https://launchpad.net/ubuntu/+archive/test-rebuild-20221215-lunar-glibc-2.37/+build/25157301 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos01-arm64-021 5.4.0-135-generic #152-Ubuntu SMP Wed Nov 23 20:19:17 UTC 2022 aarch64 Buildd toolchain package versions: launchpad-buildd_225~602~ubuntu20.04.1 python3-lpbuildd_225~602~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.6 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 5 Jan 02:11:33 ntpdate[1886]: adjust time server 10.211.37.1 offset 0.000810 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=lunar --arch=armhf PACKAGEBUILD-25157301 --image-type chroot /home/buildd/filecache-default/33b5cc1d95848e4895e3aa3c2962c834df4e2086 Creating target for build PACKAGEBUILD-25157301 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=lunar --arch=armhf PACKAGEBUILD-25157301 Starting target for build PACKAGEBUILD-25157301 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=lunar --arch=armhf PACKAGEBUILD-25157301 'deb http://ppa.launchpadcontent.net/ubuntu-toolchain-r/glibc/ubuntu lunar main' 'deb http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu lunar main' 'deb http://ftpmaster.internal/ubuntu lunar main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-25157301 RUN: /usr/share/launchpad-buildd/bin/in-target add-trusted-keys --backend=chroot --series=lunar --arch=armhf PACKAGEBUILD-25157301 Adding trusted keys to build-PACKAGEBUILD-25157301 pub rsa1024/1E9377A2BA9EF27F 2009-10-22 [SC] Key fingerprint = 60C3 1780 3A41 BA51 845E 371A 1E93 77A2 BA9E F27F uid Launchpad Toolchain builds RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=lunar --arch=armhf PACKAGEBUILD-25157301 Updating target for build PACKAGEBUILD-25157301 Get:1 http://ftpmaster.internal/ubuntu lunar InRelease [267 kB] Get:2 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/glibc/ubuntu lunar InRelease [17.5 kB] Get:3 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu lunar InRelease [23.8 kB] Get:4 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/glibc/ubuntu lunar/main armhf Packages [9256 B] Get:5 http://ftpmaster.internal/ubuntu lunar/main armhf Packages [1327 kB] Get:6 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/glibc/ubuntu lunar/main Translation-en [2120 B] Get:7 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu lunar/main armhf Packages [3240 B] Get:8 http://ftpmaster.internal/ubuntu lunar/main Translation-en [511 kB] Get:9 http://ftpmaster.internal/ubuntu lunar/restricted armhf Packages [11.0 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/restricted Translation-en [18.9 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/universe armhf Packages [13.8 MB] Get:12 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu lunar/main Translation-en [3632 B] Get:13 http://ftpmaster.internal/ubuntu lunar/universe Translation-en [5873 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/multiverse armhf Packages [174 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/multiverse Translation-en [113 kB] Fetched 22.1 MB in 5s (4824 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.34 perl-modules-5.34 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libjansson4 libperl5.36 perl-modules-5.36 The following packages will be upgraded: binutils binutils-arm-linux-gnueabihf binutils-common ca-certificates cpp-12 dash g++-12 gcc-12 gcc-12-base libapparmor1 libasan8 libatomic1 libaudit-common libaudit1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcc1-0 libctf-nobfd0 libctf0 libgcc-12-dev libgcc-s1 libgomp1 libkeyutils1 libkmod2 liblz4-1 libmpc3 libssl3 libstdc++-12-dev libstdc++6 libubsan1 lto-disabled-list openssl perl perl-base 37 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 61.1 MB of archives. After this operation, 41.5 MB of additional disk space will be used. Get:1 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/glibc/ubuntu lunar/main armhf libc6-dev armhf 2.37~~snapshot-20221213.0.g5dcd2d0ad0-0ubuntu1~ppa1 [1340 kB] Get:2 http://ftpmaster.internal/ubuntu lunar/main armhf dash armhf 0.5.11+git20210903+057cd650a4ed-9ubuntu1 [79.7 kB] Get:3 http://ftpmaster.internal/ubuntu lunar/main armhf perl-modules-5.36 all 5.36.0-4ubuntu2 [2984 kB] Get:4 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/glibc/ubuntu lunar/main armhf libc-dev-bin armhf 2.37~~snapshot-20221213.0.g5dcd2d0ad0-0ubuntu1~ppa1 [18.7 kB] Get:5 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/glibc/ubuntu lunar/main armhf libc6 armhf 2.37~~snapshot-20221213.0.g5dcd2d0ad0-0ubuntu1~ppa1 [2516 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main armhf libperl5.36 armhf 5.36.0-4ubuntu2 [4043 kB] Get:7 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/glibc/ubuntu lunar/main armhf libc-bin armhf 2.37~~snapshot-20221213.0.g5dcd2d0ad0-0ubuntu1~ppa1 [536 kB] Get:8 http://ftpmaster.internal/ubuntu lunar/main armhf perl armhf 5.36.0-4ubuntu2 [235 kB] Get:9 http://ftpmaster.internal/ubuntu lunar/main armhf perl-base armhf 5.36.0-4ubuntu2 [1621 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/main armhf libcc1-0 armhf 12.2.0-10ubuntu1 [38.9 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/main armhf libctf0 armhf 2.39.50.20221224-1ubuntu1 [86.0 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main armhf libctf-nobfd0 armhf 2.39.50.20221224-1ubuntu1 [85.1 kB] Get:13 http://ftpmaster.internal/ubuntu lunar/main armhf libjansson4 armhf 2.14-2 [28.9 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main armhf binutils-arm-linux-gnueabihf armhf 2.39.50.20221224-1ubuntu1 [2777 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main armhf libbinutils armhf 2.39.50.20221224-1ubuntu1 [484 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main armhf binutils-common armhf 2.39.50.20221224-1ubuntu1 [225 kB] Get:17 http://ftpmaster.internal/ubuntu lunar/main armhf binutils armhf 2.39.50.20221224-1ubuntu1 [3118 B] Get:18 http://ftpmaster.internal/ubuntu lunar/main armhf gcc-12-base armhf 12.2.0-10ubuntu1 [19.6 kB] Get:19 http://ftpmaster.internal/ubuntu lunar/main armhf libgcc-s1 armhf 12.2.0-10ubuntu1 [41.4 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main armhf libgomp1 armhf 12.2.0-10ubuntu1 [109 kB] Get:21 http://ftpmaster.internal/ubuntu lunar/main armhf libatomic1 armhf 12.2.0-10ubuntu1 [7660 B] Get:22 http://ftpmaster.internal/ubuntu lunar/main armhf libasan8 armhf 12.2.0-10ubuntu1 [2382 kB] Get:23 http://ftpmaster.internal/ubuntu lunar/main armhf libubsan1 armhf 12.2.0-10ubuntu1 [950 kB] Get:24 http://ftpmaster.internal/ubuntu lunar/main armhf g++-12 armhf 12.2.0-10ubuntu1 [9309 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main armhf libstdc++-12-dev armhf 12.2.0-10ubuntu1 [2238 kB] Get:26 http://ftpmaster.internal/ubuntu lunar/main armhf libgcc-12-dev armhf 12.2.0-10ubuntu1 [857 kB] Get:27 http://ftpmaster.internal/ubuntu lunar/main armhf gcc-12 armhf 12.2.0-10ubuntu1 [16.2 MB] Get:28 http://ftpmaster.internal/ubuntu lunar/main armhf cpp-12 armhf 12.2.0-10ubuntu1 [8151 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main armhf libstdc++6 armhf 12.2.0-10ubuntu1 [603 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main armhf libmpc3 armhf 1.3.1-1 [46.4 kB] Get:31 http://ftpmaster.internal/ubuntu lunar/main armhf libaudit-common all 1:3.0.7-1ubuntu3 [4864 B] Get:32 http://ftpmaster.internal/ubuntu lunar/main armhf libaudit1 armhf 1:3.0.7-1ubuntu3 [42.6 kB] Get:33 http://ftpmaster.internal/ubuntu lunar/main armhf liblz4-1 armhf 1.9.4-1 [57.6 kB] Get:34 http://ftpmaster.internal/ubuntu lunar/main armhf libssl3 armhf 3.0.5-2ubuntu2 [1560 kB] Get:35 http://ftpmaster.internal/ubuntu lunar/main armhf openssl armhf 3.0.5-2ubuntu2 [1148 kB] Get:36 http://ftpmaster.internal/ubuntu lunar/main armhf ca-certificates all 20211016ubuntu1 [141 kB] Get:37 http://ftpmaster.internal/ubuntu lunar/main armhf libapparmor1 armhf 3.0.8-1ubuntu1 [32.4 kB] Get:38 http://ftpmaster.internal/ubuntu lunar/main armhf libkeyutils1 armhf 1.6.3-2 [8062 B] Get:39 http://ftpmaster.internal/ubuntu lunar/main armhf libkmod2 armhf 30+20220905-1ubuntu1 [41.9 kB] Get:40 http://ftpmaster.internal/ubuntu lunar/main armhf lto-disabled-list all 37 [12.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 61.1 MB in 6s (10.1 MB/s) (Reading database ... 13371 files and directories currently installed.) Preparing to unpack .../dash_0.5.11+git20210903+057cd650a4ed-9ubuntu1_armhf.deb ... Unpacking dash (0.5.11+git20210903+057cd650a4ed-9ubuntu1) over (0.5.11+git20210903+057cd650a4ed-8ubuntu1) ... Setting up dash (0.5.11+git20210903+057cd650a4ed-9ubuntu1) ... (Reading database ... 13371 files and directories currently installed.) Preparing to unpack .../perl_5.36.0-4ubuntu2_armhf.deb ... Unpacking perl (5.36.0-4ubuntu2) over (5.34.0-5ubuntu1) ... Selecting previously unselected package perl-modules-5.36. Preparing to unpack .../perl-modules-5.36_5.36.0-4ubuntu2_all.deb ... Unpacking perl-modules-5.36 (5.36.0-4ubuntu2) ... Selecting previously unselected package libperl5.36:armhf. Preparing to unpack .../libperl5.36_5.36.0-4ubuntu2_armhf.deb ... Unpacking libperl5.36:armhf (5.36.0-4ubuntu2) ... Preparing to unpack .../perl-base_5.36.0-4ubuntu2_armhf.deb ... Unpacking perl-base (5.36.0-4ubuntu2) over (5.34.0-5ubuntu1) ... Setting up perl-base (5.36.0-4ubuntu2) ... (Reading database ... 15293 files and directories currently installed.) Preparing to unpack .../00-libc6-dev_2.37~~snapshot-20221213.0.g5dcd2d0ad0-0ubuntu1~ppa1_armhf.deb ... Unpacking libc6-dev:armhf (2.37~~snapshot-20221213.0.g5dcd2d0ad0-0ubuntu1~ppa1) over (2.36-0ubuntu4) ... Preparing to unpack .../01-libc-dev-bin_2.37~~snapshot-20221213.0.g5dcd2d0ad0-0ubuntu1~ppa1_armhf.deb ... Unpacking libc-dev-bin (2.37~~snapshot-20221213.0.g5dcd2d0ad0-0ubuntu1~ppa1) over (2.36-0ubuntu4) ... Preparing to unpack .../02-libcc1-0_12.2.0-10ubuntu1_armhf.deb ... Unpacking libcc1-0:armhf (12.2.0-10ubuntu1) over (12.2.0-9ubuntu1) ... Preparing to unpack .../03-libctf0_2.39.50.20221224-1ubuntu1_armhf.deb ... Unpacking libctf0:armhf (2.39.50.20221224-1ubuntu1) over (2.39-8ubuntu2) ... Preparing to unpack .../04-libctf-nobfd0_2.39.50.20221224-1ubuntu1_armhf.deb ... Unpacking libctf-nobfd0:armhf (2.39.50.20221224-1ubuntu1) over (2.39-8ubuntu2) ... 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Preparing to unpack .../3-libapparmor1_3.0.8-1ubuntu1_armhf.deb ... Unpacking libapparmor1:armhf (3.0.8-1ubuntu1) over (3.0.7-1ubuntu4) ... Preparing to unpack .../4-libkeyutils1_1.6.3-2_armhf.deb ... Unpacking libkeyutils1:armhf (1.6.3-2) over (1.6.3-1) ... Preparing to unpack .../5-libkmod2_30+20220905-1ubuntu1_armhf.deb ... Unpacking libkmod2:armhf (30+20220905-1ubuntu1) over (30+20220630-3ubuntu1) ... Preparing to unpack .../6-lto-disabled-list_37_all.deb ... Unpacking lto-disabled-list (37) over (36) ... Setting up libkeyutils1:armhf (1.6.3-2) ... Setting up lto-disabled-list (37) ... Setting up libapparmor1:armhf (3.0.8-1ubuntu1) ... Setting up binutils-common:armhf (2.39.50.20221224-1ubuntu1) ... Setting up libssl3:armhf (3.0.5-2ubuntu2) ... Setting up libctf-nobfd0:armhf (2.39.50.20221224-1ubuntu1) ... Setting up libgomp1:armhf (12.2.0-10ubuntu1) ... Setting up libjansson4:armhf (2.14-2) ... Setting up perl-modules-5.36 (5.36.0-4ubuntu2) ... Setting up libmpc3:armhf (1.3.1-1) ... Setting up libatomic1:armhf (12.2.0-10ubuntu1) ... Setting up libubsan1:armhf (12.2.0-10ubuntu1) ... Setting up libasan8:armhf (12.2.0-10ubuntu1) ... Setting up libbinutils:armhf (2.39.50.20221224-1ubuntu1) ... Setting up libc-dev-bin (2.37~~snapshot-20221213.0.g5dcd2d0ad0-0ubuntu1~ppa1) ... Setting up openssl (3.0.5-2ubuntu2) ... Setting up libcc1-0:armhf (12.2.0-10ubuntu1) ... Setting up libperl5.36:armhf (5.36.0-4ubuntu2) ... Setting up libkmod2:armhf (30+20220905-1ubuntu1) ... Setting up libctf0:armhf (2.39.50.20221224-1ubuntu1) ... Setting up cpp-12 (12.2.0-10ubuntu1) ... Setting up ca-certificates (20211016ubuntu1) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 0 added, 3 removed; done. Setting up perl (5.36.0-4ubuntu2) ... Setting up libgcc-12-dev:armhf (12.2.0-10ubuntu1) ... Setting up libc6-dev:armhf (2.37~~snapshot-20221213.0.g5dcd2d0ad0-0ubuntu1~ppa1) ... Setting up binutils-arm-linux-gnueabihf (2.39.50.20221224-1ubuntu1) ... Setting up libstdc++-12-dev:armhf (12.2.0-10ubuntu1) ... Setting up binutils (2.39.50.20221224-1ubuntu1) ... Setting up gcc-12 (12.2.0-10ubuntu1) ... Setting up g++-12 (12.2.0-10ubuntu1) ... Processing triggers for debianutils (5.7-0.4) ... Processing triggers for libc-bin (2.37~~snapshot-20221213.0.g5dcd2d0ad0-0ubuntu1~ppa1) ... Processing triggers for ca-certificates (20211016ubuntu1) ... 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-25157301 armhf lunar -c chroot:build-PACKAGEBUILD-25157301 --arch=armhf --dist=lunar --nolog vienna-rna_2.4.17+dfsg-2build2.dsc Initiating build PACKAGEBUILD-25157301 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-135-generic #152-Ubuntu SMP Wed Nov 23 20:19:17 UTC 2022 armv7l sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos01-arm64-021.buildd +==============================================================================+ | vienna-rna 2.4.17+dfsg-2build2 (armhf) Thu, 05 Jan 2023 02:12:04 +0000 | +==============================================================================+ Package: vienna-rna Version: 2.4.17+dfsg-2build2 Source Version: 2.4.17+dfsg-2build2 Distribution: lunar Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-25157301/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/vienna-rna-hZSO5A/resolver-Qn935F' 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-hZSO5A/vienna-rna-2.4.17+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/vienna-rna-hZSO5A' with '<>' +------------------------------------------------------------------------------+ | 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, build-essential, fakeroot 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, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [511 B] Get:5 copy:/<>/apt_archive ./ Packages [590 B] Fetched 2058 B in 0s (92.4 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libperl5.34 perl-modules-5.34 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 libapache-pom-java libarchive-zip-perl libavahi-client3 libavahi-common-data libavahi-common3 libbrotli1 libbsd0 libcairo2 libcdt5 libcgraph6 libclang-cpp14 libclang1-14 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 libfontenc1 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 libicu71 libidn12 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore libkpathsea6 liblab-gamut1 liblerc4 libllvm14 liblocale-gettext-perl libltdl7 libmagic-mgc libmagic1 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 libsm6 libsub-override-perl libsvm-dev libsvm3 libsynctex2 libteckit0 libtexlua53-5 libtexluajit2 libtext-unidecode-perl libthai-data libthai0 libtiff5 libtool libuchardet0 libwebp7 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 xfonts-encodings xfonts-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 low-memory-monitor 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 wp2latex python3-pygments icc-profiles libfile-which-perl texlive-latex-extra-doc texlive-science texlive-latex-recommended-doc texlive-luatex texlive-pstricks dot2tex prerex texlive-pictures-doc vprerex Recommended packages: curl | wget | lynx fonts-liberation2 dbus libarchive-cpio-perl 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 default-jre libspreadsheet-parseexcel-perl texlive-fonts-recommended texlive-plain-generic ruby tk libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev 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 libapache-pom-java libarchive-zip-perl libavahi-client3 libavahi-common-data libavahi-common3 libbrotli1 libbsd0 libcairo2 libcdt5 libcgraph6 libclang-cpp14 libclang1-14 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 libfontenc1 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 libicu71 libidn12 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore libkpathsea6 liblab-gamut1 liblerc4 libllvm14 liblocale-gettext-perl libltdl7 libmagic-mgc libmagic1 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 libsm6 libsub-override-perl libsvm-dev libsvm3 libsynctex2 libteckit0 libtexlua53-5 libtexluajit2 libtext-unidecode-perl libthai-data libthai0 libtiff5 libtool libuchardet0 libwebp7 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-main-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 xfonts-encodings xfonts-utils xxd zlib1g-dev 0 upgraded, 180 newly installed, 0 to remove and 0 not upgraded. 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[56.1 kB] Get:22 http://ftpmaster.internal/ubuntu lunar/main armhf xxd armhf 2:9.0.0242-1ubuntu1 [49.8 kB] Get:23 http://ftpmaster.internal/ubuntu lunar/main armhf bsdextrautils armhf 2.38.1-4ubuntu1 [76.4 kB] Get:24 http://ftpmaster.internal/ubuntu lunar/main armhf libmagic-mgc armhf 1:5.41-4 [257 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main armhf libmagic1 armhf 1:5.41-4 [80.1 kB] Get:26 http://ftpmaster.internal/ubuntu lunar/main armhf file armhf 1:5.41-4 [20.6 kB] Get:27 http://ftpmaster.internal/ubuntu lunar/main armhf gettext-base armhf 0.21-10 [37.3 kB] Get:28 http://ftpmaster.internal/ubuntu lunar/main armhf libuchardet0 armhf 0.0.7-1build2 [75.7 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main armhf groff-base armhf 1.22.4-9 [849 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main armhf libedit2 armhf 3.1-20221030-2 [78.3 kB] Get:31 http://ftpmaster.internal/ubuntu lunar/main armhf libpipeline1 armhf 1.5.7-1 [26.2 kB] Get:32 http://ftpmaster.internal/ubuntu 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libclang-cpp14 armhf 1:14.0.6-9 [11.0 MB] Get:64 http://ftpmaster.internal/ubuntu lunar/universe armhf libclang1-14 armhf 1:14.0.6-9 [6187 kB] Get:65 http://ftpmaster.internal/ubuntu lunar/universe armhf libxapian30 armhf 1.4.21-1 [658 kB] Get:66 http://ftpmaster.internal/ubuntu lunar/universe armhf doxygen armhf 1.9.1-2ubuntu2 [4194 kB] Get:67 http://ftpmaster.internal/ubuntu lunar/main armhf libbrotli1 armhf 1.0.9-2build7 [295 kB] Get:68 http://ftpmaster.internal/ubuntu lunar/main armhf libfreetype6 armhf 2.12.1+dfsg-3 [324 kB] Get:69 http://ftpmaster.internal/ubuntu lunar/main armhf fonts-dejavu-core all 2.37-2build2 [1137 kB] Get:70 http://ftpmaster.internal/ubuntu lunar/main armhf libfontenc1 armhf 1:1.1.4-1build3 [12.2 kB] Get:71 http://ftpmaster.internal/ubuntu lunar/main armhf x11-common all 1:7.7+23ubuntu2 [23.4 kB] Get:72 http://ftpmaster.internal/ubuntu lunar/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] Get:73 http://ftpmaster.internal/ubuntu lunar/main armhf xfonts-utils armhf 1:7.7+6build2 [89.8 kB] Get:74 http://ftpmaster.internal/ubuntu lunar/main armhf fonts-urw-base35 all 20200910-6 [6588 kB] Get:75 http://ftpmaster.internal/ubuntu lunar/main armhf fontconfig-config all 2.13.1-4.4ubuntu1 [28.2 kB] Get:76 http://ftpmaster.internal/ubuntu lunar/main armhf libfontconfig1 armhf 2.13.1-4.4ubuntu1 [107 kB] Get:77 http://ftpmaster.internal/ubuntu lunar/main armhf fontconfig armhf 2.13.1-4.4ubuntu1 [181 kB] Get:78 http://ftpmaster.internal/ubuntu lunar/universe armhf fonts-lmodern all 2.005-1 [4799 kB] Get:79 http://ftpmaster.internal/ubuntu lunar/universe armhf gengetopt armhf 2.23+dfsg1-1 [146 kB] Get:80 http://ftpmaster.internal/ubuntu lunar/main armhf libgs9-common all 9.56.1~dfsg1-0ubuntu3 [749 kB] Get:81 http://ftpmaster.internal/ubuntu lunar/main armhf libavahi-common-data armhf 0.8-6ubuntu1 [24.0 kB] Get:82 http://ftpmaster.internal/ubuntu lunar/main armhf libavahi-common3 armhf 0.8-6ubuntu1 [20.0 kB] Get:83 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lunar/main armhf libjbig0 armhf 2.1-6ubuntu1 [24.6 kB] Get:94 http://ftpmaster.internal/ubuntu lunar/main armhf liblerc4 armhf 4.0.0+ds-2ubuntu2 [151 kB] Get:95 http://ftpmaster.internal/ubuntu lunar/main armhf libwebp7 armhf 1.2.2-2build1 [165 kB] Get:96 http://ftpmaster.internal/ubuntu lunar/main armhf libtiff5 armhf 4.4.0-6ubuntu1 [171 kB] Get:97 http://ftpmaster.internal/ubuntu lunar/main armhf libgs9 armhf 9.56.1~dfsg1-0ubuntu3 [4586 kB] Get:98 http://ftpmaster.internal/ubuntu lunar/main armhf ghostscript armhf 9.56.1~dfsg1-0ubuntu3 [49.2 kB] Get:99 http://ftpmaster.internal/ubuntu lunar/universe armhf libcdt5 armhf 2.42.2-7build1 [18.6 kB] Get:100 http://ftpmaster.internal/ubuntu lunar/universe armhf libcgraph6 armhf 2.42.2-7build1 [37.5 kB] Get:101 http://ftpmaster.internal/ubuntu lunar/main armhf libxpm4 armhf 1:3.5.12-1build2 [31.0 kB] Get:102 http://ftpmaster.internal/ubuntu lunar/main armhf libgd3 armhf 2.3.3-7ubuntu1 [106 kB] Get:103 http://ftpmaster.internal/ubuntu lunar/universe armhf libgts-0.7-5 armhf 0.7.6+darcs121130-5 [146 kB] Get:104 http://ftpmaster.internal/ubuntu lunar/main armhf libpixman-1-0 armhf 0.42.2-1 [184 kB] Get:105 http://ftpmaster.internal/ubuntu lunar/main armhf libxcb-render0 armhf 1.15-1 [15.2 kB] Get:106 http://ftpmaster.internal/ubuntu lunar/main armhf libxcb-shm0 armhf 1.15-1 [5852 B] Get:107 http://ftpmaster.internal/ubuntu lunar/main armhf libxrender1 armhf 1:0.9.10-1.1 [16.5 kB] Get:108 http://ftpmaster.internal/ubuntu lunar/main armhf libcairo2 armhf 1.16.0-7 [439 kB] Get:109 http://ftpmaster.internal/ubuntu lunar/main armhf libltdl7 armhf 2.4.7-5 [37.3 kB] Get:110 http://ftpmaster.internal/ubuntu lunar/main armhf libgraphite2-3 armhf 1.3.14-1build2 [65.2 kB] Get:111 http://ftpmaster.internal/ubuntu lunar/main armhf libharfbuzz0b armhf 5.2.0-2 [381 kB] Get:112 http://ftpmaster.internal/ubuntu lunar/main armhf libthai-data all 0.1.29-1build1 [162 kB] Get:113 http://ftpmaster.internal/ubuntu lunar/main armhf 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armhf 2:6.2.1+dfsg1-1.1ubuntu1 [9134 B] Get:134 http://ftpmaster.internal/ubuntu lunar/main armhf libgmp-dev armhf 2:6.2.1+dfsg1-1.1ubuntu1 [284 kB] Get:135 http://ftpmaster.internal/ubuntu lunar/universe armhf libgslcblas0 armhf 2.7.1+dfsg-3 [73.7 kB] Get:136 http://ftpmaster.internal/ubuntu lunar/universe armhf libgsl27 armhf 2.7.1+dfsg-3 [842 kB] Get:137 http://ftpmaster.internal/ubuntu lunar/universe armhf libgsl-dev armhf 2.7.1+dfsg-3 [1080 kB] Get:138 http://ftpmaster.internal/ubuntu lunar/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] Get:139 http://ftpmaster.internal/ubuntu lunar/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-2 [118 kB] Get:140 http://ftpmaster.internal/ubuntu lunar/main armhf libjs-sphinxdoc all 5.3.0-2 [129 kB] Get:141 http://ftpmaster.internal/ubuntu lunar/main armhf libkpathsea6 armhf 2022.20220321.62855-5 [54.2 kB] Get:142 http://ftpmaster.internal/ubuntu lunar/main armhf libmpfr-dev armhf 4.1.0-3build3 [231 kB] Get:143 http://ftpmaster.internal/ubuntu lunar/main armhf libpaper-utils armhf 1.1.28build2 [8242 B] Get:144 http://ftpmaster.internal/ubuntu lunar/main armhf libptexenc1 armhf 2022.20220321.62855-5 [35.1 kB] Get:145 http://ftpmaster.internal/ubuntu lunar/main armhf libpython3.10 armhf 3.10.9-1 [1704 kB] Get:146 http://ftpmaster.internal/ubuntu lunar/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4.1ubuntu1 [155 kB] Get:147 http://ftpmaster.internal/ubuntu lunar/main armhf libpython3.10-dev armhf 3.10.9-1 [3532 kB] Get:148 http://ftpmaster.internal/ubuntu lunar/main armhf libpython3-dev armhf 3.10.6-1ubuntu1 [7128 B] Get:149 http://ftpmaster.internal/ubuntu lunar/universe armhf libsvm3 armhf 3.24+ds-6 [36.5 kB] Get:150 http://ftpmaster.internal/ubuntu lunar/universe armhf libsvm-dev armhf 3.24+ds-6 [46.5 kB] Get:151 http://ftpmaster.internal/ubuntu lunar/main armhf libsynctex2 armhf 2022.20220321.62855-5 [44.0 kB] Get:152 http://ftpmaster.internal/ubuntu lunar/universe armhf libteckit0 armhf 2.5.11+ds1-1 [336 kB] Get:153 http://ftpmaster.internal/ubuntu lunar/main armhf libtexlua53-5 armhf 2022.20220321.62855-5 [94.4 kB] Get:154 http://ftpmaster.internal/ubuntu lunar/main armhf libtexluajit2 armhf 2022.20220321.62855-5 [211 kB] Get:155 http://ftpmaster.internal/ubuntu lunar/universe armhf libtext-unidecode-perl all 1.30-3 [105 kB] Get:156 http://ftpmaster.internal/ubuntu lunar/main armhf libxi6 armhf 2:1.8-1build1 [26.6 kB] Get:157 http://ftpmaster.internal/ubuntu lunar/main armhf libxml-namespacesupport-perl all 1.12-2 [13.5 kB] Get:158 http://ftpmaster.internal/ubuntu lunar/main armhf libxml-sax-base-perl all 1.09-3 [18.9 kB] Get:159 http://ftpmaster.internal/ubuntu lunar/main armhf libxml-sax-perl all 1.02+dfsg-3 [57.0 kB] Get:160 http://ftpmaster.internal/ubuntu lunar/main armhf libxml-libxml-perl armhf 2.0207+dfsg+really+2.0134-1build1 [301 kB] Get:161 http://ftpmaster.internal/ubuntu lunar/universe armhf libzzip-0-13 armhf 0.13.72+dfsg.1-1.1 [23.0 kB] Get:162 http://ftpmaster.internal/ubuntu lunar/main armhf perl-doc all 5.36.0-4ubuntu2 [7900 kB] Get:163 http://ftpmaster.internal/ubuntu lunar/main armhf pkg-config armhf 0.29.2-1ubuntu3 [46.0 kB] Get:164 http://ftpmaster.internal/ubuntu lunar/universe armhf tex-common all 6.18 [32.8 kB] Get:165 http://ftpmaster.internal/ubuntu lunar/universe armhf preview-latex-style all 12.2-1ubuntu1 [185 kB] Get:166 http://ftpmaster.internal/ubuntu lunar/main armhf python3.10-dev armhf 3.10.9-1 [507 kB] Get:167 http://ftpmaster.internal/ubuntu lunar/main armhf python3-dev armhf 3.10.6-1ubuntu1 [26.0 kB] Get:168 http://ftpmaster.internal/ubuntu lunar/universe armhf swig4.0 armhf 4.1.0-0.2 [1089 kB] Get:169 http://ftpmaster.internal/ubuntu lunar/universe armhf swig all 4.1.0-0.2 [5598 B] Get:170 http://ftpmaster.internal/ubuntu lunar/main armhf t1utils armhf 1.41-4build2 [53.1 kB] Get:171 http://ftpmaster.internal/ubuntu lunar/universe armhf texinfo armhf 6.8-6build2 [1410 kB] Get:172 http://ftpmaster.internal/ubuntu lunar/universe armhf texlive-binaries armhf 2022.20220321.62855-5 [8518 kB] Get:173 http://ftpmaster.internal/ubuntu lunar/main armhf xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] Get:174 http://ftpmaster.internal/ubuntu lunar/universe armhf texlive-base all 2022.20221123-1 [21.7 MB] Get:175 http://ftpmaster.internal/ubuntu lunar/universe armhf texlive-latex-base all 2022.20221123-1 [1159 kB] Get:176 http://ftpmaster.internal/ubuntu lunar/universe armhf libfontbox-java all 1:1.8.16-2 [207 kB] Get:177 http://ftpmaster.internal/ubuntu lunar/universe armhf libpdfbox-java all 1:1.8.16-2 [5199 kB] Get:178 http://ftpmaster.internal/ubuntu lunar/universe armhf texlive-latex-recommended all 2022.20221123-1 [8866 kB] Get:179 http://ftpmaster.internal/ubuntu lunar/universe armhf texlive-pictures all 2022.20221123-1 [15.8 MB] Get:180 http://ftpmaster.internal/ubuntu lunar/universe armhf texlive-latex-extra all 2022.20221123-1 [18.8 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 201 MB in 11s (18.2 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 15300 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-5_armhf.deb ... Unpacking liblocale-gettext-perl (1.07-5) ... Selecting previously unselected package libpython3.10-minimal:armhf. Preparing to unpack .../libpython3.10-minimal_3.10.9-1_armhf.deb ... Unpacking libpython3.10-minimal:armhf (3.10.9-1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.5.0-1_armhf.deb ... Unpacking libexpat1:armhf (2.5.0-1) ... Selecting previously unselected package python3.10-minimal. Preparing to unpack .../python3.10-minimal_3.10.9-1_armhf.deb ... Unpacking python3.10-minimal (3.10.9-1) ... Setting up libpython3.10-minimal:armhf (3.10.9-1) ... Setting up libexpat1:armhf (2.5.0-1) ... Setting up python3.10-minimal (3.10.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 15617 files and directories currently installed.) 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Setting up libpipeline1:armhf (1.5.7-1) ... Setting up libgraphite2-3:armhf (1.3.14-1build2) ... Setting up libpixman-1-0:armhf (0.42.2-1) ... Setting up libicu71:armhf (71.1-3ubuntu1) ... Setting up libxapian30:armhf (1.4.21-1) ... Setting up libxau6:armhf (1:1.0.9-1build5) ... Setting up gengetopt (2.23+dfsg1-1) ... Setting up liblerc4:armhf (4.0.0+ds-2ubuntu2) ... Setting up bsdextrautils (2.38.1-4ubuntu1) ... Setting up libdatrie1:armhf (0.2.13-2) ... Setting up libgslcblas0:armhf (2.7.1+dfsg-3) ... Setting up libmagic-mgc (1:5.41-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:armhf (2.74.2-1) ... No schema files found: doing nothing. Setting up libijs-0.35:armhf (0.35-15build2) ... Setting up libtexluajit2:armhf (2022.20220321.62855-5) ... Setting up libdebhelper-perl (13.10.1ubuntu1) ... Setting up libbrotli1:armhf (1.0.9-2build7) ... Setting up libfontbox-java (1:1.8.16-2) ... Setting up liblab-gamut1:armhf (2.42.2-7build1) ... Setting up x11-common (1:7.7+23ubuntu2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libmagic1:armhf (1:5.41-4) ... Setting up libdeflate0:armhf (1.14-1) ... Setting up perl-doc (5.36.0-4ubuntu2) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up gettext-base (0.21-10) ... Setting up libgsl27:armhf (2.7.1+dfsg-3) ... Setting up m4 (1.4.19-1) ... Setting up libzzip-0-13:armhf (0.13.72+dfsg.1-1.1) ... Setting up file (1:5.41-4) ... Setting up cthreadpool-dev (0.0+git20201207.b259a6e-1) ... Setting up libjbig0:armhf (2.1-6ubuntu1) ... Setting up xxd (2:9.0.0242-1ubuntu1) ... Setting up poppler-data (0.4.11-1) ... Setting up libgts-0.7-5:armhf (0.7.6+darcs121130-5) ... Setting up libxml-sax-base-perl (1.09-3) ... Setting up libfontenc1:armhf (1:1.1.4-1build3) ... Setting up autotools-dev (20220109.1) ... Setting up libgmpxx4ldbl:armhf (2:6.2.1+dfsg1-1.1ubuntu1) ... Setting up libexpat1-dev:armhf (2.5.0-1) ... Setting up libfreetype6:armhf (2.12.1+dfsg-3) ... Setting up libx11-data (2:1.8.1-2) ... Setting up libjbig2dec0:armhf (0.19-3build2) ... Setting up libteckit0:armhf (2.5.11+ds1-1) ... Setting up libpathplan4:armhf (2.42.2-7build1) ... Setting up libapache-pom-java (25-2) ... Setting up libavahi-common-data:armhf (0.8-6ubuntu1) ... Setting up libdbus-1-3:armhf (1.14.0-2ubuntu3) ... Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... Setting up libfribidi0:armhf (1.0.8-2.1ubuntu1) ... Setting up t1utils (1.41-4build2) ... Setting up libtexlua53-5:armhf (2022.20220321.62855-5) ... Setting up libidn12:armhf (1.41-1) ... Setting up autopoint (0.21-10) ... Setting up pkg-config (0.29.2-1ubuntu3) ... Setting up fonts-dejavu-core (2.37-2build2) ... Setting up ucf (3.0043) ... Setting up libjpeg-turbo8:armhf (2.1.2-0ubuntu1) ... Setting up libltdl7:armhf (2.4.7-5) ... Setting up libkpathsea6:armhf (2022.20220321.62855-5) ... Setting up autoconf (2.71-2) ... Setting up libwebp7:armhf (1.2.2-2build1) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-4.1ubuntu1) ... Setting up libuchardet0:armhf (0.0.7-1build2) ... Setting up libmpdec3:armhf (2.5.1-2build2) ... Setting up fonts-lmodern (2.005-1) ... Setting up libopenjp2-7:armhf (2.5.0-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libharfbuzz0b:armhf (5.2.0-2) ... Setting up libthai-data (0.1.29-1build1) ... Setting up libcdt5:armhf (2.42.2-7build1) ... Setting up libcgraph6:armhf (2.42.2-7build1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up swig4.0 (4.1.0-0.2) ... Setting up libtext-unidecode-perl (1.30-3) ... Setting up libbsd0:armhf (0.11.7-1) ... Setting up libelf1:armhf (0.188-1) ... Setting up libxml2:armhf (2.9.14+dfsg-1.1) ... Setting up xdg-utils (1.1.3-4.1ubuntu3) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up liblocale-gettext-perl (1.07-5) ... Setting up libsvm3:armhf (3.24+ds-6) ... Setting up libsynctex2:armhf (2022.20220321.62855-5) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-2) ... Setting up libjpeg8:armhf (8c-2ubuntu10) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.0-2) ... Setting up libpaper1:armhf (1.1.28build2) ... Creating config file /etc/papersize with new version Setting up libice6:armhf (2:1.0.10-1build2) ... Setting up libdw1:armhf (0.188-1) ... Setting up libxdmcp6:armhf (1:1.1.3-0ubuntu5) ... Setting up libxcb1:armhf (1.15-1) ... Setting up gettext (0.21-10) ... Setting up libgsl-dev (2.7.1+dfsg-3) ... Setting up swig (4.1.0-0.2) ... Setting up libgmp-dev:armhf (2:6.2.1+dfsg1-1.1ubuntu1) ... Setting up libpdfbox-java (1:1.8.16-2) ... Setting up libtool (2.4.7-5) ... Setting up libxcb-render0:armhf (1.15-1) ... Setting up fontconfig-config (2.13.1-4.4ubuntu1) ... Setting up libedit2:armhf (3.1-20221030-2) ... Setting up libcommons-parent-java (55-1) ... Setting up libavahi-common3:armhf (0.8-6ubuntu1) ... Setting up libcommons-logging-java (1.2-3) ... Setting up libxcb-shm0:armhf (1.15-1) ... Setting up libpaper-utils (1.1.28build2) ... Setting up xfonts-utils (1:7.7+6build2) ... Setting up libmpfr-dev:armhf (4.1.0-3build3) ... 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+20060710.6) ... Setting up help2man (1.49.3) ... Setting up libpython3.10-stdlib:armhf (3.10.9-1) ... Setting up dh-autoreconf (20) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libthai0:armhf (0.1.29-1build1) ... Setting up libptexenc1:armhf (2022.20220321.62855-5) ... Setting up libsvm-dev:armhf (3.24+ds-6) ... Setting up libjs-sphinxdoc (5.3.0-2) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1build1) ... 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 (1.13.0-2) ... Setting up libllvm14:armhf (1:14.0.6-9) ... Setting up libgvpr2:armhf (2.42.2-7build1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-9) ... Setting up debugedit (1:5.0-5) ... Setting up libx11-6:armhf (2:1.8.1-2) ... Setting up libtiff5:armhf (4.4.0-6ubuntu1) ... Setting up libfontconfig1:armhf (2.13.1-4.4ubuntu1) ... Setting up libsm6:armhf (2:1.2.3-1build2) ... Setting up libavahi-client3:armhf (0.8-6ubuntu1) ... Setting up libpython3-stdlib:armhf (3.10.6-1ubuntu1) ... Setting up libpython3.10:armhf (3.10.9-1) ... Setting up fontconfig (2.13.1-4.4ubuntu1) ... Regenerating fonts cache... done. Setting up python3.10 (3.10.9-1) ... Setting up libxpm4:armhf (1:3.5.12-1build2) ... Setting up libxrender1:armhf (1:0.9.10-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up preview-latex-style (12.2-1ubuntu1) ... Setting up libpango-1.0-0:armhf (1.50.10+ds-1) ... Setting up libxext6:armhf (2:1.3.4-1build1) ... Setting up libclang1-14 (1:14.0.6-9) ... Setting up python3 (3.10.6-1ubuntu1) ... Setting up fonts-urw-base35 (20200910-6) ... Setting up man-db (2.11.1-1) ... 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:armhf (1.16.0-7) ... Setting up libgd3:armhf (2.3.3-7ubuntu1) ... Setting up libpython3.10-dev:armhf (3.10.9-1) ... Setting up libclang-cpp14 (1:14.0.6-9) ... Setting up libxt6:armhf (1:1.2.1-1) ... Setting up texinfo (6.8-6build2) ... Running mktexlsr. This may take some time. ... done. Setting up libcups2:armhf (2.4.2-1ubuntu2) ... Setting up python3.10-dev (3.10.9-1) ... Setting up libpangoft2-1.0-0:armhf (1.50.10+ds-1) ... Setting up python3-lib2to3 (3.10.8-1) ... Setting up libpangocairo-1.0-0:armhf (1.50.10+ds-1) ... Setting up python3-distutils (3.10.8-1) ... Setting up dh-python (5.20221230) ... Setting up libgs9-common (9.56.1~dfsg1-0ubuntu3) ... Setting up libxmu6:armhf (2:1.1.3-3) ... Setting up libpython3-dev:armhf (3.10.6-1ubuntu1) ... Setting up libgs9:armhf (9.56.1~dfsg1-0ubuntu3) ... Setting up libxi6:armhf (2:1.8-1build1) ... Setting up debhelper (13.10.1ubuntu1) ... Setting up libxaw7:armhf (2:1.0.14-1) ... Setting up ghostscript (9.56.1~dfsg1-0ubuntu3) ... Setting up doxygen (1.9.1-2ubuntu2) ... Setting up python3-dev (3.10.6-1ubuntu1) ... Setting up libgvc6 (2.42.2-7build1) ... Setting up texlive-binaries (2022.20220321.62855-5) ... 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 (2022.20221123-1) ... 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 (2.42.2-7build1) ... Setting up texlive-latex-base (2022.20221123-1) ... Setting up texlive-latex-recommended (2022.20221123-1) ... Setting up texlive-pictures (2022.20221123-1) ... Setting up texlive-latex-extra (2022.20221123-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for systemd (251.4-1ubuntu7) ... Processing triggers for libc-bin (2.37~~snapshot-20221213.0.g5dcd2d0ad0-0ubuntu1~ppa1) ... Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-135-generic #152-Ubuntu SMP Wed Nov 23 20:19:17 UTC 2022 arm64 (armv7l) Toolchain package versions: binutils_2.39.50.20221224-1ubuntu1 dpkg-dev_1.21.11ubuntu2 g++-12_12.2.0-10ubuntu1 gcc-12_12.2.0-10ubuntu1 libc6-dev_2.37~~snapshot-20221213.0.g5dcd2d0ad0-0ubuntu1~ppa1 libstdc++-12-dev_12.2.0-10ubuntu1 libstdc++6_12.2.0-10ubuntu1 linux-libc-dev_5.19.0-21.21 Package versions: adduser_3.121ubuntu1 advancecomp_2.4-1 apt_2.5.4 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-10 autotools-dev_20220109.1 base-files_12.3ubuntu1 base-passwd_3.6.1 bash_5.2-1ubuntu2 binutils_2.39.50.20221224-1ubuntu1 binutils-arm-linux-gnueabihf_2.39.50.20221224-1ubuntu1 binutils-common_2.39.50.20221224-1ubuntu1 bsdextrautils_2.38.1-4ubuntu1 bsdutils_1:2.38.1-4ubuntu1 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20211016ubuntu1 coreutils_8.32-4.1ubuntu1 cpp_4:12.2.0-1ubuntu1 cpp-12_12.2.0-10ubuntu1 cthreadpool-dev_0.0+git20201207.b259a6e-1 dash_0.5.11+git20210903+057cd650a4ed-9ubuntu1 debconf_1.5.79ubuntu1 debhelper_13.10.1ubuntu1 debianutils_5.7-0.4 debugedit_1:5.0-5 dh-autoreconf_20 dh-python_5.20221230 dh-strip-nondeterminism_1.13.0-2 diffutils_1:3.8-1 doxygen_1.9.1-2ubuntu2 dpkg_1.21.11ubuntu2 dpkg-dev_1.21.11ubuntu2 dwz_0.15-1 e2fsprogs_1.46.6~rc1-1ubuntu1 fakeroot_1.30.1-1ubuntu1 file_1:5.41-4 findutils_4.9.0-3ubuntu1 fontconfig_2.13.1-4.4ubuntu1 fontconfig-config_2.13.1-4.4ubuntu1 fonts-dejavu-core_2.37-2build2 fonts-lmodern_2.005-1 fonts-urw-base35_20200910-6 g++_4:12.2.0-1ubuntu1 g++-12_12.2.0-10ubuntu1 gcc_4:12.2.0-1ubuntu1 gcc-12_12.2.0-10ubuntu1 gcc-12-base_12.2.0-10ubuntu1 gengetopt_2.23+dfsg1-1 gettext_0.21-10 gettext-base_0.21-10 ghostscript_9.56.1~dfsg1-0ubuntu3 gpg_2.2.40-1ubuntu1 gpg-agent_2.2.40-1ubuntu1 gpgconf_2.2.40-1ubuntu1 gpgv_2.2.40-1ubuntu1 graphviz_2.42.2-7build1 grep_3.8-3 groff-base_1.22.4-9 gzip_1.12-1ubuntu1 help2man_1.49.3 hostname_3.23ubuntu2 init_1.65.2 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-2 libapache-pom-java_25-2 libapparmor1_3.0.8-1ubuntu1 libapt-pkg6.0_2.5.4 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.3 libasan8_12.2.0-10ubuntu1 libassuan0_2.5.5-5 libatomic1_12.2.0-10ubuntu1 libattr1_1:2.5.1-3 libaudit-common_1:3.0.7-1ubuntu3 libaudit1_1:3.0.7-1ubuntu3 libavahi-client3_0.8-6ubuntu1 libavahi-common-data_0.8-6ubuntu1 libavahi-common3_0.8-6ubuntu1 libbinutils_2.39.50.20221224-1ubuntu1 libblkid1_2.38.1-4ubuntu1 libbrotli1_1.0.9-2build7 libbsd0_0.11.7-1 libbz2-1.0_1.0.8-5build1 libc-bin_2.37~~snapshot-20221213.0.g5dcd2d0ad0-0ubuntu1~ppa1 libc-dev-bin_2.37~~snapshot-20221213.0.g5dcd2d0ad0-0ubuntu1~ppa1 libc6_2.37~~snapshot-20221213.0.g5dcd2d0ad0-0ubuntu1~ppa1 libc6-dev_2.37~~snapshot-20221213.0.g5dcd2d0ad0-0ubuntu1~ppa1 libcairo2_1.16.0-7 libcap-ng0_0.8.3-1build1 libcap2_1:2.44-1build3 libcc1-0_12.2.0-10ubuntu1 libcdt5_2.42.2-7build1 libcgraph6_2.42.2-7build1 libclang-cpp14_1:14.0.6-9 libclang1-14_1:14.0.6-9 libcom-err2_1.46.6~rc1-1ubuntu1 libcommons-logging-java_1.2-3 libcommons-parent-java_55-1 libcrypt-dev_1:4.4.33-1 libcrypt1_1:4.4.33-1 libcryptsetup12_2:2.5.0-6ubuntu3 libctf-nobfd0_2.39.50.20221224-1ubuntu1 libctf0_2.39.50.20221224-1ubuntu1 libcups2_2.4.2-1ubuntu2 libdatrie1_0.2.13-2 libdb5.3_5.3.28+dfsg1-0.10 libdbus-1-3_1.14.0-2ubuntu3 libdebconfclient0_0.264ubuntu1 libdebhelper-perl_13.10.1ubuntu1 libdeflate0_1.14-1 libdevmapper1.02.1_2:1.02.185-1ubuntu1 libdpkg-perl_1.21.11ubuntu2 libdw1_0.188-1 libedit2_3.1-20221030-2 libelf1_0.188-1 libexpat1_2.5.0-1 libexpat1-dev_2.5.0-1 libext2fs2_1.46.6~rc1-1ubuntu1 libfakeroot_1.30.1-1ubuntu1 libfdisk1_2.38.1-4ubuntu1 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.0-2 libfontbox-java_1:1.8.16-2 libfontconfig1_2.13.1-4.4ubuntu1 libfontenc1_1:1.1.4-1build3 libfreetype6_2.12.1+dfsg-3 libfribidi0_1.0.8-2.1ubuntu1 libgcc-12-dev_12.2.0-10ubuntu1 libgcc-s1_12.2.0-10ubuntu1 libgcrypt20_1.10.1-2ubuntu1 libgd3_2.3.3-7ubuntu1 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libglib2.0-0_2.74.2-1 libgmp-dev_2:6.2.1+dfsg1-1.1ubuntu1 libgmp10_2:6.2.1+dfsg1-1.1ubuntu1 libgmpxx4ldbl_2:6.2.1+dfsg1-1.1ubuntu1 libgnutls30_3.7.7-2ubuntu2 libgomp1_12.2.0-10ubuntu1 libgpg-error0_1.46-1 libgraphite2-3_1.3.14-1build2 libgs9_9.56.1~dfsg1-0ubuntu3 libgs9-common_9.56.1~dfsg1-0ubuntu3 libgsl-dev_2.7.1+dfsg-3 libgsl27_2.7.1+dfsg-3 libgslcblas0_2.7.1+dfsg-3 libgssapi-krb5-2_1.20.1-1 libgts-0.7-5_0.7.6+darcs121130-5 libgvc6_2.42.2-7build1 libgvpr2_2.42.2-7build1 libharfbuzz0b_5.2.0-2 libhogweed6_3.8.1-2 libice6_2:1.0.10-1build2 libicu71_71.1-3ubuntu1 libidn12_1.41-1 libidn2-0_2.3.3-1build1 libijs-0.35_0.35-15build2 libip4tc2_1.8.7-1ubuntu7 libisl23_0.25-1 libjansson4_2.14-2 libjbig0_2.1-6ubuntu1 libjbig2dec0_0.19-3build2 libjpeg-turbo8_2.1.2-0ubuntu1 libjpeg8_8c-2ubuntu10 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-sphinxdoc_5.3.0-2 libjs-underscore_1.13.4~dfsg+~1.11.4-2 libjson-c5_0.16-2 libk5crypto3_1.20.1-1 libkeyutils1_1.6.3-2 libkmod2_30+20220905-1ubuntu1 libkpathsea6_2022.20220321.62855-5 libkrb5-3_1.20.1-1 libkrb5support0_1.20.1-1 liblab-gamut1_2.42.2-7build1 liblerc4_4.0.0+ds-2ubuntu2 libllvm14_1:14.0.6-9 liblocale-gettext-perl_1.07-5 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 libltdl7_2.4.7-5 liblz4-1_1.9.4-1 liblzma5_5.2.9-0.0 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmd0_1.0.4-2 libmount1_2.38.1-4ubuntu1 libmpc3_1.3.1-1 libmpdec3_2.5.1-2build2 libmpfr-dev_4.1.0-3build3 libmpfr6_4.1.0-3build3 libncurses6_6.3+20220423-2 libncursesw6_6.3+20220423-2 libnettle8_3.8.1-2 libnpth0_1.6-3build2 libnsl-dev_1.3.0-2build2 libnsl2_1.3.0-2build2 libopenjp2-7_2.5.0-1 libp11-kit0_0.24.1-1ubuntu2 libpam-modules_1.5.2-5ubuntu1 libpam-modules-bin_1.5.2-5ubuntu1 libpam-runtime_1.5.2-5ubuntu1 libpam0g_1.5.2-5ubuntu1 libpango-1.0-0_1.50.10+ds-1 libpangocairo-1.0-0_1.50.10+ds-1 libpangoft2-1.0-0_1.50.10+ds-1 libpaper-utils_1.1.28build2 libpaper1_1.1.28build2 libpathplan4_2.42.2-7build1 libpcre2-8-0_10.40-1ubuntu1 libpcre3_2:8.39-14 libpdfbox-java_1:1.8.16-2 libperl5.34_5.34.0-5ubuntu1 libperl5.36_5.36.0-4ubuntu2 libpipeline1_1.5.7-1 libpixman-1-0_0.42.2-1 libpng16-16_1.6.39-2 libprocps8_2:3.3.17-7ubuntu1 libptexenc1_2022.20220321.62855-5 libpython3-dev_3.10.6-1ubuntu1 libpython3-stdlib_3.10.6-1ubuntu1 libpython3.10_3.10.9-1 libpython3.10-dev_3.10.9-1 libpython3.10-minimal_3.10.9-1 libpython3.10-stdlib_3.10.9-1 libreadline8_8.2-1.2 libseccomp2_2.5.4-1ubuntu2 libselinux1_3.4-1build1 libsemanage-common_3.4-1build1 libsemanage2_3.4-1build1 libsepol2_3.4-2 libsm6_2:1.2.3-1build2 libsmartcols1_2.38.1-4ubuntu1 libsqlite3-0_3.40.0-1 libss2_1.46.6~rc1-1ubuntu1 libssl3_3.0.5-2ubuntu2 libstdc++-12-dev_12.2.0-10ubuntu1 libstdc++6_12.2.0-10ubuntu1 libsub-override-perl_0.09-4 libsvm-dev_3.24+ds-6 libsvm3_3.24+ds-6 libsynctex2_2022.20220321.62855-5 libsystemd-shared_251.4-1ubuntu7 libsystemd0_251.4-1ubuntu7 libtasn1-6_4.19.0-2 libteckit0_2.5.11+ds1-1 libtexlua53-5_2022.20220321.62855-5 libtexluajit2_2022.20220321.62855-5 libtext-unidecode-perl_1.30-3 libthai-data_0.1.29-1build1 libthai0_0.1.29-1build1 libtiff5_4.4.0-6ubuntu1 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-5 libubsan1_12.2.0-10ubuntu1 libuchardet0_0.0.7-1build2 libudev1_251.4-1ubuntu7 libunistring2_1.0-2 libuuid1_2.38.1-4ubuntu1 libwebp7_1.2.2-2build1 libx11-6_2:1.8.1-2 libx11-data_2:1.8.1-2 libxapian30_1.4.21-1 libxau6_1:1.0.9-1build5 libxaw7_2:1.0.14-1 libxcb-render0_1.15-1 libxcb-shm0_1.15-1 libxcb1_1.15-1 libxdmcp6_1:1.1.3-0ubuntu5 libxext6_2:1.3.4-1build1 libxi6_2:1.8-1build1 libxml-libxml-perl_2.0207+dfsg+really+2.0134-1build1 libxml-namespacesupport-perl_1.12-2 libxml-sax-base-perl_1.09-3 libxml-sax-perl_1.02+dfsg-3 libxml2_2.9.14+dfsg-1.1 libxmu6_2:1.1.3-3 libxpm4_1:3.5.12-1build2 libxrender1_1:0.9.10-1.1 libxt6_1:1.2.1-1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 libzzip-0-13_0.13.72+dfsg.1-1.1 linux-libc-dev_5.19.0-21.21 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-1ubuntu1 logsave_1.46.6~rc1-1ubuntu1 lsb-base_11.2ubuntu1 lto-disabled-list_37 m4_1.4.19-1 make_4.3-4.1build1 man-db_2.11.1-1 mawk_1.3.4.20200120-3.1 media-types_8.0.0 mount_2.38.1-4ubuntu1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 openssl_3.0.5-2ubuntu2 optipng_0.7.7-2build1 passwd_1:4.13+dfsg1-1ubuntu1 patch_2.7.6-7build2 perl_5.36.0-4ubuntu2 perl-base_5.36.0-4ubuntu2 perl-doc_5.36.0-4ubuntu2 perl-modules-5.34_5.34.0-5ubuntu1 perl-modules-5.36_5.36.0-4ubuntu2 pinentry-curses_1.2.1-1ubuntu1 pkg-config_0.29.2-1ubuntu3 pkgbinarymangler_149 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 poppler-data_0.4.11-1 preview-latex-style_12.2-1ubuntu1 procps_2:3.3.17-7ubuntu1 python3_3.10.6-1ubuntu1 python3-dev_3.10.6-1ubuntu1 python3-distutils_3.10.8-1 python3-lib2to3_3.10.8-1 python3-minimal_3.10.6-1ubuntu1 python3.10_3.10.9-1 python3.10-dev_3.10.9-1 python3.10-minimal_3.10.9-1 readline-common_8.2-1.2 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1ubuntu2 sensible-utils_0.0.17 swig_4.1.0-0.2 swig4.0_4.1.0-0.2 systemd_251.4-1ubuntu7 systemd-sysv_251.4-1ubuntu7 sysvinit-utils_3.04-1ubuntu1 t1utils_1.41-4build2 tar_1.34+dfsg-1.1 tex-common_6.18 texinfo_6.8-6build2 texlive-base_2022.20221123-1 texlive-binaries_2022.20220321.62855-5 texlive-latex-base_2022.20221123-1 texlive-latex-extra_2022.20221123-1 texlive-latex-recommended_2022.20221123-1 texlive-pictures_2022.20221123-1 tzdata_2022g-0ubuntu2 ubuntu-keyring_2021.03.26 ucf_3.0043 usrmerge_33ubuntu1 util-linux_2.38.1-4ubuntu1 util-linux-extra_2.38.1-4ubuntu1 x11-common_1:7.7+23ubuntu2 xdg-utils_1.1.3-4.1ubuntu3 xfonts-encodings_1:1.0.5-0ubuntu2 xfonts-utils_1:7.7+6build2 xxd_2:9.0.0242-1ubuntu1 xz-utils_5.2.9-0.0 zlib1g_1:1.2.11.dfsg-4.1ubuntu1 zlib1g-dev_1:1.2.11.dfsg-4.1ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: vienna-rna Binary: vienna-rna, python3-rna, librna-perl Architecture: any Version: 2.4.17+dfsg-2build2 Maintainer: Ubuntu Developers Uploaders: Olivier Sallou , Steffen Moeller Homepage: https://www.tbi.univie.ac.at/RNA/ Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/vienna-rna Vcs-Git: https://salsa.debian.org/med-team/vienna-rna.git Build-Depends: debhelper-compat (= 13), dh-python, python3-dev, 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 Package-List: librna-perl deb non-free/perl optional arch=any python3-rna deb non-free/python optional arch=any vienna-rna deb non-free/science optional arch=any Checksums-Sha1: de4367f91afec4d84f3ddb7305a0fe7f511d8726 8710784 vienna-rna_2.4.17+dfsg.orig.tar.xz d6abf0476d2776f8515a43c32b9674e0254bd266 10260 vienna-rna_2.4.17+dfsg-2build2.debian.tar.xz Checksums-Sha256: c946d9c790b9f64240ee6196af928812efe63b3b0b18e6d76bd0d2d95f36ab3d 8710784 vienna-rna_2.4.17+dfsg.orig.tar.xz 67eef0db9db2b5296716c77433a0af074b9dcbecb614d2310b76204f0d5b5526 10260 vienna-rna_2.4.17+dfsg-2build2.debian.tar.xz Files: b9d9a85b55e596df8ef7cfe9bbe1b3ce 8710784 vienna-rna_2.4.17+dfsg.orig.tar.xz fce5532913eb9385d4b2754b1147860f 10260 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RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./vienna-rna_2.4.17+dfsg-2build2.dsc: no acceptable signature found dpkg-source: info: extracting vienna-rna in /<> 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=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-25157301 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-25157301 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-25157301 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package vienna-rna dpkg-buildpackage: info: source version 2.4.17+dfsg-2build2 dpkg-buildpackage: info: source distribution jammy dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean rm -f doc/RNAlib* rm -f doc/*.db rm -f interfaces/Perl/Makefile.perl.old rm -f interfaces/Python/install.record rm -rf doc/html rm -rf doc/latex rm -rf src/cthreadpool #find . \( -type f -a \( -name config.status -o -name config.sub -o -name config.guess \) \) -delete find src/ViennaRNA -name "*.hex" -delete find . -name "*eps-converted-to.pdf" -delete rm -f src/bin/RNAfold_cmdl.[ch] rm -f aclocal.m4 src/Kinfold/aclocal.m4 grep -rl "DO NOT MODIFY THIS FILE! It was generated by help2man" man | xargs -r rm -f grep -lri "DO NOT EDIT THIS FILE." src | grep -v debian | xargs -r rm grep -lri "File autogenerated by gengetopt" src | grep -v debian | xargs -r rm grep -lri "Generated from configure.ac" . | grep -v debian | xargs -r rm grep -lri "generated by GNU Gengetopt" . | grep -v debian | xargs -r rm grep -lri "DO NOT MODIFY THIS FILE" man | grep -v debian | xargs -r rm grep -lri "made by GNU Bison" src | grep -v debian | xargs -r rm grep -lri "produced by makeinfo version" man | grep -v debian | xargs -r rm #rm -f src/Kinfold/INSTALL src/RNAforester/INSTALL src/RNAlocmin/RNAlocmin # removal of self-added symbolic links rm -rf src/cthreadpool/ find . -name Makefile.in -delete #rm -f config/ar-lib config/compile config/depcomp config/install-sh config/ltmain.sh config/missing config/test-driver config/texinfo.tex rm -f configure rm -f m4/libtool.m4 rm -f src/{RNAforester,RNAlocmin,Kinfold,Kinwalker}/{compile,depcomp,install-sh,missing,aclocal.m4,ylwrap} rm -f src/{Kinwalker,RNAforester}/{aclocal.m4,ylwrap,install-sh rm -f src/Kinfold/config.guess src/Kinfold/config.sub src/Kinfold/configure rm -f src/Kinwalker/configure rm -f src/RNAforester/configure src/RNAforester/g2-0.72/configure rm -f src/RNAlocmin/config.guess src/RNAlocmin/config.sub src/RNAlocmin/configure rm -f config/ltmain.sh src/Kinfold/INSTALL src/RNAforester/INSTALL # removing self-created man pages find man/ -name "*.1" -delete make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-arch --with python3 dh_update_autotools_config -a dh_autoreconf -a configure.ac: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.m4:100: 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 '/<>' 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=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-cluster --without-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... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for gcc... (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... 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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 arm-linux-gnueabihf-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-arm-linux-gnueabihf.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 (/<>/src/Kinfold) configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr' '--build=arm-linux-gnueabihf' '--includedir=${prefix}/include' '--mandir=${prefix}/share/man' '--infodir=${prefix}/share/info' '--sysconfdir=/etc' '--localstatedir=/var' '--disable-silent-rules' '--libdir=${prefix}/lib/arm-linux-gnueabihf' '--runstatedir=/run' '--disable-maintainer-mode' '--disable-dependency-tracking' '--with-cluster' '--without-python' '--with-python3' '--without-forester' '--without-doc' '--without-tutorial' 'build_alias=arm-linux-gnueabihf' 'CFLAGS=-I/usr/include/json-c/ -I/usr/include/libsvm/' 'LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro' 'CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2' 'CXXFLAGS=-I/usr/include/json-c/ -I/usr/include/libsvm/' 'CC=gcc' 'CXX=g++' 'AR=gcc-ar' 'RANLIB=gcc-ranlib' 'NM=gcc-nm' 'VRNA_CFLAGS=-I$(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... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking for strdup... yes checking for memset... yes checking for strchr... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for RNAlib2 >= 2.2.0... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for exp in -lm... yes checking for an ANSI C-conforming const... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Example/Makefile config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands === configuring in src/RNAlocmin (/<>/src/RNAlocmin) configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr' '--build=arm-linux-gnueabihf' '--includedir=${prefix}/include' '--mandir=${prefix}/share/man' '--infodir=${prefix}/share/info' '--sysconfdir=/etc' '--localstatedir=/var' '--disable-silent-rules' '--libdir=${prefix}/lib/arm-linux-gnueabihf' '--runstatedir=/run' '--disable-maintainer-mode' '--disable-dependency-tracking' '--with-cluster' '--without-python' '--with-python3' '--without-forester' '--without-doc' '--without-tutorial' 'build_alias=arm-linux-gnueabihf' 'CFLAGS=-I/usr/include/json-c/ -I/usr/include/libsvm/' 'LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro' 'CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2' 'CXXFLAGS=-I/usr/include/json-c/ -I/usr/include/libsvm/' 'CC=gcc' 'CXX=g++' 'AR=gcc-ar' 'RANLIB=gcc-ranlib' 'NM=gcc-nm' 'VRNA_CFLAGS=-I$(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... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking how to run the C preprocessor... gcc -E checking whether g++ supports C++11 features by default... yes checking for strchr... yes checking for strdup... yes checking for strtol... yes checking for limits.h... yes checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for inline... inline checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking for working strtod... yes checking for size_t... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for RNAlib2... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands configure: ====================================== ViennaRNA Package 2.4.17 ====================================== 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/arm-linux-gnueabihf * Header files : /usr/include * Extra Data : /usr/share * Man pages : /usr/share/man * Documentation : Not to be installed (HTML) : (PDF) : * Perl5 Interface : (binaries) : /usr/lib/arm-linux-gnueabihf/perl/5.36.0 (scripts) : /usr/share/perl/5.36.0 * 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 '/<>' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' if [ ! -d src/cthreadpool ]; then \ mkdir -p src/cthreadpool && \ cd src/cthreadpool && \ ln -s /usr/include/cthreadpool/thpool.h . && \ ln -s /usr/share/cthreadpool/thpool.c . ; \ fi dh_auto_build make -j4 make[2]: Entering directory '/<>' make all-recursive make[3]: Entering directory '/<>' Making all in src make[4]: Entering directory '/<>/src' Making all in ViennaRNA make[5]: Entering directory '/<>/src/ViennaRNA' Making all in static make[6]: Entering directory '/<>/src/ViennaRNA/static' /usr/bin/xxd -i < postscript/structure_plot_macro_base.ps > postscript/structure_plot_macro_base.hex && echo ',0x00' >> postscript/structure_plot_macro_base.hex /usr/bin/xxd -i < postscript/structure_plot_macro_extras.ps > postscript/structure_plot_macro_extras.hex && echo ',0x00' >> postscript/structure_plot_macro_extras.hex /usr/bin/xxd -i < postscript/dot_plot_macro_base.ps > postscript/dot_plot_macro_base.hex && echo ',0x00' >> postscript/dot_plot_macro_base.hex /usr/bin/xxd -i < postscript/dot_plot_macro_turn.ps > postscript/dot_plot_macro_turn.hex && echo ',0x00' >> postscript/dot_plot_macro_turn.hex /usr/bin/xxd -i < postscript/dot_plot_macro_sd.ps > postscript/dot_plot_macro_sd.hex && echo ',0x00' >> postscript/dot_plot_macro_sd.hex /usr/bin/xxd -i < postscript/dot_plot_macro_ud.ps > postscript/dot_plot_macro_ud.hex && echo ',0x00' >> postscript/dot_plot_macro_ud.hex /usr/bin/xxd -i < postscript/dot_plot_macro_sc_motifs.ps > postscript/dot_plot_macro_sc_motifs.hex && echo ',0x00' >> postscript/dot_plot_macro_sc_motifs.hex /usr/bin/xxd -i < postscript/dot_plot_macro_linear_data.ps > postscript/dot_plot_macro_linear_data.hex && echo ',0x00' >> postscript/dot_plot_macro_linear_data.hex /usr/bin/xxd -i < postscript/aln_macro_base.ps > postscript/aln_macro_base.hex && echo ',0x00' >> postscript/aln_macro_base.hex /usr/bin/xxd -i < svg/structure_plot_header.svg > svg/structure_plot_header.hex && echo ',0x00' >> svg/structure_plot_header.hex /usr/bin/xxd -i < svg/structure_plot_footer.svg > svg/structure_plot_footer.hex && echo ',0x00' >> svg/structure_plot_footer.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/dna_mathews1999.par > misc/dna_mathews1999.hex && echo ',0x00' >> misc/dna_mathews1999.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/dna_mathews2004.par > misc/dna_mathews2004.hex && echo ',0x00' >> misc/dna_mathews2004.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/rna_andronescu2007.par > misc/rna_andronescu2007.hex && echo ',0x00' >> misc/rna_andronescu2007.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/rna_langdon2018.par > misc/rna_langdon2018.hex && echo ',0x00' >> misc/rna_langdon2018.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/rna_misc_special_hairpins.par > misc/rna_misc_special_hairpins.hex && echo ',0x00' >> misc/rna_misc_special_hairpins.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/rna_turner1999.par > misc/rna_turner1999.hex && echo ',0x00' >> misc/rna_turner1999.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/rna_turner2004.par > misc/rna_turner2004.hex && echo ',0x00' >> misc/rna_turner2004.hex make all-am make[7]: Entering directory '/<>/src/ViennaRNA/static' make[7]: Nothing to be done for 'all-am'. make[7]: Leaving directory '/<>/src/ViennaRNA/static' make[6]: Leaving directory '/<>/src/ViennaRNA/static' make[6]: Entering directory '/<>/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.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 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 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 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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 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 /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 inverse.c -fPIC -DPIC -o .libs/inverse.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 ProfileDist.c -fPIC -DPIC -o .libs/ProfileDist.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 RNAstruct.c -fPIC -DPIC -o .libs/RNAstruct.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 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 ProfileDist.c -o ProfileDist.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 inverse.c -o inverse.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_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_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.c -o mfe.o >/dev/null 2>&1 mfe_window.c: In function ‘print_block_list’: mfe_window.c:1636:21: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 1636 | printf("block %lu: en=%d, start: %lu, end: %lu, shift: %lu\n", | ~~^ | | | long unsigned int | %u 1637 | cnt, | ~~~ | | | size_t {aka unsigned int} mfe_window.c:1642:13: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 1642 | printf("%lu blocks remaining\n", cnt); | ~~^ ~~~ | | | | long unsigned int size_t {aka unsigned int} | %u /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 mfe_window_wrappers.c -o mfe_window_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 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 -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 subopt.lo subopt.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 subopt.c -fPIC -DPIC -o .libs/subopt.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 Lfold.lo Lfold.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 -fPIC -DPIC -o .libs/Lfold.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 cofold.lo cofold.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_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 cofold.c -fPIC -DPIC -o .libs/cofold.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_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 -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 -o part_func_co.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 concentrations.c -o concentrations.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 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-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 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-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 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 -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c plex_functions.c -fPIC -DPIC -o .libs/plex_functions.o 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 ali_plex.c -fPIC -DPIC -o .libs/ali_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 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--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 /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 snoop.lo snoop.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 snofold.c -fPIC -DPIC -o .libs/snofold.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/ 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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 grammar.c -fPIC -DPIC -o .libs/grammar.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 grammar.c -o grammar.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 equilibrium_probs.c -o equilibrium_probs.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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-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 commands.lo commands.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 commands.c -fPIC -DPIC -o .libs/commands.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 combinatorics.lo combinatorics.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 combinatorics.c -fPIC -DPIC -o .libs/combinatorics.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 commands.c -o commands.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 combinatorics.c -o combinatorics.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 eval.lo eval.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 eval_wrappers.lo eval_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 eval.c -fPIC -DPIC -o .libs/eval.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 move_set.lo move_set.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 eval_wrappers.c -fPIC -DPIC -o .libs/eval_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 special_const.lo special_const.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 move_set.c -fPIC -DPIC -o .libs/move_set.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 special_const.c -fPIC -DPIC -o .libs/special_const.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 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libRNA_utils.la utils/utils.lo utils/string_utils.lo utils/structure_utils.lo utils/structure_tree.lo utils/msa_utils.lo utils/higher_order_functions.lo utils/cpu.lo utils/units.lo io/io_utils.lo io/file_formats.lo io/file_formats_msa.lo search/BoyerMoore.lo commands.lo combinatorics.lo -lgsl -lgslcblas -lm libtool: link: gcc-ar cr .libs/libRNA_datastructures.a datastructures/.libs/basic_datastructures.o datastructures/.libs/lists.o datastructures/.libs/char_stream.o datastructures/.libs/stream_output.o datastructures/.libs/hash_tables.o datastructures/.libs/heap.o libtool: link: gcc-ranlib .libs/libRNA_datastructures.a libtool: link: ( cd ".libs" && rm -f "libRNA_datastructures.la" && ln -s "../libRNA_datastructures.la" "libRNA_datastructures.la" ) /bin/bash ../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z,relro 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/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 -Wl,-z,relro -o libRNA_params.la params/io.lo params/default.lo params/params.lo params/convert.lo -lgsl -lgslcblas -lm libtool: link: gcc-ar cr .libs/libRNA_params.a params/.libs/io.o params/.libs/default.o params/.libs/params.o params/.libs/convert.o libtool: link: gcc-ranlib .libs/libRNA_params.a libtool: link: ( cd ".libs" && rm -f "libRNA_params.la" && ln -s "../libRNA_params.la" "libRNA_params.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/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z,relro -o libRNA_conv.la fold_compound.lo dist_vars.lo part_func.lo part_func_wrappers.lo pf_fold.lo treedist.lo inverse.lo ProfileDist.lo 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.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 -Wl,-z,relro -o libRNA.la -rpath /usr/lib/arm-linux-gnueabihf libRNA_conv.la -lgsl -lgslcblas -lm libtool: link: (cd .libs/libRNA.lax/libRNA_conv.a && gcc-ar x "/<>/src/ViennaRNA/./.libs/libRNA_conv.a") libtool: link: gcc-ar cr .libs/libRNA.a .libs/libRNA.lax/libRNA_conv.a/2Dfold.o .libs/libRNA.lax/libRNA_conv.a/2Dpfold.o .libs/libRNA.lax/libRNA_conv.a/BoyerMoore.o .libs/libRNA.lax/libRNA_conv.a/LPfold.o .libs/libRNA.lax/libRNA_conv.a/Lfold.o .libs/libRNA.lax/libRNA_conv.a/MEA.o .libs/libRNA.lax/libRNA_conv.a/ProfileAln.o .libs/libRNA.lax/libRNA_conv.a/ProfileDist.o .libs/libRNA.lax/libRNA_conv.a/RNApuzzler.o .libs/libRNA.lax/libRNA_conv.a/RNAstruct.o .libs/libRNA.lax/libRNA_conv.a/RNAturtle.o .libs/libRNA.lax/libRNA_conv.a/SHAPE.o .libs/libRNA.lax/libRNA_conv.a/ali_plex.o .libs/libRNA.lax/libRNA_conv.a/alifold.o .libs/libRNA.lax/libRNA_conv.a/alignments.o .libs/libRNA.lax/libRNA_conv.a/alipfold.o .libs/libRNA.lax/libRNA_conv.a/alphabet.o .libs/libRNA.lax/libRNA_conv.a/basic_datastructures.o .libs/libRNA.lax/libRNA_conv.a/boltzmann_sampling.o .libs/libRNA.lax/libRNA_conv.a/bs_wrappers.o .libs/libRNA.lax/libRNA_conv.a/c_plex.o .libs/libRNA.lax/libRNA_conv.a/centroid.o .libs/libRNA.lax/libRNA_conv.a/char_stream.o .libs/libRNA.lax/libRNA_conv.a/cofold.o .libs/libRNA.lax/libRNA_conv.a/combinatorics.o .libs/libRNA.lax/libRNA_conv.a/commands.o .libs/libRNA.lax/libRNA_conv.a/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 '/<>/src/ViennaRNA' make[5]: Leaving directory '/<>/src/ViennaRNA' Making all in bin make[5]: Entering directory '/<>/src/bin' /usr/bin/gengetopt -i RNAfold.ggo gcc -DHAVE_CONFIG_H -I. -I../.. -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 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 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 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 RNAsnoop.c: In function ‘redraw_output’: RNAsnoop.c:1106:25: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 1106 | sprintf(str, "%d", count); | ^~ RNAsnoop.c:1106:24: note: directive argument in the range [1, 2147483647] 1106 | sprintf(str, "%d", count); | ^~~~ RNAsnoop.c:1106:11: note: ‘sprintf’ output between 2 and 11 bytes into a destination of size 9 1106 | sprintf(str, "%d", count); | ^~~~~~~~~~~~~~~~~~~~~~~~~ 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 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 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 -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 -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 -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 -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 -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 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-I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -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 -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAfold RNAfold_cmdl.o RNAfold.o ../../src/ViennaRNA/.libs/libRNA_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 -Wl,-z,relro -o RNAdistance RNAdistance_cmdl.o RNAdistance.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAdistance RNAdistance_cmdl.o RNAdistance.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-z,relro -o RNAinverse RNAinverse_cmdl.o RNAinverse.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAinverse RNAinverse_cmdl.o RNAinverse.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-z,relro -o RNAplot RNAplot_cmdl.o RNAplot.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAplot RNAplot_cmdl.o RNAplot.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -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 -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -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 -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 -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -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 -Wl,-z,relro -o RNAcofold RNAcofold_cmdl.o RNAcofold.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAcofold RNAcofold_cmdl.o RNAcofold.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-z,relro -o RNApaln RNApaln_cmdl.o RNApaln.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNApaln RNApaln_cmdl.o RNApaln.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -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 -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -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 -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 -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -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 -Wl,-z,relro -o RNAplfold RNAplfold_cmdl.o RNAplfold.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAplfold RNAplfold_cmdl.o RNAplfold.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-z,relro -o RNAup RNAup_cmdl.o RNAup.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAup RNAup_cmdl.o RNAup.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-z,relro -o RNAaliduplex RNAaliduplex_cmdl.o RNAaliduplex.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAaliduplex RNAaliduplex_cmdl.o RNAaliduplex.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-z,relro -o RNALalifold RNALalifold_cmdl.o RNALalifold.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNALalifold RNALalifold_cmdl.o RNALalifold.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -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 -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNA2Dfold RNA2Dfold_cmdl.o RNA2Dfold.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-z,relro -o RNAparconv RNAparconv_cmdl.o RNAparconv.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o 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 -Wl,-z,relro -o RNAPKplex RNAPKplex_cmdl.o RNAPKplex.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAPKplex RNAPKplex_cmdl.o RNAPKplex.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-z,relro -o RNAplex RNAplex_cmdl.o RNAplex.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAplex RNAplex_cmdl.o RNAplex.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-z,relro -o RNAsnoop RNAsnoop_cmdl.o RNAsnoop.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAsnoop RNAsnoop_cmdl.o RNAsnoop.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-z,relro -o RNApvmin RNApvmin_cmdl.o RNApvmin.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNApvmin RNApvmin_cmdl.o RNApvmin.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.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 -Wl,-z,relro -o RNAdos RNAdos_cmdl.o RNAdos.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o RNAdos RNAdos_cmdl.o RNAdos.o ../../src/ViennaRNA/.libs/libRNA_conv.a ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp make[5]: Leaving directory '/<>/src/bin' Making all in Utils make[5]: Entering directory '/<>/src/Utils' gcc -DHAVE_CONFIG_H -I. -I../.. -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 -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 -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 -Wl,-z,relro -o ct2db ct2db_cmdl.o ct2db.o ../../src/ViennaRNA/libRNA_conv.la -lm -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o 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 -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o b2ct b2ct.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o ct2db ct2db_cmdl.o ct2db.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lgsl -lgslcblas -lm -pthread -fopenmp make[5]: Leaving directory '/<>/src/Utils' Making all in Cluster make[5]: Entering directory '/<>/src/Cluster' gcc -DHAVE_CONFIG_H -I. -I../.. -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 -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 -Wl,-z,relro -o AnalyseSeqs statgeom.o distance_matrix.o cluster.o AS_main.o split.o treeplot.o PS3D.o ../../src/ViennaRNA/libRNA_conv.la -lgsl -lgslcblas -lm libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o AnalyseDists split.o distance_matrix.o cluster.o treeplot.o AD_main.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: gcc -fno-strict-aliasing -flto -ffat-lto-objects -fopenmp -ftree-vectorize -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -flto -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o AnalyseSeqs statgeom.o distance_matrix.o cluster.o AS_main.o split.o treeplot.o PS3D.o ../../src/ViennaRNA/.libs/libRNA_conv.a -lgsl -lgslcblas -lm -pthread -fopenmp make[5]: Leaving directory '/<>/src/Cluster' make[5]: Entering directory '/<>/src' make[5]: Nothing to be done for 'all-am'. make[5]: Leaving directory '/<>/src' make[4]: Leaving directory '/<>/src' Making all in man make[4]: Entering directory '/<>/man' restore=: && backupdir=".am$$" && \ am__cwd=`pwd` && CDPATH="${ZSH_VERSION+.}:" && cd . && \ rm -rf $backupdir && mkdir $backupdir && \ if (/bin/bash '/<>/config/missing' makeinfo --version) >/dev/null 2>&1; then \ for f in RNAlib.info RNAlib.info-[0-9] RNAlib.info-[0-9][0-9] RNAlib.i[0-9] RNAlib.i[0-9][0-9]; do \ if test -f $f; then mv $f $backupdir; restore=mv; else :; fi; \ done; \ else :; fi && \ cd "$am__cwd"; \ if /bin/bash '/<>/config/missing' makeinfo -I . \ -o RNAlib.info RNAlib.texi; \ then \ rc=0; \ CDPATH="${ZSH_VERSION+.}:" && cd .; \ else \ rc=$?; \ CDPATH="${ZSH_VERSION+.}:" && cd . && \ $restore $backupdir/* `echo "./RNAlib.info" | sed 's|[^/]*$||'`; \ fi; \ rm -rf $backupdir; exit $rc ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNA2Dfold.ggo | perl -pe 's/\\e\\e/\\e/g' > RNA2Dfold.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAaliduplex.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAaliduplex.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAalifold.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAalifold.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAcofold.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAcofold.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAduplex.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAduplex.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAeval.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAeval.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAfold.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAfold.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAheat.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAheat.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAinverse.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAinverse.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNALalifold.ggo | perl -pe 's/\\e\\e/\\e/g' > RNALalifold.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNALfold.ggo | perl -pe 's/\\e\\e/\\e/g' > RNALfold.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNApaln.ggo | perl -pe 's/\\e\\e/\\e/g' > RNApaln.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAparconv.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAparconv.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAplfold.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAplfold.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAplot.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAplot.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNApvmin.ggo | perl -pe 's/\\e\\e/\\e/g' > RNApvmin.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAsubopt.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAsubopt.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAup.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAup.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAPKplex.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAPKplex.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAsnoop.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAsnoop.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAplex.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAplex.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAdistance.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAdistance.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNApdist.ggo | perl -pe 's/\\e\\e/\\e/g' > RNApdist.1 ./help2manWrapper.sh \ "/usr/bin/help2man" ../src/bin/RNAdos.ggo | perl -pe 's/\\e\\e/\\e/g' > RNAdos.1 /usr/bin/help2man \ -N \ --help-option=--detailed-help \ --opt-include=./include/ref_package.inc \ "./cmdlopt.sh ../src/Utils/ct2db" > ct2db.1 make[4]: Leaving directory '/<>/man' Making all in misc make[4]: Entering directory '/<>/misc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/misc' Making all in doc make[4]: Entering directory '/<>/doc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/doc' Making all in RNA-Tutorial make[4]: Entering directory '/<>/RNA-Tutorial' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/RNA-Tutorial' Making all in interfaces make[4]: Entering directory '/<>/interfaces' Making all in Perl make[5]: Entering directory '/<>/interfaces/Perl' /usr/bin/swig -I../../src \ -I. -I. \ \ -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/arm-linux-gnueabihf/perl/5.36/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/arm-linux-gnueabihf/perl/5.36/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/arm-linux-gnueabihf/perl/5.36/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 -Wl,-z,relro -o RNA.la -rpath /usr/lib/arm-linux-gnueabihf/perl/5.36.0/auto/RNA RNA_la-RNA_wrap.lo ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/12/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/arm-linux-gnueabihf/12 -L/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/12/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/12/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/crtn.o -flto -fopenmp -pthread -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -fopenmp -pthread -Wl,-soname -Wl,RNA.so -o .libs/RNA.so libtool: link: ( cd ".libs" && rm -f "RNA.la" && ln -s "../RNA.la" "RNA.la" ) ( /usr/bin/mkdir -p auto/RNA ) && \ ( \ /bin/bash ../../libtool --config > libtoolconfig.tmp && \ ( . ./libtoolconfig.tmp; cp "$objdir/RNA.so" auto/RNA ) && \ rm -f libtoolconfig.tmp \ ) make[5]: Leaving directory '/<>/interfaces/Perl' Making all in Python3 make[5]: Entering directory '/<>/interfaces/Python3' /usr/bin/swig -I../../src \ -I. -I. \ -DPY3 \ \ -python -py3 -c++ -keyword -w511 \ -o RNA_wrap.cpp \ ./../RNA.i Deprecated command line option: -py3. Ignored, this option is no longer supported. /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 -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/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 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 .cpython-310-arm-linux-gnueabihf.so -Wl,-Bsymbolic-functions -Wl,-z,relro -o _RNA.la -rpath /usr/lib/python3.10/site-packages/RNA _RNA_la-RNA_wrap.lo ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lgsl -lgslcblas -lm libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/12/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/arm-linux-gnueabihf/12 -L/usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/12/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/12/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/crtn.o -flto -fopenmp -pthread -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -fopenmp -pthread -Wl,-soname -Wl,_RNA.cpython-310-arm-linux-gnueabihf.so -o .libs/_RNA.cpython-310-arm-linux-gnueabihf.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 $objdir/_RNA.cpython-310-arm-linux-gnueabihf.so RNA ) && \ rm -f libtoolconfig.tmp ( PYTHONPATH="RNA:$PYTHONPATH" /usr/bin/python3 -c "import _RNA" ; \ PYTHONPATH=".:$PYTHONPATH" /usr/bin/python3 -c "import RNA" ) ( PYTHONPATH="RNA:$PYTHONPATH" /usr/bin/python3 -O -c "import _RNA" ; \ PYTHONPATH=".:$PYTHONPATH" /usr/bin/python3 -O -c "import RNA" ) make[5]: Leaving directory '/<>/interfaces/Python3' make[5]: Entering directory '/<>/interfaces' make[5]: Nothing to be done for 'all-am'. make[5]: Leaving directory '/<>/interfaces' make[4]: Leaving directory '/<>/interfaces' Making all in src/Kinfold make[4]: Entering directory '/<>/src/Kinfold' make all-recursive make[5]: Entering directory '/<>/src/Kinfold' Making all in Example make[6]: Entering directory '/<>/src/Kinfold/Example' make[6]: Nothing to be done for 'all'. make[6]: Leaving directory '/<>/src/Kinfold/Example' make[6]: Entering directory '/<>/src/Kinfold' gcc -DHAVE_CONFIG_H -I. -I./src -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 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 -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 '/<>/src/Kinfold' make[5]: Leaving directory '/<>/src/Kinfold' make[4]: Leaving directory '/<>/src/Kinfold' Making all in src/RNAlocmin make[4]: Entering directory '/<>/src/RNAlocmin' make all-am make[5]: Entering directory '/<>/src/RNAlocmin' gengetopt -i RNAlocmin.ggo g++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -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 -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 '/<>/src/RNAlocmin' make[4]: Leaving directory '/<>/src/RNAlocmin' Making all in tests make[4]: Entering directory '/<>/tests' make all-am make[5]: Entering directory '/<>/tests' make[5]: Nothing to be done for 'all-am'. make[5]: Leaving directory '/<>/tests' make[4]: Leaving directory '/<>/tests' Making all in examples make[4]: Entering directory '/<>/examples' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/examples' Making all in packaging/macosx make[4]: Entering directory '/<>/packaging/macosx' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/packaging/macosx' make[4]: Entering directory '/<>' make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' if [ -r doc/RNAlib-*pdf; then cd doc && ln -f RNAlib-*.pdf RNAlib.pdf; fi /bin/bash: line 1: [: missing `]' make[1]: Leaving directory '/<>' dh_auto_test -a make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 make[1]: Entering directory '/<>' Making check in src make[2]: Entering directory '/<>/src' Making check in ViennaRNA make[3]: Entering directory '/<>/src/ViennaRNA' Making check in static make[4]: Entering directory '/<>/src/ViennaRNA/static' make check-am make[5]: Entering directory '/<>/src/ViennaRNA/static' make[5]: Nothing to be done for 'check-am'. make[5]: Leaving directory '/<>/src/ViennaRNA/static' make[4]: Leaving directory '/<>/src/ViennaRNA/static' make[4]: Entering directory '/<>/src/ViennaRNA' make[4]: Nothing to be done for 'check-am'. make[4]: Leaving directory '/<>/src/ViennaRNA' make[3]: Leaving directory '/<>/src/ViennaRNA' Making check in bin make[3]: Entering directory '/<>/src/bin' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/src/bin' Making check in Utils make[3]: Entering directory '/<>/src/Utils' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/src/Utils' Making check in Cluster make[3]: Entering directory '/<>/src/Cluster' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/src/Cluster' make[3]: Entering directory '/<>/src' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>/src' Making check in man make[2]: Entering directory '/<>/man' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/man' Making check in misc make[2]: Entering directory '/<>/misc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/misc' Making check in doc make[2]: Entering directory '/<>/doc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/doc' Making check in RNA-Tutorial make[2]: Entering directory '/<>/RNA-Tutorial' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/RNA-Tutorial' Making check in interfaces make[2]: Entering directory '/<>/interfaces' Making check in Perl make[3]: Entering directory '/<>/interfaces/Perl' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/interfaces/Perl' Making check in Python3 make[3]: Entering directory '/<>/interfaces/Python3' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/interfaces/Python3' make[3]: Entering directory '/<>/interfaces' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/<>/interfaces' make[2]: Leaving directory '/<>/interfaces' Making check in src/Kinfold make[2]: Entering directory '/<>/src/Kinfold' Making check in Example make[3]: Entering directory '/<>/src/Kinfold/Example' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/src/Kinfold/Example' make[3]: Entering directory '/<>/src/Kinfold' make[3]: Leaving directory '/<>/src/Kinfold' make[2]: Leaving directory '/<>/src/Kinfold' Making check in src/RNAlocmin make[2]: Entering directory '/<>/src/RNAlocmin' make[2]: Leaving directory '/<>/src/RNAlocmin' Making check in tests make[2]: Entering directory '/<>/tests' make check-am make[3]: Entering directory '/<>/tests' make make[4]: Entering directory '/<>/tests' make all-am make[5]: Entering directory '/<>/tests' make[5]: Nothing to be done for 'all-am'. make[5]: Leaving directory '/<>/tests' make[4]: Leaving directory '/<>/tests' make check-TESTS make[4]: Entering directory '/<>/tests' make[5]: Entering directory '/<>/tests' PASS: RNAfold/partfunc.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 ../config/test-driver: line 112: 28594 Segmentation fault (core dumped) "$@" >> "$log_file" 2>&1 FAIL: perl5/test-RNA-mfe_eval.pl ../config/test-driver: line 112: 28604 Segmentation fault (core dumped) "$@" >> "$log_file" 2>&1 FAIL: perl5/test-RNA-mfe_window.pl ../config/test-driver: line 112: 28614 Segmentation fault (core dumped) "$@" >> "$log_file" 2>&1 FAIL: perl5/test-RNA-pf_window.pl PASS: perl5/test-RNA-boltzmann-sampling.pl PASS: perl5/test-RNA-constraints.pl PASS: perl5/test-RNA-constraints-soft.pl ../config/test-driver: line 112: 28651 Segmentation fault (core dumped) "$@" >> "$log_file" 2>&1 FAIL: perl5/test-RNA-constraints-SHAPE.pl ../config/test-driver: line 112: 28661 Segmentation fault (core dumped) "$@" >> "$log_file" 2>&1 FAIL: 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 ============================================ ViennaRNA 2.4.17: tests/test-suite.log ============================================ # TOTAL: 36 # PASS: 31 # SKIP: 0 # XFAIL: 0 # FAIL: 5 # XPASS: 0 # ERROR: 0 .. contents:: :depth: 2 FAIL: perl5/test-RNA-mfe_eval ============================= 1..11 test_mfe (((.(((...)))))) [ -5.60] ok 1 test_mfe_Dimer (((.(((..)))))) [ -8.00] ok 2 FAIL perl5/test-RNA-mfe_eval.pl (exit status: 139) FAIL: perl5/test-RNA-mfe_window =============================== 1..21 test_mfe_window ok 1 test_Lfold_cb ok 2 ok 3 ok 4 ok 5 ok 6 test_mfe_window_cb ok 7 ok 8 ok 9 ok 10 ok 11 FAIL perl5/test-RNA-mfe_window.pl (exit status: 139) FAIL: perl5/test-RNA-pf_window ============================== 1..37 Useless use of a constant ("\n") in void context at ./perl5/test-RNA-pf_window.pl line 488. Checking whether pfl_fold() returns reasonable results... ok 1 ok 2 ok 3 ok 4 Checking whether pfl_fold_up() returns reasonable results... ok 5 ok 6 ok 7 ok 8 ok 9 Checking whether we can do the same with a single call to probs_window()... FAIL perl5/test-RNA-pf_window.pl (exit status: 139) FAIL: perl5/test-RNA-constraints-SHAPE ====================================== 1..4 test_sc_add_deigan -999 0.117 0.117 0.117 0.273 0.117 0 0.156 0.039 0.117 0.039 0 0.039 0.156 0 0.273 0.078 0.351 0.623 0.429 0.234 0.273 0.156 0.156 0.117 0 0.039 0.078 0.078 0 0.039 0.039 0.234 0.234 0.156 0.117 0.039 0.117 0.702 5.419 4.717 1.169 0 0.156 0.078 0 0.195 0 0.078 0.078 0.351 1.209 6.979 5.068 1.832 0.663 0.195 0.273 0.156 0.429 0 0.195 0.585 0.78 0.195 0.389 0.234 0.234 0.389 0.234 0.273 0.234 0.389 0.078 0.234 0.585 -999 0.546 0.857 0.74 1.286 0.585 0.117 0 0.078 0.195 0.156 0.117 0.156 0.234 0.312 0.039 1.131 0.974 0.897 -999 -999 -999 -999 -999 -999 -999 0.312 0.429 -999 1.326 0.234 -999 0.819 0.74 3.82 0.351 0.623 0.117 0.195 0.234 0.117 0.078 0.117 0.195 0.117 0.039 0.195 0 0.195 0.234 0.546 0.234 9.045 1.248 0.897 1.014 1.169 0.936 0.506 0.156 1.131 0.351 0.468 0.663 1.091 1.482 0.74 0.936 0.234 0.234 0 0.234 0.506 1.131 3.977 4.756 4.483 2.183 0.117 0.039 0 0.078 0.195 0.506 0.078 0.702 1.248 0.897 0.585 0.468 0.078 1.131 0.663 0.078 -999 -999 -999 0.819 1.794 (((((((((.(((((.((((.........(((((((((................)))))))))......)).)))))))..((((((((((((.......))))))))).))).((((((((((.....)))))))).))..(((((((....))))))).....))))))))) [-121.55] ok 1 test_sc_add_SHAPE_deigan2Use of uninitialized value in method with known name at ./perl5/test-RNA-constraints-SHAPE.pl line 91. Use of uninitialized value in method with known name at ./perl5/test-RNA-constraints-SHAPE.pl line 91. Use of uninitialized value in method with known name at ./perl5/test-RNA-constraints-SHAPE.pl line 91. Can't locate object method "new" via package "" (perhaps you forgot to load ""?) at ./perl5/test-RNA-constraints-SHAPE.pl line 91. FAIL perl5/test-RNA-constraints-SHAPE.pl (exit status: 139) FAIL: perl5/test-RNA-constraints-special ======================================== 1..1 "my" variable $fc masks earlier declaration in same scope at ./perl5/test-RNA-constraints-special.pl line 28. test_sc_add_hi_motif((((...((((((((......)))))...)))...))))...((.((((((((((.((((((.((.((((....)))).))..)))))).)))))))))))).. [-33.82] ok 1 .(((((..((((((((((((((((((....(((((((............)))))))........)))))))))))))...)))))))))).............. [ -26.50 ] ((((...((((((((......)))))...)))...))))...((.((((((((((.((((((.((.((((....)))).))..)))))).)))))))))))).. [ -33.82 ] ((((...((((.....(.(.....).).))))...))))...((.((((((((((.((((((.((.((((....)))).))..)))))).)))))))))))).. [ -35.60 ] FAIL perl5/test-RNA-constraints-special.pl (exit status: 139) ============================================================================ Testsuite summary for ViennaRNA 2.4.17 ============================================================================ # TOTAL: 36 # PASS: 31 # SKIP: 0 # XFAIL: 0 # FAIL: 5 # XPASS: 0 # ERROR: 0 ============================================================================ See tests/test-suite.log Please report to rna@tbi.univie.ac.at ============================================================================ make[5]: *** [Makefile:1129: test-suite.log] Error 1 make[5]: Leaving directory '/<>/tests' make[4]: *** [Makefile:1237: check-TESTS] Error 2 make[4]: Leaving directory '/<>/tests' make[3]: *** [Makefile:1471: check-am] Error 2 make[3]: Leaving directory '/<>/tests' make[2]: *** [Makefile:1473: check] Error 2 make[2]: Leaving directory '/<>/tests' make[1]: *** [Makefile:678: check-recursive] Error 1 make[1]: Leaving directory '/<>' dh_auto_test: error: make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 returned exit code 2 make: *** [debian/rules:5: binary-arch] Error 25 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2023-01-05T02:27:45Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build Type: any Build-Space: 338096 Build-Time: 809 Distribution: lunar Fail-Stage: build Host Architecture: armhf Install-Time: 130 Job: vienna-rna_2.4.17+dfsg-2build2.dsc Machine Architecture: arm64 Package: vienna-rna Package-Time: 941 Source-Version: 2.4.17+dfsg-2build2 Space: 338096 Status: attempted Version: 2.4.17+dfsg-2build2 -------------------------------------------------------------------------------- Finished at 2023-01-05T02:27:45Z Build needed 00:15:41, 338096k disk space E: Build failure (dpkg-buildpackage died) Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=lunar --arch=armhf PACKAGEBUILD-25157301 Scanning for processes to kill in build PACKAGEBUILD-25157301