAlocmin' make[4]: Leaving directory '/<>/src/RNAlocmin' Making all in tests make[4]: Entering directory '/<>/tests' cp ../interfaces/Perl/RNA/t/Design.t ./perl5/test-RNA-Design.t make all-am make[5]: Entering directory '/<>/tests' make[5]: Nothing to be done for 'all-am'. make[5]: Leaving directory '/<>/tests' make[4]: Leaving directory '/<>/tests' Making all in examples make[4]: Entering directory '/<>/examples' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/examples' Making all in packaging/macosx make[4]: Entering directory '/<>/packaging/macosx' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/packaging/macosx' make[4]: Entering directory '/<>' make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' if [ -r doc/RNAlib-*pdf; then cd doc && ln -f RNAlib-*.pdf RNAlib.pdf; fi /bin/bash: line 1: [: missing `]' make[1]: Leaving directory '/<>' dh_auto_test -a make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 make[1]: Entering directory '/<>' Making check in src make[2]: Entering directory '/<>/src' Making check in ViennaRNA make[3]: Entering directory '/<>/src/ViennaRNA' Making check in static make[4]: Entering directory '/<>/src/ViennaRNA/static' make check-am make[5]: Entering directory '/<>/src/ViennaRNA/static' make[5]: Nothing to be done for 'check-am'. make[5]: Leaving directory '/<>/src/ViennaRNA/static' make[4]: Leaving directory '/<>/src/ViennaRNA/static' Making check in plotting/naview make[4]: Entering directory '/<>/src/ViennaRNA/plotting/naview' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/<>/src/ViennaRNA/plotting/naview' make[4]: Entering directory '/<>/src/ViennaRNA' make[4]: Nothing to be done for 'check-am'. make[4]: Leaving directory '/<>/src/ViennaRNA' make[3]: Leaving directory '/<>/src/ViennaRNA' Making check in bin make[3]: Entering directory '/<>/src/bin' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/src/bin' Making check in Utils make[3]: Entering directory '/<>/src/Utils' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/src/Utils' Making check in Cluster make[3]: Entering directory '/<>/src/Cluster' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/src/Cluster' make[3]: Entering directory '/<>/src' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>/src' Making check in man make[2]: Entering directory '/<>/man' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/man' Making check in misc make[2]: Entering directory '/<>/misc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/misc' Making check in doc make[2]: Entering directory '/<>/doc' Making check in CLA make[3]: Entering directory '/<>/doc/CLA' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/doc/CLA' make[3]: Entering directory '/<>/doc' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/<>/doc' make[2]: Leaving directory '/<>/doc' Making check in RNA-Tutorial make[2]: Entering directory '/<>/RNA-Tutorial' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/RNA-Tutorial' Making check in interfaces make[2]: Entering directory '/<>/interfaces' Making check in Perl make[3]: Entering directory '/<>/interfaces/Perl' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/interfaces/Perl' Making check in Python make[3]: Entering directory '/<>/interfaces/Python' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/interfaces/Python' make[3]: Entering directory '/<>/interfaces' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/<>/interfaces' make[2]: Leaving directory '/<>/interfaces' Making check in src/Kinfold make[2]: Entering directory '/<>/src/Kinfold' Making check in Example make[3]: Entering directory '/<>/src/Kinfold/Example' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/src/Kinfold/Example' make[3]: Entering directory '/<>/src/Kinfold' make[3]: Leaving directory '/<>/src/Kinfold' make[2]: Leaving directory '/<>/src/Kinfold' Making check in src/RNAlocmin make[2]: Entering directory '/<>/src/RNAlocmin' make[2]: Leaving directory '/<>/src/RNAlocmin' Making check in tests make[2]: Entering directory '/<>/tests' make check-am make[3]: Entering directory '/<>/tests' make make[4]: Entering directory '/<>/tests' make all-am make[5]: Entering directory '/<>/tests' make[5]: Nothing to be done for 'all-am'. make[5]: Leaving directory '/<>/tests' make[4]: Leaving directory '/<>/tests' make check-TESTS make[4]: Entering directory '/<>/tests' make[5]: Entering directory '/<>/tests' PASS: RNAfold/partfunc 1 - Partition function (centroid, MEA) PASS: RNAfold/partfunc 2 - Partition function (base pair probabilities) PASS: RNAfold/partfunc 3 - Partition function (stack probabilities) PASS: RNAfold/long 1 - MFE prediction (.seq file) PASS: RNAfold/long 2 - MFE prediction (.fasta file) PASS: RNAfold/general 1 - correct version number PASS: RNAfold/general 2 - MFE prediction (RNAfold -d0) PASS: RNAfold/general 3 - MFE prediction (RNAfold -d1) PASS: RNAfold/general 4 - MFE prediction (RNAfold -d2) PASS: RNAfold/general 5 - MFE prediction (RNAfold -d3) PASS: RNAfold/general 6 - MFE prediction (RNAfold --noLP) PASS: RNAfold/general 7 - MFE prediction (RNAfold -T 25) PASS: RNAfold/general 8 - MFE prediction (RNAfold -T 40) PASS: RNAfold/general 9 - MFE prediction (RNAfold --maxBPspan=30) PASS: RNAfold/general 10 - MFE prediction and automatic sequence ID feature PASS: RNAfold/general 11 - MFE prediction (-P dna_mathews1999.par) PASS: RNAfold/general 12 - MFE prediction (-P dna_mathews2004.par) PASS: RNAfold/general 13 - MFE prediction (-P rna_andronescu2007.par) PASS: RNAfold/general 14 - MFE prediction (-P rna_turner1999.par) PASS: RNAfold/special 1 - G-Quadruplex feature (MFE, centroid, MEA) PASS: RNAfold/special 2 - G-Quadruplex feature (probabilities) PASS: RNAfold/special 3 - Aptamer Motif - Theophylline (MFE, centroid, MEA) PASS: RNAfold/special 4 - Aptamer Motif - Theophylline (probabilities) PASS: RNAfold/special 5 - Command file - Constraints and Ligand motifs (MFE, centroid, MEA) PASS: RNAfold/special 6 - Command file - Constraints and Ligand motifs (probabilities) PASS: RNAfold/special 7 - SHAPE probing data (TPP_riboswitch_E.coli) Deigan et al. 2009 method PASS: RNAfold/special 8 - SHAPE probing data (TPP_riboswitch_E.coli) Zarringhalam et al. 2012 method PASS: RNAfold/special 9 - SHAPE probing data (TPP_riboswitch_E.coli) Washietl et al. 2012 method PASS: RNAfold/special 10 - SHAPE probing data (Lysine_riboswitch_T._martima) Deigan et al. 2009 method PASS: RNAfold/special 11 - SHAPE probing data (Lysine_riboswitch_T._martima) Zarringhalam et al. 2012 method PASS: RNAfold/special 12 - SHAPE probing data (Lysine_riboswitch_T._martima) Washietl et al. 2012 method PASS: RNAfold/special 13 - SHAPE probing data (5domain16S_rRNA_H.volcanii) Deigan et al. 2009 method PASS: RNAfold/special 14 - SHAPE probing data (5domain16S_rRNA_H.volcanii) Zarringhalam et al. 2012 method PASS: RNAfold/special 15 - SHAPE probing data (5domain16S_rRNA_H.volcanii) Washietl et al. 2012 method PASS: RNAfold/special 16 - SHAPE probing data (5domain16S_rRNA_E.coli) Deigan et al. 2009 method PASS: RNAfold/special 17 - SHAPE probing data (5domain16S_rRNA_E.coli) Zarringhalam et al. 2012 method PASS: RNAfold/special 18 - SHAPE probing data (5domain16S_rRNA_E.coli) Washietl et al. 2012 method PASS: RNAfold/special 19 - MFE/PF prediction (RNAfold -p0 --circ) PASS: RNAfold/special 20 - MFE/PF prediction (circular RNAs + Hard constraints) PASS: RNAfold/special 21 - MFE/PF prediction (circular RNAs + Soft constraints) PASS: RNAcofold/general 1 - Version number (RNAcofold --version) PASS: RNAcofold/general 2 - MFE prediction (RNAcofold -d0) PASS: RNAcofold/general 3 - MFE prediction (RNAcofold -d1) PASS: RNAcofold/general 4 - MFE prediction (RNAcofold -d2) PASS: RNAcofold/general 5 - MFE prediction (RNAcofold -d3) PASS: RNAcofold/general 6 - MFE prediction (RNAcofold --noLP) PASS: RNAcofold/general 7 - MFE prediction (RNAcofold -T 25) PASS: RNAcofold/general 8 - MFE prediction (RNAcofold -T 40) PASS: RNAcofold/general 9 - MFE prediction (RNAcofold --maxBPspan=30) PASS: RNAcofold/general 10 - MFE prediction and automatic sequence ID feature PASS: RNAcofold/general 11 - MFE prediction (-P dna_mathews1999.par) PASS: RNAcofold/general 12 - MFE prediction (-P dna_mathews2004.par) PASS: RNAcofold/general 13 - MFE prediction (-P rna_andronescu2007.par) PASS: RNAcofold/general 14 - MFE prediction (-P rna_turner1999.par) PASS: RNAalifold/partfunc 1 - Partition function (centroid, MEA) PASS: RNAalifold/partfunc 2 - Partition function (base pair probabilities) PASS: perl5/test-RNA.pl 1 - Version number ($RNA::VERSION) PASS: perl5/test-RNA.pl 2 - Hamming distance (RNA::hamming) PASS: perl5/test-RNA.pl 3 - Base pair distance (RNA::bp_distance) PASS: perl5/test-RNA.pl 4 - Global default temperature ($RNA::temperature) PASS: perl5/test-RNA.pl 5 - MFE folding - obsolete way (RNA::fold) PASS: perl5/test-RNA.pl 6 - MFE folding - new way (RNA::fold) PASS: perl5/test-RNA.pl 7 - Compare MFE prediction against energy evaluation (RNA::energy_of_struct) PASS: perl5/test-RNA.pl 8 - Constrained MFE prediction - structure (RNA::fold) PASS: perl5/test-RNA.pl 9 - Constrained MFE prediction - energy (RNA::energy_of_struct) PASS: perl5/test-RNA.pl 10 - MFE cofold prediction - structure (RNA::cofold) PASS: perl5/test-RNA.pl 11 - MFE cofold prediction - energy (RNA::energy_of_struct) PASS: perl5/test-RNA.pl 12 - Partition function cofold - Ensemble energy (RNA::co_pf_fold) PASS: perl5/test-RNA.pl 13 - Partition function cofold - concentrations (RNA::get_concentrations) PASS: perl5/test-RNA.pl 14 - Partition function - MFE vs. ensemble energy comparison PASS: perl5/test-RNA.pl 15 - Tree edit distance (RNA::tree_edit_distance) PASS: perl5/test-RNA.pl 16 - Access to global iindx array ($RNA::iindx) PASS: perl5/test-RNA.pl 17 - Access to global xsubi array ($RNA::xsubi) PASS: perl5/test-RNA.pl 18 - Access to global pr array for base pair probabilities (RNA::get_pr and via RNA::intP_getitem) PASS: perl5/test-RNA.pl 19 - Base pair profile (RNA::Make_bp_profile) PASS: perl5/test-RNA.pl 20 - Structure compression (RNA::pack_structure and RNA::unpack_structure) PASS: perl5/test-RNA.pl 21 - Structure parsing - (RNA::parse_structure and $RNA::loops) PASS: perl5/test-RNA.pl 22 - Structure parsing - (RNA::parse_structure and $RNA::pairs) PASS: perl5/test-RNA.pl 23 - Structure parsing - (RNA::parse_structure and $RNA::unpaired) PASS: perl5/test-RNA.pl 24 - Structure parsing - (RNA::parse_structure and $RNA::loop_degree) PASS: perl5/test-RNA.pl 25 - Inverse folding (RNA::inverse) PASS: perl5/test-RNA.pl 26 - Energy evaluation - dimer (RNA::energy_of_struct) PASS: perl5/test-RNA.pl 27 - Duplex MFE prediction (RNA::duplexfold) PASS: perl5/test-RNA.pl 28 - Comparative MFE prediction - structure (RNA::alifold) PASS: perl5/test-RNA.pl 29 - Comparative MFE prediction - most informative sequence (RNA::consens_mis) PASS: perl5/test-RNA.pl 30 - Move set - gradient descent (RNA::move_standard) PASS: perl5/test-RNA.pl 31 - Move set - First (RNA::move_standard) PASS: perl5/test-RNA.pl 32 - Model details - default dangles (RNA::md->new()->{dangles}) PASS: perl5/test-RNA.pl 33 - Model details - default temperature (RNA::md->new()->{temperature}) PASS: perl5/test-RNA.pl 34 - Global model settings - set dangles ($RNA::dangles) PASS: perl5/test-RNA.pl 35 - Global model settings - set temperature ($RNA::temperature) PASS: perl5/test-RNA.pl 36 - Model details - globally set dangles ($RNA::dangles and RNA::md->new()->{dangles}) PASS: perl5/test-RNA.pl 37 - Model details - globally set temperature ($RNA::temperature and RNA::md->new()->{temperature}) PASS: perl5/test-RNA.pl 38 - Energy parameters - default temperature (RNA::param->new()->{temperature}) PASS: perl5/test-RNA.pl 39 - Energy parameters - initialized with non-defaut temperature (RNA::param->new($md)->{temperature}) PASS: perl5/test-RNA.pl 40 - Boltzmann factors - default temperature (RNA::exp_param->new()->{temperature}) PASS: perl5/test-RNA.pl 41 - Boltzmann factors - initialized with non-defaut temperature (RNA::exp_param->new($md)->{temperature}) PASS: perl5/test-RNA.pl 42 - Fold compound - default type (new RNA::fold_compound($seq)->{type}) PASS: perl5/test-RNA.pl 43 - Fold compound - alignment type (new RNA::fold_compound($alignment)->{type}) PASS: perl5/test-RNA.pl 44 - Fold compound method - centroid structure ($fc->centroid()) PASS: perl5/test-RNA.pl 45 - Fold compound method - centroid distance ($fc->centroid()) PASS: perl5/test-RNA.pl 46 - Fold compound method - partition function ($fc->pf()) PASS: perl5/test-RNA.pl 47 - Fold compound method - mean base pair distance ($fc->centroid()) PASS: perl5/test-RNA.pl 48 PASS: perl5/test-RNA.pl 49 PASS: perl5/test-RNA.pl 50 PASS: perl5/test-RNA.pl 51 PASS: perl5/test-RNA.pl 52 PASS: perl5/test-RNA.pl 53 PASS: perl5/test-RNA.pl 54 PASS: perl5/test-RNA.pl 55 PASS: perl5/test-RNA.pl 56 PASS: perl5/test-RNA-callbacks.pl 1 PASS: perl5/test-RNA-combinatorics.pl 1 - Enumerate Necklaces (4 sequences, 1 strand per sequences) PASS: perl5/test-RNA-combinatorics.pl 2 - Enumerate necklaces (3 sequences, different number of strands per sequence) PASS: perl5/test-RNA-Design.t 1 - use RNA; PASS: perl5/test-RNA-Design.t 2 - use RNA::Design; PASS: perl5/test-RNA-Design.t 3 - use RNA::Utils; PASS: perl5/test-RNA-Design.t 4 - 'Object initialized' isa 'RNA::Design' PASS: perl5/test-RNA-Design.t 5 - RNA::Design -- Default Options PASS: perl5/test-RNA-Design.t 6 - RNA::Design -- Internal Functions PASS: perl5/test-RNA-Design.t 7 - find_dependency_paths -- one bpair PASS: perl5/test-RNA-Design.t 8 - find_dependency_paths -- three knots PASS: perl5/test-RNA-Design.t 9 - find_dependency_paths -- "[,]" knot PASS: perl5/test-RNA-Design.t 10 - find_dependency_paths -- nested knots PASS: perl5/test-RNA-Design.t 11 - find_dependency_paths -- two pathways PASS: perl5/test-RNA-Design.t 12 - find_dependency_paths -- duplicate struct PASS: perl5/test-RNA-Design.t 13 - find_dependency_paths -- cycles,pathways,basepairs PASS: perl5/test-RNA-Design.t 14 - explore_sequence_space() PASS: perl5/test-RNA-ensemble_defect.pl 1 - Ensemble Defect PASS: perl5/test-RNA-ensemble_defect.pl 2 - Ensemble Defect (pair table) PASS: perl5/test-RNA-ensemble_defect.pl 3 - Ensemble Defect (pk) PASS: perl5/test-RNA-ensemble_defect.pl 4 - Ensemble Defect (pk, pair table) PASS: perl5/test-RNA-ensemble_defect.pl 5 - Ensemble Defect (Sanity check 1) PASS: perl5/test-RNA-ensemble_defect.pl 6 - Ensemble Defect (Sanity check 2) PASS: perl5/test-RNA-file-formats.pl 1 PASS: perl5/test-RNA-file-formats.pl 2 PASS: perl5/test-RNA-file-formats.pl 3 PASS: perl5/test-RNA-file-formats.pl 4 PASS: perl5/test-RNA-file-formats.pl 5 PASS: perl5/test-RNA-file-formats.pl 6 PASS: perl5/test-RNA-file-formats.pl 7 PASS: perl5/test-RNA-file-formats.pl 8 PASS: perl5/test-RNA-file-formats.pl 9 PASS: perl5/test-RNA-file-formats.pl 10 PASS: perl5/test-RNA-file-formats.pl 11 PASS: perl5/test-RNA-file-formats.pl 12 PASS: perl5/test-RNA-file-formats.pl 13 PASS: perl5/test-RNA-file-formats.pl 14 PASS: perl5/test-RNA-file-formats.pl 15 PASS: perl5/test-RNA-file-formats.pl 16 PASS: perl5/test-RNA-file-formats.pl 17 PASS: perl5/test-RNA-file-formats.pl 18 PASS: perl5/test-RNA-file-formats.pl 19 PASS: perl5/test-RNA-file-formats.pl 20 PASS: perl5/test-RNA-file-formats.pl 21 PASS: perl5/test-RNA-file-formats.pl 22 PASS: perl5/test-RNA-file-formats.pl 23 PASS: perl5/test-RNA-file-formats.pl 24 PASS: perl5/test-RNA-file-formats.pl 25 PASS: perl5/test-RNA-file-formats.pl 26 PASS: perl5/test-RNA-file-formats.pl 27 PASS: perl5/test-RNA-file-formats.pl 28 PASS: perl5/test-RNA-mfe_eval.pl 1 PASS: perl5/test-RNA-mfe_eval.pl 2 PASS: perl5/test-RNA-mfe_eval.pl 3 PASS: perl5/test-RNA-mfe_eval.pl 4 PASS: perl5/test-RNA-mfe_eval.pl 5 PASS: perl5/test-RNA-mfe_eval.pl 6 PASS: perl5/test-RNA-mfe_eval.pl 7 PASS: perl5/test-RNA-mfe_eval.pl 8 PASS: perl5/test-RNA-mfe_eval.pl 9 PASS: perl5/test-RNA-mfe_eval.pl 10 PASS: perl5/test-RNA-mfe_eval.pl 11 PASS: perl5/test-RNA-mfe_window.pl 1 PASS: perl5/test-RNA-mfe_window.pl 2 PASS: perl5/test-RNA-mfe_window.pl 3 PASS: perl5/test-RNA-mfe_window.pl 4 PASS: perl5/test-RNA-mfe_window.pl 5 PASS: perl5/test-RNA-mfe_window.pl 6 PASS: perl5/test-RNA-mfe_window.pl 7 PASS: perl5/test-RNA-mfe_window.pl 8 PASS: perl5/test-RNA-mfe_window.pl 9 PASS: perl5/test-RNA-mfe_window.pl 10 PASS: perl5/test-RNA-mfe_window.pl 11 PASS: perl5/test-RNA-mfe_window.pl 12 PASS: perl5/test-RNA-mfe_window.pl 13 PASS: perl5/test-RNA-mfe_window.pl 14 PASS: perl5/test-RNA-mfe_window.pl 15 PASS: perl5/test-RNA-mfe_window.pl 16 PASS: perl5/test-RNA-mfe_window.pl 17 PASS: perl5/test-RNA-mfe_window.pl 18 PASS: perl5/test-RNA-mfe_window.pl 19 PASS: perl5/test-RNA-mfe_window.pl 20 PASS: perl5/test-RNA-mfe_window.pl 21 PASS: perl5/test-RNA-pf_window.pl 1 PASS: perl5/test-RNA-pf_window.pl 2 PASS: perl5/test-RNA-pf_window.pl 3 PASS: perl5/test-RNA-pf_window.pl 4 PASS: perl5/test-RNA-pf_window.pl 5 PASS: perl5/test-RNA-pf_window.pl 6 PASS: perl5/test-RNA-pf_window.pl 7 PASS: perl5/test-RNA-pf_window.pl 8 PASS: perl5/test-RNA-pf_window.pl 9 PASS: perl5/test-RNA-pf_window.pl 10 PASS: perl5/test-RNA-pf_window.pl 11 PASS: perl5/test-RNA-pf_window.pl 12 PASS: perl5/test-RNA-pf_window.pl 13 PASS: perl5/test-RNA-pf_window.pl 14 PASS: perl5/test-RNA-pf_window.pl 15 PASS: perl5/test-RNA-pf_window.pl 16 PASS: perl5/test-RNA-pf_window.pl 17 PASS: perl5/test-RNA-pf_window.pl 18 PASS: perl5/test-RNA-pf_window.pl 19 PASS: perl5/test-RNA-pf_window.pl 20 PASS: perl5/test-RNA-pf_window.pl 21 PASS: perl5/test-RNA-pf_window.pl 22 PASS: perl5/test-RNA-pf_window.pl 23 PASS: perl5/test-RNA-pf_window.pl 24 PASS: perl5/test-RNA-pf_window.pl 25 PASS: perl5/test-RNA-pf_window.pl 26 PASS: perl5/test-RNA-pf_window.pl 27 PASS: perl5/test-RNA-pf_window.pl 28 PASS: perl5/test-RNA-pf_window.pl 29 PASS: perl5/test-RNA-pf_window.pl 30 PASS: perl5/test-RNA-pf_window.pl 31 PASS: perl5/test-RNA-pf_window.pl 32 PASS: perl5/test-RNA-pf_window.pl 33 PASS: perl5/test-RNA-pf_window.pl 34 PASS: perl5/test-RNA-pf_window.pl 35 PASS: perl5/test-RNA-pf_window.pl 36 PASS: perl5/test-RNA-pf_window.pl 37 PASS: perl5/test-RNA-boltzmann-sampling.pl 1 PASS: perl5/test-RNA-boltzmann-sampling.pl 2 PASS: perl5/test-RNA-boltzmann-sampling.pl 3 PASS: perl5/test-RNA-boltzmann-sampling.pl 4 PASS: perl5/test-RNA-boltzmann-sampling.pl 5 PASS: perl5/test-RNA-boltzmann-sampling.pl 6 PASS: perl5/test-RNA-boltzmann-sampling.pl 7 PASS: perl5/test-RNA-boltzmann-sampling.pl 8 PASS: perl5/test-RNA-boltzmann-sampling.pl 9 PASS: perl5/test-RNA-boltzmann-sampling.pl 10 PASS: perl5/test-RNA-boltzmann-sampling.pl 11 PASS: perl5/test-RNA-boltzmann-sampling.pl 12 PASS: perl5/test-RNA-boltzmann-sampling.pl 13 PASS: perl5/test-RNA-boltzmann-sampling.pl 14 PASS: perl5/test-RNA-boltzmann-sampling.pl 15 PASS: perl5/test-RNA-boltzmann-sampling.pl 16 PASS: perl5/test-RNA-boltzmann-sampling.pl 17 PASS: perl5/test-RNA-boltzmann-sampling.pl 18 PASS: perl5/test-RNA-boltzmann-sampling.pl 19 PASS: perl5/test-RNA-boltzmann-sampling.pl 20 PASS: perl5/test-RNA-boltzmann-sampling.pl 21 PASS: perl5/test-RNA-boltzmann-sampling.pl 22 PASS: perl5/test-RNA-boltzmann-sampling.pl 23 PASS: perl5/test-RNA-boltzmann-sampling.pl 24 PASS: perl5/test-RNA-boltzmann-sampling.pl 25 PASS: perl5/test-RNA-boltzmann-sampling.pl 26 PASS: perl5/test-RNA-boltzmann-sampling.pl 27 PASS: perl5/test-RNA-boltzmann-sampling.pl 28 PASS: perl5/test-RNA-boltzmann-sampling.pl 29 PASS: perl5/test-RNA-boltzmann-sampling.pl 30 PASS: perl5/test-RNA-boltzmann-sampling.pl 31 PASS: perl5/test-RNA-boltzmann-sampling.pl 32 PASS: perl5/test-RNA-constraints.pl 1 - Fold compound method - constraints_add - hard constraints PASS: perl5/test-RNA-constraints.pl 2 - Fold compound method - hc_init PASS: perl5/test-RNA-constraints.pl 3 - Fold compound method - constraints_add - soft constraints PASS: perl5/test-RNA-constraints.pl 4 - Fold compound method - hc_add_up PASS: perl5/test-RNA-constraints.pl 5 - Fold compound method - hc_add_bp_nonspecific PASS: perl5/test-RNA-constraints.pl 6 - Fold compound method - hc_ad_bp PASS: perl5/test-RNA-constraints.pl 7 - Fold compound method - hc_add_from_db PASS: perl5/test-RNA-constraints.pl 8 - Fold compound method - hc_add_bp - sliding window MFE PASS: perl5/test-RNA-constraints-soft.pl 1 PASS: perl5/test-RNA-constraints-soft.pl 2 PASS: perl5/test-RNA-constraints-soft.pl 3 PASS: perl5/test-RNA-constraints-soft.pl 4 PASS: perl5/test-RNA-constraints-SHAPE.pl 1 PASS: perl5/test-RNA-constraints-SHAPE.pl 2 PASS: perl5/test-RNA-constraints-SHAPE.pl 3 PASS: perl5/test-RNA-constraints-SHAPE.pl 4 PASS: perl5/test-RNA-constraints-special.pl 1 PASS: python/test-RNA-combinatorics.py 1 - Enumerate necklaces (4 sequences, 1 strand per sequences) PASS: python/test-RNA-combinatorics.py 2 - Enumerate necklaces (3 sequences, different number of strands per sequence) PASS: python/test-RNA-constraints.py 1 - Add (hard and soft) contraints from file PASS: python/test-RNA-constraints.py 2 - Add hard constraints - base pairs PASS: python/test-RNA-constraints.py 3 - Add hard constraints - base pairing unspecific PASS: python/test-RNA-constraints.py 4 - Add hard constraints from dot-bracket string PASS: python/test-RNA-constraints.py 5 - Add hard constraints - unpaired PASS: python/test-RNA-constraints.py 6 - Hard constraints - base pairs in sliding-window MFE prediction PASS: python/test-RNA-constraints-soft.py 1 - Soft constraints - base pairs sliding window MFE PASS: python/test-RNA-constraints-soft.py 2 - Soft constraints - unpaired nucleotides sliding window MFE PASS: python/test-RNA-constraints-soft.py 3 - Soft constraints - base pairs PASS: python/test-RNA-constraints-soft.py 4 - Soft constraints - unpaired nucleotides PASS: python/test-RNA-constraints-soft.py 5 - Soft constraints - shift energy landscape PASS: python/test-RNA-constraints-SHAPE.py 1 - SHAPE data Deigan et al. 2009 method - TPP riboswitch PASS: python/test-RNA-constraints-SHAPE.py 2 - SHAPE data Deigan et al. 2009 method - Comparative MFE prediction PASS: python/test-RNA-constraints-SHAPE.py 3 - SHAPE data Zarringhalam et al 2012 method PASS: python/test-RNA-constraints-SHAPE.py 4 - SHAPE data Deigan et al. 2009 method - Lysine riboswitch PASS: python/test-RNA-constraints-special.py 1 - Soft constraints - Motif - Hairpin PASS: python/test-RNA-constraints-special.py 2 - Soft constraints - Motif - Theophylline aptamer PASS: python/test-RNA-ensemble_defect.py 1 - Ensembe defect PASS: python/test-RNA-ensemble_defect.py 2 - Ensemble defect (pk) PASS: python/test-RNA-ensemble_defect.py 3 - Ensembe defect (sanity check) PASS: python/test-RNA-file-formats.py 1 - Detect CLUSTAL formatted MSA file PASS: python/test-RNA-file-formats.py 2 - Detect FASTA formatted MSA file PASS: python/test-RNA-file-formats.py 3 - Detect MAF formatted MSA file PASS: python/test-RNA-file-formats.py 4 - Detect STOCKHOLM formatted MSA file PASS: python/test-RNA-file-formats.py 5 - Detect unknown MSA file format PASS: python/test-RNA-file-formats.py 6 - Read Clustal formatted MSA file PASS: python/test-RNA-file-formats.py 7 - Read FASTA formatted MSA file PASS: python/test-RNA-file-formats.py 8 - Read MAF formatted MSA file PASS: python/test-RNA-file-formats.py 9 - Read multiple MSAs from MAF file PASS: python/test-RNA-file-formats.py 10 - Read Multiple MSAs from Stockholm file PASS: python/test-RNA-file-formats.py 11 - Read Stockholm formatted MSA file PASS: python/test-RNA-mfe_eval.py 1 - Structure energy evaluation - Covariance energy contribution PASS: python/test-RNA-mfe_eval.py 2 - Loop energy evaluation PASS: python/test-RNA-mfe_eval.py 3 - Move energy evaluation - base pair removal PASS: python/test-RNA-mfe_eval.py 4 - Move energy evaluation - base pair insertion PASS: python/test-RNA-mfe_eval.py 5 - Move energy evaluation - base pair removal - pair table PASS: python/test-RNA-mfe_eval.py 6 - Structure energy evaluation - dot-bracket string PASS: python/test-RNA-mfe_eval.py 7 - Structure energy evaluation - pair table PASS: python/test-RNA-mfe_eval.py 8 - Structure energy evaluation - pair table - verbose output PASS: python/test-RNA-mfe_eval.py 9 - Structure energy evaluation - dot-bracket string - verbose output PASS: python/test-RNA-mfe_eval.py 10 - MFE prediction - single sequence PASS: python/test-RNA-mfe_eval.py 11 - MFE prediction - dimer PASS: python/test-RNA-mfe_window.py 1 - MFE prediction - RNA.Lfold_cb PASS: python/test-RNA-mfe_window.py 2 - MFE prediction - sequence aignments - RNA.aliLfold_cb PASS: python/test-RNA-mfe_window.py 3 - MFE prediction - fold_compound.mfe_window() PASS: python/test-RNA-mfe_window.py 4 - MFE prediction - sequence alignments - fold_compound.mfe_window_cb PASS: python/test-RNA-pf_window.py 1 - SHAPE data PASS: python/test-RNA-pf_window.py 2 - RNA.pfl_fold() - sanity check for base pair probabilities PASS: python/test-RNA-pf_window.py 3 - RNA.pfl_fold_up() - sanity check for unpaired probabilities PASS: python/test-RNA-pf_window.py 4 - Soft constraints - energy landscape shift - base pair probabilities PASS: python/test-RNA-pf_window.py 5 - Compare results from local and global predictions PASS: python/test-RNA-pf_window.py 6 - Soft constraints - energy landscape shift - unpaired probabilities PASS: python/test-RNA-pf_window.py 7 - Unpaired probabilities for u=1 are the same as obtained from global fold PASS: python/test-RNA-pf_window.py 8 - Unpaired probabilties for short RNAs are identical to what we get from exhaustive enumeration PASS: python/test-RNA-pf_window.py 9 - Reporting check for probs_window() callback PASS: python/test-RNA-sc-callbacks.py 1 - Hairpin backtracking (basepair) PASS: python/test-RNA-sc-callbacks.py 2 - Hairpin backtracking (Dictionary) PASS: python/test-RNA-sc-callbacks.py 3 - Hairpin backtracking (Tuples) PASS: python/test-RNA-sc-callbacks.py 4 - Revert MFE to MaximumMatching PASS: python/test-RNA-subopt.py 1 - RNA.subopt (pointer mode) PASS: python/test-RNA-subopt.py 2 - RNA.subopt (list mode) PASS: python/test-RNA-subopt.py 3 - fold_compound.subopt() PASS: python/test-RNA-subopt.py 4 - fold_compound.subopt_cb() PASS: python/test-RNA-subopt.py 5 - fold_compound.subopt_zuker() PASS: python/test-RNA-subopt.py 6 - RNA.zukersubopt() (pointer mode) PASS: python/test-RNA-boltzmann-sampling.py 1 - Boltzmann sampling (single structure, a.k.a. pbacktrack) PASS: python/test-RNA-boltzmann-sampling.py 2 - Boltzmann sampling (single sub-structure, a.k.a. pbacktrack5) PASS: python/test-RNA-boltzmann-sampling.py 3 - Boltzmann sampling (multiple sub-structures, a.k.a. pbacktrack5_cb) PASS: python/test-RNA-boltzmann-sampling.py 4 - Boltzmann sampling (multiple sub-structures, a.k.a. pbacktrack5_num) PASS: python/test-RNA-boltzmann-sampling.py 5 - Boltzmann sampling (multiple structures, a.k.a. pbacktrack_cb) PASS: python/test-RNA-boltzmann-sampling.py 6 - Boltzmann sampling (multiple structures, a.k.a. pbacktrack_num) PASS: python/test-RNA-boltzmann-sampling.py 7 - Boltzmann sampling - non redundant PASS: python/test-RNA-boltzmann-sampling.py 8 - Boltzmann sampling - non redundant - callback PASS: python/test-RNA-boltzmann-sampling.py 9 - Boltzmann sampling - non redundant resume PASS: python/test-RNA-boltzmann-sampling.py 10 - Boltzmann sampling - non redundant resume - callback PASS: python/test-RNA-utils.py 1 - Base pair distance PASS: python/test-RNA-utils.py 2 - Base Pair Distance - PairTable PASS: python/test-RNA-utils.py 3 - Base Pair Distance (pk) - PairTable PASS: python/test-RNA-utils.py 4 - Sanitize (too) long file names PASS: python/test-RNA-utils.py 5 - Sanitize file names - with directories and special characters PASS: python/test-RNA-utils.py 6 - Sanitize file names - special characters PASS: python/test-RNA-utils.py 7 - Create pair table PASS: python/test-RNA-utils.py 8 - RNA,plist() PASS: python/test-RNA.py 1 - fold_compound method - centroid structure PASS: python/test-RNA.py 2 - Creating fold_compound - Single sequence 2D fold PASS: python/test-RNA.py 3 - Creating fold_compound - Multiple sequence alignment PASS: python/test-RNA.py 4 - Creating fold_compound - Single sequence PASS: python/test-RNA.py 5 - fold_compound method - Partition function, mean base pair distance PASS: python/test-RNA.py 6 - fold_compound method - Partition function for dimer PASS: python/test-RNA.py 7 - Comparative MFE prediction (alifold) PASS: python/test-RNA.py 8 - Cofolding of two sequences, MFE and Partition function, base pairing probabilities PASS: python/test-RNA.py 9 - Simple constrained MFE folding PASS: python/test-RNA.py 10 - Reduced symbol set PASS: python/test-RNA.py 11 - Duplex fold structure prediction PASS: python/test-RNA.py 12 - Energy of dimer structure PASS: python/test-RNA.py 13 - Energy Parameter structure - Boltzmann factors PASS: python/test-RNA.py 14 - Simple MFE prediction, structure, energy PASS: python/test-RNA.py 15 - Compute hamming distance between sequences and structures PASS: python/test-RNA.py 16 - Model details data structure - default values PASS: python/test-RNA.py 17 - Model details data structure - default values from global settings PASS: python/test-RNA.py 18 - Move set - gradient descent (energy, structure) PASS: python/test-RNA.py 19 - Move set - First (structure) PASS: python/test-RNA.py 20 - Energy Parameter structure PASS: python/test-RNA.py 21 - Structure parsing and splitting into components PASS: python/test-RNA.py 22 - Creating structure layout and base pair probability EPS plots PASS: python/test-RNA.py 23 - Simple XY coordinates PASS: python/test-RNA.py 24 - Default global Temperature PASS: python/test-RNA.py 25 - Tree edit distance PASS: python/test-RNA.py 26 - Version number PASS: RNAalifold/general 1 - correct version number PASS: RNAalifold/general 2 - MFE prediction (RNAalifold -d0) PASS: RNAalifold/general 3 - MFE prediction (RNAalifold -d2) PASS: RNAalifold/general 4 - MFE prediction (RNAalifold --noLP) PASS: RNAalifold/general 5 - MFE prediction (RNAalifold -T 25) PASS: RNAalifold/general 6 - MFE prediction (RNAalifold -T 40) PASS: RNAalifold/general 7 - MFE prediction (RNAalifold --maxBPspan=30) PASS: RNAalifold/general 8 - MFE prediction and automatic alignment ID feature PASS: RNAalifold/general 9 - MFE prediction (-P dna_mathews1999.par) PASS: RNAalifold/general 10 - MFE prediction (-P dna_mathews2004.par) PASS: RNAalifold/general 11 - MFE prediction (-P rna_andronescu2007.par) PASS: RNAalifold/general 12 - MFE prediction (-P rna_turner1999.par) PASS: RNAalifold/general 13 - MFE prediction with ribosum scoring (RNAalifold -r) PASS: RNAalifold/general 14 - MFE prediction with different file formats (alignment_clustal.aln) PASS: RNAalifold/general 15 - MFE prediction with different file formats (alignment_fasta.fa) PASS: RNAalifold/general 16 - MFE prediction with different file formats (alignment_maf.maf) PASS: RNAalifold/general 17 - MFE prediction with different file formats (alignment_stockholm.stk) PASS: RNAcofold/partfunc 1 - Partition function (centroid, MEA) PASS: RNAcofold/partfunc 2 - Partition function (centroid, dimers, monomers) PASS: RNAcofold/partfunc 3 - Partition function (base pair probabilities - Hetero-dimer) PASS: RNAcofold/partfunc 4 - Partition function (base pair probabilities - Homo-dimers) PASS: RNAcofold/partfunc 5 - Partition function (base pair probabilities - Monomers) PASS: RNAcofold/partfunc 6 - Partition function (concentrations) PASS: RNAalifold/special 1 - G-Quadruplex feature (MFE, centroid, MEA) PASS: RNAalifold/special 2 - Parallel processing of input data PASS: RNAalifold/special 3 - SHAPE probing data (070313_ecoli_cdiff_16S_clustalw.aln) Deigan et al. 2009 method PASS: RNAalifold/special 4 - MFE/PF prediction (RNAalifold -p0 --circ) ============================================================================ Testsuite summary for ViennaRNA 2.5.1 ============================================================================ # TOTAL: 419 # PASS: 419 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/<>/tests' make[4]: Leaving directory '/<>/tests' make[3]: Leaving directory '/<>/tests' make[2]: Leaving directory '/<>/tests' Making check in examples make[2]: Entering directory '/<>/examples' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/examples' Making check in packaging/macosx make[2]: Entering directory '/<>/packaging/macosx' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/packaging/macosx' make[2]: Entering directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a dh_installdirs -a debian/rules override_dh_auto_install make[1]: Entering directory '/<>' # rename perl scripts to remove the *.pl extension and create manpage via perldoc mkdir -p /<>/debian/tmp/usr/bin mkdir -p /<>/debian/tmp/usr/share/man/man1 #for script in `ls Utils/*.pl` ; do \ # newscript=`basename ${script} .pl` ; \ # cp -a ${script} /<>/debian/tmp/usr/bin/${newscript} ; \ # perldoc -onroff -F ${script} | \ # sed -e "s/${newscript}\.pl/${newscript}/g" \ # > /<>/debian/tmp/usr/share/man/man1/${newscript}.1 ; \ # if [ ! -s /<>/debian/tmp/usr/share/man/man1/${newscript}.1 ] ; then \ # rm -f /<>/debian/tmp/usr/share/man/man1/${newscript}.1 ; \ # fi ; \ #done dh_auto_install make -j1 install DESTDIR=/<>/vienna-rna-2.5.1\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/<>' Making install in src make[3]: Entering directory '/<>/src' Making install in ViennaRNA make[4]: Entering directory '/<>/src/ViennaRNA' Making install in static make[5]: Entering directory '/<>/src/ViennaRNA/static' make install-am make[6]: Entering directory '/<>/src/ViennaRNA/static' make[7]: Entering directory '/<>/src/ViennaRNA/static' make[7]: Nothing to be done for 'install-exec-am'. make[7]: Nothing to be done for 'install-data-am'. make[7]: Leaving directory '/<>/src/ViennaRNA/static' make[6]: Leaving directory '/<>/src/ViennaRNA/static' make[5]: Leaving directory '/<>/src/ViennaRNA/static' Making install in plotting/naview make[5]: Entering directory '/<>/src/ViennaRNA/plotting/naview' make[6]: Entering directory '/<>/src/ViennaRNA/plotting/naview' make[6]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/include/ViennaRNA/plotting/naview' /usr/bin/install -c -m 644 naview.h '/<>/debian/tmp/usr/include/ViennaRNA/plotting/naview' make[6]: Leaving directory '/<>/src/ViennaRNA/plotting/naview' make[5]: Leaving directory '/<>/src/ViennaRNA/plotting/naview' make[5]: Entering directory '/<>/src/ViennaRNA' make[6]: Entering directory '/<>/src/ViennaRNA' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/arm-linux-gnueabihf' /bin/bash ../../libtool --mode=install /usr/bin/install -c libRNA.la '/<>/debian/tmp/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c .libs/libRNA.lai /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libRNA.la libtool: install: /usr/bin/install -c .libs/libRNA.a /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libRNA.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libRNA.a libtool: install: gcc-ranlib /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libRNA.a libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf' /usr/bin/mkdir -p '/<>/debian/tmp/usr/include/ViennaRNA' /usr/bin/install -c -m 644 vrna_config.h '/<>/debian/tmp/usr/include/ViennaRNA' /usr/bin/mkdir -p '/<>/debian/tmp/usr/include/ViennaRNA' /usr/bin/install -c -m 644 concentrations.h wrap_dlib.h pair_mat.h RNAstruct.h dist_vars.h mfe.h mfe_window.h fold.h part_func.h part_func_window.h pf_multifold.h stringdist.h edit_cost.h fold_vars.h profiledist.h treedist.h inverse.h subopt.h subopt_zuker.h cofold.h duplex.h alifold.h part_func_co.h ProfileAln.h LPfold.h Lfold.h part_func_up.h ribo.h findpath.h data_structures.h char_stream.h stream_output.h fold_compound.h MEA.h mm.h loop_energies.h exterior_loops.h hairpin_loops.h interior_loops.h multibranch_loops.h '/<>/debian/tmp/usr/include/ViennaRNA' /usr/bin/install -c -m 644 2Dfold.h 2Dpfold.h PKplex.h pk_plex.h ali_plex.h plex.h snofold.h snoop.h move_set.h gquad.h constraints.h eval.h perturbation_fold.h centroid.h utils.h structure_utils.h string_utils.h aln_util.h model.h dp_matrices.h PS_dot.h plot_structure.h plot_aln.h plot_utils.h plot_layouts.h boltzmann_sampling.h equilibrium_probs.h constraints_ligand.h constraints_SHAPE.h constraints_hard.h constraints_soft.h alphabet.h sequence.h grammar.h structured_domains.h unstructured_domains.h file_utils.h file_formats.h file_formats_msa.h energy_par.h '/<>/debian/tmp/usr/include/ViennaRNA' /usr/bin/install -c -m 644 energy_const.h params.h read_epars.h convert_epars.h commands.h units.h combinatorics.h neighbor.h walk.h heat_capacity.h naview.h '/<>/debian/tmp/usr/include/ViennaRNA' /usr/bin/mkdir -p '/<>/debian/tmp/usr/include/ViennaRNA/constraints' /usr/bin/install -c -m 644 constraints/basic.h constraints/ligand.h constraints/SHAPE.h constraints/hard.h constraints/soft.h '/<>/debian/tmp/usr/include/ViennaRNA/constraints' /usr/bin/mkdir -p '/<>/debian/tmp/usr/include/ViennaRNA/datastructures' /usr/bin/install -c -m 644 datastructures/basic.h datastructures/lists.h datastructures/char_stream.h datastructures/stream_output.h datastructures/hash_tables.h datastructures/heap.h '/<>/debian/tmp/usr/include/ViennaRNA/datastructures' /usr/bin/mkdir -p '/<>/debian/tmp/usr/include/ViennaRNA/io' /usr/bin/install -c -m 644 io/utils.h io/file_formats.h io/file_formats_msa.h '/<>/debian/tmp/usr/include/ViennaRNA/io' /usr/bin/mkdir -p '/<>/debian/tmp/usr/include/ViennaRNA/landscape' /usr/bin/install -c -m 644 landscape/paths.h landscape/findpath.h landscape/neighbor.h landscape/walk.h landscape/move.h '/<>/debian/tmp/usr/include/ViennaRNA/landscape' /usr/bin/mkdir -p '/<>/debian/tmp/usr/include/ViennaRNA/loops' /usr/bin/install -c -m 644 loops/all.h loops/external.h loops/hairpin.h loops/internal.h loops/multibranch.h '/<>/debian/tmp/usr/include/ViennaRNA/loops' /usr/bin/mkdir -p '/<>/debian/tmp/usr/include/ViennaRNA/params' /usr/bin/install -c -m 644 params/default.h params/constants.h params/basic.h params/io.h params/convert.h '/<>/debian/tmp/usr/include/ViennaRNA/params' /usr/bin/mkdir -p '/<>/debian/tmp/usr/include/ViennaRNA/plotting' /usr/bin/install -c -m 644 plotting/alignments.h plotting/layouts.h plotting/probabilities.h plotting/structures.h plotting/utils.h '/<>/debian/tmp/usr/include/ViennaRNA/plotting' /usr/bin/mkdir -p '/<>/debian/tmp/usr/include/ViennaRNA/plotting/RNApuzzler' /usr/bin/install -c -m 644 plotting/RNApuzzler/RNApuzzler.h plotting/RNApuzzler/RNAturtle.h '/<>/debian/tmp/usr/include/ViennaRNA/plotting/RNApuzzler' /usr/bin/mkdir -p '/<>/debian/tmp/usr/include/ViennaRNA/search' /usr/bin/install -c -m 644 search/BoyerMoore.h '/<>/debian/tmp/usr/include/ViennaRNA/search' /usr/bin/mkdir -p '/<>/debian/tmp/usr/include/ViennaRNA/utils' /usr/bin/install -c -m 644 utils/basic.h utils/strings.h utils/structures.h utils/alignments.h utils/higher_order_functions.h utils/cpu.h utils/units.h '/<>/debian/tmp/usr/include/ViennaRNA/utils' make[6]: Leaving directory '/<>/src/ViennaRNA' make[5]: Leaving directory '/<>/src/ViennaRNA' make[4]: Leaving directory '/<>/src/ViennaRNA' Making install in bin make[4]: Entering directory '/<>/src/bin' make[5]: Entering directory '/<>/src/bin' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /bin/bash ../../libtool --mode=install /usr/bin/install -c RNAfold RNAeval RNAheat RNApdist RNAdistance RNAinverse RNAplot RNAsubopt RNALfold RNAcofold RNApaln RNAduplex RNAalifold RNAplfold RNAup RNAaliduplex RNALalifold RNA2Dfold RNAparconv RNAPKplex RNAplex RNAsnoop RNApvmin RNAdos RNAmultifold '/<>/debian/tmp/usr/bin' libtool: install: /usr/bin/install -c RNAfold /<>/debian/tmp/usr/bin/RNAfold libtool: install: /usr/bin/install -c RNAeval /<>/debian/tmp/usr/bin/RNAeval libtool: install: /usr/bin/install -c RNAheat /<>/debian/tmp/usr/bin/RNAheat libtool: install: /usr/bin/install -c RNApdist /<>/debian/tmp/usr/bin/RNApdist libtool: install: /usr/bin/install -c RNAdistance /<>/debian/tmp/usr/bin/RNAdistance libtool: install: /usr/bin/install -c RNAinverse /<>/debian/tmp/usr/bin/RNAinverse libtool: install: /usr/bin/install -c RNAplot /<>/debian/tmp/usr/bin/RNAplot libtool: install: /usr/bin/install -c RNAsubopt /<>/debian/tmp/usr/bin/RNAsubopt libtool: install: /usr/bin/install -c RNALfold /<>/debian/tmp/usr/bin/RNALfold libtool: install: /usr/bin/install -c RNAcofold /<>/debian/tmp/usr/bin/RNAcofold libtool: install: /usr/bin/install -c RNApaln /<>/debian/tmp/usr/bin/RNApaln libtool: install: /usr/bin/install -c RNAduplex /<>/debian/tmp/usr/bin/RNAduplex libtool: install: /usr/bin/install -c RNAalifold /<>/debian/tmp/usr/bin/RNAalifold libtool: install: /usr/bin/install -c RNAplfold /<>/debian/tmp/usr/bin/RNAplfold libtool: install: /usr/bin/install -c RNAup /<>/debian/tmp/usr/bin/RNAup libtool: install: /usr/bin/install -c RNAaliduplex /<>/debian/tmp/usr/bin/RNAaliduplex libtool: install: /usr/bin/install -c RNALalifold /<>/debian/tmp/usr/bin/RNALalifold libtool: install: /usr/bin/install -c RNA2Dfold /<>/debian/tmp/usr/bin/RNA2Dfold libtool: install: /usr/bin/install -c RNAparconv /<>/debian/tmp/usr/bin/RNAparconv libtool: install: /usr/bin/install -c RNAPKplex /<>/debian/tmp/usr/bin/RNAPKplex libtool: install: /usr/bin/install -c RNAplex /<>/debian/tmp/usr/bin/RNAplex libtool: install: /usr/bin/install -c RNAsnoop /<>/debian/tmp/usr/bin/RNAsnoop libtool: install: /usr/bin/install -c RNApvmin /<>/debian/tmp/usr/bin/RNApvmin libtool: install: /usr/bin/install -c RNAdos /<>/debian/tmp/usr/bin/RNAdos libtool: install: /usr/bin/install -c RNAmultifold /<>/debian/tmp/usr/bin/RNAmultifold make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/<>/src/bin' make[4]: Leaving directory '/<>/src/bin' Making install in Utils make[4]: Entering directory '/<>/src/Utils' make[5]: Entering directory '/<>/src/Utils' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /bin/bash ../../libtool --mode=install /usr/bin/install -c b2ct popt ct2db '/<>/debian/tmp/usr/bin' libtool: install: /usr/bin/install -c b2ct /<>/debian/tmp/usr/bin/b2ct libtool: install: /usr/bin/install -c popt /<>/debian/tmp/usr/bin/popt libtool: install: /usr/bin/install -c ct2db /<>/debian/tmp/usr/bin/ct2db /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/ViennaRNA/bin' /usr/bin/install -c b2mt.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl coloraln.pl refold.pl switch.pl RNAdesign.pl '/<>/debian/tmp/usr/share/ViennaRNA/bin' make install-data-hook make[6]: Entering directory '/<>/src/Utils' for i in b2mt.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl coloraln.pl refold.pl switch.pl RNAdesign.pl; \ do \ /usr/bin/perl -npi -e 's|^#!\S+|#!'/usr/bin/perl'|' /<>/debian/tmp/usr/share/ViennaRNA/bin/$i ; \ done make[6]: Leaving directory '/<>/src/Utils' make[5]: Leaving directory '/<>/src/Utils' make[4]: Leaving directory '/<>/src/Utils' Making install in Cluster make[4]: Entering directory '/<>/src/Cluster' make[5]: Entering directory '/<>/src/Cluster' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /bin/bash ../../libtool --mode=install /usr/bin/install -c AnalyseDists AnalyseSeqs '/<>/debian/tmp/usr/bin' libtool: install: /usr/bin/install -c AnalyseDists /<>/debian/tmp/usr/bin/AnalyseDists libtool: install: /usr/bin/install -c AnalyseSeqs /<>/debian/tmp/usr/bin/AnalyseSeqs /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 AnalyseDists.1 AnalyseSeqs.1 '/<>/debian/tmp/usr/share/man/man1' make[5]: Leaving directory '/<>/src/Cluster' make[4]: Leaving directory '/<>/src/Cluster' make[4]: Entering directory '/<>/src' make[5]: Entering directory '/<>/src' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/<>/src' make[4]: Leaving directory '/<>/src' make[3]: Leaving directory '/<>/src' Making install in man make[3]: Entering directory '/<>/man' make[4]: Entering directory '/<>/man' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/info' /usr/bin/install -c -m 644 ./RNAlib.info '/<>/debian/tmp/usr/share/info' /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 RNA2Dfold.1 RNAaliduplex.1 RNAalifold.1 RNAcofold.1 RNAduplex.1 RNAeval.1 RNAfold.1 RNAheat.1 RNAinverse.1 RNALalifold.1 RNALfold.1 RNAmultifold.1 RNApaln.1 RNAparconv.1 RNAplfold.1 RNAplot.1 RNApvmin.1 RNAsubopt.1 RNAup.1 RNAPKplex.1 RNAsnoop.1 RNAplex.1 RNAdistance.1 RNApdist.1 RNAdos.1 ct2db.1 '/<>/debian/tmp/usr/share/man/man1' make[4]: Leaving directory '/<>/man' make[3]: Leaving directory '/<>/man' Making install in misc make[3]: Entering directory '/<>/misc' make[4]: Entering directory '/<>/misc' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/ViennaRNA' /usr/bin/install -c -m 644 2Dlandscape_mfe.gri 2Dlandscape_pf.gri rna_turner1999.par rna_turner2004.par rna_andronescu2007.par dna_mathews1999.par dna_mathews2004.par rna_langdon2018.par rna_misc_special_hairpins.par 2Dlandscape.R '/<>/debian/tmp/usr/share/ViennaRNA' make[4]: Leaving directory '/<>/misc' make[3]: Leaving directory '/<>/misc' Making install in doc make[3]: Entering directory '/<>/doc' Making install in CLA make[4]: Entering directory '/<>/doc/CLA' make[5]: Entering directory '/<>/doc/CLA' make[5]: Nothing to be done for 'install-exec-am'. for dir in "/<>/debian/tmp/usr/share/doc/ViennaRNA"; do \ test -z "$dir" || /usr/bin/mkdir -p "$dir"; \ done test -f ./ViennaRNA-CLA-Individual.pdf || ln -s ./ViennaRNA-CLA-Individual.pdf ./ViennaRNA-CLA-Individual.pdf /usr/bin/install -c -m 644 ./ViennaRNA-CLA-Individual.pdf /<>/debian/tmp/usr/share/doc/ViennaRNA { test ! -h ./ViennaRNA-CLA-Individual.pdf || rm -f ./ViennaRNA-CLA-Individual.pdf; } test -f ./ViennaRNA-CLA-Entity.pdf || ln -s ./ViennaRNA-CLA-Entity.pdf ./ViennaRNA-CLA-Entity.pdf /usr/bin/install -c -m 644 ./ViennaRNA-CLA-Entity.pdf /<>/debian/tmp/usr/share/doc/ViennaRNA { test ! -h ./ViennaRNA-CLA-Entity.pdf || rm -f ./ViennaRNA-CLA-Entity.pdf; } make[5]: Leaving directory '/<>/doc/CLA' make[4]: Leaving directory '/<>/doc/CLA' make[4]: Entering directory '/<>/doc' make[5]: Entering directory '/<>/doc' make[5]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/ViennaRNA' /usr/bin/install -c -m 644 viennarna.bib DoxygenLayout.xml '/<>/debian/tmp/usr/share/ViennaRNA' make[5]: Leaving directory '/<>/doc' make[4]: Leaving directory '/<>/doc' make[3]: Leaving directory '/<>/doc' Making install in RNA-Tutorial make[3]: Entering directory '/<>/RNA-Tutorial' make[4]: Entering directory '/<>/RNA-Tutorial' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Leaving directory '/<>/RNA-Tutorial' make[3]: Leaving directory '/<>/RNA-Tutorial' Making install in interfaces make[3]: Entering directory '/<>/interfaces' Making install in Perl make[4]: Entering directory '/<>/interfaces/Perl' make[5]: Entering directory '/<>/interfaces/Perl' make[5]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/perl/5.38.2' /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/perl/5.38.2/RNA' /usr/bin/install -c -m 644 RNA/Benchmark.pm RNA/Design.pm RNA/Files.pm RNA/Reliability.pm RNA/Utils.pm RNA/Params.pm '/<>/debian/tmp/usr/share/perl/5.38.2/RNA' /usr/bin/install -c -m 644 RNA.pm '/<>/debian/tmp/usr/share/perl/5.38.2/.' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/arm-linux-gnueabihf/perl/5.38.2/auto/RNA' /bin/bash ../../libtool --mode=install /usr/bin/install -c RNA.la '/<>/debian/tmp/usr/lib/arm-linux-gnueabihf/perl/5.38.2/auto/RNA' libtool: install: /usr/bin/install -c .libs/RNA.so /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/perl/5.38.2/auto/RNA/RNA.so libtool: install: /usr/bin/install -c .libs/RNA.lai /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/perl/5.38.2/auto/RNA/RNA.la libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf/perl/5.38.2/auto/RNA' make install-data-hook make[6]: Entering directory '/<>/interfaces/Perl' rm -f /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/perl/5.38.2/auto/RNA/RNA.la make[6]: Leaving directory '/<>/interfaces/Perl' make[5]: Leaving directory '/<>/interfaces/Perl' make[4]: Leaving directory '/<>/interfaces/Perl' Making install in Python make[4]: Entering directory '/<>/interfaces/Python' make[5]: Entering directory '/<>/interfaces/Python' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/python3.12/site-packages/RNA' /usr/bin/install -c -m 644 RNA/__init__.py '/<>/debian/tmp/usr/lib/python3.12/site-packages/RNA' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/python3.12/site-packages/RNA' /bin/bash ../../libtool --mode=install /usr/bin/install -c _RNA.la '/<>/debian/tmp/usr/lib/python3.12/site-packages/RNA' libtool: install: /usr/bin/install -c .libs/_RNA.so /<>/debian/tmp/usr/lib/python3.12/site-packages/RNA/_RNA.so libtool: install: /usr/bin/install -c .libs/_RNA.lai /<>/debian/tmp/usr/lib/python3.12/site-packages/RNA/_RNA.la libtool: warning: remember to run 'libtool --finish /usr/lib/python3.12/site-packages/RNA' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/python3.12/site-packages/RNA/__pycache__' /usr/bin/install -c -m 644 RNA/__pycache__/__init__.cpython-312.pyc RNA/__pycache__/__init__.cpython-312.opt-1.pyc '/<>/debian/tmp/usr/lib/python3.12/site-packages/RNA/__pycache__' make install-data-hook make[6]: Entering directory '/<>/interfaces/Python' rm -f /<>/debian/tmp/usr/lib/python3.12/site-packages/RNA/_RNA.la make[6]: Leaving directory '/<>/interfaces/Python' make[5]: Leaving directory '/<>/interfaces/Python' make[4]: Leaving directory '/<>/interfaces/Python' make[4]: Entering directory '/<>/interfaces' make[5]: Entering directory '/<>/interfaces' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/<>/interfaces' make[4]: Leaving directory '/<>/interfaces' make[3]: Leaving directory '/<>/interfaces' Making install in src/Kinfold make[3]: Entering directory '/<>/src/Kinfold' Making install in Example make[4]: Entering directory '/<>/src/Kinfold/Example' make[5]: Entering directory '/<>/src/Kinfold/Example' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/<>/src/Kinfold/Example' make[4]: Leaving directory '/<>/src/Kinfold/Example' make[4]: Entering directory '/<>/src/Kinfold' make[5]: Entering directory '/<>/src/Kinfold' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c Kinfold '/<>/debian/tmp/usr/bin' /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 Kinfold.1 '/<>/debian/tmp/usr/share/man/man1' make[5]: Leaving directory '/<>/src/Kinfold' make[4]: Leaving directory '/<>/src/Kinfold' make[3]: Leaving directory '/<>/src/Kinfold' Making install in src/RNAlocmin make[3]: Entering directory '/<>/src/RNAlocmin' make[4]: Entering directory '/<>/src/RNAlocmin' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c RNAlocmin '/<>/debian/tmp/usr/bin' /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 RNAlocmin.1 '/<>/debian/tmp/usr/share/man/man1' make[4]: Leaving directory '/<>/src/RNAlocmin' make[3]: Leaving directory '/<>/src/RNAlocmin' Making install in tests make[3]: Entering directory '/<>/tests' make install-am make[4]: Entering directory '/<>/tests' make[5]: Entering directory '/<>/tests' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/<>/tests' make[4]: Leaving directory '/<>/tests' make[3]: Leaving directory '/<>/tests' Making install in examples make[3]: Entering directory '/<>/examples' make[4]: Entering directory '/<>/examples' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/ViennaRNA/examples' /usr/bin/install -c -m 644 callback_subopt.c example1.c example_old.c fold_compound_md.c fold_compound_mfe.c helloworld_mfe.c helloworld_mfe_comparative.c helloworld_probabilities.c soft_constraints_up.c '/<>/debian/tmp/usr/share/ViennaRNA/examples' /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/ViennaRNA/examples/data' /usr/bin/install -c -m 644 files/alignment_clustal.aln files/alignment_fasta.fa files/alignment_stockholm.stk files/alignment_maf.maf '/<>/debian/tmp/usr/share/ViennaRNA/examples/data' /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/ViennaRNA/examples/perl5' /usr/bin/install -c -m 644 Perl5/helloworld_mfe.pl Perl5/helloworld_mfe_comparative.pl Perl5/helloworld_nondefault.pl Perl5/maximum_matching.pl Perl5/oo_example1.pl '/<>/debian/tmp/usr/share/ViennaRNA/examples/perl5' /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/ViennaRNA/examples/python' /usr/bin/install -c -m 644 Python/boltzmann_sampling.py Python/helloworld_mfe_comparative.py Python/helloworld_mfe.py Python/helloworld_nondefault.py Python/maximum_matching.py Python/oo_example1.py Python/subopt.py Python/RNAfold_MEA.py '/<>/debian/tmp/usr/share/ViennaRNA/examples/python' make[4]: Leaving directory '/<>/examples' make[3]: Leaving directory '/<>/examples' Making install in packaging/macosx make[3]: Entering directory '/<>/packaging/macosx' make[4]: Entering directory '/<>/packaging/macosx' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/packaging/macosx' make[3]: Leaving directory '/<>/packaging/macosx' make[3]: Entering directory '/<>' make[4]: Entering directory '/<>' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig' /usr/bin/install -c -m 644 RNAlib2.pc '/<>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig' make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' find debian/ -name .gitignore -delete make[1]: Leaving directory '/<>' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_installinfo -a dh_python3 -a I: dh_python3 fs:418: renaming _RNA.so to _RNA.cpython-312-arm-linux-gnueabihf.so dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a debian/rules override_dh_compress make[1]: Entering directory '/<>' dh_compress --exclude=.pdf make[1]: Leaving directory '/<>' dh_fixperms -a dh_dwz -a dwz: debian/python3-rna/usr/lib/python3/dist-packages/RNA/_RNA.cpython-312-arm-linux-gnueabihf.so: .debug_info section not present dwz: debian/vienna-rna/usr/bin/AnalyseDists: .debug_info section not present dwz: debian/vienna-rna/usr/bin/AnalyseSeqs: .debug_info section not present dwz: debian/vienna-rna/usr/bin/Kinfold: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNA2Dfold: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNALalifold: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNALfold: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNAPKplex: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNAaliduplex: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNAalifold: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNAcofold: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNAdistance: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNAdos: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNAduplex: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNAeval: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNAfold: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNAheat: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNAinverse: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNAlocmin: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNAmultifold: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNApaln: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNAparconv: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNApdist: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNAplex: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNAplfold: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNAplot: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNApvmin: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNAsnoop: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNAsubopt: .debug_info section not present dwz: debian/vienna-rna/usr/bin/RNAup: .debug_info section not present dwz: debian/vienna-rna/usr/bin/b2ct: .debug_info section not present dwz: debian/vienna-rna/usr/bin/ct2db: .debug_info section not present dwz: debian/vienna-rna/usr/bin/popt: .debug_info section not present dwz: Too few files for multifile optimization dh_dwz: warning: No dwz multifile created, but not explicitly requested either so ignoring it. dh_dwz: warning: Common issues include no debug information at all (missing -g) and dh_dwz: warning: compressed debug information (#931891). dh_strip -a 6dafd579efd392d9af49e88b0fe298f05a610138 82f20cb8cac5af038a2f6df7c22e6180f1baf820 1eeb77e740efaf3c224358897de9fb40694c3613 a28618600857bc74dfe45a79ef5dac1ba567afbf 584f84fb124d40f86f930dd771d9213714f2a5c6 bc6a378d0d2829ea9302ab1e0b09c7d7b25d060e 383d5041b0d4d3075ba38825339e2f04a04e147f fc432b097622c7580d29b2420aa448fb01fc33e7 6d241fc9f261823622f2a5a0298ae7a37e4e086c 0e4d53205b75be5c85657c218a705b2e0d626a15 ffbe59db373f2de9c7f37b0ebded2f39be88b665 314faabd0069c9f38f77a3e16cee3a453d99dbd9 d48dcc845d8f09248ed8e6c50c9bbcb716ae47dc 558905b8a0bfa19a7d0bab751ecc890fcd29874d 15c3eeab5c9ece35fb82323e6b00ec183793677e c39000a77d93b501904ff2dbba0e3ad62bae643b ee4face9dc38e7e64b4b38bafade58076ed8ff86 76f0e34ff680a348e368c57119c61d1877698d2f bb53438f96ef16e1e919a01d09a35f2bb8826141 00759ea12e3dfb42430ea98f49918bb7b9716b28 e3b6631ea9cdc900f66508135b523fe75461722e c07e5b4ab8005e29fce1165efd29213fb8b7325c 6888c1be953c0d3e4c45379762effabe8004b868 3f645917b055d89c862714ff9cc3cc2654162eb4 f68d66fffd70b8eaf42e72b87af2011e370eb29d 385c475696eb9ccd4b97cf0116a2b6659012b00d 6edca429ad47484b76867d3336ef25263a9d7007 36909fd9261bce68cede6128ee8a08a92f099f72 1c5c830d06733d4df64dade0c7940fcb436f0e23 7d9d7a5d5878e0808524cb767c110e6e10f3ed86 8956e8fb6a8ad27f2c2c9f674d8cbf8eea443066 4b9c2b3a52199e50a43a4d67bed7e8ac3ae3ad81 fc548aeb608636763495f120cf38cd08618c0afa dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dpkg-shlibdeps: warning: debian/python3-rna/usr/lib/python3/dist-packages/RNA/_RNA.cpython-312-arm-linux-gnueabihf.so contains an unresolvable reference to symbol PyBool_FromLong: it's probably a plugin dpkg-shlibdeps: warning: 111 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: debian/vienna-rna/usr/bin/RNAmultifold contains an unresolvable reference to symbol __aeabi_atexit@GLIBC_2.4: it's probably a plugin dpkg-shlibdeps: warning: debian/vienna-rna/usr/bin/RNAlocmin contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: Depends field of package librna-perl: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing librna-perl (in debian/librna-perl); do_strip: , oemstrip: INFO: pkgstriptranslations version 154 pkgstriptranslations: processing vienna-rna (in debian/vienna-rna); do_strip: , oemstrip: pkgstriptranslations: processing python3-rna (in debian/python3-rna); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/librna-perl/DEBIAN/control, package librna-perl, directory debian/librna-perl INFO: pkgstripfiles: waiting for lock (librna-perl) ... pkgstripfiles: processing control file: debian/python3-rna/DEBIAN/control, package python3-rna, directory debian/python3-rna INFO: pkgstripfiles: waiting for lock (python3-rna) ... INFO: pkgstripfiles: waiting for lock (librna-perl) ... INFO: pkgstripfiles: waiting for lock (python3-rna) ... INFO: pkgstripfiles: waiting for lock (librna-perl) ... INFO: pkgstripfiles: waiting for lock (python3-rna) ... INFO: pkgstripfiles: waiting for lock (librna-perl) ... INFO: pkgstripfiles: waiting for lock (python3-rna) ... INFO: pkgstripfiles: waiting for lock (librna-perl) ... INFO: pkgstripfiles: waiting for lock (python3-rna) ... pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com INFO: pkgstripfiles: waiting for lock (librna-perl) ... INFO: pkgstripfiles: waiting for lock (python3-rna) ... pkgstripfiles: processing control file: debian/vienna-rna/DEBIAN/control, package vienna-rna, directory debian/vienna-rna pkgstripfiles: Running PNG optimization (using 4 cpus) for package vienna-rna ... pkgstripfiles: No PNG files. dpkg-deb: building package 'vienna-rna' in '../vienna-rna_2.5.1+dfsg-1build3_armhf.deb'. INFO: pkgstripfiles: waiting for lock (librna-perl) ... pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-rna ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-rna' in '../python3-rna_2.5.1+dfsg-1build3_armhf.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package librna-perl ... pkgstripfiles: No PNG files. dpkg-deb: building package 'librna-perl' in '../librna-perl_2.5.1+dfsg-1build3_armhf.deb'. INFO: pkgstriptranslations version 154 pkgstriptranslations: processing python3-rna-dbgsym (in debian/.debhelper/python3-rna/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/.debhelper/python3-rna/dbgsym-root/DEBIAN/control, package python3-rna-dbgsym, directory debian/.debhelper/python3-rna/dbgsym-root dpkg-deb: building package 'python3-rna-dbgsym' in 'debian/.debhelper/scratch-space/build-python3-rna/python3-rna-dbgsym_2.5.1+dfsg-1build3_armhf.deb'. Renaming python3-rna-dbgsym_2.5.1+dfsg-1build3_armhf.deb to python3-rna-dbgsym_2.5.1+dfsg-1build3_armhf.ddeb INFO: pkgstriptranslations version 154 pkgstriptranslations: processing vienna-rna-dbgsym (in debian/.debhelper/vienna-rna/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/.debhelper/vienna-rna/dbgsym-root/DEBIAN/control, package vienna-rna-dbgsym, directory debian/.debhelper/vienna-rna/dbgsym-root dpkg-deb: building package 'vienna-rna-dbgsym' in 'debian/.debhelper/scratch-space/build-vienna-rna/vienna-rna-dbgsym_2.5.1+dfsg-1build3_armhf.deb'. Renaming vienna-rna-dbgsym_2.5.1+dfsg-1build3_armhf.deb to vienna-rna-dbgsym_2.5.1+dfsg-1build3_armhf.ddeb dpkg-genbuildinfo --build=any -O../vienna-rna_2.5.1+dfsg-1build3_armhf.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../vienna-rna_2.5.1+dfsg-1build3_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-04-03T06:12:19Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ vienna-rna_2.5.1+dfsg-1build3_armhf.changes: -------------------------------------------- Format: 1.8 Date: Mon, 01 Apr 2024 16:24:05 +1100 Source: vienna-rna Binary: librna-perl python3-rna vienna-rna Built-For-Profiles: noudeb Architecture: armhf Version: 2.5.1+dfsg-1build3 Distribution: noble-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: William Grant Description: librna-perl - ViennaRNA perl wrappers python3-rna - ViennaRNA Python wrappers vienna-rna - RNA sequence analysis Changes: vienna-rna (2.5.1+dfsg-1build3) noble; urgency=medium . * No-change rebuild for CVE-2024-3094 Checksums-Sha1: 6cb9e147fc2254c7e7986453db76845618a7c805 49348 librna-perl_2.5.1+dfsg-1build3_armhf.deb 7c36b486703b409e51ee7fe2d1d07015f7e49246 192332 python3-rna-dbgsym_2.5.1+dfsg-1build3_armhf.ddeb 038f24ff2ee6a9a616ea13f9b5aef53a15076323 1076024 python3-rna_2.5.1+dfsg-1build3_armhf.deb 69eb92246855f9ad6fc19af4fd9b008d42219946 527214 vienna-rna-dbgsym_2.5.1+dfsg-1build3_armhf.ddeb 9fa26c50a44e75ca2c0e8bff5146d829cf9834c9 14181 vienna-rna_2.5.1+dfsg-1build3_armhf.buildinfo 50c223fcc488a7cde575473d8e71002480ff1396 2134778 vienna-rna_2.5.1+dfsg-1build3_armhf.deb Checksums-Sha256: 35ca23f637a6be82d59f73c7d1b0024d2c36e5a83d633813706bbe50e1d0c4a3 49348 librna-perl_2.5.1+dfsg-1build3_armhf.deb 45ab8c7eed2c02b6a277939a7b87a0522dc487c28fb68a4ff3e053199dc58c17 192332 python3-rna-dbgsym_2.5.1+dfsg-1build3_armhf.ddeb 44bd58ae911a3ca3e0eaa3efac3cdb89c7d22a8c858719316712af9773b97c37 1076024 python3-rna_2.5.1+dfsg-1build3_armhf.deb 76254f0f098936aeb54c7a4d59d49c37831686f5cc84d87ab6aa7884d4dffc59 527214 vienna-rna-dbgsym_2.5.1+dfsg-1build3_armhf.ddeb 6b848acad810d1d71fa50bd365c0c05900f26a637f16eb1b9709996c7b7fb391 14181 vienna-rna_2.5.1+dfsg-1build3_armhf.buildinfo 32ce0047908c4c974c6f285c035814223d1376e6501371de334a2f0723f93fc8 2134778 vienna-rna_2.5.1+dfsg-1build3_armhf.deb Files: 5855eef1f44e913e0f8a95f92d6c83c2 49348 non-free/perl optional librna-perl_2.5.1+dfsg-1build3_armhf.deb 503f376d8a2299d62ad9362ba9d72a04 192332 non-free/debug optional python3-rna-dbgsym_2.5.1+dfsg-1build3_armhf.ddeb 57dc097aca9650a77b7145009610750f 1076024 non-free/python optional python3-rna_2.5.1+dfsg-1build3_armhf.deb 5e6ed8b4d16ce0a4264b4a8ba9a436e3 527214 non-free/debug optional vienna-rna-dbgsym_2.5.1+dfsg-1build3_armhf.ddeb b4ffe6abc74ca659363fdcdd2f5f266d 14181 non-free/science optional vienna-rna_2.5.1+dfsg-1build3_armhf.buildinfo fd43b7160efed11fa731aa390f41cf28 2134778 non-free/science optional vienna-rna_2.5.1+dfsg-1build3_armhf.deb Original-Maintainer: Debian Med Packaging Team /<>/vienna-rna_2.5.1+dfsg-1build3_armhf.changes.new could not be renamed to /<>/vienna-rna_2.5.1+dfsg-1build3_armhf.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: vienna-rna Binary: librna-perl python3-rna python3-rna-dbgsym vienna-rna vienna-rna-dbgsym Architecture: armhf Version: 2.5.1+dfsg-1build3 Checksums-Md5: 5855eef1f44e913e0f8a95f92d6c83c2 49348 librna-perl_2.5.1+dfsg-1build3_armhf.deb 503f376d8a2299d62ad9362ba9d72a04 192332 python3-rna-dbgsym_2.5.1+dfsg-1build3_armhf.ddeb 57dc097aca9650a77b7145009610750f 1076024 python3-rna_2.5.1+dfsg-1build3_armhf.deb 5e6ed8b4d16ce0a4264b4a8ba9a436e3 527214 vienna-rna-dbgsym_2.5.1+dfsg-1build3_armhf.ddeb fd43b7160efed11fa731aa390f41cf28 2134778 vienna-rna_2.5.1+dfsg-1build3_armhf.deb Checksums-Sha1: 6cb9e147fc2254c7e7986453db76845618a7c805 49348 librna-perl_2.5.1+dfsg-1build3_armhf.deb 7c36b486703b409e51ee7fe2d1d07015f7e49246 192332 python3-rna-dbgsym_2.5.1+dfsg-1build3_armhf.ddeb 038f24ff2ee6a9a616ea13f9b5aef53a15076323 1076024 python3-rna_2.5.1+dfsg-1build3_armhf.deb 69eb92246855f9ad6fc19af4fd9b008d42219946 527214 vienna-rna-dbgsym_2.5.1+dfsg-1build3_armhf.ddeb 50c223fcc488a7cde575473d8e71002480ff1396 2134778 vienna-rna_2.5.1+dfsg-1build3_armhf.deb Checksums-Sha256: 35ca23f637a6be82d59f73c7d1b0024d2c36e5a83d633813706bbe50e1d0c4a3 49348 librna-perl_2.5.1+dfsg-1build3_armhf.deb 45ab8c7eed2c02b6a277939a7b87a0522dc487c28fb68a4ff3e053199dc58c17 192332 python3-rna-dbgsym_2.5.1+dfsg-1build3_armhf.ddeb 44bd58ae911a3ca3e0eaa3efac3cdb89c7d22a8c858719316712af9773b97c37 1076024 python3-rna_2.5.1+dfsg-1build3_armhf.deb 76254f0f098936aeb54c7a4d59d49c37831686f5cc84d87ab6aa7884d4dffc59 527214 vienna-rna-dbgsym_2.5.1+dfsg-1build3_armhf.ddeb 32ce0047908c4c974c6f285c035814223d1376e6501371de334a2f0723f93fc8 2134778 vienna-rna_2.5.1+dfsg-1build3_armhf.deb Build-Origin: Ubuntu Build-Architecture: armhf Build-Date: Wed, 03 Apr 2024 06:12:17 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3ubuntu1), autopoint (= 0.21-14ubuntu1), autotools-dev (= 20220109.1), base-files (= 13ubuntu9), base-passwd (= 3.6.3), bash (= 5.2.21-2ubuntu4), binutils (= 2.42-4ubuntu2), binutils-arm-linux-gnueabihf (= 2.42-4ubuntu2), binutils-common (= 2.42-4ubuntu2), bsdextrautils (= 2.39.3-9ubuntu4), bsdutils (= 1:2.39.3-9ubuntu4), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5.1), coreutils (= 9.4-3ubuntu5), cpp (= 4:13.2.0-7ubuntu1), cpp-13 (= 13.2.0-23ubuntu3), cpp-13-arm-linux-gnueabihf (= 13.2.0-23ubuntu3), cpp-arm-linux-gnueabihf (= 4:13.2.0-7ubuntu1), cthreadpool-dev (= 0.0+git20231218.4eb5a69-1build1), dash (= 0.5.12-6ubuntu5), debconf (= 1.5.86), debhelper (= 13.14.1ubuntu5), debianutils (= 5.17build1), debugedit (= 1:5.0-5build1), dh-autoreconf (= 20), dh-python (= 6.20240401), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), doxygen (= 1.9.8+ds-2build5), dpkg (= 1.22.6ubuntu6), dpkg-dev (= 1.22.6ubuntu6), dwz (= 0.15-1build6), file (= 1:5.45-3build1), findutils (= 4.9.0-5), fontconfig (= 2.15.0-1.1ubuntu2), fontconfig-config (= 2.15.0-1.1ubuntu2), fonts-dejavu-core (= 2.37-8), fonts-dejavu-mono (= 2.37-8), fonts-lmodern (= 2.005-1), fonts-urw-base35 (= 20200910-8), g++ (= 4:13.2.0-7ubuntu1), g++-13 (= 13.2.0-23ubuntu3), g++-13-arm-linux-gnueabihf (= 13.2.0-23ubuntu3), g++-arm-linux-gnueabihf (= 4:13.2.0-7ubuntu1), gcc (= 4:13.2.0-7ubuntu1), gcc-13 (= 13.2.0-23ubuntu3), gcc-13-arm-linux-gnueabihf (= 13.2.0-23ubuntu3), gcc-13-base (= 13.2.0-23ubuntu3), gcc-14-base (= 14-20240330-1ubuntu2), gcc-arm-linux-gnueabihf (= 4:13.2.0-7ubuntu1), gengetopt (= 2.23+dfsg1-1), gettext (= 0.21-14ubuntu1), gettext-base (= 0.21-14ubuntu1), ghostscript (= 10.02.1~dfsg1-0ubuntu6), graphviz (= 2.42.2-9build1), grep (= 3.11-4), groff-base (= 1.23.0-3build2), gzip (= 1.12-1ubuntu2), help2man (= 1.49.3), hostname (= 3.23+nmu2ubuntu1), init-system-helpers (= 1.66ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-1), libapache-pom-java (= 29-2), libarchive-zip-perl (= 1.68-1), libasan8 (= 14-20240330-1ubuntu2), libatomic1 (= 14-20240330-1ubuntu2), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-2.1build1), libaudit1 (= 1:3.1.2-2.1build1), libavahi-client3 (= 0.8-13ubuntu5), libavahi-common-data (= 0.8-13ubuntu5), libavahi-common3 (= 0.8-13ubuntu5), libbinutils (= 2.42-4ubuntu2), libblas-dev (= 3.12.0-3), libblas3 (= 3.12.0-3), libblkid1 (= 2.39.3-9ubuntu4), libbrotli1 (= 1.1.0-2build2), libbsd0 (= 0.12.1-1build1), 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), libcairo2 (= 1.18.0-3), libcap-ng0 (= 0.8.4-2build2), libcap2 (= 1:2.66-5ubuntu1), libcc1-0 (= 14-20240330-1ubuntu2), libcdt5 (= 2.42.2-9build1), libcgraph6 (= 2.42.2-9build1), libclang-cpp18 (= 1:18.1.2-1ubuntu3), libclang1-18 (= 1:18.1.2-1ubuntu3), libcom-err2 (= 1.47.0-2.4~exp1ubuntu3), libcommons-logging-java (= 1.3.0-1ubuntu1), libcommons-parent-java (= 56-1), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42-4ubuntu2), libctf0 (= 2.42-4ubuntu2), libcups2t64 (= 2.4.7-1.2ubuntu3), libdatrie1 (= 0.2.13-3), libdb5.3t64 (= 5.3.28+dfsg2-6build1), libdbus-1-3 (= 1.14.10-4ubuntu3), libdebconfclient0 (= 0.271ubuntu3), libdebhelper-perl (= 13.14.1ubuntu5), libdeflate0 (= 1.19-1), libdlib-data (= 19.24+dfsg-1.1build1), libdlib-dev (= 19.24+dfsg-1.1build1), libdlib19.1t64 (= 19.24+dfsg-1.1build1), libdpkg-perl (= 1.22.6ubuntu6), libdrm-amdgpu1 (= 2.4.120-2), libdrm-common (= 2.4.120-2), libdrm-nouveau2 (= 2.4.120-2), libdrm-radeon1 (= 2.4.120-2), libdrm2 (= 2.4.120-2), libdw1t64 (= 0.190-1.1build3), libedit2 (= 3.1-20230828-1), libelf1t64 (= 0.190-1.1build3), libexpat1 (= 2.6.1-2build1), libexpat1-dev (= 2.6.1-2build1), libffi8 (= 3.4.6-1), libfile-stripnondeterminism-perl (= 1.13.1-1), libfmt9 (= 9.1.0+ds1-2), libfontbox-java (= 1:1.8.16-5), libfontconfig1 (= 2.15.0-1.1ubuntu2), libfontenc1 (= 1:1.1.8-1build1), libfreetype6 (= 2.13.2+dfsg-1build3), libfribidi0 (= 1.0.13-3), libgcc-13-dev (= 13.2.0-23ubuntu3), libgcc-s1 (= 14-20240330-1ubuntu2), libgcrypt20 (= 1.10.3-2), libgd3 (= 2.3.3-9ubuntu4), libgdbm-compat4t64 (= 1.23-5.1build1), libgdbm6t64 (= 1.23-5.1build1), 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1:1.1.3-0ubuntu5), libxdmcp6 (= 1:1.1.3-0ubuntu5), libxext6 (= 2:1.3.4-1build1), libxfixes3 (= 1:6.0.0-2), libxi6 (= 2:1.8.1-1), libxml-libxml-perl (= 2.0207+dfsg+really+2.0134-1build4), libxml-namespacesupport-perl (= 1.12-2), libxml-sax-base-perl (= 1.09-3), libxml-sax-perl (= 1.02+dfsg-3), libxml2 (= 2.9.14+dfsg-1.3ubuntu3), libxmu6 (= 2:1.1.3-3build2), libxpm4 (= 1:3.5.17-1build2), libxrender1 (= 1:0.9.10-1.1), libxshmfence1 (= 1.3-1build4), libxt6t64 (= 1:1.2.1-1.2build1), libxxf86vm1 (= 1:1.1.4-1build3), libzstd1 (= 1.5.5+dfsg2-2), libzzip-0-13t64 (= 0.13.72+dfsg.1-1.2build1), linux-libc-dev (= 6.8.0-20.20), login (= 1:4.13+dfsg1-4ubuntu1), lto-disabled-list (= 47), m4 (= 1.4.19-4), make (= 4.3-4.1build1), man-db (= 2.12.0-4build1), mawk (= 1.3.4.20240123-1), media-types (= 10.1.0), ncurses-base (= 6.4+20240113-1ubuntu1), ncurses-bin (= 6.4+20240113-1ubuntu1), netbase (= 6.4), patch (= 2.7.6-7build2), perl (= 5.38.2-3.2build1), perl-base (= 5.38.2-3.2build1), perl-doc (= 5.38.2-3.2build1), perl-modules-5.38 (= 5.38.2-3.2build1), pkg-config (= 1.8.1-2), pkgconf (= 1.8.1-2), pkgconf-bin (= 1.8.1-2), po-debconf (= 1.0.21+nmu1), poppler-data (= 0.4.12-1), preview-latex-style (= 13.2-1), pybind11-dev (= 2.11.1-2), python3 (= 3.12.2-0ubuntu2), python3-dev (= 3.12.2-0ubuntu2), python3-minimal (= 3.12.2-0ubuntu2), python3-pkg-resources (= 68.1.2-2ubuntu1), python3-setuptools (= 68.1.2-2ubuntu1), python3.12 (= 3.12.2-5ubuntu3), python3.12-dev (= 3.12.2-5ubuntu3), python3.12-minimal (= 3.12.2-5ubuntu3), readline-common (= 8.2-4build1), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-2), sensible-utils (= 0.0.22), swig (= 4.2.0-2ubuntu1), sysvinit-utils (= 3.08-6ubuntu2), t1utils (= 1.41-4build2), tar (= 1.35+dfsg-3), tex-common (= 6.18), texinfo (= 7.1-3build2), texinfo-lib (= 7.1-3build2), texlive-base (= 2023.20240207-1), texlive-binaries (= 2023.20230311.66589-9build3), texlive-latex-base (= 2023.20240207-1), texlive-latex-extra (= 2023.20240207-1), texlive-latex-recommended (= 2023.20240207-1), texlive-pictures (= 2023.20240207-1), tzdata (= 2024a-1ubuntu1), ucf (= 3.0043+nmu1), util-linux (= 2.39.3-9ubuntu4), x11-common (= 1:7.7+23ubuntu2), x11proto-dev (= 2023.2-1), xdg-utils (= 1.1.3-4.1ubuntu3), xfonts-encodings (= 1:1.0.5-0ubuntu2), xfonts-utils (= 1:7.7+6build2), xorg-sgml-doctools (= 1:1.11-1.1), xtrans-dev (= 1.4.0-1), xxd (= 2:9.1.0016-1ubuntu7), xz-utils (= 5.6.1+really5.4.5-1), zlib1g (= 1:1.3.dfsg-3.1ubuntu2), zlib1g-dev (= 1:1.3.dfsg-3.1ubuntu2) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1711949045" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ librna-perl_2.5.1+dfsg-1build3_armhf.deb ---------------------------------------- new Debian package, version 2.0. size 49348 bytes: control archive=822 bytes. 606 bytes, 17 lines control 597 bytes, 9 lines md5sums Package: librna-perl Source: vienna-rna Version: 2.5.1+dfsg-1build3 Architecture: armhf Maintainer: Ubuntu Developers Installed-Size: 251 Depends: perl:any Section: non-free/perl Priority: optional Homepage: https://www.tbi.univie.ac.at/RNA/ Description: ViennaRNA perl wrappers Perl wrappers above ViennaRNA library. . The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2024-04-01 05:24 ./ drwxr-xr-x root/root 0 2024-04-01 05:24 ./usr/ drwxr-xr-x root/root 0 2024-04-01 05:24 ./usr/share/ drwxr-xr-x root/root 0 2024-04-01 05:24 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-04-01 05:24 ./usr/share/doc/librna-perl/ -rw-r--r-- root/root 1349 2024-04-01 05:24 ./usr/share/doc/librna-perl/changelog.Debian.gz -rw-r--r-- root/root 7117 2023-02-10 06:19 ./usr/share/doc/librna-perl/copyright drwxr-xr-x root/root 0 2024-04-01 05:24 ./usr/share/perl5/ -rw-r--r-- root/root 109828 2024-04-01 05:24 ./usr/share/perl5/RNA.pm drwxr-xr-x root/root 0 2024-04-01 05:24 ./usr/share/perl5/RNA/ -rw-r--r-- root/root 14079 2024-04-01 05:24 ./usr/share/perl5/RNA/Benchmark.pm -rw-r--r-- root/root 39458 2024-04-01 05:24 ./usr/share/perl5/RNA/Design.pm -rw-r--r-- root/root 4614 2024-04-01 05:24 ./usr/share/perl5/RNA/Files.pm -rw-r--r-- root/root 57391 2024-04-01 05:24 ./usr/share/perl5/RNA/Params.pm -rw-r--r-- root/root 1818 2024-04-01 05:24 ./usr/share/perl5/RNA/Reliability.pm -rw-r--r-- root/root 8342 2024-04-01 05:24 ./usr/share/perl5/RNA/Utils.pm python3-rna_2.5.1+dfsg-1build3_armhf.deb ---------------------------------------- new Debian package, version 2.0. size 1076024 bytes: control archive=1103 bytes. 832 bytes, 17 lines control 338 bytes, 4 lines md5sums 269 bytes, 12 lines * postinst #!/bin/sh 382 bytes, 12 lines * prerm #!/bin/sh Package: python3-rna Source: vienna-rna Version: 2.5.1+dfsg-1build3 Architecture: armhf Maintainer: Ubuntu Developers Installed-Size: 6506 Depends: python3 (<< 3.13), python3 (>= 3.12~), python3:any, libc6 (>= 2.38), libdlib19.1t64 (>= 19.24+dfsg), libgcc-s1 (>= 3.5), libgomp1 (>= 4.9), libgsl27 (>= 2.7.1), libgslcblas0 (>= 2.7.1), libmpfr6 (>= 3.1.3), libstdc++6 (>= 13.1) Section: non-free/python Priority: optional Homepage: https://www.tbi.univie.ac.at/RNA/ Description: ViennaRNA Python wrappers Python wrappers above ViennaRNA library. . The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2024-04-01 05:24 ./ drwxr-xr-x root/root 0 2024-04-01 05:24 ./usr/ drwxr-xr-x root/root 0 2024-04-01 05:24 ./usr/lib/ drwxr-xr-x root/root 0 2024-04-01 05:24 ./usr/lib/python3/ drwxr-xr-x root/root 0 2024-04-01 05:24 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2024-04-01 05:24 ./usr/lib/python3/dist-packages/RNA/ -rw-r--r-- root/root 6505544 2024-04-01 05:24 ./usr/lib/python3/dist-packages/RNA/_RNA.cpython-312-arm-linux-gnueabihf.so -rw-r--r-- root/root 133330 2024-04-01 05:24 ./usr/lib/python3/dist-packages/RNA/__init__.py drwxr-xr-x root/root 0 2024-04-01 05:24 ./usr/share/ drwxr-xr-x root/root 0 2024-04-01 05:24 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-04-01 05:24 ./usr/share/doc/python3-rna/ -rw-r--r-- root/root 1345 2024-04-01 05:24 ./usr/share/doc/python3-rna/changelog.Debian.gz -rw-r--r-- root/root 7117 2023-02-10 06:19 ./usr/share/doc/python3-rna/copyright vienna-rna_2.5.1+dfsg-1build3_armhf.deb --------------------------------------- new Debian package, version 2.0. size 2134778 bytes: control archive=3066 bytes. 1879 bytes, 35 lines control 4497 bytes, 74 lines md5sums Package: vienna-rna Version: 2.5.1+dfsg-1build3 Architecture: armhf Maintainer: Ubuntu Developers Installed-Size: 80469 Depends: libc6 (>= 2.38), libdlib19.1t64 (>= 19.24+dfsg), libgcc-s1 (>= 3.5), libgomp1 (>= 4.9), libgsl27 (>= 2.7.1), libgslcblas0 (>= 2.7.1), liblapack3 | liblapack.so.3, libmpfr6 (>= 3.1.3), libstdc++6 (>= 13.1) Recommends: readseq Section: non-free/science Priority: optional Homepage: https://www.tbi.univie.ac.at/RNA/ Description: RNA sequence analysis The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. It is developed and maintained by the group of Ivo Hofacker in Vienna. . RNA secondary structure prediction through energy minimization is the most used function in the package. It provides three kinds of dynamic programming algorithms for structure prediction: * the minimum free energy algorithm of (Zuker & Stiegler 1981) which yields a single optimal structure, * the partition function algorithm of (McCaskill 1990) which calculates base pair probabilities in the thermodynamic ensemble, and the suboptimal folding algorithm of (Wuchty et.al 1999) which generates all suboptimal structures within a given energy range of the optimal energy. . For secondary structure comparison, the package contains several measures of distance (dissimilarities) using either string alignment or tree-editing (Shapiro & Zhang 1990). Finally, is provided an algorithm to design sequences with a predefined structure (inverse folding). The RNAforester package is a tool for aligning RNA secondary structures and it's user interface integrates to those of the tools of the Vienna RNA package. 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./usr/share/man/man1/dpzoom.1.gz -rw-r--r-- root/root 405 2024-04-01 05:24 ./usr/share/man/man1/popt.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build Type: any Build-Space: 595420 Build-Time: 1830 Distribution: noble-proposed Host Architecture: armhf Install-Time: 994 Job: vienna-rna_2.5.1+dfsg-1build3.dsc Machine Architecture: arm64 Package: vienna-rna Package-Time: 2839 Source-Version: 2.5.1+dfsg-1build3 Space: 595420 Status: successful Version: 2.5.1+dfsg-1build3 -------------------------------------------------------------------------------- Finished at 2024-04-03T06:12:19Z Build needed 00:47:19, 595420k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27999130 Scanning for processes to kill in build PACKAGEBUILD-27999130