https://launchpad.net/ubuntu/+source/vienna-rna/2.4.17+dfsg-2build2/+build/23057752 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-045 4.15.0-166-generic #174-Ubuntu SMP Wed Dec 8 19:08:37 UTC 2021 aarch64 Buildd toolchain package versions: launchpad-buildd_206~519~ubuntu18.04.1 python3-lpbuildd_206~519~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.9 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 14 Jan 14:08:38 ntpdate[1683]: adjust time server 10.211.37.1 offset 0.037041 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=jammy --arch=arm64 PACKAGEBUILD-23057752 --image-type chroot /home/buildd/filecache-default/d7d0133902b8cc1df688a841d4b96e994eeac2e0 Creating target for build PACKAGEBUILD-23057752 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=jammy --arch=arm64 PACKAGEBUILD-23057752 Starting target for build PACKAGEBUILD-23057752 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=jammy --arch=arm64 PACKAGEBUILD-23057752 'deb http://ftpmaster.internal/ubuntu jammy main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu jammy-security main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu jammy-updates main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu jammy-proposed main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-23057752 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=jammy --arch=arm64 PACKAGEBUILD-23057752 Updating target for build PACKAGEBUILD-23057752 Get:1 http://ftpmaster.internal/ubuntu jammy InRelease [270 kB] Get:2 http://ftpmaster.internal/ubuntu jammy-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed InRelease [121 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main arm64 Packages [1408 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main Translation-en [519 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/restricted arm64 Packages [5356 B] Get:8 http://ftpmaster.internal/ubuntu jammy/restricted Translation-en [13.3 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/universe arm64 Packages [13.6 MB] Get:10 http://ftpmaster.internal/ubuntu jammy/universe Translation-en [5585 kB] Get:11 http://ftpmaster.internal/ubuntu jammy/multiverse arm64 Packages [183 kB] Get:12 http://ftpmaster.internal/ubuntu jammy/multiverse Translation-en [111 kB] Get:13 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 Packages [139 kB] Get:14 http://ftpmaster.internal/ubuntu jammy-proposed/main Translation-en [58.0 kB] Get:15 http://ftpmaster.internal/ubuntu jammy-proposed/restricted arm64 Packages [2064 B] Get:16 http://ftpmaster.internal/ubuntu jammy-proposed/restricted Translation-en [7140 B] Get:17 http://ftpmaster.internal/ubuntu jammy-proposed/universe arm64 Packages [604 kB] Get:18 http://ftpmaster.internal/ubuntu jammy-proposed/universe Translation-en [235 kB] Get:19 http://ftpmaster.internal/ubuntu jammy-proposed/multiverse arm64 Packages [21.2 kB] Get:20 http://ftpmaster.internal/ubuntu jammy-proposed/multiverse Translation-en [13.0 kB] Fetched 23.0 MB in 7s (3137 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libssl1.1 Use 'sudo apt autoremove' to remove it. The following packages will be REMOVED: libsemanage1* The following NEW packages will be installed: libsemanage2 libsepol2 libssl3 The following packages will be upgraded: apt base-files bash binutils binutils-aarch64-linux-gnu binutils-common bsdutils bzip2 ca-certificates cpp-11 dash debconf debianutils dpkg dpkg-dev e2fsprogs g++-11 gcc-11 gcc-11-base gpg gpg-agent gpgconf gpgv grep init init-system-helpers libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libattr1 libbinutils libblkid1 libbz2-1.0 libcap-ng0 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdpkg-perl libext2fs2 libgcc-11-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libhwasan0 libidn2-0 libip4tc2 libisl23 libitm1 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblsan0 libmount1 libmpc3 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsmartcols1 libsqlite3-0 libss2 libstdc++-11-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtsan0 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev lockfile-progs login logsave lto-disabled-list make mount ncurses-base ncurses-bin openssl passwd pkgbinarymangler readline-common sed sensible-utils systemd systemd-sysv systemd-timesyncd tzdata usrmerge util-linux 112 upgraded, 3 newly installed, 1 to remove and 0 not upgraded. Need to get 83.1 MB of archives. After this operation, 379 MB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu jammy/main arm64 debconf all 1.5.79 [126 kB] Get:2 http://ftpmaster.internal/ubuntu jammy/main arm64 libpam0g arm64 1.4.0-10ubuntu2 [61.3 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main arm64 libcrypt-dev arm64 1:4.4.27-1 [119 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main arm64 libcrypt1 arm64 1:4.4.27-1 [86.8 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main arm64 base-files arm64 12ubuntu2 [63.2 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main arm64 debianutils arm64 5.5-1ubuntu1 [106 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main arm64 bash arm64 5.1-6ubuntu1 [762 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main arm64 bsdutils arm64 1:2.37.2-4ubuntu1 [84.5 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main arm64 libgpg-error0 arm64 1.43-1 [69.3 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main arm64 libgcrypt20 arm64 1.9.4-3ubuntu2 [456 kB] Get:11 http://ftpmaster.internal/ubuntu jammy/main arm64 bzip2 arm64 1.0.8-5 [34.5 kB] Get:12 http://ftpmaster.internal/ubuntu jammy/main arm64 libbz2-1.0 arm64 1.0.8-5 [36.0 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main arm64 libubsan1 arm64 11.2.0-13ubuntu1 [908 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main arm64 libtsan0 arm64 11.2.0-13ubuntu1 [2232 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main arm64 gcc-11-base arm64 11.2.0-13ubuntu1 [21.1 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main arm64 libgcc-s1 arm64 11.2.0-13ubuntu1 [39.3 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main arm64 libgomp1 arm64 11.2.0-13ubuntu1 [115 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main arm64 libitm1 arm64 11.2.0-13ubuntu1 [28.4 kB] Get:19 http://ftpmaster.internal/ubuntu jammy/main arm64 libatomic1 arm64 11.2.0-13ubuntu1 [10.8 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main arm64 libasan6 arm64 11.2.0-13ubuntu1 [2229 kB] Get:21 http://ftpmaster.internal/ubuntu jammy/main arm64 liblsan0 arm64 11.2.0-13ubuntu1 [942 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main arm64 libhwasan0 arm64 11.2.0-13ubuntu1 [1010 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main arm64 cpp-11 arm64 11.2.0-13ubuntu1 [9736 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main arm64 libcc1-0 arm64 11.2.0-13ubuntu1 [54.1 kB] Get:25 http://ftpmaster.internal/ubuntu jammy/main arm64 g++-11 arm64 11.2.0-13ubuntu1 [11.1 MB] Get:26 http://ftpmaster.internal/ubuntu jammy/main arm64 gcc-11 arm64 11.2.0-13ubuntu1 [19.5 MB] Get:27 http://ftpmaster.internal/ubuntu jammy/main arm64 libgcc-11-dev arm64 11.2.0-13ubuntu1 [1150 kB] Get:28 http://ftpmaster.internal/ubuntu jammy/main arm64 libstdc++-11-dev arm64 11.2.0-13ubuntu1 [2102 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main arm64 libstdc++6 arm64 11.2.0-13ubuntu1 [624 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main arm64 libisl23 arm64 0.24-2 [690 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main arm64 libmpc3 arm64 1.2.1-1 [48.1 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main arm64 libzstd1 arm64 1.4.8+dfsg-3 [311 kB] Get:33 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libctf0 arm64 2.37.50.20220106-2ubuntu1 [102 kB] Get:34 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libctf-nobfd0 arm64 2.37.50.20220106-2ubuntu1 [106 kB] Get:35 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libbinutils arm64 2.37.50.20220106-2ubuntu1 [822 kB] Get:36 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 binutils-common arm64 2.37.50.20220106-2ubuntu1 [220 kB] Get:37 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 binutils arm64 2.37.50.20220106-2ubuntu1 [3156 B] Get:38 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 binutils-aarch64-linux-gnu arm64 2.37.50.20220106-2ubuntu1 [3246 kB] Get:39 http://ftpmaster.internal/ubuntu jammy/main arm64 libssl3 arm64 3.0.1-0ubuntu1 [1767 kB] Get:40 http://ftpmaster.internal/ubuntu jammy/main arm64 libblkid1 arm64 2.37.2-4ubuntu1 [103 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main arm64 libuuid1 arm64 2.37.2-4ubuntu1 [23.8 kB] Get:42 http://ftpmaster.internal/ubuntu jammy/main arm64 libcryptsetup12 arm64 2:2.4.2-1ubuntu4 [205 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main arm64 libidn2-0 arm64 2.3.2-2 [67.1 kB] Get:44 http://ftpmaster.internal/ubuntu jammy/main arm64 libp11-kit0 arm64 0.24.0-6 [231 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/main arm64 libtasn1-6 arm64 4.18.0-4 [42.6 kB] Get:46 http://ftpmaster.internal/ubuntu jammy/main arm64 libgnutls30 arm64 3.7.2-5ubuntu1 [917 kB] Get:47 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 systemd-sysv arm64 249.5-2ubuntu4 [10.5 kB] Get:48 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 systemd-timesyncd arm64 249.5-2ubuntu4 [29.6 kB] Get:49 http://ftpmaster.internal/ubuntu jammy/main arm64 libapparmor1 arm64 3.0.3-0ubuntu5 [37.7 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main arm64 libip4tc2 arm64 1.8.7-1ubuntu4 [19.8 kB] Get:51 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libkmod2 arm64 29-1ubuntu1 [46.4 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/main arm64 libpcre2-8-0 arm64 10.39-3 [201 kB] Get:53 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libselinux1 arm64 3.3-1build1 [74.3 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/main arm64 libmount1 arm64 2.37.2-4ubuntu1 [120 kB] Get:55 http://ftpmaster.internal/ubuntu jammy/main arm64 libseccomp2 arm64 2.5.2-2ubuntu2 [47.9 kB] Get:56 http://ftpmaster.internal/ubuntu jammy/main arm64 login arm64 1:4.8.1-2ubuntu1 [186 kB] Get:57 http://ftpmaster.internal/ubuntu jammy/main arm64 util-linux arm64 2.37.2-4ubuntu1 [1059 kB] Get:58 http://ftpmaster.internal/ubuntu jammy/main arm64 mount arm64 2.37.2-4ubuntu1 [113 kB] Get:59 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 systemd arm64 249.5-2ubuntu4 [4381 kB] Get:60 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libsystemd0 arm64 249.5-2ubuntu4 [315 kB] Get:61 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libudev1 arm64 249.5-2ubuntu4 [75.9 kB] Get:62 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libxxhash0 arm64 0.8.1-0.1 [19.9 kB] Get:63 http://ftpmaster.internal/ubuntu jammy/main arm64 libapt-pkg6.0 arm64 2.3.14 [865 kB] Get:64 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 dpkg arm64 1.21.1ubuntu1 [1235 kB] Get:65 http://ftpmaster.internal/ubuntu jammy/main arm64 dash arm64 0.5.11+git20210903+057cd650a4ed-3 [91.7 kB] Get:66 http://ftpmaster.internal/ubuntu jammy/main arm64 grep arm64 3.7-1 [152 kB] Get:67 http://ftpmaster.internal/ubuntu jammy/main arm64 libncurses6 arm64 6.3-1 [108 kB] Get:68 http://ftpmaster.internal/ubuntu jammy/main arm64 libncursesw6 arm64 6.3-1 [142 kB] Get:69 http://ftpmaster.internal/ubuntu jammy/main arm64 libtinfo6 arm64 6.3-1 [104 kB] Get:70 http://ftpmaster.internal/ubuntu jammy/main arm64 ncurses-bin arm64 6.3-1 [183 kB] Get:71 http://ftpmaster.internal/ubuntu jammy/main arm64 sed arm64 4.8-1ubuntu1 [186 kB] Get:72 http://ftpmaster.internal/ubuntu jammy/main arm64 init-system-helpers all 1.61 [39.3 kB] Get:73 http://ftpmaster.internal/ubuntu jammy/main arm64 ncurses-base all 6.3-1 [19.9 kB] Get:74 http://ftpmaster.internal/ubuntu jammy/main arm64 gpgv arm64 2.2.27-3ubuntu1 [133 kB] Get:75 http://ftpmaster.internal/ubuntu jammy/main arm64 apt arm64 2.3.14 [1354 kB] Get:76 http://ftpmaster.internal/ubuntu jammy/main arm64 libsepol2 arm64 3.3-1 [274 kB] Get:77 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libsemanage-common all 3.3-1build1 [10.0 kB] Get:78 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libsemanage2 arm64 3.3-1build1 [89.4 kB] Get:79 http://ftpmaster.internal/ubuntu jammy/main arm64 passwd arm64 1:4.8.1-2ubuntu1 [761 kB] Get:80 http://ftpmaster.internal/ubuntu jammy/main arm64 libpam-modules-bin arm64 1.4.0-10ubuntu2 [38.6 kB] Get:81 http://ftpmaster.internal/ubuntu jammy/main arm64 libpam-modules arm64 1.4.0-10ubuntu2 [278 kB] Get:82 http://ftpmaster.internal/ubuntu jammy/main arm64 logsave arm64 1.46.5-2ubuntu1 [10.5 kB] Get:83 http://ftpmaster.internal/ubuntu jammy/main arm64 libext2fs2 arm64 1.46.5-2ubuntu1 [212 kB] Get:84 http://ftpmaster.internal/ubuntu jammy/main arm64 e2fsprogs arm64 1.46.5-2ubuntu1 [587 kB] Get:85 http://ftpmaster.internal/ubuntu jammy/main arm64 init arm64 1.61 [6102 B] Get:86 http://ftpmaster.internal/ubuntu jammy/main arm64 libattr1 arm64 1:2.5.1-1 [13.3 kB] Get:87 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libcap-ng0 arm64 0.7.9-2.2build3 [11.2 kB] Get:88 http://ftpmaster.internal/ubuntu jammy/main arm64 libcom-err2 arm64 1.46.5-2ubuntu1 [9728 B] Get:89 http://ftpmaster.internal/ubuntu jammy/main arm64 libk5crypto3 arm64 1.19.2-0ubuntu1 [91.6 kB] Get:90 http://ftpmaster.internal/ubuntu jammy/main arm64 libkrb5support0 arm64 1.19.2-0ubuntu1 [32.5 kB] Get:91 http://ftpmaster.internal/ubuntu jammy/main arm64 libkrb5-3 arm64 1.19.2-0ubuntu1 [356 kB] Get:92 http://ftpmaster.internal/ubuntu jammy/main arm64 libgssapi-krb5-2 arm64 1.19.2-0ubuntu1 [142 kB] Get:93 http://ftpmaster.internal/ubuntu jammy/main arm64 libpam-runtime all 1.4.0-10ubuntu2 [40.2 kB] Get:94 http://ftpmaster.internal/ubuntu jammy/main arm64 libsmartcols1 arm64 2.37.2-4ubuntu1 [49.6 kB] Get:95 http://ftpmaster.internal/ubuntu jammy/main arm64 libss2 arm64 1.46.5-2ubuntu1 [11.9 kB] Get:96 http://ftpmaster.internal/ubuntu jammy/main arm64 sensible-utils all 0.0.17 [20.1 kB] Get:97 http://ftpmaster.internal/ubuntu jammy/main arm64 usrmerge all 25ubuntu2 [54.7 kB] Get:98 http://ftpmaster.internal/ubuntu jammy/main arm64 openssl arm64 3.0.1-0ubuntu1 [1157 kB] Get:99 http://ftpmaster.internal/ubuntu jammy/main arm64 ca-certificates all 20211016 [148 kB] Get:100 http://ftpmaster.internal/ubuntu jammy/main arm64 readline-common all 8.1.2-1 [53.5 kB] Get:101 http://ftpmaster.internal/ubuntu jammy/main arm64 libreadline8 arm64 8.1.2-1 [153 kB] Get:102 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libsqlite3-0 arm64 3.37.2-1 [635 kB] Get:103 http://ftpmaster.internal/ubuntu jammy/main arm64 tzdata all 2021e-1ubuntu1 [343 kB] Get:104 http://ftpmaster.internal/ubuntu jammy/main arm64 libgdbm6 arm64 1.22-1 [35.1 kB] Get:105 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 dpkg-dev all 1.21.1ubuntu1 [922 kB] Get:106 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libdpkg-perl all 1.21.1ubuntu1 [236 kB] Get:107 http://ftpmaster.internal/ubuntu jammy/main arm64 make arm64 4.3-4ubuntu2 [176 kB] Get:108 http://ftpmaster.internal/ubuntu jammy/main arm64 lto-disabled-list all 18 [12.2 kB] Get:109 http://ftpmaster.internal/ubuntu jammy/main arm64 gpg arm64 2.2.27-3ubuntu1 [507 kB] Get:110 http://ftpmaster.internal/ubuntu jammy/main arm64 gpgconf arm64 2.2.27-3ubuntu1 [92.4 kB] Get:111 http://ftpmaster.internal/ubuntu jammy/main arm64 gpg-agent arm64 2.2.27-3ubuntu1 [204 kB] Get:112 http://ftpmaster.internal/ubuntu jammy/main arm64 libgdbm-compat4 arm64 1.22-1 [6370 B] Get:113 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 linux-libc-dev arm64 5.15.0-16.16 [1234 kB] Get:114 http://ftpmaster.internal/ubuntu jammy/main arm64 lockfile-progs arm64 0.1.19 [9778 B] Get:115 http://ftpmaster.internal/ubuntu jammy/main arm64 pkgbinarymangler all 149 [32.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 83.1 MB in 3s (25.3 MB/s) (Reading database ... 13240 files and directories currently installed.) Preparing to unpack .../debconf_1.5.79_all.deb ... Unpacking debconf (1.5.79) over (1.5.77) ... Setting up debconf (1.5.79) ... (Reading database ... 13239 files and directories currently installed.) Preparing to unpack .../libpam0g_1.4.0-10ubuntu2_arm64.deb ... Unpacking libpam0g:arm64 (1.4.0-10ubuntu2) over (1.3.1-5ubuntu11) ... Setting up libpam0g:arm64 (1.4.0-10ubuntu2) ... Checking for services that may need to be restarted...Checking init scripts... Nothing to restart. (Reading database ... 13239 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.27-1_arm64.deb ... Unpacking libcrypt-dev:arm64 (1:4.4.27-1) over (1:4.4.18-4ubuntu2) ... Preparing to unpack .../libcrypt1_1%3a4.4.27-1_arm64.deb ... Unpacking libcrypt1:arm64 (1:4.4.27-1) over (1:4.4.18-4ubuntu2) ... Setting up libcrypt1:arm64 (1:4.4.27-1) ... (Reading database ... 13239 files and directories currently installed.) Preparing to unpack .../base-files_12ubuntu2_arm64.deb ... 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Setting up libgomp1:arm64 (11.2.0-13ubuntu1) ... Setting up bzip2 (1.0.8-5) ... Setting up libasan6:arm64 (11.2.0-13ubuntu1) ... Setting up tzdata (2021e-1ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Jan 14 14:09:37 UTC 2022. Universal Time is now: Fri Jan 14 14:09:37 UTC 2022. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up make (4.3-4ubuntu2) ... Setting up libncurses6:arm64 (6.3-1) ... Setting up libmpc3:arm64 (1.2.1-1) ... Setting up systemd-timesyncd (249.5-2ubuntu4) ... Setting up lockfile-progs (0.1.19) ... Setting up libatomic1:arm64 (11.2.0-13ubuntu1) ... Setting up usrmerge (25ubuntu2) ... Setting up libss2:arm64 (1.46.5-2ubuntu1) ... Setting up libncursesw6:arm64 (6.3-1) ... Setting up libdpkg-perl (1.21.1ubuntu1) ... Setting up logsave (1.46.5-2ubuntu1) ... Setting up libubsan1:arm64 (11.2.0-13ubuntu1) ... Setting up sensible-utils (0.0.17) ... Setting up libhwasan0:arm64 (11.2.0-13ubuntu1) ... 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Setting up ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 7 added, 8 removed; done. Setting up libgdbm-compat4:arm64 (1.22-1) ... Setting up libgcc-11-dev:arm64 (11.2.0-13ubuntu1) ... Setting up gcc-11 (11.2.0-13ubuntu1) ... Setting up gpgconf (2.2.27-3ubuntu1) ... Setting up gpg (2.2.27-3ubuntu1) ... Setting up gpg-agent (2.2.27-3ubuntu1) ... Setting up libstdc++-11-dev:arm64 (11.2.0-13ubuntu1) ... Setting up g++-11 (11.2.0-13ubuntu1) ... Processing triggers for libc-bin (2.34-0ubuntu3) ... Processing triggers for ca-certificates (20211016) ... 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-23057752 arm64 jammy-proposed -c chroot:build-PACKAGEBUILD-23057752 --arch=arm64 --dist=jammy-proposed --nolog vienna-rna_2.4.17+dfsg-2build2.dsc Initiating build PACKAGEBUILD-23057752 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-166-generic #174-Ubuntu SMP Wed Dec 8 19:08:37 UTC 2021 aarch64 sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-arm64-045.buildd +==============================================================================+ | vienna-rna 2.4.17+dfsg-2build2 (arm64) Fri, 14 Jan 2022 14:09:48 +0000 | +==============================================================================+ Package: vienna-rna Version: 2.4.17+dfsg-2build2 Source Version: 2.4.17+dfsg-2build2 Distribution: jammy-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-23057752/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- vienna-rna_2.4.17+dfsg-2build2.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/vienna-rna-N8wCwR/vienna-rna-2.4.17+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/vienna-rna-N8wCwR' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-KHmUq5/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-KHmUq5/apt_archive ./ InRelease Get:2 copy:/<>/resolver-KHmUq5/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-KHmUq5/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-KHmUq5/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-KHmUq5/apt_archive ./ Packages [433 B] Fetched 1739 B in 0s (54.4 kB/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libssl1.1 systemd-timesyncd Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 652 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-KHmUq5/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [652 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 652 B in 0s (52.0 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 13442 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, python3-dev, swig (>= 4.0.2), perl-doc, perl, graphviz, libgsl-dev, xxd, texlive-latex-extra, help2man, autoconf, automake, m4, pkg-config, libtool, gettext, libsvm-dev, gengetopt, libmpfr-dev, cthreadpool-dev, ghostscript, doxygen, texinfo Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3-dev, swig (>= 4.0.2), perl-doc, perl, graphviz, libgsl-dev, xxd, texlive-latex-extra, help2man, autoconf, automake, m4, pkg-config, libtool, gettext, libsvm-dev, gengetopt, libmpfr-dev, cthreadpool-dev, ghostscript, doxygen, texinfo dpkg-deb: building package 'sbuild-build-depends-vienna-rna-dummy' in '/<>/resolver-KHmUq5/apt_archive/sbuild-build-depends-vienna-rna-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-vienna-rna-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-KHmUq5/apt_archive ./ InRelease Get:2 copy:/<>/resolver-KHmUq5/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-KHmUq5/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-KHmUq5/apt_archive ./ Sources [642 B] Get:5 copy:/<>/resolver-KHmUq5/apt_archive ./ Packages [724 B] Fetched 2329 B in 0s (73.7 kB/s) Reading package lists... Reading package lists... Install vienna-rna 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: libssl1.1 systemd-timesyncd Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils cthreadpool-dev debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism doxygen dwz file fontconfig fontconfig-config fonts-dejavu-core fonts-lmodern fonts-urw-base35 gengetopt gettext gettext-base ghostscript graphviz groff-base help2man intltool-debian libann0 libapache-pom-java libarchive-zip-perl libavahi-client3 libavahi-common-data libavahi-common3 libbrotli1 libbsd0 libcairo2 libcdt5 libcgraph6 libclang-cpp12 libclang1-12 libcommons-logging-java libcommons-parent-java libcups2 libdatrie1 libdbus-1-3 libdebhelper-perl libdeflate0 libdw1 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfreetype6 libfribidi0 libgd3 libglib2.0-0 libgmp-dev libgmpxx4ldbl libgraphite2-3 libgs9 libgs9-common libgsl-dev libgsl27 libgslcblas0 libgts-0.7-5 libgvc6 libgvpr2 libharfbuzz0b libice6 libicu67 libidn12 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore libkpathsea6 liblab-gamut1 libllvm12 liblocale-gettext-perl libltdl7 libmagic-mgc libmagic1 libmd0 libmpdec3 libmpfr-dev libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpathplan4 libpdfbox-java libpipeline1 libpixman-1-0 libptexenc1 libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib libsigsegv2 libsm6 libsub-override-perl libsvm-dev libsvm3 libsynctex2 libteckit0 libtexlua53 libtext-unidecode-perl libthai-data libthai0 libtiff5 libtool libuchardet0 libwebp6 libx11-6 libx11-data libxapian30 libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml2 libxmu6 libxpm4 libxrender1 libxt6 libzzip-0-13 m4 man-db media-types perl-doc pkg-config po-debconf poppler-data preview-latex-style python3 python3-dev python3-distutils python3-lib2to3 python3-minimal python3.10 python3.10-dev python3.10-minimal swig swig4.0 t1utils tex-common texinfo texlive-base texlive-binaries texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures ucf x11-common xdg-utils xxd zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make flit python3-build python3-tomli python3-installer doxygen-latex doxygen-doc doxygen-gui fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gettext-doc libasprintf-dev libgettextpo-dev ghostscript-x gsfonts graphviz-doc groff libavalon-framework-java libcommons-logging-java-doc libexcalibur-logkit-java liblog4j1.2-java cups-common libgd-tools gmp-doc libgmp10-doc gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libmpfr-doc libtool-doc gfortran | fortran95-compiler gcj-jdk xapian-tools 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 python3-doc python3-tk python3-venv python3.10-venv python3.10-doc binfmt-support swig-doc swig-examples swig4.0-examples swig4.0-doc texlive-plain-generic texlive-fonts-recommended perl-tk xpdf | pdf-viewer xzdec texlive-latex-base-doc python3-pygments icc-profiles libfile-which-perl libspreadsheet-parseexcel-perl texlive-latex-extra-doc texlive-latex-recommended-doc texlive-luatex texlive-pstricks dot2tex prerex texlive-pictures-doc vprerex Recommended packages: curl | wget | lynx fonts-liberation dbus libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs fonts-droid-fallback libgts-bin javascript-common libltdl-dev libwww-perl libxml-sax-expat-perl libmail-sendmail-perl lmodern dvisvgm 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 bsdextrautils cthreadpool-dev debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism doxygen dwz file fontconfig fontconfig-config fonts-dejavu-core fonts-lmodern fonts-urw-base35 gengetopt gettext gettext-base ghostscript graphviz groff-base help2man intltool-debian libann0 libapache-pom-java libarchive-zip-perl libavahi-client3 libavahi-common-data libavahi-common3 libbrotli1 libbsd0 libcairo2 libcdt5 libcgraph6 libclang-cpp12 libclang1-12 libcommons-logging-java libcommons-parent-java libcups2 libdatrie1 libdbus-1-3 libdebhelper-perl libdeflate0 libdw1 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfreetype6 libfribidi0 libgd3 libglib2.0-0 libgmp-dev libgmpxx4ldbl libgraphite2-3 libgs9 libgs9-common libgsl-dev libgsl27 libgslcblas0 libgts-0.7-5 libgvc6 libgvpr2 libharfbuzz0b libice6 libicu67 libidn12 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore libkpathsea6 liblab-gamut1 libllvm12 liblocale-gettext-perl libltdl7 libmagic-mgc libmagic1 libmd0 libmpdec3 libmpfr-dev libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpathplan4 libpdfbox-java libpipeline1 libpixman-1-0 libptexenc1 libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib libsigsegv2 libsm6 libsub-override-perl libsvm-dev libsvm3 libsynctex2 libteckit0 libtexlua53 libtext-unidecode-perl libthai-data libthai0 libtiff5 libtool libuchardet0 libwebp6 libx11-6 libx11-data libxapian30 libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml2 libxmu6 libxpm4 libxrender1 libxt6 libzzip-0-13 m4 man-db media-types perl-doc pkg-config po-debconf poppler-data preview-latex-style python3 python3-dev python3-distutils python3-lib2to3 python3-minimal python3.10 python3.10-dev python3.10-minimal sbuild-build-depends-vienna-rna-dummy swig swig4.0 t1utils tex-common texinfo texlive-base texlive-binaries texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures ucf x11-common xdg-utils xxd zlib1g-dev 0 upgraded, 178 newly installed, 0 to remove and 0 not upgraded. Need to get 190 MB of archives. After this operation, 693 MB of additional disk space will be used. Get:1 copy:/<>/resolver-KHmUq5/apt_archive ./ sbuild-build-depends-vienna-rna-dummy 0.invalid.0 [806 B] Get:2 http://ftpmaster.internal/ubuntu jammy/main arm64 liblocale-gettext-perl arm64 1.07-4build2 [17.0 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libpython3.10-minimal arm64 3.10.1-5 [805 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main arm64 libexpat1 arm64 2.4.2-1 [75.8 kB] Get:5 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 python3.10-minimal arm64 3.10.1-5 [2144 kB] Get:6 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 python3-minimal arm64 3.10.1-0ubuntu1 [24.7 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main arm64 media-types all 4.0.0 [22.2 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main arm64 libmd0 arm64 1.0.4-1 [23.8 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main arm64 libbsd0 arm64 0.11.3-1ubuntu3 [43.5 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main arm64 libedit2 arm64 3.1-20210910-1 [95.9 kB] Get:11 http://ftpmaster.internal/ubuntu jammy/main arm64 libmpdec3 arm64 2.5.1-2build1 [89.0 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libpython3.10-stdlib arm64 3.10.1-5 [1820 kB] Get:13 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 python3.10 arm64 3.10.1-5 [480 kB] Get:14 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libpython3-stdlib arm64 3.10.1-0ubuntu1 [7320 B] Get:15 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 python3 arm64 3.10.1-0ubuntu1 [22.8 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main arm64 poppler-data all 0.4.11-1 [2171 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main arm64 ucf all 3.0043 [56.1 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/universe arm64 tex-common all 6.17 [33.7 kB] Get:19 http://ftpmaster.internal/ubuntu jammy/main arm64 libdbus-1-3 arm64 1.12.20-2ubuntu2 [188 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main arm64 libelf1 arm64 0.186-1 [51.1 kB] Get:21 http://ftpmaster.internal/ubuntu jammy/main arm64 libfribidi0 arm64 1.0.8-2ubuntu2 [26.1 kB] Get:22 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libglib2.0-0 arm64 2.71.0-2 [1414 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main arm64 libicu67 arm64 67.1-7ubuntu1 [10.0 MB] Get:24 http://ftpmaster.internal/ubuntu jammy/main arm64 libxml2 arm64 2.9.12+dfsg-5 [725 kB] Get:25 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 xxd arm64 2:8.2.3565-1ubuntu5 [50.7 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main arm64 bsdextrautils arm64 2.37.2-4ubuntu1 [70.1 kB] Get:27 http://ftpmaster.internal/ubuntu jammy/main arm64 libmagic-mgc arm64 1:5.41-2 [257 kB] Get:28 http://ftpmaster.internal/ubuntu jammy/main arm64 libmagic1 arm64 1:5.41-2 [84.9 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main arm64 file arm64 1:5.41-2 [21.6 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main arm64 gettext-base arm64 0.21-4ubuntu3 [35.2 kB] Get:31 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http://ftpmaster.internal/ubuntu jammy/universe arm64 texlive-latex-extra all 2021.20211217-1 [13.8 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 190 MB in 8s (23.6 MB/s) Selecting previously unselected package liblocale-gettext-perl. 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Setting up bsdextrautils (2.37.2-4ubuntu1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:arm64 (67.1-7ubuntu1) ... Setting up libdatrie1:arm64 (0.2.13-1ubuntu3) ... Setting up libgslcblas0:arm64 (2.7.1+dfsg-3) ... Setting up libmagic-mgc (1:5.41-2) ... Setting up libtexlua53:arm64 (2021.20210626.59705-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:arm64 (2.71.0-2) ... No schema files found: doing nothing. Setting up libijs-0.35:arm64 (0.35-15build1) ... Setting up libdebhelper-perl (13.5.2ubuntu1) ... Setting up libbrotli1:arm64 (1.0.9-2build4) ... Setting up libfontbox-java (1:1.8.16-2) ... Setting up liblab-gamut1:arm64 (2.42.2-5build2) ... Setting up x11-common (1:7.7+23ubuntu1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libmagic1:arm64 (1:5.41-2) ... Setting up libdeflate0:arm64 (1.8-1ubuntu1) ... Setting up perl-doc (5.32.1-3ubuntu3) ... Setting up libxml-namespacesupport-perl (1.12-1.1) ... Setting up gettext-base (0.21-4ubuntu3) ... Setting up libgsl27:arm64 (2.7.1+dfsg-3) ... Setting up libzzip-0-13:arm64 (0.13.72+dfsg.1-1.1) ... Setting up file (1:5.41-2) ... Setting up fonts-urw-base35 (20200910-1) ... Setting up cthreadpool-dev (0.0+git20201207.b259a6e-1) ... Setting up libjbig0:arm64 (2.1-3.1build2) ... Setting up xxd (2:8.2.3565-1ubuntu5) ... Setting up poppler-data (0.4.11-1) ... Setting up libgts-0.7-5:arm64 (0.7.6+darcs121130-5) ... Setting up libxml-sax-base-perl (1.09-1.1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libgmpxx4ldbl:arm64 (2:6.2.1+dfsg-1ubuntu3) ... Setting up libexpat1-dev:arm64 (2.4.2-1) ... Setting up libfreetype6:arm64 (2.11.1+dfsg-1) ... Setting up libx11-data (2:1.7.2-2) ... Setting up libjbig2dec0:arm64 (0.19-3build1) ... Setting up libteckit0:arm64 (2.5.11+ds1-1) ... Setting up libpathplan4:arm64 (2.42.2-5build2) ... 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Setting up libfile-stripnondeterminism-perl (1.13.0-1) ... Setting up libpaper1:arm64 (1.1.28build1) ... Creating config file /etc/papersize with new version Setting up libice6:arm64 (2:1.0.10-1build1) ... Setting up libdw1:arm64 (0.186-1) ... Setting up libxdmcp6:arm64 (1:1.1.3-0ubuntu4) ... Setting up libxcb1:arm64 (1.14-3ubuntu2) ... Setting up gettext (0.21-4ubuntu3) ... Setting up libgsl-dev (2.7.1+dfsg-3) ... Setting up swig (4.0.2-1ubuntu1) ... Setting up libgmp-dev:arm64 (2:6.2.1+dfsg-1ubuntu3) ... Setting up libpdfbox-java (1:1.8.16-2) ... Setting up libtool (2.4.6-15build1) ... Setting up libxcb-render0:arm64 (1.14-3ubuntu2) ... Setting up fontconfig-config (2.13.1-4.2ubuntu4) ... Setting up libedit2:arm64 (3.1-20210910-1) ... Setting up libcommons-parent-java (43-1) ... Setting up libavahi-common3:arm64 (0.8-5ubuntu4) ... Setting up libcommons-logging-java (1.2-2) ... Setting up m4 (1.4.18-5ubuntu1) ... Setting up libxcb-shm0:arm64 (1.14-3ubuntu2) ... Setting up libpaper-utils (1.1.28build1) ... Setting up libmpfr-dev:arm64 (4.1.0-3build2) ... 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 intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.48.5) ... Setting up libpython3.10-stdlib:arm64 (3.10.1-5) ... Setting up tex-common (6.17) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libthai0:arm64 (0.1.29-1) ... Setting up libptexenc1:arm64 (2021.20210626.59705-1) ... Setting up libllvm12:arm64 (1:12.0.1-17build1) ... Setting up libsvm-dev:arm64 (3.24+ds-6) ... Setting up libjs-sphinxdoc (4.3.2-1) ... Setting up autoconf (2.71-2) ... Setting up libxml-libxml-perl (2.0134+dfsg-2build2) ... 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 dh-strip-nondeterminism (1.13.0-1) ... Setting up libgvpr2:arm64 (2.42.2-5build2) ... Setting up dwz (0.14-1build1) ... Setting up groff-base (1.22.4-8) ... Setting up debugedit (1:5.0-4) ... Setting up libx11-6:arm64 (2:1.7.2-2) ... Setting up libtiff5:arm64 (4.3.0-2) ... Setting up libfontconfig1:arm64 (2.13.1-4.2ubuntu4) ... Setting up libsm6:arm64 (2:1.2.3-1build1) ... Setting up libavahi-client3:arm64 (0.8-5ubuntu4) ... Setting up libpython3-stdlib:arm64 (3.10.1-0ubuntu1) ... Setting up automake (1:1.16.5-1.1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libpython3.10:arm64 (3.10.1-5) ... Setting up fontconfig (2.13.1-4.2ubuntu4) ... Regenerating fonts cache... done. Setting up python3.10 (3.10.1-5) ... Setting up libxpm4:arm64 (1:3.5.12-1build1) ... Setting up libxrender1:arm64 (1:0.9.10-1build3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up preview-latex-style (12.2-1ubuntu1) ... Setting up libpango-1.0-0:arm64 (1.50.3+ds1-3) ... Setting up libxext6:arm64 (2:1.3.4-1) ... Setting up python3 (3.10.1-0ubuntu1) ... Setting up man-db (2.9.4-4) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libcairo2:arm64 (1.16.0-5ubuntu2) ... Setting up libclang1-12 (1:12.0.1-17build1) ... Setting up dh-autoreconf (20) ... Setting up libclang-cpp12 (1:12.0.1-17build1) ... Setting up libgd3:arm64 (2.3.0-2ubuntu1) ... Setting up libpython3.10-dev:arm64 (3.10.1-5) ... Setting up libxt6:arm64 (1:1.2.0-1build1) ... Setting up texinfo (6.8-4) ... Running mktexlsr. This may take some time. ... done. Setting up libcups2:arm64 (2.3.3op2-7ubuntu2) ... Setting up python3.10-dev (3.10.1-5) ... Setting up libpangoft2-1.0-0:arm64 (1.50.3+ds1-3) ... Setting up python3-lib2to3 (3.9.9-3) ... Setting up libpangocairo-1.0-0:arm64 (1.50.3+ds1-3) ... Setting up python3-distutils (3.9.9-3) ... Setting up dh-python (5.20220101) ... Setting up libxmu6:arm64 (2:1.1.3-0ubuntu2) ... Setting up libpython3-dev:arm64 (3.10.1-0ubuntu1) ... Setting up libgs9:arm64 (9.55.0~dfsg1-0ubuntu4) ... Setting up libxi6:arm64 (2:1.8-1) ... Setting up debhelper (13.5.2ubuntu1) ... Setting up libxaw7:arm64 (2:1.0.13-1.1build1) ... Setting up ghostscript (9.55.0~dfsg1-0ubuntu4) ... Setting up doxygen (1.9.1-2ubuntu1) ... Setting up python3-dev (3.10.1-0ubuntu1) ... Setting up libgvc6 (2.42.2-5build2) ... Setting up texlive-binaries (2021.20210626.59705-1) ... 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 (2021.20211217-1) ... 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 graphviz (2.42.2-5build2) ... Setting up texlive-latex-base (2021.20211217-1) ... Setting up texlive-latex-recommended (2021.20211217-1) ... Setting up texlive-pictures (2021.20211217-1) ... Setting up texlive-latex-extra (2021.20211217-1) ... Setting up sbuild-build-depends-vienna-rna-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.34-0ubuntu3) ... Processing triggers for tex-common (6.17) ... 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. +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-166-generic arm64 (aarch64) Toolchain package versions: binutils_2.37.50.20220106-2ubuntu1 dpkg-dev_1.21.1ubuntu1 g++-11_11.2.0-13ubuntu1 gcc-11_11.2.0-13ubuntu1 libc6-dev_2.34-0ubuntu3 libstdc++-11-dev_11.2.0-13ubuntu1 libstdc++6_11.2.0-13ubuntu1 linux-libc-dev_5.15.0-16.16 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1ubuntu1 apt_2.3.14 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4ubuntu3 autotools-dev_20180224.1+nmu1 base-files_12ubuntu2 base-passwd_3.5.52 bash_5.1-6ubuntu1 binutils_2.37.50.20220106-2ubuntu1 binutils-aarch64-linux-gnu_2.37.50.20220106-2ubuntu1 binutils-common_2.37.50.20220106-2ubuntu1 bsdextrautils_2.37.2-4ubuntu1 bsdutils_1:2.37.2-4ubuntu1 build-essential_12.9ubuntu2 bzip2_1.0.8-5 ca-certificates_20211016 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sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-vienna-rna-dummy_0.invalid.0 sed_4.8-1ubuntu1 sensible-utils_0.0.17 swig_4.0.2-1ubuntu1 swig4.0_4.0.2-1ubuntu1 systemd_249.5-2ubuntu4 systemd-sysv_249.5-2ubuntu4 systemd-timesyncd_249.5-2ubuntu4 sysvinit-utils_2.96-7ubuntu2 t1utils_1.41-4build1 tar_1.34+dfsg-1build2 tex-common_6.17 texinfo_6.8-4 texlive-base_2021.20211217-1 texlive-binaries_2021.20210626.59705-1 texlive-latex-base_2021.20211217-1 texlive-latex-extra_2021.20211217-1 texlive-latex-recommended_2021.20211217-1 texlive-pictures_2021.20211217-1 tzdata_2021e-1ubuntu1 ubuntu-keyring_2021.03.26 ucf_3.0043 usrmerge_25ubuntu2 util-linux_2.37.2-4ubuntu1 x11-common_1:7.7+23ubuntu1 xdg-utils_1.1.3-4.1ubuntu1 xxd_2:8.2.3565-1ubuntu5 xz-utils_5.2.5-2build1 zlib1g_1:1.2.11.dfsg-2ubuntu7 zlib1g-dev_1:1.2.11.dfsg-2ubuntu7 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri Jan 14 14:01:41 2022 UTC gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify signature ./vienna-rna_2.4.17+dfsg-2build2.dsc dpkg-source: info: extracting vienna-rna in /<>/vienna-rna-2.4.17+dfsg dpkg-source: info: unpacking vienna-rna_2.4.17+dfsg.orig.tar.xz dpkg-source: info: unpacking vienna-rna_2.4.17+dfsg-2build2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying g2.patch dpkg-source: info: applying tutorial.patch dpkg-source: info: applying addHelp2ManWrapper.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-23057752 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-23057752 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-23057752 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package vienna-rna dpkg-buildpackage: info: source version 2.4.17+dfsg-2build2 dpkg-buildpackage: info: source distribution jammy dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/vienna-rna-2.4.17+dfsg' 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 '/<>/vienna-rna-2.4.17+dfsg' dh_clean debian/rules binary-arch dh binary-arch --with python3 dh_update_autotools_config -a dh_autoreconf -a configure.ac:74: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:74: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:74: the top level 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:111: warning: The macro `AC_CYGWIN' is obsolete. configure.ac:111: You should run autoupdate. ./lib/autoconf/specific.m4:319: AC_CYGWIN is expanded from... configure.ac:111: the top level configure.ac:135: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:135: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:135: the top level configure.ac:142: warning: AC_OUTPUT should be used without arguments. configure.ac:142: You should run autoupdate. configure.ac:10: warning: 'AM_CONFIG_HEADER': this macro is obsolete. configure.ac:10: You should use the 'AC_CONFIG_HEADERS' macro instead. ./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from... aclocal.m4:1039: AM_CONFIG_HEADER is expanded from... configure.ac:10: the top level configure.ac:16: warning: AC_PROG_LEX without either yywrap or noyywrap is obsolete ./lib/autoconf/programs.m4:716: _AC_PROG_LEX is expanded from... ./lib/autoconf/programs.m4:709: AC_PROG_LEX is expanded from... aclocal.m4:944: AM_PROG_LEX is expanded from... configure.ac:16: the top level configure.ac:59: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:59: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:59: the top level configure.ac:83: warning: AC_OUTPUT should be used without arguments. configure.ac:83: You should run autoupdate. 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:35: warning: AC_OUTPUT should be used without arguments. configure.ac:35: You should run autoupdate. configure.ac:14: installing './compile' configure.ac:4: installing './install-sh' configure.ac:4: installing './missing' Makefile.am: installing './depcomp' configure.ac:47: warning: AC_OUTPUT should be used without arguments. configure.ac:47: You should run autoupdate. 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:54: warning: The macro `AC_PROG_CC_C99' is obsolete. configure.ac:54: You should run autoupdate. ./lib/autoconf/c.m4:1659: AC_PROG_CC_C99 is expanded from... configure.ac:54: the top level configure.ac:56: warning: The macro `AC_PROG_LIBTOOL' is obsolete. configure.ac:56: You should run autoupdate. m4/libtool.m4:99: AC_PROG_LIBTOOL is expanded from... configure.ac:56: the top level configure.ac:65: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:65: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:65: the top level configure.ac:80: warning: $as_echo is obsolete; use AS_ECHO(["message"]) instead lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... m4/ax_pthread.m4:88: AX_PTHREAD is expanded from... m4/ac_rna_macros.m4:63: RNA_FEATURE_IF_ENABLED is expanded from... m4/ac_rna_features.m4:213: RNA_ENABLE_PTHREADS is expanded from... m4/ac_rna.m4:11: AC_RNA_INIT is expanded from... configure.ac:80: the top level configure.ac:47: 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' interfaces/Perl/Makefile.am: installing 'config/depcomp' man/Makefile.am:5: installing 'config/texinfo.tex' parallel-tests: installing 'config/test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>/vienna-rna-2.4.17+dfsg' 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-python --with-python3 --without-forester --without-doc --without-tutorial ./configure --build=aarch64-linux-gnu --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/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-cluster --without-python --with-python3 --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 dependency style of gcc... none checking if malloc debugging is wanted... no checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu 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... (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 for ar... ar checking the archiver (ar) interface... ar checking whether make sets $(MAKE)... (cached) yes checking for grep that handles long lines and -e... /usr/bin/grep checking for a sed that does not truncate output... /usr/bin/sed checking whether ln -s works... yes checking how to print strings... printf checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for exp in -lm... yes checking for egrep... (cached) /usr/bin/grep -E checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for malloc.h... yes checking for float.h... yes checking for limits.h... yes 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 math.h... yes checking for stdarg.h... yes checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking for working strtod... yes checking for floor... yes checking for strdup... yes checking for strstr... yes checking for strchr... yes checking for strrchr... yes checking for strstr... (cached) yes checking for strtol... yes checking for strtoul... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for erand48... yes checking for memset... yes checking for memmove... yes checking for erand48... (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-3.24/svm.cpp... no checking for ./src/libsvm-3.24/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... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking whether more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking compiler support for AVX 512 instructions... no checking compiler support for SSE 4.1 instructions... no checking whether C compiler accepts -ftree-vectorize... yes checking for mpfr.h... yes checking whether we can compile programs with mpfr support... yes checking for ./interfaces/Makefile.am... yes checking for swig... /usr/bin/swig checking SWIG version... 4.0.2 checking for SWIG library... /usr/share/swig4.0 checking for ./interfaces/Perl/Makefile.am... yes checking for /usr/bin/perl... (cached) /usr/bin/perl checking for Perl prefix... /usr checking for Perl siteprefix... /usr/local checking for Perl vendorprefix... /usr checking for Perl extension include path... /usr/lib/aarch64-linux-gnu/perl/5.32/CORE checking for Perl extension target directory... /usr/local/lib/aarch64-linux-gnu/perl/5.32.1 checking for architecture dependent Perl extension site target directory... /usr/local/lib/aarch64-linux-gnu/perl/5.32.1 checking for architecture dependent Perl extension vendor target directory... /usr/lib/aarch64-linux-gnu/perl5/5.32 checking for architecture independent Perl extension site target directory... /usr/local/share/perl/5.32.1 checking for architecture independent Perl extension vendor target directory... /usr/share/perl5 checking for Perl extensions C preprocessor flags... -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include checking for Perl extensions linker flags... -shared -L/usr/local/lib -fstack-protector-strong checking for Perl dynamic library extension... .so checking for ./interfaces/Python3/Makefile.am... yes checking for python3... /usr/bin/python3 checking for Python3 include path... :1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives :1: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead /usr/include/python3.10 checking for /usr/include/python3.10/Python.h... yes checking for Python3 ldflags... checking for Python3 extension linker... :1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives :1: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 checking for directory to install Python3 scripts in... :1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives :1: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead ${prefix}/lib/python3.10/site-packages checking for directory to install architecture dependent python3 things in... :1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives :1: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead ${exec_prefix}/lib/python3.10/site-packages checking for Python3 module extension... :1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives :1: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead .cpython-310-aarch64-linux-gnu.so checking for Python3 tag for cached compiled scripts... cpython-310 checking for Python3 extension of cached and optimized bytecode... cpython-310.opt-1.pyc checking for doxygen... /usr/bin/doxygen checking for dot... /usr/bin/dot checking for egrep... /usr/bin/egrep checking for perl... /usr/bin/perl checking for htlatex... no 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 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 interfaces/Perl/Makefile config.status: creating interfaces/Perl/version.i config.status: creating interfaces/Python3/Makefile config.status: creating interfaces/Python3/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 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 (/<>/vienna-rna-2.4.17+dfsg/src/Kinfold) configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr' '--build=aarch64-linux-gnu' '--includedir=${prefix}/include' '--mandir=${prefix}/share/man' '--infodir=${prefix}/share/info' '--sysconfdir=/etc' '--localstatedir=/var' '--disable-silent-rules' '--libdir=${prefix}/lib/aarch64-linux-gnu' '--runstatedir=/run' '--disable-maintainer-mode' '--disable-dependency-tracking' '--with-cluster' '--without-python' '--with-python3' '--without-forester' '--without-doc' '--without-tutorial' 'build_alias=aarch64-linux-gnu' 'CFLAGS=-I/usr/include/json-c/ -I/usr/include/libsvm/' 'LDFLAGS=-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro' 'CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2' 'CXXFLAGS=-I/usr/include/json-c/ -I/usr/include/libsvm/' 'CC=gcc' 'CXX=g++' 'AR=gcc-ar' 'RANLIB=gcc-ranlib' 'NM=gcc-nm' 'VRNA_CFLAGS=-I$(top_srcdir)/../../src/ViennaRNA -I$(top_srcdir)/../../src' 'VRNA_LIBS=-fno-strict-aliasing -flto -L$(top_builddir)/../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -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... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu 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 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 (/<>/vienna-rna-2.4.17+dfsg/src/RNAlocmin) configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr' '--build=aarch64-linux-gnu' '--includedir=${prefix}/include' '--mandir=${prefix}/share/man' '--infodir=${prefix}/share/info' '--sysconfdir=/etc' '--localstatedir=/var' '--disable-silent-rules' '--libdir=${prefix}/lib/aarch64-linux-gnu' '--runstatedir=/run' '--disable-maintainer-mode' '--disable-dependency-tracking' '--with-cluster' '--without-python' '--with-python3' '--without-forester' '--without-doc' '--without-tutorial' 'build_alias=aarch64-linux-gnu' 'CFLAGS=-I/usr/include/json-c/ -I/usr/include/libsvm/' 'LDFLAGS=-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro' 'CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2' 'CXXFLAGS=-I/usr/include/json-c/ -I/usr/include/libsvm/' 'CC=gcc' 'CXX=g++' 'AR=gcc-ar' 'RANLIB=gcc-ranlib' 'NM=gcc-nm' 'VRNA_CFLAGS=-I$(top_srcdir)/../../src/ViennaRNA -I$(top_srcdir)/../../src' 'VRNA_LIBS=-fno-strict-aliasing -flto -L$(top_builddir)/../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -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... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu 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 2.4.17 ====================================== 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 -------- * Boustrophedon : yes * 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 2 : no * Python 3 : yes Documentation ------------- * Reference Manual (PDF) : no * Reference Manual (HTML) : no * Tutorial (PDF) : no * Tutorial (HTML) : no Unit Tests ---------- * Executable Programs : yes * C-Library : no * Perl 5 Interface : yes * Python 2 Interface : no * Python 3 Interface : yes MacOS X ------- * Universal Binary : no * Installer : no * SDK : custom Install Directories ------------------- * Executables : /usr/bin * Libraries : /usr/lib/aarch64-linux-gnu * 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/aarch64-linux-gnu/perl/5.32.1 (scripts) : /usr/share/perl/5.32.1 * Python2 Interface : Not to be installed (binaries) : (scripts) : * Python3 Interface : (binaries) : /usr/lib/python3.10/site-packages (scripts) : /usr/lib/python3.10/site-packages 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 '/<>/vienna-rna-2.4.17+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/<>/vienna-rna-2.4.17+dfsg' 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 '/<>/vienna-rna-2.4.17+dfsg' make all-recursive make[3]: Entering directory '/<>/vienna-rna-2.4.17+dfsg' Making all in src make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src' Making all in ViennaRNA make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA' Making all in static make[6]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/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 '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA/static' make[7]: Nothing to be done for 'all-am'. make[7]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA/static' make[6]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA/static' make[6]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA' /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c dist_vars.c -o dist_vars.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 -o part_func_wrappers.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c fold_compound.c -o fold_compound.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c part_func.c -o part_func.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c pf_fold.c -o pf_fold.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c treedist.c -o treedist.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c inverse.c -o inverse.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c RNAstruct.c -o RNAstruct.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c ProfileDist.c -o ProfileDist.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c mfe_wrappers.c -o mfe_wrappers.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c mfe.c -o mfe.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 -o mfe_window_wrappers.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c mfe_window.c -o mfe_window.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c fold.c -o fold.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c stringdist.c -o stringdist.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time 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gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c Lfold.c -o Lfold.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o concentrations.lo concentrations.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c concentrations.c -fPIC -DPIC -o .libs/concentrations.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 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-I/usr/include/libsvm/ -c ProfileAln.c -fPIC -DPIC -o .libs/ProfileAln.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c ProfileAln.c -o ProfileAln.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c duplex.c -o duplex.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c alifold.c -o alifold.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile 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-I/usr/include/libsvm/ -c -o part_func_up.lo part_func_up.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 .libs/part_func_up.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o ribo.lo ribo.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o MEA.lo MEA.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c LPfold.c -o LPfold.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c ribo.c -o ribo.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c MEA.c -o MEA.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 -o part_func_up.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c mm.c -o mm.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c 2Dfold.c -o 2Dfold.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c 2Dpfold.c -o 2Dpfold.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c c_plex.c -o c_plex.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto 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>/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o ugly_bt.lo ugly_bt.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c ugly_bt.c -fPIC -DPIC -o .libs/ugly_bt.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c move_set.c -o move_set.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp 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"/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA/./.libs/libRNA_datastructures.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_utils.a && gcc-ar x "/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA/./.libs/libRNA_utils.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_plotting.a && gcc-ar x "/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA/./.libs/libRNA_plotting.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_params.a && gcc-ar x "/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA/./.libs/libRNA_params.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_eval.a && gcc-ar x "/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA/./.libs/libRNA_eval.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_loops.a && gcc-ar x "/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA/./.libs/libRNA_loops.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_landscape.a && gcc-ar x "/<>/vienna-rna-2.4.17+dfsg/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/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/Lfold.o .libs/cofold.o .libs/part_func_co.o .libs/concentrations.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_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_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++ -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -avoid-version -static -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o libRNA.la -rpath /usr/lib/aarch64-linux-gnu libRNA_conv.la -lgsl -lgslcblas -lm libtool: link: (cd .libs/libRNA.lax/libRNA_conv.a && gcc-ar x "/<>/vienna-rna-2.4.17+dfsg/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/concentrations.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_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/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/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/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 '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA' make[5]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA' Making all in bin make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/bin' /usr/bin/gengetopt -i RNAfold.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c parallel_helpers.c -o parallel_helpers.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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 -o input_id_helpers.o >/dev/null 2>&1 /usr/bin/gengetopt -i RNAheat.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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 gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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 gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c ../cthreadpool/thpool.c -o ../cthreadpool/thpool.o >/dev/null 2>&1 gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../../src/cthreadpool -Wdate-time -D_FORTIFY_SOURCE=2 -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 /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/ -avoid-version -static -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o libhelpers.la input_id_helpers.lo parallel_helpers.lo ../cthreadpool/thpool.lo -lgsl -lgslcblas -lm libtool: link: gcc-ar cr .libs/libhelpers.a input_id_helpers.o parallel_helpers.o ../cthreadpool/thpool.o libtool: link: gcc-ranlib .libs/libhelpers.a libtool: link: ( cd ".libs" && rm -f "libhelpers.la" && ln -s "../libhelpers.la" "libhelpers.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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o RNAfold RNAfold_cmdl.o RNAfold.o ../../src/ViennaRNA/libRNA_special_const.la ../../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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o RNAeval RNAeval_cmdl.o RNAeval.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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o RNAheat RNAheat_cmdl.o RNAheat.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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o RNApdist RNApdist_cmdl.o RNApdist.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 -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o RNApdist RNApdist_cmdl.o RNApdist.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp libtool: 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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o RNAeval RNAeval_cmdl.o RNAeval.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp libtool: 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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o RNAheat RNAheat_cmdl.o RNAheat.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp libtool: 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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o RNAfold RNAfold_cmdl.o RNAfold.o ../../src/ViennaRNA/.libs/libRNA_special_const.a ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -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 -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o RNAdistance RNAdistance_cmdl.o RNAdistance.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -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 -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o RNAinverse RNAinverse_cmdl.o RNAinverse.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -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 -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o RNAplot RNAplot_cmdl.o RNAplot.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o RNAsubopt RNAsubopt_cmdl.o RNAsubopt.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 -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o RNAsubopt RNAsubopt_cmdl.o RNAsubopt.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o RNALfold RNALfold_cmdl.o RNALfold.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 -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o RNALfold RNALfold_cmdl.o RNALfold.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -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 -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o RNAcofold RNAcofold_cmdl.o RNAcofold.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -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 -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o RNApaln RNApaln_cmdl.o RNApaln.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o RNAduplex RNAduplex_cmdl.o RNAduplex.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 -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o RNAduplex RNAduplex_cmdl.o RNAduplex.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o RNAalifold RNAalifold_cmdl.o RNAalifold.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 -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o RNAalifold RNAalifold_cmdl.o RNAalifold.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -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 -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o RNAplfold RNAplfold_cmdl.o RNAplfold.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -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 -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o RNAup RNAup_cmdl.o RNAup.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -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 -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o RNAaliduplex RNAaliduplex_cmdl.o RNAaliduplex.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -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 -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o RNALalifold RNALalifold_cmdl.o RNALalifold.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o RNA2Dfold RNA2Dfold_cmdl.o RNA2Dfold.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 -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o RNA2Dfold RNA2Dfold_cmdl.o RNA2Dfold.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -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 -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o RNAparconv RNAparconv_cmdl.o RNAparconv.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -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 -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o RNAPKplex RNAPKplex_cmdl.o RNAPKplex.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -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 -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o RNAplex RNAplex_cmdl.o RNAplex.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -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 -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o RNAsnoop RNAsnoop_cmdl.o RNAsnoop.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -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 -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o RNApvmin RNApvmin_cmdl.o RNApvmin.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -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 -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o RNAdos RNAdos_cmdl.o RNAdos.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp make[5]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/bin' Making all in Utils make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/Utils' gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -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 -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o popt popt.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lgsl -lgslcblas -lm -pthread -fopenmp libtool: 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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o b2ct b2ct.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lgsl -lgslcblas -lm -pthread -fopenmp libtool: 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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o ct2db ct2db_cmdl.o ct2db.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lgsl -lgslcblas -lm -pthread -fopenmp make[5]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/Utils' Making all in Cluster make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/Cluster' gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../.. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../.. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../.. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../.. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../.. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../.. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../.. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -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../.. -I../../src -I../.. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -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 -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o AnalyseDists split.o distance_matrix.o cluster.o treeplot.o AD_main.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lgsl -lgslcblas -lm -pthread -fopenmp libtool: 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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z -Wl,relro -o AnalyseSeqs statgeom.o distance_matrix.o cluster.o AS_main.o split.o treeplot.o PS3D.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lgsl -lgslcblas -lm -pthread -fopenmp make[5]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/Cluster' make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src' make[5]: Nothing to be done for 'all-am'. make[5]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src' Making all in man make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/man' restore=: && backupdir=".am$$" && \ am__cwd=`pwd` && CDPATH="${ZSH_VERSION+.}:" && cd . && \ rm -rf $backupdir && mkdir $backupdir && \ if (/bin/bash '/<>/vienna-rna-2.4.17+dfsg/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 '/<>/vienna-rna-2.4.17+dfsg/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 ./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 '/<>/vienna-rna-2.4.17+dfsg/man' Making all in misc make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/misc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/misc' Making all in doc make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/doc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/doc' Making all in RNA-Tutorial make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/RNA-Tutorial' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/RNA-Tutorial' Making all in interfaces make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/interfaces' Making all in Perl make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/interfaces/Perl' /usr/bin/swig -I../../src \ -I. -I. \ \ -perl5 -proxy -const -c++ \ -module RNA -o RNA_wrap.cpp \ ./../RNA.i /usr/bin/swig -I../../src \ -I. -I. \ \ -perl5 -proxy -const -c++ \ -module RNA -o RNA_wrap.cpp \ ./../RNA.i /bin/bash ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/lib/aarch64-linux-gnu/perl/5.32/CORE -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/lib/aarch64-linux-gnu/perl/5.32/CORE -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/lib/aarch64-linux-gnu/perl/5.32/CORE -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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 -o RNA_la-RNA_wrap.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CXX --mode=link g++ -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 -avoid-version -module -shared -export-dynamic -shrext .so -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o RNA.la -rpath /usr/lib/aarch64-linux-gnu/perl/5.32.1/auto/RNA RNA_la-RNA_wrap.lo ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: g++ -fPIC -DPIC -shared -nostdlib 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( . ./libtoolconfig.tmp; cp "$objdir/RNA.so" auto/RNA ) && \ rm -f libtoolconfig.tmp \ ) make[5]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/interfaces/Perl' Making all in Python3 make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/interfaces/Python3' /usr/bin/swig -I../../src \ -I. -I. \ -DPY3 \ \ -python -py3 -c++ -keyword -w511 \ -o RNA_wrap.cpp \ ./../RNA.i /bin/bash ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/include/python3.10 -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -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++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/include/python3.10 -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -flto 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-lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/11/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/11/crtbeginS.o .libs/_RNA_la-RNA_wrap.o -Wl,--whole-archive ../../src/ViennaRNA/.libs/libRNA_conv.a -Wl,--no-whole-archive -lmpfr -lgmp -lgsl -lgslcblas -L/usr/lib/gcc/aarch64-linux-gnu/11 -L/usr/lib/gcc/aarch64-linux-gnu/11/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/11/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/11/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/11/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/11/../../../aarch64-linux-gnu/crtn.o -flto -fopenmp -pthread -pthread -Wl,-Bsymbolic-functions -flto=auto -flto=auto -Wl,-z -Wl,relro -fopenmp -pthread -Wl,-soname -Wl,_RNA.cpython-310-aarch64-linux-gnu.so -o .libs/_RNA.cpython-310-aarch64-linux-gnu.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 $objdir/_RNA.cpython-310-aarch64-linux-gnu.so RNA ) && \ rm -f libtoolconfig.tmp ( PYTHONPATH="RNA:$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 '/<>/vienna-rna-2.4.17+dfsg/interfaces/Python3' make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/interfaces' make[5]: Nothing to be done for 'all-am'. make[5]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/interfaces' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/interfaces' Making all in src/Kinfold make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/Kinfold' make all-recursive make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/Kinfold' Making all in Example make[6]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/Kinfold/Example' make[6]: Nothing to be done for 'all'. make[6]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/Kinfold/Example' make[6]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/Kinfold' gcc -DHAVE_CONFIG_H -I. -I./src -Wdate-time -D_FORTIFY_SOURCE=2 -I./../../src/ViennaRNA -I./../../src -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o baum.o baum.c gcc -DHAVE_CONFIG_H -I. -I./src -Wdate-time -D_FORTIFY_SOURCE=2 -I./../../src/ViennaRNA -I./../../src -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 -Wdate-time -D_FORTIFY_SOURCE=2 -I./../../src/ViennaRNA -I./../../src -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o main.o main.c gcc -DHAVE_CONFIG_H -I. -I./src -Wdate-time -D_FORTIFY_SOURCE=2 -I./../../src/ViennaRNA -I./../../src -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o nachbar.o nachbar.c nachbar.c: In function ‘sel_nb’: nachbar.c:318:30: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 318 | sprintf(format, "%%-%ds %%6.2f %%10.3f", strlen(GAV.farbe_full)+1); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int size_t {aka long unsigned int} | %ld gcc -DHAVE_CONFIG_H -I. -I./src -Wdate-time -D_FORTIFY_SOURCE=2 -I./../../src/ViennaRNA -I./../../src -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o cmdline.o cmdline.c gcc -DHAVE_CONFIG_H -I. -I./src -Wdate-time -D_FORTIFY_SOURCE=2 -I./../../src/ViennaRNA -I./../../src -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 -I/usr/include/json-c/ -I/usr/include/libsvm/ -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -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 -lmpfr -lgmp -lm make[6]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/Kinfold' make[5]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/Kinfold' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/Kinfold' Making all in src/RNAlocmin make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/RNAlocmin' make all-am make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/RNAlocmin' gengetopt -i RNAlocmin.ggo g++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -Wno-write-strings -Wdate-time -D_FORTIFY_SOURCE=2 -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 -Wno-write-strings -Wdate-time -D_FORTIFY_SOURCE=2 -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 -Wno-write-strings -Wdate-time -D_FORTIFY_SOURCE=2 -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 -Wno-write-strings -Wdate-time -D_FORTIFY_SOURCE=2 -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; | ^~~ g++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -Wno-write-strings -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o hash_util.o hash_util.cpp 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; | ^~~ 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 -Wno-write-strings -Wdate-time -D_FORTIFY_SOURCE=2 -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 -Wno-write-strings -Wdate-time -D_FORTIFY_SOURCE=2 -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 -Wno-write-strings -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o move_set_pk.o move_set_pk.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; | ^~~ g++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -Wno-write-strings -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o neighbourhood.o neighbourhood.cpp 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; | ^~~ g++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -Wno-write-strings -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o pknots.o pknots.cpp 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 -Wno-write-strings -Wdate-time -D_FORTIFY_SOURCE=2 -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 -Wno-write-strings -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o treeplot.o treeplot.cpp 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; | ^~~ gcc -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -Wno-write-strings -Wdate-time -D_FORTIFY_SOURCE=2 -fexceptions -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAlocmin_cmdline.o RNAlocmin_cmdline.c g++ -I/usr/include/json-c/ -I/usr/include/libsvm/ -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -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 -lmpfr -lgmp make[5]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/RNAlocmin' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/RNAlocmin' Making all in tests make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/tests' make all-am make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/tests' make[5]: Nothing to be done for 'all-am'. make[5]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/tests' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/tests' Making all in examples make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/examples' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/examples' Making all in packaging/macosx make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/packaging/macosx' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/packaging/macosx' make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg' make[3]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg' make[2]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg' if [ -r doc/RNAlib-*pdf; then cd doc && ln -f RNAlib-*.pdf RNAlib.pdf; fi /bin/bash: line 1: [: missing `]' make[1]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg' dh_auto_test -a make -j4 check VERBOSE=1 make[1]: Entering directory '/<>/vienna-rna-2.4.17+dfsg' Making check in src make[2]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src' Making check in ViennaRNA make[3]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA' Making check in static make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA/static' make check-am make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA/static' make[5]: Nothing to be done for 'check-am'. make[5]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA/static' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA/static' make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA' make[4]: Nothing to be done for 'check-am'. make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA' make[3]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA' Making check in bin make[3]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/bin' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/bin' Making check in Utils make[3]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/Utils' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/Utils' Making check in Cluster make[3]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/Cluster' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/Cluster' make[3]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src' make[2]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src' Making check in man make[2]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/man' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/man' Making check in misc make[2]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/misc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/misc' Making check in doc make[2]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/doc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/doc' Making check in RNA-Tutorial make[2]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/RNA-Tutorial' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/RNA-Tutorial' Making check in interfaces make[2]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/interfaces' Making check in Perl make[3]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/interfaces/Perl' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/interfaces/Perl' Making check in Python3 make[3]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/interfaces/Python3' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/interfaces/Python3' make[3]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/interfaces' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/interfaces' make[2]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/interfaces' Making check in src/Kinfold make[2]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/Kinfold' Making check in Example make[3]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/Kinfold/Example' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/Kinfold/Example' make[3]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/Kinfold' make[3]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/Kinfold' make[2]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/Kinfold' Making check in src/RNAlocmin make[2]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/RNAlocmin' make[2]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/RNAlocmin' Making check in tests make[2]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/tests' make check-am make[3]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/tests' make make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/tests' make all-am make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/tests' make[5]: Nothing to be done for 'all-am'. make[5]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/tests' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/tests' make check-TESTS make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/tests' make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/tests' PASS: RNAfold/partfunc.sh PASS: RNAfold/long.sh PASS: RNAfold/general.sh PASS: RNAfold/special.sh PASS: RNAcofold/general.sh PASS: RNAalifold/partfunc.sh PASS: perl5/test-RNA.pl PASS: perl5/test-RNA-callbacks.pl PASS: perl5/test-RNA-combinatorics.pl PASS: perl5/test-RNA-Design.t PASS: perl5/test-RNA-file-formats.pl PASS: perl5/test-RNA-mfe_eval.pl PASS: perl5/test-RNA-mfe_window.pl PASS: perl5/test-RNA-pf_window.pl PASS: perl5/test-RNA-boltzmann-sampling.pl PASS: perl5/test-RNA-constraints.pl PASS: perl5/test-RNA-constraints-soft.pl PASS: perl5/test-RNA-constraints-SHAPE.pl PASS: perl5/test-RNA-constraints-special.pl PASS: python3/test-RNA-combinatorics.py3 PASS: python3/test-RNA-constraints.py3 PASS: python3/test-RNA-constraints-soft.py3 PASS: python3/test-RNA-constraints-SHAPE.py3 PASS: python3/test-RNA-constraints-special.py3 PASS: python3/test-RNA-file-formats.py3 PASS: python3/test-RNA-mfe_eval.py3 PASS: python3/test-RNA-mfe_window.py3 PASS: python3/test-RNA-pf_window.py3 PASS: python3/test-RNA-sc-callbacks.py3 PASS: python3/test-RNA-subopt.py3 PASS: python3/test-RNA-boltzmann-sampling.py3 PASS: python3/test-RNA-utils.py3 PASS: python3/test-RNA.py3 PASS: RNAalifold/general.sh PASS: RNAcofold/partfunc.sh PASS: RNAalifold/special.sh ============================================================================ Testsuite summary for ViennaRNA 2.4.17 ============================================================================ # TOTAL: 36 # PASS: 36 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/tests' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/tests' make[3]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/tests' make[2]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/tests' Making check in examples make[2]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/examples' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/examples' Making check in packaging/macosx make[2]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/packaging/macosx' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/packaging/macosx' make[2]: Entering directory '/<>/vienna-rna-2.4.17+dfsg' make[2]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg' make[1]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg' create-stamp debian/debhelper-build-stamp dh_prep -a dh_installdirs -a debian/rules override_dh_auto_install make[1]: Entering directory '/<>/vienna-rna-2.4.17+dfsg' # rename perl scripts to remove the *.pl extension and create manpage via perldoc mkdir -p /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin mkdir -p /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/man/man1 #for script in `ls Utils/*.pl` ; do \ # newscript=`basename ${script} .pl` ; \ # cp -a ${script} /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/${newscript} ; \ # perldoc -onroff -F ${script} | \ # sed -e "s/${newscript}\.pl/${newscript}/g" \ # > /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/man/man1/${newscript}.1 ; \ # if [ ! -s /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/man/man1/${newscript}.1 ] ; then \ # rm -f /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/man/man1/${newscript}.1 ; \ # fi ; \ #done dh_auto_install make -j1 install DESTDIR=/<>/vienna-rna-2.4.17\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/<>/vienna-rna-2.4.17+dfsg' Making install in src make[3]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src' Making install in ViennaRNA make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA' Making install in static make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA/static' make install-am make[6]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA/static' make[7]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/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 '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA/static' make[6]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA/static' make[5]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA/static' make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA' make[6]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' /bin/bash ../../libtool --mode=install /usr/bin/install -c libRNA.la '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libRNA.lai /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libRNA.la libtool: install: /usr/bin/install -c .libs/libRNA.a /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libRNA.a libtool: install: chmod 644 /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libRNA.a libtool: install: gcc-ranlib /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libRNA.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/include/ViennaRNA' /usr/bin/install -c -m 644 vrna_config.h '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/include/ViennaRNA' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/include/ViennaRNA' /usr/bin/install -c -m 644 pair_mat.h RNAstruct.h dist_vars.h mfe.h mfe_window.h fold.h part_func.h part_func_window.h stringdist.h edit_cost.h fold_vars.h profiledist.h treedist.h inverse.h subopt.h cofold.h duplex.h alifold.h part_func_co.h concentrations.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 2Dfold.h 2Dpfold.h PKplex.h '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/include/ViennaRNA' /usr/bin/install -c -m 644 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 naview.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 energy_const.h params.h read_epars.h '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/include/ViennaRNA' /usr/bin/install -c -m 644 convert_epars.h commands.h units.h combinatorics.h neighbor.h walk.h heat_capacity.h '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/include/ViennaRNA' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/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 '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/include/ViennaRNA/constraints' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/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 '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/include/ViennaRNA/datastructures' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/include/ViennaRNA/io' /usr/bin/install -c -m 644 io/utils.h io/file_formats.h io/file_formats_msa.h '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/include/ViennaRNA/io' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/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 '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/include/ViennaRNA/landscape' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/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 '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/include/ViennaRNA/loops' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/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 '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/include/ViennaRNA/params' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/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 plotting/naview.h '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/include/ViennaRNA/plotting' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/include/ViennaRNA/plotting/RNApuzzler' /usr/bin/install -c -m 644 plotting/RNApuzzler/RNApuzzler.h plotting/RNApuzzler/RNAturtle.h '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/include/ViennaRNA/plotting/RNApuzzler' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/include/ViennaRNA/search' /usr/bin/install -c -m 644 search/BoyerMoore.h '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/include/ViennaRNA/search' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/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 '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/include/ViennaRNA/utils' make[6]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA' make[5]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/ViennaRNA' Making install in bin make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/bin' make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/bin' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/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 '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin' libtool: install: /usr/bin/install -c RNAfold /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/RNAfold libtool: install: /usr/bin/install -c RNAeval /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/RNAeval libtool: install: /usr/bin/install -c RNAheat /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/RNAheat libtool: install: /usr/bin/install -c RNApdist /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/RNApdist libtool: install: /usr/bin/install -c RNAdistance /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/RNAdistance libtool: install: /usr/bin/install -c RNAinverse /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/RNAinverse libtool: install: /usr/bin/install -c RNAplot /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/RNAplot libtool: install: /usr/bin/install -c RNAsubopt /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/RNAsubopt libtool: install: /usr/bin/install -c RNALfold /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/RNALfold libtool: install: /usr/bin/install -c RNAcofold /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/RNAcofold libtool: install: /usr/bin/install -c RNApaln /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/RNApaln libtool: install: /usr/bin/install -c RNAduplex /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/RNAduplex libtool: install: /usr/bin/install -c RNAalifold /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/RNAalifold libtool: install: /usr/bin/install -c RNAplfold /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/RNAplfold libtool: install: /usr/bin/install -c RNAup /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/RNAup libtool: install: /usr/bin/install -c RNAaliduplex /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/RNAaliduplex libtool: install: /usr/bin/install -c RNALalifold /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/RNALalifold libtool: install: /usr/bin/install -c RNA2Dfold /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/RNA2Dfold libtool: install: /usr/bin/install -c RNAparconv /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/RNAparconv libtool: install: /usr/bin/install -c RNAPKplex /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/RNAPKplex libtool: install: /usr/bin/install -c RNAplex /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/RNAplex libtool: install: /usr/bin/install -c RNAsnoop /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/RNAsnoop libtool: install: /usr/bin/install -c RNApvmin /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/RNApvmin libtool: install: /usr/bin/install -c RNAdos /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/RNAdos make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/bin' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/bin' Making install in Utils make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/Utils' make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/Utils' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin' /bin/bash ../../libtool --mode=install /usr/bin/install -c b2ct popt ct2db '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin' libtool: install: /usr/bin/install -c b2ct /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/b2ct libtool: install: /usr/bin/install -c popt /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/popt libtool: install: /usr/bin/install -c ct2db /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/ct2db /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/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 '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/ViennaRNA/bin' make install-data-hook make[6]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/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'|' /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/ViennaRNA/bin/$i ; \ done make[6]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/Utils' make[5]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/Utils' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/Utils' Making install in Cluster make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/Cluster' make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/Cluster' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin' /bin/bash ../../libtool --mode=install /usr/bin/install -c AnalyseDists AnalyseSeqs '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin' libtool: install: /usr/bin/install -c AnalyseDists /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/AnalyseDists libtool: install: /usr/bin/install -c AnalyseSeqs /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin/AnalyseSeqs /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 AnalyseDists.1 AnalyseSeqs.1 '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/man/man1' make[5]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/Cluster' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/Cluster' make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src' make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/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 '/<>/vienna-rna-2.4.17+dfsg/src' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src' make[3]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src' Making install in man make[3]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/man' make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/man' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/info' /usr/bin/install -c -m 644 ./RNAlib.info '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/info' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/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 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 '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/man/man1' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/man' make[3]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/man' Making install in misc make[3]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/misc' make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/misc' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/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 '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/ViennaRNA' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/misc' make[3]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/misc' Making install in doc make[3]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/doc' make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/doc' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/ViennaRNA' /usr/bin/install -c -m 644 viennarna.bib DoxygenLayout.xml '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/ViennaRNA' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/doc' make[3]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/doc' Making install in RNA-Tutorial make[3]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/RNA-Tutorial' make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/RNA-Tutorial' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/RNA-Tutorial' make[3]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/RNA-Tutorial' Making install in interfaces make[3]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/interfaces' Making install in Perl make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/interfaces/Perl' make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/interfaces/Perl' make[5]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/perl/5.32.1' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/perl/5.32.1/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 '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/perl/5.32.1/RNA' /usr/bin/install -c -m 644 RNA.pm '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/perl/5.32.1/.' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/perl/5.32.1/auto/RNA' /bin/bash ../../libtool --mode=install /usr/bin/install -c RNA.la '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/perl/5.32.1/auto/RNA' libtool: install: /usr/bin/install -c .libs/RNA.so /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/perl/5.32.1/auto/RNA/RNA.so libtool: install: /usr/bin/install -c .libs/RNA.lai /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/perl/5.32.1/auto/RNA/RNA.la libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu/perl/5.32.1/auto/RNA' make install-data-hook make[6]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/interfaces/Perl' rm -f /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/perl/5.32.1/auto/RNA/RNA.la make[6]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/interfaces/Perl' make[5]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/interfaces/Perl' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/interfaces/Perl' Making install in Python3 make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/interfaces/Python3' make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/interfaces/Python3' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/lib/python3.10/site-packages/RNA' /usr/bin/install -c -m 644 RNA/__init__.py '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/lib/python3.10/site-packages/RNA' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/lib/python3.10/site-packages/RNA' /bin/bash ../../libtool --mode=install /usr/bin/install -c _RNA.la '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/lib/python3.10/site-packages/RNA' libtool: install: /usr/bin/install -c .libs/_RNA.cpython-310-aarch64-linux-gnu.so /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/lib/python3.10/site-packages/RNA/_RNA.cpython-310-aarch64-linux-gnu.so libtool: install: /usr/bin/install -c .libs/_RNA.lai /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/lib/python3.10/site-packages/RNA/_RNA.la libtool: warning: remember to run 'libtool --finish /usr/lib/python3.10/site-packages/RNA' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/lib/python3.10/site-packages/RNA/__pycache__' /usr/bin/install -c -m 644 RNA/__pycache__/__init__.cpython-310.pyc RNA/__pycache__/__init__.cpython-310.opt-1.pyc '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/lib/python3.10/site-packages/RNA/__pycache__' make install-data-hook make[6]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/interfaces/Python3' rm -f /<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/lib/python3.10/site-packages/RNA/_RNA.la make[6]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/interfaces/Python3' make[5]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/interfaces/Python3' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/interfaces/Python3' make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/interfaces' make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/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 '/<>/vienna-rna-2.4.17+dfsg/interfaces' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/interfaces' make[3]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/interfaces' Making install in src/Kinfold make[3]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/Kinfold' Making install in Example make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/Kinfold/Example' make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/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 '/<>/vienna-rna-2.4.17+dfsg/src/Kinfold/Example' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/Kinfold/Example' make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/Kinfold' make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/Kinfold' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin' /usr/bin/install -c Kinfold '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 Kinfold.1 '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/man/man1' make[5]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/Kinfold' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/Kinfold' make[3]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/Kinfold' Making install in src/RNAlocmin make[3]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/RNAlocmin' make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/src/RNAlocmin' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin' /usr/bin/install -c RNAlocmin '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/bin' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 RNAlocmin.1 '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/man/man1' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/RNAlocmin' make[3]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/src/RNAlocmin' Making install in tests make[3]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/tests' make install-am make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/tests' make[5]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/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 '/<>/vienna-rna-2.4.17+dfsg/tests' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/tests' make[3]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/tests' Making install in examples make[3]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/examples' make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/examples' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/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 '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/ViennaRNA/examples' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/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 '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/ViennaRNA/examples/data' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/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 '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/ViennaRNA/examples/perl5' /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/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 '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/share/ViennaRNA/examples/python' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/examples' make[3]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/examples' Making install in packaging/macosx make[3]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/packaging/macosx' make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg/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 '/<>/vienna-rna-2.4.17+dfsg/packaging/macosx' make[3]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg/packaging/macosx' make[3]: Entering directory '/<>/vienna-rna-2.4.17+dfsg' make[4]: Entering directory '/<>/vienna-rna-2.4.17+dfsg' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 RNAlib2.pc '/<>/vienna-rna-2.4.17+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' make[4]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg' make[3]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg' make[2]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg' find debian/ -name .gitignore -delete make[1]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_installinfo -a dh_python3 -a dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a debian/rules override_dh_compress make[1]: Entering directory '/<>/vienna-rna-2.4.17+dfsg' dh_compress --exclude=.pdf make[1]: Leaving directory '/<>/vienna-rna-2.4.17+dfsg' dh_fixperms -a dh_dwz -a dwz: debian/python3-rna/usr/lib/python3/dist-packages/RNA/_RNA.cpython-310-aarch64-linux-gnu.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/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 6846793c94c90d48c5763b1ddd577ee245cac2be ddcecff64a9ca0be12a6b58d386785297f3cee04 45aa14755edba9157231f2b02decb793289ff55a 7f1640bbb8a7e6cf55da956bcdb310cc3f64a793 0f1a402afa0fcdce5d9e999085c8fa909e0e68ed a319954989c9bc36027215912be4b7d339a5aeab da684e8ab7d3e881742eacec6e37e8ec96556aaa ed2a7d9ae73b081e8a808de0aa049cbb070bed97 df1ed80580d185c00fbacd32ee30f595af9d794e a95aa01ddf6a860f01e420a574452b0e90b33dd3 6b56425369de0567422225219bb6853fab449a86 34cef43a5b769788dcb7df1e7e46a37ab20a23ec 76a6da279db405b3c6cd4c96904b393071630652 17fc3560a8275cf5b675e6fee7fe49a15a48b91e 174b589d300e976623fdcfbc3e2d09b6a0915e6b d6551743a0dd2754dd637b6fb964e70dc6b4f789 3bbfca49b0b0203413ff4995a322ba4fd68a63a8 f8c3930ce61438e7b720aacc9959c653064aa955 3158b43633e9328f86dc2209cd439636cb22625d 6b8c17c054e2138db1042b62f0c98d13b60d6374 19019ea717585cc3436e94d3aa195b5a166fde26 68ed61ecf35390cbb62698de1edb714f68a5739a b42fc51d4fab2307164f548333ab66865eef7281 fd60ed5beac7644bba63f6ca6cbf52c8583b3614 ad455d1ee7302649a76a06540abe924a98879e84 403cd783d66b1f92626eb7412e6cb4476bf98a8b c055856c0cff3d3cbb311537c519d1d8fe2d0b43 3ef973949bcbef5f9a8108434c740904edf35f37 ad9b7690ef4eab1dc66125dd994b8c9205cbcc37 732cf9305e21a324ee7ac17398c599311735159b e0e3930f914bebca7fd68ea2f3401fe1e8e82eef 2ecb98bb43ad89b3989a1a1d4b993951c9b8feb6 dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/python3-rna/usr/lib/python3/dist-packages/RNA/_RNA.cpython-310-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyDict_GetItem: it's probably a plugin dpkg-shlibdeps: warning: 106 other similar warnings have been skipped (use -v to see them all) dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: Depends field of package librna-perl: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package python3-rna: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-rna: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package python3-rna: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-rna: substitution variable ${python3:Versions} unused, but is defined dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing python3-rna (in debian/python3-rna); do_strip: , oemstrip: pkgstriptranslations: processing librna-perl (in debian/librna-perl); do_strip: , oemstrip: pkgstriptranslations: processing vienna-rna (in debian/vienna-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/python3-rna/DEBIAN/control, package python3-rna, directory debian/python3-rna pkgstripfiles: processing control file: debian/librna-perl/DEBIAN/control, package librna-perl, directory debian/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) ... INFO: pkgstripfiles: waiting for lock (librna-perl) ... INFO: pkgstripfiles: waiting for lock (python3-rna) ... INFO: pkgstripfiles: waiting for lock (librna-perl) ... pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com 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_2.4.17+dfsg-2build2_arm64.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_2.4.17+dfsg-2build2_arm64.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_2.4.17+dfsg-2build2_arm64.deb'. INFO: pkgstriptranslations version 149 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_2.4.17+dfsg-2build2_arm64.deb'. Renaming python3-rna-dbgsym_2.4.17+dfsg-2build2_arm64.deb to python3-rna-dbgsym_2.4.17+dfsg-2build2_arm64.ddeb INFO: pkgstriptranslations version 149 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_2.4.17+dfsg-2build2_arm64.deb'. Renaming vienna-rna-dbgsym_2.4.17+dfsg-2build2_arm64.deb to vienna-rna-dbgsym_2.4.17+dfsg-2build2_arm64.ddeb dpkg-genbuildinfo --build=any -O../vienna-rna_2.4.17+dfsg-2build2_arm64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../vienna-rna_2.4.17+dfsg-2build2_arm64.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 2022-01-14T14:31:15Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ vienna-rna_2.4.17+dfsg-2build2_arm64.changes: --------------------------------------------- Format: 1.8 Date: Fri, 14 Jan 2022 14:01:38 +0000 Source: vienna-rna Binary: librna-perl python3-rna vienna-rna Built-For-Profiles: noudeb Architecture: arm64 Version: 2.4.17+dfsg-2build2 Distribution: jammy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Graham Inggs Description: librna-perl - ViennaRNA perl wrappers python3-rna - ViennaRNA Python wrappers vienna-rna - RNA sequence analysis Changes: vienna-rna (2.4.17+dfsg-2build2) jammy; urgency=medium . * No-change rebuild with Python 3.10 as default version Checksums-Sha1: 9e24dff54c129e7ac9c21eec5a3d2994eff8bee1 48356 librna-perl_2.4.17+dfsg-2build2_arm64.deb 2fc600a0d1021ee69313428ad451b9a22e7baa4a 141080 python3-rna-dbgsym_2.4.17+dfsg-2build2_arm64.ddeb 3aa66a24c20800940f8f19a468d57b3954da0a12 977270 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libpython3.10-dev (= 3.10.1-5), libpython3.10-minimal (= 3.10.1-5), libpython3.10-stdlib (= 3.10.1-5), libseccomp2 (= 2.5.2-2ubuntu2), libselinux1 (= 3.3-1build1), libsigsegv2 (= 2.13-1ubuntu2), libsm6 (= 2:1.2.3-1build1), libsmartcols1 (= 2.37.2-4ubuntu1), libsqlite3-0 (= 3.37.2-1), libssl3 (= 3.0.1-0ubuntu1), libstdc++-11-dev (= 11.2.0-13ubuntu1), libstdc++6 (= 11.2.0-13ubuntu1), libsub-override-perl (= 0.09-2), libsvm-dev (= 3.24+ds-6), libsvm3 (= 3.24+ds-6), libsynctex2 (= 2021.20210626.59705-1), libsystemd0 (= 249.5-2ubuntu4), libtasn1-6 (= 4.18.0-4), libteckit0 (= 2.5.11+ds1-1), libtexlua53 (= 2021.20210626.59705-1), libtext-unidecode-perl (= 1.30-1), libthai-data (= 0.1.29-1), libthai0 (= 0.1.29-1), libtiff5 (= 4.3.0-2), libtinfo6 (= 6.3-1), libtirpc-common (= 1.3.2-2), libtirpc-dev (= 1.3.2-2), libtirpc3 (= 1.3.2-2), libtool (= 2.4.6-15build1), libtsan0 (= 11.2.0-13ubuntu1), libubsan1 (= 11.2.0-13ubuntu1), libuchardet0 (= 0.0.7-1build1), libudev1 (= 249.5-2ubuntu4), libunistring2 (= 0.9.10-6), libuuid1 (= 2.37.2-4ubuntu1), libwebp6 (= 0.6.1-2.1build1), libx11-6 (= 2:1.7.2-2), libx11-data (= 2:1.7.2-2), libxapian30 (= 1.4.18-4), libxau6 (= 1:1.0.9-1build4), libxaw7 (= 2:1.0.13-1.1build1), libxcb-render0 (= 1.14-3ubuntu2), libxcb-shm0 (= 1.14-3ubuntu2), libxcb1 (= 1.14-3ubuntu2), libxdmcp6 (= 1:1.1.3-0ubuntu4), libxext6 (= 2:1.3.4-1), libxi6 (= 2:1.8-1), libxml-libxml-perl (= 2.0134+dfsg-2build2), libxml-namespacesupport-perl (= 1.12-1.1), libxml-sax-base-perl (= 1.09-1.1), libxml-sax-perl (= 1.02+dfsg-3), libxml2 (= 2.9.12+dfsg-5), libxmu6 (= 2:1.1.3-0ubuntu2), libxpm4 (= 1:3.5.12-1build1), libxrender1 (= 1:0.9.10-1build3), libxt6 (= 1:1.2.0-1build1), libzstd1 (= 1.4.8+dfsg-3), libzzip-0-13 (= 0.13.72+dfsg.1-1.1), linux-libc-dev (= 5.15.0-16.16), login (= 1:4.8.1-2ubuntu1), lsb-base (= 11.1.0ubuntu3), lto-disabled-list (= 18), m4 (= 1.4.18-5ubuntu1), make (= 4.3-4ubuntu2), man-db (= 2.9.4-4), mawk (= 1.3.4.20200120-2build1), media-types (= 4.0.0), 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texlive-latex-recommended (= 2021.20211217-1), texlive-pictures (= 2021.20211217-1), ucf (= 3.0043), util-linux (= 2.37.2-4ubuntu1), x11-common (= 1:7.7+23ubuntu1), xdg-utils (= 1.1.3-4.1ubuntu1), xxd (= 2:8.2.3565-1ubuntu5), xz-utils (= 5.2.5-2build1), zlib1g (= 1:1.2.11.dfsg-2ubuntu7), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu7) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1642168898" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ librna-perl_2.4.17+dfsg-2build2_arm64.deb ----------------------------------------- new Debian package, version 2.0. size 48356 bytes: control archive=820 bytes. 607 bytes, 17 lines control 597 bytes, 9 lines md5sums Package: librna-perl Source: vienna-rna Version: 2.4.17+dfsg-2build2 Architecture: arm64 Maintainer: Ubuntu Developers Installed-Size: 236 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 2022-01-14 14:01 ./ drwxr-xr-x root/root 0 2022-01-14 14:01 ./usr/ drwxr-xr-x root/root 0 2022-01-14 14:01 ./usr/share/ drwxr-xr-x root/root 0 2022-01-14 14:01 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-01-14 14:01 ./usr/share/doc/librna-perl/ -rw-r--r-- root/root 1147 2022-01-14 14:01 ./usr/share/doc/librna-perl/changelog.Debian.gz -rw-r--r-- root/root 7117 2020-12-11 08:52 ./usr/share/doc/librna-perl/copyright drwxr-xr-x root/root 0 2022-01-14 14:01 ./usr/share/perl5/ -rw-r--r-- root/root 94981 2022-01-14 14:01 ./usr/share/perl5/RNA.pm drwxr-xr-x root/root 0 2022-01-14 14:01 ./usr/share/perl5/RNA/ -rw-r--r-- root/root 14079 2022-01-14 14:01 ./usr/share/perl5/RNA/Benchmark.pm -rw-r--r-- root/root 39458 2022-01-14 14:01 ./usr/share/perl5/RNA/Design.pm -rw-r--r-- root/root 4614 2022-01-14 14:01 ./usr/share/perl5/RNA/Files.pm -rw-r--r-- root/root 57391 2022-01-14 14:01 ./usr/share/perl5/RNA/Params.pm -rw-r--r-- root/root 1818 2022-01-14 14:01 ./usr/share/perl5/RNA/Reliability.pm -rw-r--r-- root/root 8342 2022-01-14 14:01 ./usr/share/perl5/RNA/Utils.pm python3-rna_2.4.17+dfsg-2build2_arm64.deb ----------------------------------------- new Debian package, version 2.0. size 977270 bytes: control archive=1203 bytes. 776 bytes, 17 lines control 336 bytes, 4 lines md5sums 259 bytes, 12 lines * postinst #!/bin/sh 408 bytes, 12 lines * prerm #!/bin/sh 64 bytes, 1 lines shlibs 74 bytes, 2 lines triggers Package: python3-rna Source: vienna-rna Version: 2.4.17+dfsg-2build2 Architecture: arm64 Maintainer: Ubuntu Developers Installed-Size: 7463 Depends: python3 (<< 3.11), python3 (>= 3.10~), python3:any, libc6 (>= 2.33), libgcc-s1 (>= 3.3.1), libgomp1 (>= 4.9), libgsl27 (>= 2.7.1), libmpfr6 (>= 3.1.3), libstdc++6 (>= 11) 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 2022-01-14 14:01 ./ drwxr-xr-x root/root 0 2022-01-14 14:01 ./usr/ drwxr-xr-x root/root 0 2022-01-14 14:01 ./usr/lib/ drwxr-xr-x root/root 0 2022-01-14 14:01 ./usr/lib/python3/ drwxr-xr-x root/root 0 2022-01-14 14:01 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2022-01-14 14:01 ./usr/lib/python3/dist-packages/RNA/ -rw-r--r-- root/root 7467440 2022-01-14 14:01 ./usr/lib/python3/dist-packages/RNA/_RNA.cpython-310-aarch64-linux-gnu.so -rw-r--r-- root/root 149665 2022-01-14 14:01 ./usr/lib/python3/dist-packages/RNA/__init__.py drwxr-xr-x root/root 0 2022-01-14 14:01 ./usr/share/ drwxr-xr-x root/root 0 2022-01-14 14:01 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-01-14 14:01 ./usr/share/doc/python3-rna/ -rw-r--r-- root/root 1147 2022-01-14 14:01 ./usr/share/doc/python3-rna/changelog.Debian.gz -rw-r--r-- root/root 7117 2020-12-11 08:52 ./usr/share/doc/python3-rna/copyright vienna-rna_2.4.17+dfsg-2build2_arm64.deb ---------------------------------------- new Debian package, version 2.0. size 2302794 bytes: control archive=2969 bytes. 1792 bytes, 35 lines control 4371 bytes, 72 lines md5sums Package: vienna-rna Version: 2.4.17+dfsg-2build2 Architecture: arm64 Maintainer: Ubuntu Developers Installed-Size: 85534 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libgsl27 (>= 2.7.1), libmpfr6 (>= 3.1.3), libstdc++6 (>= 11) 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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+------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Type: any Build-Space: n/a Build-Time: 1170 Distribution: jammy-proposed Host Architecture: arm64 Install-Time: 113 Job: vienna-rna_2.4.17+dfsg-2build2.dsc Machine Architecture: arm64 Package: vienna-rna Package-Time: 1287 Source-Version: 2.4.17+dfsg-2build2 Space: n/a Status: successful Version: 2.4.17+dfsg-2build2 -------------------------------------------------------------------------------- Finished at 2022-01-14T14:31:15Z Build needed 00:21:27, no disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=jammy --arch=arm64 PACKAGEBUILD-23057752 Scanning for processes to kill in build PACKAGEBUILD-23057752