DC-Build-Header: clustalo 1.2.0-1 / 2013-07-17 03:43:19 +0000 DC-Task: source:clustalo version:1.2.0-1 architecture:any chroot:unstable esttime:119 logfile:/tmp/clustalo_1.2.0-1_unstable_clang.log modes:binary-only:clang DC-Sbuild-call: su user -c 'sbuild -n --apt-update -d unstable -v --chroot-setup-commands=/tmp/switch-to-clang --append-to-version "clang1" --maintainer "Lucas Nussbaum " --uploader "Lucas Nussbaum " clustalo_1.2.0-1' sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on ip-10-235-1-254.ec2.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ clustalo 1.2.0-1clang1 (amd64) 17 Jul 2013 03:43 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: clustalo Version: 1.2.0-1clang1 Source Version: 1.2.0-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/clustalo-HbeR8w/clustalo-1.2.0' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/clustalo-HbeR8w' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-7a4642bc-c4fb-451f-90f7-e84b3c2f4f89' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Get:1 http://localhost:9999 unstable InRelease [204 kB] Get:2 http://localhost:9999 unstable/main Sources/DiffIndex [7876 B] Get:3 http://localhost:9999 unstable/main amd64 Packages/DiffIndex [7876 B] Get:4 http://localhost:9999 unstable/main Translation-en/DiffIndex [7876 B] Get:5 http://localhost:9999 unstable/main 2013-07-13-2032.15.pdiff [23.1 kB] Get:6 http://localhost:9999 unstable/main amd64 2013-07-13-2032.15.pdiff [16.9 kB] Get:7 http://localhost:9999 unstable/main 2013-07-13-2032.15.pdiff [23.1 kB] Get:8 http://localhost:9999 unstable/main 2013-07-13-2032.15.pdiff [1809 B] Get:9 http://localhost:9999 unstable/main amd64 2013-07-13-2032.15.pdiff [16.9 kB] Get:10 http://localhost:9999 unstable/main 2013-07-14-0231.07.pdiff [12.9 kB] Get:11 http://localhost:9999 unstable/main 2013-07-13-2032.15.pdiff [1809 B] Get:12 http://localhost:9999 unstable/main amd64 2013-07-14-0231.07.pdiff [14.9 kB] Get:13 http://localhost:9999 unstable/main 2013-07-14-0231.07.pdiff [12.9 kB] Get:14 http://localhost:9999 unstable/main 2013-07-14-0231.07.pdiff [1384 B] Get:15 http://localhost:9999 unstable/main amd64 2013-07-14-0231.07.pdiff [14.9 kB] Get:16 http://localhost:9999 unstable/main 2013-07-14-0832.16.pdiff [4670 B] Get:17 http://localhost:9999 unstable/main 2013-07-14-0231.07.pdiff [1384 B] Get:18 http://localhost:9999 unstable/main amd64 2013-07-14-0832.16.pdiff [1624 B] Get:19 http://localhost:9999 unstable/main 2013-07-14-0832.16.pdiff [4670 B] Get:20 http://localhost:9999 unstable/main 2013-07-14-0832.16.pdiff [337 B] Get:21 http://localhost:9999 unstable/main amd64 2013-07-14-0832.16.pdiff [1624 B] Get:22 http://localhost:9999 unstable/main 2013-07-14-1431.18.pdiff [11.4 kB] Get:23 http://localhost:9999 unstable/main 2013-07-14-0832.16.pdiff [337 B] Get:24 http://localhost:9999 unstable/main amd64 2013-07-14-1431.18.pdiff [8223 B] Get:25 http://localhost:9999 unstable/main 2013-07-14-1431.18.pdiff [11.4 kB] Get:26 http://localhost:9999 unstable/main 2013-07-14-1431.18.pdiff [887 B] Get:27 http://localhost:9999 unstable/main amd64 2013-07-14-1431.18.pdiff [8223 B] Get:28 http://localhost:9999 unstable/main 2013-07-14-2031.21.pdiff [9038 B] Get:29 http://localhost:9999 unstable/main 2013-07-14-1431.18.pdiff [887 B] Get:30 http://localhost:9999 unstable/main amd64 2013-07-14-2031.21.pdiff [9955 B] Get:31 http://localhost:9999 unstable/main 2013-07-14-2031.21.pdiff [9038 B] Get:32 http://localhost:9999 unstable/main 2013-07-14-2031.21.pdiff [2736 B] Get:33 http://localhost:9999 unstable/main amd64 2013-07-14-2031.21.pdiff [9955 B] Get:34 http://localhost:9999 unstable/main 2013-07-15-0229.01.pdiff [9715 B] Get:35 http://localhost:9999 unstable/main 2013-07-14-2031.21.pdiff [2736 B] Get:36 http://localhost:9999 unstable/main amd64 2013-07-15-0229.01.pdiff [12.7 kB] Get:37 http://localhost:9999 unstable/main 2013-07-15-0229.01.pdiff [9715 B] Get:38 http://localhost:9999 unstable/main 2013-07-15-0229.01.pdiff [2239 B] Get:39 http://localhost:9999 unstable/main amd64 2013-07-15-0229.01.pdiff [12.7 kB] Get:40 http://localhost:9999 unstable/main 2013-07-15-0830.19.pdiff [3273 B] Get:41 http://localhost:9999 unstable/main 2013-07-15-0229.01.pdiff [2239 B] Get:42 http://localhost:9999 unstable/main amd64 2013-07-15-0830.19.pdiff [3964 B] Get:43 http://localhost:9999 unstable/main 2013-07-15-0830.19.pdiff [3273 B] Get:44 http://localhost:9999 unstable/main 2013-07-15-0830.19.pdiff [1357 B] Get:45 http://localhost:9999 unstable/main amd64 2013-07-15-0830.19.pdiff [3964 B] Get:46 http://localhost:9999 unstable/main 2013-07-15-1432.36.pdiff [5326 B] Get:47 http://localhost:9999 unstable/main 2013-07-15-0830.19.pdiff [1357 B] Get:48 http://localhost:9999 unstable/main amd64 2013-07-15-1432.36.pdiff [9809 B] Get:49 http://localhost:9999 unstable/main 2013-07-15-1432.36.pdiff [5326 B] Get:50 http://localhost:9999 unstable/main 2013-07-15-1432.36.pdiff [322 B] Get:51 http://localhost:9999 unstable/main amd64 2013-07-15-1432.36.pdiff [9809 B] Get:52 http://localhost:9999 unstable/main 2013-07-15-2031.50.pdiff [12.2 kB] Get:53 http://localhost:9999 unstable/main 2013-07-15-1432.36.pdiff [322 B] Get:54 http://localhost:9999 unstable/main amd64 2013-07-15-2031.50.pdiff [24.4 kB] Get:55 http://localhost:9999 unstable/main 2013-07-15-2031.50.pdiff [12.2 kB] Get:56 http://localhost:9999 unstable/main 2013-07-15-2031.50.pdiff [537 B] Get:57 http://localhost:9999 unstable/main amd64 2013-07-15-2031.50.pdiff [24.4 kB] Get:58 http://localhost:9999 unstable/main 2013-07-16-0233.12.pdiff [14.8 kB] Get:59 http://localhost:9999 unstable/main 2013-07-15-2031.50.pdiff [537 B] Get:60 http://localhost:9999 unstable/main amd64 2013-07-16-0233.12.pdiff [49.5 kB] Get:61 http://localhost:9999 unstable/main 2013-07-16-0233.12.pdiff [14.8 kB] Get:62 http://localhost:9999 unstable/main 2013-07-16-0233.12.pdiff [3247 B] Get:63 http://localhost:9999 unstable/main amd64 2013-07-16-0233.12.pdiff [49.5 kB] Get:64 http://localhost:9999 unstable/main 2013-07-16-0834.41.pdiff [7447 B] Get:65 http://localhost:9999 unstable/main 2013-07-16-0233.12.pdiff [3247 B] Get:66 http://localhost:9999 unstable/main amd64 2013-07-16-0834.41.pdiff [4493 B] Get:67 http://localhost:9999 unstable/main 2013-07-16-0834.41.pdiff [7447 B] Get:68 http://localhost:9999 unstable/main 2013-07-16-0834.41.pdiff [5852 B] Get:69 http://localhost:9999 unstable/main amd64 2013-07-16-0834.41.pdiff [4493 B] Get:70 http://localhost:9999 unstable/main 2013-07-16-1433.54.pdiff [21.2 kB] Get:71 http://localhost:9999 unstable/main 2013-07-16-0834.41.pdiff [5852 B] Get:72 http://localhost:9999 unstable/main amd64 2013-07-16-1433.54.pdiff [19.3 kB] Get:73 http://localhost:9999 unstable/main 2013-07-16-1433.54.pdiff [21.2 kB] Get:74 http://localhost:9999 unstable/main 2013-07-16-1433.54.pdiff [1941 B] Get:75 http://localhost:9999 unstable/main amd64 2013-07-16-1433.54.pdiff [19.3 kB] Get:76 http://localhost:9999 unstable/main 2013-07-16-2046.09.pdiff [19.4 kB] Get:77 http://localhost:9999 unstable/main 2013-07-16-1433.54.pdiff [1941 B] Get:78 http://localhost:9999 unstable/main amd64 2013-07-16-2046.09.pdiff [18.4 kB] Get:79 http://localhost:9999 unstable/main 2013-07-16-2046.09.pdiff [19.4 kB] Get:80 http://localhost:9999 unstable/main 2013-07-16-2046.09.pdiff [465 B] Get:81 http://localhost:9999 unstable/main amd64 2013-07-16-2046.09.pdiff [18.4 kB] Get:82 http://localhost:9999 unstable/main 2013-07-16-2046.09.pdiff [465 B] Fetched 600 kB in 48s (12.4 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: cpp-4.7 gcc-4.7 gcc-4.7-base initscripts libgcc-4.7-dev sysv-rc sysvinit sysvinit-utils 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 14.2 MB of archives. After this operation, 18.4 kB disk space will be freed. Get:1 http://localhost:9999/debian/ unstable/main sysvinit amd64 2.88dsf-42 [134 kB] Get:2 http://localhost:9999/debian/ unstable/main sysv-rc all 2.88dsf-42 [80.4 kB] Get:3 http://localhost:9999/debian/ unstable/main sysvinit-utils amd64 2.88dsf-42 [103 kB] Get:4 http://localhost:9999/debian/ unstable/main initscripts amd64 2.88dsf-42 [87.1 kB] Get:5 http://localhost:9999/debian/ unstable/main gcc-4.7 amd64 4.7.3-6 [5819 kB] Get:6 http://localhost:9999/debian/ unstable/main cpp-4.7 amd64 4.7.3-6 [5385 kB] Get:7 http://localhost:9999/debian/ unstable/main libgcc-4.7-dev amd64 4.7.3-6 [2465 kB] Get:8 http://localhost:9999/debian/ unstable/main gcc-4.7-base amd64 4.7.3-6 [149 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 14.2 MB in 0s (25.2 MB/s) (Reading database ... 13844 files and directories currently installed.) Preparing to replace sysvinit 2.88dsf-41 (using .../sysvinit_2.88dsf-42_amd64.deb) ... Unpacking replacement sysvinit ... Setting up sysvinit (2.88dsf-42) ... Not restarting sysvinit (Reading database ... 13844 files and directories currently installed.) Preparing to replace sysv-rc 2.88dsf-41 (using .../sysv-rc_2.88dsf-42_all.deb) ... Unpacking replacement sysv-rc ... Preparing to replace sysvinit-utils 2.88dsf-41 (using .../sysvinit-utils_2.88dsf-42_amd64.deb) ... Unpacking replacement sysvinit-utils ... Setting up sysvinit-utils (2.88dsf-42) ... Setting up sysv-rc (2.88dsf-42) ... (Reading database ... 13844 files and directories currently installed.) Preparing to replace initscripts 2.88dsf-41 (using .../initscripts_2.88dsf-42_amd64.deb) ... Removing unmodified and obsolete conffile /etc/init.d/mtab.sh ... Unpacking replacement initscripts ... Setting up initscripts (2.88dsf-42) ... Installing new version of config file /etc/init.d/bootmisc.sh ... Installing new version of config file /etc/init.d/checkfs.sh ... Installing new version of config file /etc/init.d/checkroot.sh ... Installing new version of config file /etc/init.d/checkroot-bootclean.sh ... Installing new version of config file /etc/init.d/mountdevsubfs.sh ... Installing new version of config file /etc/init.d/mountkernfs.sh ... Installing new version of config file /etc/init.d/rmnologin ... Installing new version of config file /etc/network/if-up.d/mountnfs ... (Reading database ... 13843 files and directories currently installed.) Preparing to replace gcc-4.7 4.7.3-5 (using .../gcc-4.7_4.7.3-6_amd64.deb) ... Unpacking replacement gcc-4.7 ... Preparing to replace cpp-4.7 4.7.3-5 (using .../cpp-4.7_4.7.3-6_amd64.deb) ... Unpacking replacement cpp-4.7 ... Preparing to replace libgcc-4.7-dev:amd64 4.7.3-5 (using .../libgcc-4.7-dev_4.7.3-6_amd64.deb) ... Unpacking replacement libgcc-4.7-dev:amd64 ... Preparing to replace gcc-4.7-base:amd64 4.7.3-5 (using .../gcc-4.7-base_4.7.3-6_amd64.deb) ... Unpacking replacement gcc-4.7-base:amd64 ... Setting up gcc-4.7-base:amd64 (4.7.3-6) ... Setting up cpp-4.7 (4.7.3-6) ... Setting up libgcc-4.7-dev:amd64 (4.7.3-6) ... Setting up gcc-4.7 (4.7.3-6) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'clustalo' packaging is maintained in the 'Svn' version control system at: svn://anonscm.debian.org/debian-med/trunk/packages/clustalo/trunk/ Need to get 1163 kB of source archives. Get:1 http://localhost:9999/debian/ unstable/main clustalo 1.2.0-1 (dsc) [2100 B] Get:2 http://localhost:9999/debian/ unstable/main clustalo 1.2.0-1 (tar) [1157 kB] Get:3 http://localhost:9999/debian/ unstable/main clustalo 1.2.0-1 (diff) [3730 B] Fetched 1163 kB in 0s (4236 kB/s) Download complete and in download only mode Check arch ────────── ┌──────────────────────────────────────────────────────────────────────────────┐ │ Chroot Setup Commands │ └──────────────────────────────────────────────────────────────────────────────┘ /tmp/switch-to-clang ──────────────────── + echo 'Entering customization script...' Entering customization script... + echo 'Install of clang' Install of clang + apt-get update Hit http://localhost:9999 unstable InRelease Hit http://localhost:9999 unstable/main Sources/DiffIndex Hit http://localhost:9999 unstable/main amd64 Packages/DiffIndex Hit http://localhost:9999 unstable/main Translation-en/DiffIndex Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-3.3 Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libclang-common-3.3-dev libclang1-3.3 libffi6 libllvm3.3 libobjc-4.7-dev libobjc4 libstdc++6-4.7-dev Suggested packages: libstdc++6-4.7-doc Recommended packages: llvm-3.3-dev python The following NEW packages will be installed: clang-3.3 libclang-common-3.3-dev libclang1-3.3 libffi6 libllvm3.3 libobjc-4.7-dev libobjc4 libstdc++6-4.7-dev 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. Need to get 27.2 MB of archives. After this operation, 80.8 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libffi6 amd64 3.0.13-4 [21.6 kB] Get:2 http://localhost:9999/debian/ unstable/main libllvm3.3 amd64 1:3.3-3 [8575 kB] Get:3 http://localhost:9999/debian/ unstable/main libobjc4 amd64 4.8.1-6 [160 kB] Get:4 http://localhost:9999/debian/ unstable/main libstdc++6-4.7-dev amd64 4.7.3-6 [1694 kB] Get:5 http://localhost:9999/debian/ unstable/main libobjc-4.7-dev amd64 4.7.3-6 [719 kB] Get:6 http://localhost:9999/debian/ unstable/main libclang-common-3.3-dev amd64 1:3.3-3 [574 kB] Get:7 http://localhost:9999/debian/ unstable/main libclang1-3.3 amd64 1:3.3-3 [4579 kB] Get:8 http://localhost:9999/debian/ unstable/main clang-3.3 amd64 1:3.3-3 [10.9 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 27.2 MB in 1s (25.6 MB/s) Selecting previously unselected package libffi6:amd64. (Reading database ... 13843 files and directories currently installed.) Unpacking libffi6:amd64 (from .../libffi6_3.0.13-4_amd64.deb) ... Selecting previously unselected package libllvm3.3:amd64. Unpacking libllvm3.3:amd64 (from .../libllvm3.3_1%3a3.3-3_amd64.deb) ... Selecting previously unselected package libobjc4:amd64. Unpacking libobjc4:amd64 (from .../libobjc4_4.8.1-6_amd64.deb) ... Selecting previously unselected package libstdc++6-4.7-dev:amd64. Unpacking libstdc++6-4.7-dev:amd64 (from .../libstdc++6-4.7-dev_4.7.3-6_amd64.deb) ... Selecting previously unselected package libobjc-4.7-dev:amd64. Unpacking libobjc-4.7-dev:amd64 (from .../libobjc-4.7-dev_4.7.3-6_amd64.deb) ... Selecting previously unselected package libclang-common-3.3-dev. Unpacking libclang-common-3.3-dev (from .../libclang-common-3.3-dev_1%3a3.3-3_amd64.deb) ... Selecting previously unselected package libclang1-3.3. Unpacking libclang1-3.3 (from .../libclang1-3.3_1%3a3.3-3_amd64.deb) ... Selecting previously unselected package clang-3.3. Unpacking clang-3.3 (from .../clang-3.3_1%3a3.3-3_amd64.deb) ... Setting up libffi6:amd64 (3.0.13-4) ... Setting up libllvm3.3:amd64 (1:3.3-3) ... Setting up libobjc4:amd64 (4.8.1-6) ... Setting up libstdc++6-4.7-dev:amd64 (4.7.3-6) ... Setting up libobjc-4.7-dev:amd64 (4.7.3-6) ... Setting up libclang-common-3.3-dev (1:3.3-3) ... Setting up libclang1-3.3 (1:3.3-3) ... Setting up clang-3.3 (1:3.3-3) ... Processing triggers for libc-bin ... + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8' + cd /usr/bin + for VERSION in '$VERSIONS' + rm -f g++-4.6 gcc-4.6 cpp-4.6 + ln -s clang++ g++-4.6 + ln -s clang gcc-4.6 + ln -s clang cpp-4.6 + for VERSION in '$VERSIONS' + rm -f g++-4.7 gcc-4.7 cpp-4.7 + ln -s clang++ g++-4.7 + ln -s clang gcc-4.7 + ln -s clang cpp-4.7 + for VERSION in '$VERSIONS' + rm -f g++-4.8 gcc-4.8 cpp-4.8 + ln -s clang++ g++-4.8 + ln -s clang gcc-4.8 + ln -s clang cpp-4.8 + cd - /«BUILDDIR» + echo 'Block the installation of new gcc version' Block the installation of new gcc version + dpkg --set-selections + echo 'gcc-4.6 hold' + dpkg --set-selections + echo 'cpp-4.6 hold' + dpkg --set-selections + echo 'g++-4.6 hold' + dpkg --set-selections + echo 'gcc-4.7 hold' + dpkg --set-selections + echo 'cpp-4.7 hold' + dpkg --set-selections + echo 'g++-4.7 hold' + dpkg --set-selections + echo 'gcc-4.8 hold' + dpkg --set-selections + echo 'cpp-4.8 hold' + dpkg --set-selections + echo 'g++-4.8 hold' + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + grep clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version I: Finished running '/tmp/switch-to-clang'. Finished processing commands. ──────────────────────────────────────────────────────────────────────────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-9NfTFx/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/710 B of archives. After this operation, 0 B of additional disk space will be used. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14698 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), libargtable2-dev, doxygen, graphviz Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), libargtable2-dev, doxygen, graphviz dpkg-deb: building package `sbuild-build-depends-clustalo-dummy' in `/«BUILDDIR»/resolver-Rm3Xtn/apt_archive/sbuild-build-depends-clustalo-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install clustalo build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils debhelper doxygen file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base graphviz groff-base intltool-debian libargtable2-0 libargtable2-dev libargtable2-docs libasprintf0c2 libcairo2 libcdt4 libcgraph5 libcroco3 libdatrie1 libdrm2 libegl1-mesa libexpat1 libfontconfig1 libfreetype6 libgbm1 libgd3 libgl1-mesa-glx libglapi-mesa libglib2.0-0 libgraph4 libgraphite2-3 libgvc5 libgvpr1 libharfbuzz0a libice6 libjbig0 libjpeg8 libllvm3.2 libltdl7 libmagic1 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 libpipeline1 libpixman-1-0 libpng12-0 libsm6 libthai-data libthai0 libtiff4 libudev0 libunistring0 libvpx1 libwayland-client0 libwayland-server0 libx11-6 libx11-data libx11-xcb1 libxau6 libxaw7 libxcb-dri2-0 libxcb-glx0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-xfixes0 libxcb1 libxdamage1 libxdmcp6 libxdot4 libxext6 libxfixes3 libxml2 libxmu6 libxpm4 libxrender1 libxt6 libxxf86vm1 man-db po-debconf ttf-dejavu-core x11-common Suggested packages: wamerican wordlist whois vacation dh-make doxygen-doc doxygen-gui gettext-doc gsfonts graphviz-doc groff libgd-tools ttf-baekmuk ttf-arphic-gbsn00lp ttf-arphic-bsmi00lp ttf-arphic-gkai00mp ttf-arphic-bkai00mp less www-browser libmail-box-perl Recommended packages: doxygen-latex curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev ttf-liberation libegl1-mesa-drivers libgl1-mesa-dri libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper doxygen file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base graphviz groff-base intltool-debian libargtable2-0 libargtable2-dev libargtable2-docs libasprintf0c2 libcairo2 libcdt4 libcgraph5 libcroco3 libdatrie1 libdrm2 libegl1-mesa libexpat1 libfontconfig1 libfreetype6 libgbm1 libgd3 libgl1-mesa-glx libglapi-mesa libglib2.0-0 libgraph4 libgraphite2-3 libgvc5 libgvpr1 libharfbuzz0a libice6 libjbig0 libjpeg8 libllvm3.2 libltdl7 libmagic1 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 libpipeline1 libpixman-1-0 libpng12-0 libsm6 libthai-data libthai0 libtiff4 libudev0 libunistring0 libvpx1 libwayland-client0 libwayland-server0 libx11-6 libx11-data libx11-xcb1 libxau6 libxaw7 libxcb-dri2-0 libxcb-glx0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-xfixes0 libxcb1 libxdamage1 libxdmcp6 libxdot4 libxext6 libxfixes3 libxml2 libxmu6 libxpm4 libxrender1 libxt6 libxxf86vm1 man-db po-debconf sbuild-build-depends-clustalo-dummy ttf-dejavu-core x11-common 0 upgraded, 86 newly installed, 0 to remove and 0 not upgraded. Need to get 34.8 MB/34.8 MB of archives. After this operation, 85.8 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libpipeline1 amd64 1.2.4-1 [41.0 kB] Get:2 http://localhost:9999/debian/ unstable/main libudev0 amd64 175-7.2 [126 kB] Get:3 http://localhost:9999/debian/ unstable/main groff-base amd64 1.22.2-3 [747 kB] Get:4 http://localhost:9999/debian/ unstable/main bsdmainutils amd64 9.0.5 [211 kB] Get:5 http://localhost:9999/debian/ unstable/main man-db amd64 2.6.5-2 [976 kB] Get:6 http://localhost:9999/debian/ unstable/main libasprintf0c2 amd64 0.18.3-1 [29.6 kB] Get:7 http://localhost:9999/debian/ unstable/main libmagic1 amd64 1:5.14-2 [216 kB] Get:8 http://localhost:9999/debian/ unstable/main libxml2 amd64 2.9.1+dfsg1-2 [911 kB] Get:9 http://localhost:9999/debian/ unstable/main libdrm2 amd64 2.4.45-3 [468 kB] Get:10 http://localhost:9999/debian/ unstable/main libglapi-mesa amd64 9.1.4-1 [49.2 kB] Get:11 http://localhost:9999/debian/ unstable/main libllvm3.2 amd64 1:3.2repack-10 [8040 kB] Get:12 http://localhost:9999/debian/ unstable/main libxau6 amd64 1:1.0.8-1 [20.7 kB] Get:13 http://localhost:9999/debian/ unstable/main libxdmcp6 amd64 1:1.1.1-1 [26.3 kB] Get:14 http://localhost:9999/debian/ unstable/main libxcb1 amd64 1.9.1-3 [50.3 kB] Get:15 http://localhost:9999/debian/ unstable/main libxcb-dri2-0 amd64 1.9.1-3 [12.9 kB] Get:16 http://localhost:9999/debian/ unstable/main libgbm1 amd64 9.1.4-1 [469 kB] Get:17 http://localhost:9999/debian/ unstable/main libwayland-client0 amd64 1.1.0-2 [23.0 kB] Get:18 http://localhost:9999/debian/ unstable/main libwayland-server0 amd64 1.1.0-2 [33.0 kB] Get:19 http://localhost:9999/debian/ unstable/main libx11-data all 2:1.6.0-1 [191 kB] Get:20 http://localhost:9999/debian/ unstable/main libx11-6 amd64 2:1.6.0-1 [919 kB] Get:21 http://localhost:9999/debian/ unstable/main libx11-xcb1 amd64 2:1.6.0-1 [153 kB] Get:22 http://localhost:9999/debian/ unstable/main libxcb-render0 amd64 1.9.1-3 [19.0 kB] Get:23 http://localhost:9999/debian/ unstable/main libxcb-shape0 amd64 1.9.1-3 [11.5 kB] Get:24 http://localhost:9999/debian/ unstable/main libxcb-xfixes0 amd64 1.9.1-3 [14.9 kB] Get:25 http://localhost:9999/debian/ unstable/main libegl1-mesa amd64 9.1.4-1 [83.7 kB] Get:26 http://localhost:9999/debian/ unstable/main libexpat1 amd64 2.1.0-4 [138 kB] Get:27 http://localhost:9999/debian/ unstable/main libfreetype6 amd64 2.4.9-1.1 [451 kB] Get:28 http://localhost:9999/debian/ unstable/main fonts-dejavu-core all 2.33+svn2514-3 [1042 kB] Get:29 http://localhost:9999/debian/ unstable/main ttf-dejavu-core all 2.33+svn2514-3 [29.8 kB] Get:30 http://localhost:9999/debian/ unstable/main fontconfig-config all 2.10.2-2 [251 kB] Get:31 http://localhost:9999/debian/ unstable/main libfontconfig1 amd64 2.10.2-2 [319 kB] Get:32 http://localhost:9999/debian/ unstable/main libxcb-glx0 amd64 1.9.1-3 [32.5 kB] Get:33 http://localhost:9999/debian/ unstable/main libxfixes3 amd64 1:5.0.1-1 [22.5 kB] Get:34 http://localhost:9999/debian/ unstable/main libxdamage1 amd64 1:1.1.4-1 [15.1 kB] Get:35 http://localhost:9999/debian/ unstable/main libxext6 amd64 2:1.3.2-1 [56.5 kB] Get:36 http://localhost:9999/debian/ unstable/main libxxf86vm1 amd64 1:1.1.2-1+deb7u1 [19.5 kB] Get:37 http://localhost:9999/debian/ unstable/main libgl1-mesa-glx amd64 9.1.4-1 [133 kB] Get:38 http://localhost:9999/debian/ unstable/main libpixman-1-0 amd64 0.26.0-4 [427 kB] Get:39 http://localhost:9999/debian/ unstable/main libpng12-0 amd64 1.2.49-4 [190 kB] Get:40 http://localhost:9999/debian/ unstable/main libxcb-shm0 amd64 1.9.1-3 [10.8 kB] Get:41 http://localhost:9999/debian/ unstable/main libxrender1 amd64 1:0.9.8-1 [33.5 kB] Get:42 http://localhost:9999/debian/ unstable/main libcairo2 amd64 1.12.14-5 [1044 kB] Get:43 http://localhost:9999/debian/ unstable/main libglib2.0-0 amd64 2.36.3-3 [2048 kB] Get:44 http://localhost:9999/debian/ unstable/main libcroco3 amd64 0.6.8-2 [133 kB] Get:45 http://localhost:9999/debian/ unstable/main libdatrie1 amd64 0.2.6-2 [30.2 kB] Get:46 http://localhost:9999/debian/ unstable/main libjpeg8 amd64 8d-1 [134 kB] Get:47 http://localhost:9999/debian/ unstable/main libjbig0 amd64 2.0-2 [32.2 kB] Get:48 http://localhost:9999/debian/ unstable/main libtiff4 amd64 3.9.7-1 [205 kB] Get:49 http://localhost:9999/debian/ unstable/main libvpx1 amd64 1.2.0-2 [298 kB] Get:50 http://localhost:9999/debian/ unstable/main libxpm4 amd64 1:3.5.10-1 [49.4 kB] Get:51 http://localhost:9999/debian/ unstable/main libgd3 amd64 2.1.0-2 [171 kB] Get:52 http://localhost:9999/debian/ unstable/main libgraphite2-3 amd64 1.2.3-1 [61.3 kB] Get:53 http://localhost:9999/debian/ unstable/main libharfbuzz0a amd64 0.9.18-3 [412 kB] Get:54 http://localhost:9999/debian/ unstable/main x11-common all 1:7.7+3 [284 kB] Get:55 http://localhost:9999/debian/ unstable/main libice6 amd64 2:1.0.8-2 [63.1 kB] Get:56 http://localhost:9999/debian/ unstable/main libltdl7 amd64 2.4.2-1.3 [352 kB] Get:57 http://localhost:9999/debian/ unstable/main libthai-data all 0.1.19-2 [156 kB] Get:58 http://localhost:9999/debian/ unstable/main libthai0 amd64 0.1.19-2 [43.1 kB] Get:59 http://localhost:9999/debian/ unstable/main fontconfig amd64 2.10.2-2 [375 kB] Get:60 http://localhost:9999/debian/ unstable/main libpango-1.0-0 amd64 1.32.5-5+b1 [263 kB] Get:61 http://localhost:9999/debian/ unstable/main libpangoft2-1.0-0 amd64 1.32.5-5+b1 [187 kB] Get:62 http://localhost:9999/debian/ unstable/main libpangocairo-1.0-0 amd64 1.32.5-5+b1 [174 kB] Get:63 http://localhost:9999/debian/ unstable/main libsm6 amd64 2:1.2.1-2 [34.2 kB] Get:64 http://localhost:9999/debian/ unstable/main libunistring0 amd64 0.9.3-5 [434 kB] Get:65 http://localhost:9999/debian/ unstable/main libxt6 amd64 1:1.1.3-1+deb7u1 [212 kB] Get:66 http://localhost:9999/debian/ unstable/main libxmu6 amd64 2:1.1.1-1 [66.6 kB] Get:67 http://localhost:9999/debian/ unstable/main libxaw7 amd64 2:1.0.11-1 [228 kB] Get:68 http://localhost:9999/debian/ unstable/main file amd64 1:5.14-2 [54.0 kB] Get:69 http://localhost:9999/debian/ unstable/main gettext-base amd64 0.18.3-1 [161 kB] Get:70 http://localhost:9999/debian/ unstable/main gettext amd64 0.18.3-1 [1898 kB] Get:71 http://localhost:9999/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:72 http://localhost:9999/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB] Get:73 http://localhost:9999/debian/ unstable/main debhelper all 9.20130630 [710 kB] Get:74 http://localhost:9999/debian/ unstable/main doxygen amd64 1.8.4-1 [2740 kB] Get:75 http://localhost:9999/debian/ unstable/main libcdt4 amd64 2.26.3-15 [59.4 kB] Get:76 http://localhost:9999/debian/ unstable/main libcgraph5 amd64 2.26.3-15 [86.5 kB] Get:77 http://localhost:9999/debian/ unstable/main libgraph4 amd64 2.26.3-15 [73.4 kB] Get:78 http://localhost:9999/debian/ unstable/main libpathplan4 amd64 2.26.3-15 [64.6 kB] Get:79 http://localhost:9999/debian/ unstable/main libxdot4 amd64 2.26.3-15 [54.0 kB] Get:80 http://localhost:9999/debian/ unstable/main libgvc5 amd64 2.26.3-15 [537 kB] Get:81 http://localhost:9999/debian/ unstable/main libgvpr1 amd64 2.26.3-15 [243 kB] Get:82 http://localhost:9999/debian/ unstable/main graphviz amd64 2.26.3-15 [370 kB] Get:83 http://localhost:9999/debian/ unstable/main libargtable2-0 amd64 12-1 [19.2 kB] Get:84 http://localhost:9999/debian/ unstable/main libargtable2-docs all 12-1 [2958 kB] Get:85 http://localhost:9999/debian/ unstable/main libargtable2-dev amd64 12-1 [60.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 34.8 MB in 2s (17.1 MB/s) Selecting previously unselected package libpipeline1:amd64. (Reading database ... 14698 files and directories currently installed.) Unpacking libpipeline1:amd64 (from .../libpipeline1_1.2.4-1_amd64.deb) ... Selecting previously unselected package libudev0:amd64. Unpacking libudev0:amd64 (from .../libudev0_175-7.2_amd64.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.22.2-3_amd64.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.5_amd64.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.5-2_amd64.deb) ... Selecting previously unselected package libasprintf0c2:amd64. Unpacking libasprintf0c2:amd64 (from .../libasprintf0c2_0.18.3-1_amd64.deb) ... Selecting previously unselected package libmagic1:amd64. Unpacking libmagic1:amd64 (from .../libmagic1_1%3a5.14-2_amd64.deb) ... Selecting previously unselected package libxml2:amd64. 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Selecting previously unselected package libxcb-shape0:amd64. Unpacking libxcb-shape0:amd64 (from .../libxcb-shape0_1.9.1-3_amd64.deb) ... Selecting previously unselected package libxcb-xfixes0:amd64. Unpacking libxcb-xfixes0:amd64 (from .../libxcb-xfixes0_1.9.1-3_amd64.deb) ... Selecting previously unselected package libegl1-mesa:amd64. Unpacking libegl1-mesa:amd64 (from .../libegl1-mesa_9.1.4-1_amd64.deb) ... Selecting previously unselected package libexpat1:amd64. Unpacking libexpat1:amd64 (from .../libexpat1_2.1.0-4_amd64.deb) ... Selecting previously unselected package libfreetype6:amd64. Unpacking libfreetype6:amd64 (from .../libfreetype6_2.4.9-1.1_amd64.deb) ... Selecting previously unselected package fonts-dejavu-core. Unpacking fonts-dejavu-core (from .../fonts-dejavu-core_2.33+svn2514-3_all.deb) ... Selecting previously unselected package ttf-dejavu-core. Unpacking ttf-dejavu-core (from .../ttf-dejavu-core_2.33+svn2514-3_all.deb) ... Selecting previously unselected package fontconfig-config. Unpacking fontconfig-config (from .../fontconfig-config_2.10.2-2_all.deb) ... Selecting previously unselected package libfontconfig1:amd64. Unpacking libfontconfig1:amd64 (from .../libfontconfig1_2.10.2-2_amd64.deb) ... Selecting previously unselected package libxcb-glx0:amd64. Unpacking libxcb-glx0:amd64 (from .../libxcb-glx0_1.9.1-3_amd64.deb) ... Selecting previously unselected package libxfixes3:amd64. Unpacking libxfixes3:amd64 (from .../libxfixes3_1%3a5.0.1-1_amd64.deb) ... Selecting previously unselected package libxdamage1:amd64. Unpacking libxdamage1:amd64 (from .../libxdamage1_1%3a1.1.4-1_amd64.deb) ... Selecting previously unselected package libxext6:amd64. Unpacking libxext6:amd64 (from .../libxext6_2%3a1.3.2-1_amd64.deb) ... Selecting previously unselected package libxxf86vm1:amd64. Unpacking libxxf86vm1:amd64 (from .../libxxf86vm1_1%3a1.1.2-1+deb7u1_amd64.deb) ... Selecting previously unselected package libgl1-mesa-glx:amd64. Unpacking libgl1-mesa-glx:amd64 (from .../libgl1-mesa-glx_9.1.4-1_amd64.deb) ... Selecting previously unselected package libpixman-1-0:amd64. Unpacking libpixman-1-0:amd64 (from .../libpixman-1-0_0.26.0-4_amd64.deb) ... Selecting previously unselected package libpng12-0:amd64. Unpacking libpng12-0:amd64 (from .../libpng12-0_1.2.49-4_amd64.deb) ... Selecting previously unselected package libxcb-shm0:amd64. Unpacking libxcb-shm0:amd64 (from .../libxcb-shm0_1.9.1-3_amd64.deb) ... Selecting previously unselected package libxrender1:amd64. Unpacking libxrender1:amd64 (from .../libxrender1_1%3a0.9.8-1_amd64.deb) ... Selecting previously unselected package libcairo2:amd64. Unpacking libcairo2:amd64 (from .../libcairo2_1.12.14-5_amd64.deb) ... Selecting previously unselected package libglib2.0-0:amd64. Unpacking libglib2.0-0:amd64 (from .../libglib2.0-0_2.36.3-3_amd64.deb) ... Selecting previously unselected package libcroco3:amd64. Unpacking libcroco3:amd64 (from .../libcroco3_0.6.8-2_amd64.deb) ... Selecting previously unselected package libdatrie1:amd64. Unpacking libdatrie1:amd64 (from .../libdatrie1_0.2.6-2_amd64.deb) ... Selecting previously unselected package libjpeg8:amd64. Unpacking libjpeg8:amd64 (from .../libjpeg8_8d-1_amd64.deb) ... Selecting previously unselected package libjbig0:amd64. Unpacking libjbig0:amd64 (from .../libjbig0_2.0-2_amd64.deb) ... Selecting previously unselected package libtiff4:amd64. Unpacking libtiff4:amd64 (from .../libtiff4_3.9.7-1_amd64.deb) ... Selecting previously unselected package libvpx1:amd64. Unpacking libvpx1:amd64 (from .../libvpx1_1.2.0-2_amd64.deb) ... Selecting previously unselected package libxpm4:amd64. Unpacking libxpm4:amd64 (from .../libxpm4_1%3a3.5.10-1_amd64.deb) ... Selecting previously unselected package libgd3:amd64. Unpacking libgd3:amd64 (from .../libgd3_2.1.0-2_amd64.deb) ... Selecting previously unselected package libgraphite2-3:amd64. Unpacking libgraphite2-3:amd64 (from .../libgraphite2-3_1.2.3-1_amd64.deb) ... Selecting previously unselected package libharfbuzz0a:amd64. Unpacking libharfbuzz0a:amd64 (from .../libharfbuzz0a_0.9.18-3_amd64.deb) ... Selecting previously unselected package x11-common. Unpacking x11-common (from .../x11-common_1%3a7.7+3_all.deb) ... Selecting previously unselected package libice6:amd64. Unpacking libice6:amd64 (from .../libice6_2%3a1.0.8-2_amd64.deb) ... Selecting previously unselected package libltdl7:amd64. Unpacking libltdl7:amd64 (from .../libltdl7_2.4.2-1.3_amd64.deb) ... Selecting previously unselected package libthai-data. Unpacking libthai-data (from .../libthai-data_0.1.19-2_all.deb) ... Selecting previously unselected package libthai0:amd64. Unpacking libthai0:amd64 (from .../libthai0_0.1.19-2_amd64.deb) ... Selecting previously unselected package fontconfig. Unpacking fontconfig (from .../fontconfig_2.10.2-2_amd64.deb) ... Selecting previously unselected package libpango-1.0-0:amd64. Unpacking libpango-1.0-0:amd64 (from .../libpango-1.0-0_1.32.5-5+b1_amd64.deb) ... Selecting previously unselected package libpangoft2-1.0-0:amd64. Unpacking libpangoft2-1.0-0:amd64 (from .../libpangoft2-1.0-0_1.32.5-5+b1_amd64.deb) ... Selecting previously unselected package libpangocairo-1.0-0:amd64. Unpacking libpangocairo-1.0-0:amd64 (from .../libpangocairo-1.0-0_1.32.5-5+b1_amd64.deb) ... Selecting previously unselected package libsm6:amd64. Unpacking libsm6:amd64 (from .../libsm6_2%3a1.2.1-2_amd64.deb) ... Selecting previously unselected package libunistring0:amd64. Unpacking libunistring0:amd64 (from .../libunistring0_0.9.3-5_amd64.deb) ... Selecting previously unselected package libxt6:amd64. Unpacking libxt6:amd64 (from .../libxt6_1%3a1.1.3-1+deb7u1_amd64.deb) ... Selecting previously unselected package libxmu6:amd64. Unpacking libxmu6:amd64 (from .../libxmu6_2%3a1.1.1-1_amd64.deb) ... Selecting previously unselected package libxaw7:amd64. Unpacking libxaw7:amd64 (from .../libxaw7_2%3a1.0.11-1_amd64.deb) ... Selecting previously unselected package file. Unpacking file (from .../file_1%3a5.14-2_amd64.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.3-1_amd64.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.3-1_amd64.deb) ... Selecting previously unselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously unselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ... Selecting previously unselected package debhelper. Unpacking debhelper (from .../debhelper_9.20130630_all.deb) ... Selecting previously unselected package doxygen. Unpacking doxygen (from .../doxygen_1.8.4-1_amd64.deb) ... Selecting previously unselected package libcdt4. Unpacking libcdt4 (from .../libcdt4_2.26.3-15_amd64.deb) ... Selecting previously unselected package libcgraph5. Unpacking libcgraph5 (from .../libcgraph5_2.26.3-15_amd64.deb) ... Selecting previously unselected package libgraph4. Unpacking libgraph4 (from .../libgraph4_2.26.3-15_amd64.deb) ... Selecting previously unselected package libpathplan4. Unpacking libpathplan4 (from .../libpathplan4_2.26.3-15_amd64.deb) ... Selecting previously unselected package libxdot4. Unpacking libxdot4 (from .../libxdot4_2.26.3-15_amd64.deb) ... Selecting previously unselected package libgvc5. Unpacking libgvc5 (from .../libgvc5_2.26.3-15_amd64.deb) ... Selecting previously unselected package libgvpr1. Unpacking libgvpr1 (from .../libgvpr1_2.26.3-15_amd64.deb) ... Selecting previously unselected package graphviz. Unpacking graphviz (from .../graphviz_2.26.3-15_amd64.deb) ... Selecting previously unselected package libargtable2-0. Unpacking libargtable2-0 (from .../libargtable2-0_12-1_amd64.deb) ... Selecting previously unselected package libargtable2-docs. Unpacking libargtable2-docs (from .../libargtable2-docs_12-1_all.deb) ... Selecting previously unselected package libargtable2-dev. Unpacking libargtable2-dev (from .../libargtable2-dev_12-1_amd64.deb) ... Selecting previously unselected package sbuild-build-depends-clustalo-dummy. Unpacking sbuild-build-depends-clustalo-dummy (from .../sbuild-build-depends-clustalo-dummy.deb) ... Setting up libpipeline1:amd64 (1.2.4-1) ... Setting up libudev0:amd64 (175-7.2) ... Setting up groff-base (1.22.2-3) ... Setting up bsdmainutils (9.0.5) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up man-db (2.6.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libasprintf0c2:amd64 (0.18.3-1) ... Setting up libmagic1:amd64 (1:5.14-2) ... Setting up libxml2:amd64 (2.9.1+dfsg1-2) ... Setting up libdrm2:amd64 (2.4.45-3) ... Setting up libglapi-mesa:amd64 (9.1.4-1) ... Setting up libllvm3.2:amd64 (1:3.2repack-10) ... Setting up libxau6:amd64 (1:1.0.8-1) ... Setting up libxdmcp6:amd64 (1:1.1.1-1) ... Setting up libxcb1:amd64 (1.9.1-3) ... Setting up libxcb-dri2-0:amd64 (1.9.1-3) ... Setting up libgbm1:amd64 (9.1.4-1) ... Setting up libwayland-client0:amd64 (1.1.0-2) ... Setting up libwayland-server0:amd64 (1.1.0-2) ... Setting up libx11-data (2:1.6.0-1) ... Setting up libx11-6:amd64 (2:1.6.0-1) ... Setting up libx11-xcb1:amd64 (2:1.6.0-1) ... Setting up libxcb-render0:amd64 (1.9.1-3) ... Setting up libxcb-shape0:amd64 (1.9.1-3) ... Setting up libxcb-xfixes0:amd64 (1.9.1-3) ... Setting up libegl1-mesa:amd64 (9.1.4-1) ... Setting up libexpat1:amd64 (2.1.0-4) ... Setting up libfreetype6:amd64 (2.4.9-1.1) ... Setting up fonts-dejavu-core (2.33+svn2514-3) ... Setting up ttf-dejavu-core (2.33+svn2514-3) ... Setting up fontconfig-config (2.10.2-2) ... Setting up libfontconfig1:amd64 (2.10.2-2) ... Setting up libxcb-glx0:amd64 (1.9.1-3) ... Setting up libxfixes3:amd64 (1:5.0.1-1) ... Setting up libxdamage1:amd64 (1:1.1.4-1) ... Setting up libxext6:amd64 (2:1.3.2-1) ... Setting up libxxf86vm1:amd64 (1:1.1.2-1+deb7u1) ... Setting up libgl1-mesa-glx:amd64 (9.1.4-1) ... Setting up libpixman-1-0:amd64 (0.26.0-4) ... Setting up libpng12-0:amd64 (1.2.49-4) ... Setting up libxcb-shm0:amd64 (1.9.1-3) ... Setting up libxrender1:amd64 (1:0.9.8-1) ... Setting up libcairo2:amd64 (1.12.14-5) ... Setting up libglib2.0-0:amd64 (2.36.3-3) ... No schema files found: doing nothing. Setting up libcroco3:amd64 (0.6.8-2) ... Setting up libdatrie1:amd64 (0.2.6-2) ... Setting up libjpeg8:amd64 (8d-1) ... Setting up libjbig0:amd64 (2.0-2) ... Setting up libtiff4:amd64 (3.9.7-1) ... Setting up libvpx1:amd64 (1.2.0-2) ... Setting up libxpm4:amd64 (1:3.5.10-1) ... Setting up libgd3:amd64 (2.1.0-2) ... Setting up libgraphite2-3:amd64 (1.2.3-1) ... Setting up libharfbuzz0a:amd64 (0.9.18-3) ... Setting up x11-common (1:7.7+3) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of start. Setting up libice6:amd64 (2:1.0.8-2) ... Setting up libltdl7:amd64 (2.4.2-1.3) ... Setting up libthai-data (0.1.19-2) ... Setting up libthai0:amd64 (0.1.19-2) ... Setting up fontconfig (2.10.2-2) ... Regenerating fonts cache... done. Setting up libpango-1.0-0:amd64 (1.32.5-5+b1) ... Setting up libpangoft2-1.0-0:amd64 (1.32.5-5+b1) ... Setting up libpangocairo-1.0-0:amd64 (1.32.5-5+b1) ... Setting up libsm6:amd64 (2:1.2.1-2) ... Setting up libunistring0:amd64 (0.9.3-5) ... Setting up libxt6:amd64 (1:1.1.3-1+deb7u1) ... Setting up libxmu6:amd64 (2:1.1.1-1) ... Setting up libxaw7:amd64 (2:1.0.11-1) ... Setting up file (1:5.14-2) ... Setting up gettext-base (0.18.3-1) ... Setting up gettext (0.18.3-1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20130630) ... Setting up doxygen (1.8.4-1) ... Setting up libcdt4 (2.26.3-15) ... Setting up libcgraph5 (2.26.3-15) ... Setting up libgraph4 (2.26.3-15) ... Setting up libpathplan4 (2.26.3-15) ... Setting up libxdot4 (2.26.3-15) ... Setting up libgvc5 (2.26.3-15) ... Setting up libgvpr1 (2.26.3-15) ... Setting up graphviz (2.26.3-15) ... Setting up libargtable2-0 (12-1) ... Setting up libargtable2-docs (12-1) ... Setting up libargtable2-dev (12-1) ... Setting up sbuild-build-depends-clustalo-dummy (0.invalid.0) ... Processing triggers for libc-bin ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-xen-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.23.52.20130620-1 dpkg-dev_1.16.10 g++-4.6_4.6.4-4 g++-4.8_4.8.1-6 gcc-4.6_4.6.4-4 gcc-4.7_4.7.3-6 gcc-4.8_4.8.1-6 libc6-dev_2.17-7 libstdc++-4.8-dev_4.8.1-6 libstdc++6_4.8.1-6 libstdc++6-4.6-dev_4.6.4-4 libstdc++6-4.7-dev_4.7.3-6 linux-libc-dev_3.9.8-1 Package versions: apt_0.9.9.1 base-files_7.2 base-passwd_3.5.26 bash_4.2+dfsg-1 binutils_2.23.52.20130620-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.5 build-essential_11.6 bzip2_1.0.6-4 clang-3.3_1:3.3-3 coreutils_8.20-3 cpp_4:4.8.1-2 cpp-4.6_4.6.4-4 cpp-4.7_4.7.3-6 cpp-4.8_4.8.1-6 dash_0.5.7-3 debconf_1.5.50 debconf-i18n_1.5.50 debfoster_2.7-1.2 debhelper_9.20130630 debian-archive-keyring_2012.4 debianutils_4.3.4 diffutils_1:3.2-8 doxygen_1.8.4-1 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.8-1 e2fsprogs_1.42.8-1 fakeroot_1.19-2 file_1:5.14-2 findutils_4.4.2-6 fontconfig_2.10.2-2 fontconfig-config_2.10.2-2 fonts-dejavu-core_2.33+svn2514-3 g++_4:4.8.1-2 g++-4.6_4.6.4-4 g++-4.8_4.8.1-6 gcc_4:4.8.1-2 gcc-4.4-base_4.4.7-4 gcc-4.5-base_4.5.4-1 gcc-4.6_4.6.4-4 gcc-4.6-base_4.6.4-4 gcc-4.7_4.7.3-6 gcc-4.7-base_4.7.3-6 gcc-4.8_4.8.1-6 gcc-4.8-base_4.8.1-6 gettext_0.18.3-1 gettext-base_0.18.3-1 gnupg_1.4.12-7 gpgv_1.4.12-7 graphviz_2.26.3-15 grep_2.14-2 groff-base_1.22.2-3 gzip_1.6-1 hostname_3.13 initscripts_2.88dsf-42 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.52-1 libapt-pkg4.12_0.9.9.1 libargtable2-0_12-1 libargtable2-dev_12-1 libargtable2-docs_12-1 libasan0_4.8.1-6 libasprintf0c2_0.18.3-1 libatomic1_4.8.1-6 libattr1_1:2.4.47-1 libblkid1_2.20.1-5.5 libbz2-1.0_1.0.6-4 libc-bin_2.17-7 libc-dev-bin_2.17-7 libc6_2.17-7 libc6-dev_2.17-7 libcairo2_1.12.14-5 libcap2_1:2.22-1.2 libcdt4_2.26.3-15 libcgraph5_2.26.3-15 libclang-common-3.3-dev_1:3.3-3 libclang1-3.3_1:3.3-3 libclass-isa-perl_0.36-5 libcloog-isl4_0.18.0-2 libcloog-ppl1_0.16.1-3 libcomerr2_1.42.8-1 libcroco3_0.6.8-2 libdatrie1_0.2.6-2 libdb5.1_5.1.29-6 libdpkg-perl_1.16.10 libdrm2_2.4.45-3 libegl1-mesa_9.1.4-1 libexpat1_2.1.0-4 libffi6_3.0.13-4 libfile-fcntllock-perl_0.14-2 libfontconfig1_2.10.2-2 libfreetype6_2.4.9-1.1 libgbm1_9.1.4-1 libgc1c2_1:7.2d-5 libgcc-4.7-dev_4.7.3-6 libgcc-4.8-dev_4.8.1-6 libgcc1_1:4.8.1-6 libgd3_2.1.0-2 libgdbm3_1.8.3-12 libgl1-mesa-glx_9.1.4-1 libglapi-mesa_9.1.4-1 libglib2.0-0_2.36.3-3 libgmp10_2:5.1.2+dfsg-2 libgmpxx4ldbl_2:5.1.2+dfsg-2 libgomp1_4.8.1-6 libgpm2_1.20.4-6.1 libgraph4_2.26.3-15 libgraphite2-3_1.2.3-1 libgvc5_2.26.3-15 libgvpr1_2.26.3-15 libharfbuzz0a_0.9.18-3 libice6_2:1.0.8-2 libisl10_0.11.2-1 libitm1_4.8.1-6 libjbig0_2.0-2 libjpeg8_8d-1 libllvm3.2_1:3.2repack-10 libllvm3.3_1:3.3-3 liblocale-gettext-perl_1.05-7+b1 libltdl7_2.4.2-1.3 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.14-2 libmount1_2.20.1-5.5 libmpc2_0.9-4 libmpc3_1.0.1-1 libmpfr4_3.1.1-1 libncurses5_5.9+20130608-1 libobjc-4.7-dev_4.7.3-6 libobjc4_4.8.1-6 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpango-1.0-0_1.32.5-5+b1 libpangocairo-1.0-0_1.32.5-5+b1 libpangoft2-1.0-0_1.32.5-5+b1 libpathplan4_2.26.3-15 libpcre3_1:8.31-2 libpipeline1_1.2.4-1 libpixman-1-0_0.26.0-4 libpng12-0_1.2.49-4 libppl-c4_1:1.0-7 libppl12_1:1.0-7 libquadmath0_4.8.1-6 libreadline6_6.2+dfsg-0.1 libselinux1_2.1.13-2 libsemanage-common_2.1.10-2 libsemanage1_2.1.10-2 libsepol1_2.1.9-2 libslang2_2.2.4-15 libsm6_2:1.2.1-2 libss2_1.42.8-1 libstdc++-4.8-dev_4.8.1-6 libstdc++6_4.8.1-6 libstdc++6-4.6-dev_4.6.4-4 libstdc++6-4.7-dev_4.7.3-6 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libthai-data_0.1.19-2 libthai0_0.1.19-2 libtiff4_3.9.7-1 libtimedate-perl_1.2000-1 libtinfo5_5.9+20130608-1 libtsan0_4.8.1-6 libudev0_175-7.2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.2 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.5 libvpx1_1.2.0-2 libwayland-client0_1.1.0-2 libwayland-server0_1.1.0-2 libx11-6_2:1.6.0-1 libx11-data_2:1.6.0-1 libx11-xcb1_2:1.6.0-1 libxau6_1:1.0.8-1 libxaw7_2:1.0.11-1 libxcb-dri2-0_1.9.1-3 libxcb-glx0_1.9.1-3 libxcb-render0_1.9.1-3 libxcb-shape0_1.9.1-3 libxcb-shm0_1.9.1-3 libxcb-xfixes0_1.9.1-3 libxcb1_1.9.1-3 libxdamage1_1:1.1.4-1 libxdmcp6_1:1.1.1-1 libxdot4_2.26.3-15 libxext6_2:1.3.2-1 libxfixes3_1:5.0.1-1 libxml2_2.9.1+dfsg1-2 libxmu6_2:1.1.1-1 libxpm4_1:3.5.10-1 libxrender1_1:0.9.8-1 libxt6_1:1.1.3-1+deb7u1 libxxf86vm1_1:1.1.2-1+deb7u1 linux-libc-dev_3.9.8-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian12 make_3.81-8.2 man-db_2.6.5-2 mawk_1.3.3-17 mount_2.20.1-5.5 multiarch-support_2.17-7 ncurses-base_5.9+20130608-1 ncurses-bin_5.9+20130608-1 passwd_1:4.1.5.1-1 patch_2.7.1-3 perl_5.14.2-21 perl-base_5.14.2-21 perl-modules_5.14.2-21 po-debconf_1.0.16+nmu2 readline-common_6.2+dfsg-0.1 sbuild-build-depends-clustalo-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.2-1 sensible-utils_0.0.9 sudo_1.8.5p2-1+nmu1 sysv-rc_2.88dsf-42 sysvinit_2.88dsf-42 sysvinit-utils_2.88dsf-42 tar_1.26+dfsg-6 ttf-dejavu-core_2.33+svn2514-3 tzdata_2013c-2 ucf_3.0027+nmu1 util-linux_2.20.1-5.5 vim_2:7.3.923-3 vim-common_2:7.3.923-3 vim-runtime_2:7.3.923-3 x11-common_1:7.7+3 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Sat Jul 6 07:30:50 2013 UTC using RSA key ID 326D8438 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./clustalo_1.2.0-1.dsc dpkg-source: info: extracting clustalo in clustalo-1.2.0 dpkg-source: info: unpacking clustalo_1.2.0.orig.tar.gz dpkg-source: info: unpacking clustalo_1.2.0-1.debian.tar.gz Check disc space ──────────────── Sufficient free space for build Hack binNMU version ─────────────────── Created changelog entry for binNMU version 1.2.0-1clang1 User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=user PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=user SCHROOT_SESSION_ID=unstable-amd64-sbuild-7a4642bc-c4fb-451f-90f7-e84b3c2f4f89 SCHROOT_UID=1000 SCHROOT_USER=user SHELL=/bin/sh USER=user dpkg-buildpackage ───────────────── dpkg-buildpackage: source package clustalo dpkg-buildpackage: source version 1.2.0-1clang1 dpkg-source --before-build clustalo-1.2.0 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean debian/rules override_dh_clean make[1]: Entering directory `/«PKGBUILDDIR»' dh_clean rm -f _configs.sed rm -rf doc make[1]: Leaving directory `/«PKGBUILDDIR»' debian/rules build-arch dh build-arch dh_testdir -a dh_auto_configure -a configure: WARNING: unrecognized options: --disable-maintainer-mode configure: Welcome to Clustal Omega - version 1.2.0 (AndreaGiacomo) +NMMMMMMMMMS= MMMMM? :MMMMM8 IMMMMS MMMMM, ~MMMMN ,MMMMM =MMMMM MMMMM ?MMMMM +MMMMM MMMMMS MMMMM MMMMM MMMMM: MMMMM MMMMM+ MMMMM MMMMM~ MMMMM MMMMM MMMMMZ MMMMM MMMMM ,MMMMZ MMMM8 MMMM+ MMMMS MMMM, MMMMO MMMM ,N SMMM MMM8 +8 ,M7 M+ M+ :M8 ,MMMMMMMMMMMMI MMMMMMMMMMMM8 ,MMMMMMMMMMMM8 MMMMMMMMMMMM8 ,MMMMMMMMMMMMN MMMMMMMMMMMM8 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking for style of include used by make... GNU checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 3458764513820540925 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... yes checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for a BSD-compatible install... /usr/bin/install -c checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking dependency style of gcc... (cached) none checking how to run the C preprocessor... gcc -E checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking dependency style of g++... (cached) none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking how to run the C++ preprocessor... g++ -E checking for ANSI C header files... (cached) yes checking assert.h usability... yes checking assert.h presence... yes checking for assert.h... yes checking ctype.h usability... yes checking ctype.h presence... yes checking for ctype.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking for memory.h... (cached) yes checking stdarg.h usability... yes checking stdarg.h presence... yes checking for stdarg.h... yes checking stdio.h usability... yes checking stdio.h presence... yes checking for stdio.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking time.h usability... yes checking time.h presence... yes checking for time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking for inline... inline checking for log in -lm... yes checking for log2 in -lm... yes checking argtable2.h usability... yes checking argtable2.h presence... yes checking for argtable2.h... yes checking for arg_parse in -largtable2... yes checking for OpenMP flag of C compiler... -fopenmp checking whether byte ordering is bigendian... no checking for ntohs... yes checking for ntohl... yes checking for ntons... no checking for ntonl... no checking size of unsigned short... 2 checking size of unsigned int... 4 checking size of unsigned long... 8 checking size of unsigned long long... 8 checking for stroul... no checking for strtoull... yes checking for ftello... yes checking for fseeko... yes checking for ftello64... yes checking for fseeko64... yes checking for ftell64... no checking for fseek64... no checking for off_t... yes checking size of fpos_t... 16 checking if malloc debugging is wanted... no checking whether to build with debug information... no configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating clustalo.pc config.status: creating Doxyfile config.status: creating src/clustal/Makefile config.status: creating src/hhalign/Makefile config.status: creating src/kmpp/Makefile config.status: creating src/squid/Makefile config.status: creating src/config.h config.status: executing src/clustal-omega-config.h commands config.status: creating src/clustal-omega-config.h - prefix CLUSTAL_OMEGA for src/config.h defines config.status: src/clustal-omega-config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build -a make[1]: Entering directory `/«PKGBUILDDIR»' Making all in src make[2]: Entering directory `/«PKGBUILDDIR»/src' make all-recursive make[3]: Entering directory `/«PKGBUILDDIR»/src' Making all in hhalign make[4]: Entering directory `/«PKGBUILDDIR»/src/hhalign' /bin/bash ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o hhalign.lo hhalign.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c hhalign.cpp -fPIC -DPIC -o .libs/hhalign.o clang: warning: argument unused during compilation: '-fopenmp' In file included from hhalign.cpp:61: ./hhutil-C.h:516:35: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhutil-C.h:521:38: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ In file included from hhalign.cpp:70: ./hhhmm-C.h:188:23: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(q.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhhmm-C.h:193:21: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm-C.h:329:34: warning: when type is in parentheses, array cannot have dynamic size char *cur_seq = new(char[par.maxColCnt]); //Sequence currently read in ~ ^~~~~~~~~~~~~ ~ ./hhhmm-C.h:343:60: warning: while loop has empty body [-Wempty-body] {while (fgetline(line,LINELEN-1,dbf) && line[0]!='#'); break;} ^ ./hhhmm-C.h:343:60: note: put the semicolon on a separate line to silence this warning ./hhhmm-C.h:354:57: warning: while loop has empty body [-Wempty-body] {while (fgetline(line,LINELEN-1,dbf) && line[0]!='#'); k--; break;} ^ ./hhhmm-C.h:354:57: note: put the semicolon on a separate line to silence this warning ./hhhmm-C.h:360:25: warning: when type is in parentheses, array cannot have dynamic size seq[k-1]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm-C.h:367:26: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0' ~ ^~~~~~~~~~~~~~~~ ~ ./hhhmm-C.h:463:22: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm-C.h:735:43: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[/*MAXRES*/par.maxResLen+2]); ~ ^~~~~~~~~~~~~~~ ~ ./hhhmm-C.h:756:43: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred] = new(char[/*MAXRES*/par.maxResLen+2]); ~ ^~~~~~~~~~~~~~~ ~ ./hhhmm-C.h:777:43: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[/*MAXRES*/par.maxResLen+2]); ~ ^~~~~~~~~~~~~~~ ~ ./hhhmm-C.h:859:39: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[/*MAXRES*/par.maxResLen+2]); ~ ^~~~~~~~~~~~~~~ ~ ./hhhmm-C.h:1035:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm-C.h:1037:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm-C.h:1040:25: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ ./hhhmm-C.h:1058:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm-C.h:1062:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm-C.h:1237:61: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[/*MAXRES*/par.maxResLen+2]); ~ ^~~~~~~~~~~~~~~ ~ ./hhhmm-C.h:1258:61: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred] = new(char[/*MAXRES*/par.maxResLen+2]); ~ ^~~~~~~~~~~~~~~ ~ ./hhhmm-C.h:1279:61: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[/*MAXRES*/par.maxResLen+2]); ~ ^~~~~~~~~~~~~~~ ~ ./hhhmm-C.h:1349:53: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[/*MAXRES*/par.maxResLen+2]); ~ ^~~~~~~~~~~~~~~ ~ ./hhhmm-C.h:1529:30: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm-C.h:1531:26: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm-C.h:1534:28: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ ./hhhmm-C.h:1552:28: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm-C.h:1554:26: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm-C.h:2109:28: warning: when type is in parentheses, array cannot have dynamic size char** lines = new(char*[3*L+100000]); ~ ^~~~~~~~~~ ~ ./hhhmm-C.h:2138:29: warning: when type is in parentheses, array cannot have dynamic size lines[nline]=new(char[strlen(line)+1]); ~ ^~~~~~~~~~~~~~ ~ In file included from hhalign.cpp:71: ./hhalignment-C.h:80:21: warning: when type is in parentheses, array cannot have dynamic size sname = new(char*[maxseq+2]); /* MR1 */ ~ ^~~~~~~~ ~ ./hhalignment-C.h:81:19: warning: when type is in parentheses, array cannot have dynamic size seq = new(char*[maxseq+2]); /* MR1 */ ~ ^~~~~~~~ ~ ./hhalignment-C.h:82:15: warning: when type is in parentheses, array cannot have dynamic size l = new(int[maxres]); ~ ^~~~~~ ~ ./hhalignment-C.h:83:17: warning: when type is in parentheses, array cannot have dynamic size X = new(char*[maxseq+2]); /* MR1 */ ~ ^~~~~~~~ ~ ./hhalignment-C.h:84:31: warning: when type is in parentheses, array cannot have dynamic size I = new(short unsigned int*[maxseq+2]); /* MR1 */ ~ ^~~~~~~~ ~ ./hhalignment-C.h:85:19: warning: when type is in parentheses, array cannot have dynamic size keep = new(char[maxseq+2]); /* MR1 */ ~ ^~~~~~~~ ~ ./hhalignment-C.h:86:22: warning: when type is in parentheses, array cannot have dynamic size display = new(char[maxseq+2]); /* MR1 */ ~ ^~~~~~~~ ~ ./hhalignment-C.h:87:18: warning: when type is in parentheses, array cannot have dynamic size wg = new(float[maxseq+2]); /* MR1 */ ~ ^~~~~~~~ ~ ./hhalignment-C.h:88:19: warning: when type is in parentheses, array cannot have dynamic size nseqs = new(int[maxres+2]); /* MR1 */ ~ ^~~~~~~~ ~ ./hhalignment-C.h:141:26: warning: when type is in parentheses, array cannot have dynamic size char *cur_seq=new(char[par.maxColCnt]); ~ ^~~~~~~~~~~~~ ~ ./hhalignment-C.h:183:43: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment-C.h:185:41: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment-C.h:187:55: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment-C.h:236:39: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(cur_name)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhalignment-C.h:351:27: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment-C.h:353:25: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment-C.h:355:39: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment-C.h:423:36: warning: when type is in parentheses, array cannot have dynamic size h = new(/*short*/ unsigned int[N_in+2]); /* short -> overflow, FS, r235 -> r236 */ ~ ^~~~~~ ~ ./hhalignment-C.h:555:38: warning: when type is in parentheses, array cannot have dynamic size percent_gaps = new(float[par.maxColCnt]); ~ ^~~~~~~~~~~~~ ~ ./hhalignment-C.h:561:42: warning: when type is in parentheses, array cannot have dynamic size if (nres==NULL) nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment-C.h:783:36: warning: when type is in parentheses, array cannot have dynamic size match_state = new(char[par.maxColCnt]); ~ ^~~~~~~~~~~~~ ~ ./hhalignment-C.h:945:28: warning: when type is in parentheses, array cannot have dynamic size char *dummy = new(char[N_in+1]); ~ ^~~~~~ ~ ./hhalignment-C.h:1008:23: warning: when type is in parentheses, array cannot have dynamic size char* in=new(char[N_in+1]); // in[k]=1: seq k has been accepted; in[k]=0: seq k has not yet been accepted at current seqid ~ ^~~~~~ ~ ./hhalignment-C.h:1009:25: warning: when type is in parentheses, array cannot have dynamic size char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0; ~ ^~~~~~ ~ ./hhalignment-C.h:1010:23: warning: when type is in parentheses, array cannot have dynamic size int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering /* MR1, used to be called idmax*/ ~ ^~~ ~ ./hhalignment-C.h:1011:27: warning: when type is in parentheses, array cannot have dynamic size int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL] ~ ^~~ ~ ./hhalignment-C.h:1012:29: warning: when type is in parentheses, array cannot have dynamic size int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid) ~ ^~~~~~ ~ ./hhalignment-C.h:1013:20: warning: when type is in parentheses, array cannot have dynamic size int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i ~ ^~~ ~ ./hhalignment-C.h:1042:27: warning: when type is in parentheses, array cannot have dynamic size first=new(int[N_in]);// first non-gap position in sequence k ~ ^~~~ ~ ./hhalignment-C.h:1043:27: warning: when type is in parentheses, array cannot have dynamic size last =new(int[N_in]);// last non-gap position in sequence k ~ ^~~~ ~ ./hhalignment-C.h:1056:26: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment-C.h:1070:27: warning: when type is in parentheses, array cannot have dynamic size ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences ~ ^~~~ ~ ./hhalignment-C.h:1313:28: warning: when type is in parentheses, array cannot have dynamic size char* coreseq=new(char[N_in]); // coreseq[k]=1 if sequence belongs to core of alignment (i.e. it is very similar to query) ~ ^~~~ ~ ./hhalignment-C.h:1364:32: warning: when type is in parentheses, array cannot have dynamic size float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore ~ ^~~ ~ ./hhalignment-C.h:1373:27: warning: when type is in parentheses, array cannot have dynamic size first=new(int[N_in]);// first non-gap position in sequence k ~ ^~~~ ~ ./hhalignment-C.h:1374:27: warning: when type is in parentheses, array cannot have dynamic size last =new(int[N_in]);// last non-gap position in sequence k ~ ^~~~ ~ ./hhalignment-C.h:1387:26: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment-C.h:1669:45: warning: when type is in parentheses, array cannot have dynamic size q.seq[q.ncons]=new(char[L+2]); ~ ^~~ ~ ./hhalignment-C.h:1676:48: warning: when type is in parentheses, array cannot have dynamic size q.sname[q.nfirst]=new(char[strlen(name)+11]); ~ ^~~~~~~~~~~~~~~ ~ ./hhalignment-C.h:1680:46: warning: when type is in parentheses, array cannot have dynamic size q.seq[q.nfirst]=new(char[L+2]); ~ ^~~ ~ ./hhalignment-C.h:1738:42: warning: when type is in parentheses, array cannot have dynamic size q.sname[nn]=new(char[strlen(sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhalignment-C.h:1741:40: warning: when type is in parentheses, array cannot have dynamic size q.seq[nn]=new(char[strlen(seq[k])+1]); ~ ^~~~~~~~~~~~~~~~ ~ ./hhalignment-C.h:1828:27: warning: when type is in parentheses, array cannot have dynamic size float *Neff = new(float[par.maxResLen]); // diversity of subalignment i ~ ^~~~~~~~~~~~~ ~ ./hhalignment-C.h:1835:18: warning: when type is in parentheses, array cannot have dynamic size wi = new(float[N_in+2]); ~ ^~~~~~ ~ ./hhalignment-C.h:1844:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment-C.h:1907:43: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]0) wi[k]=wg[k]; else wi[k]=0.0; ^ ./hhalignment-C.h:2256:29: warning: when type is in parentheses, array cannot have dynamic size float *Neff = new(float[par.maxResLen]); // diversity of subalignment i ~ ^~~~~~~~~~~~~ ~ ./hhalignment-C.h:2265:20: warning: when type is in parentheses, array cannot have dynamic size wi = new(float[N_in+2]); /* FIXME: FS */ ~ ^~~~~~ ~ ./hhalignment-C.h:2275:18: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment-C.h:2346:76: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]==GAP) wi[k]=wg[k]; else wi[k]=0.0; ^ ./hhalignment-C.h:2546:22: warning: when type is in parentheses, array cannot have dynamic size int* imatch=new(int[hit.j2+1]); ~ ^~~~~~~~ ~ ./hhalignment-C.h:2678:25: warning: when type is in parentheses, array cannot have dynamic size char* new_seq=new(char[2*maxcol]); ~ ^~~~~~~~ ~ ./hhalignment-C.h:2691:21: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[h]); ~ ^ ~ ./hhalignment-C.h:2694:19: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[h]); ~ ^ ~ ./hhalignment-C.h:2696:33: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[h]); ~ ^ ~ ./hhalignment-C.h:2698:23: warning: when type is in parentheses, array cannot have dynamic size sname[N_in]=new(char[strlen(Tali.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment-C.h:2729:19: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment-C.h:2779:15: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment-C.h:2896:39: warning: when type is in parentheses, array cannot have dynamic size I[k] = new(short unsigned int[iLen+2+GOOD_MEASURE]); ~ ^~~~~~~~~~~~~~~~~~~ ~ ./hhalignment-C.h:2897:25: warning: when type is in parentheses, array cannot have dynamic size X[k] = new(char[iLen+2+GOOD_MEASURE]); ~ ^~~~~~~~~~~~~~~~~~~ ~ ./hhalignment-C.h:2898:27: warning: when type is in parentheses, array cannot have dynamic size seq[k] = new(char[iLen+2+GOOD_MEASURE]); ~ ^~~~~~~~~~~~~~~~~~~ ~ In file included from hhalign.cpp:72: ./hhhit-C.h:179:17: warning: when type is in parentheses, array cannot have dynamic size bMM=new(char*[Nq]); ~ ^~ ~ ./hhhit-C.h:180:17: warning: when type is in parentheses, array cannot have dynamic size bMI=new(char*[Nq]); ~ ^~ ~ ./hhhit-C.h:181:17: warning: when type is in parentheses, array cannot have dynamic size bIM=new(char*[Nq]); ~ ^~ ~ ./hhhit-C.h:182:17: warning: when type is in parentheses, array cannot have dynamic size bDG=new(char*[Nq]); ~ ^~ ~ ./hhhit-C.h:183:17: warning: when type is in parentheses, array cannot have dynamic size bGD=new(char*[Nq]); ~ ^~ ~ ./hhhit-C.h:184:22: warning: when type is in parentheses, array cannot have dynamic size cell_off=new(char*[Nq]); ~ ^~ ~ ./hhhit-C.h:187:23: warning: when type is in parentheses, array cannot have dynamic size bMM[i]=new(char[Nt]); ~ ^~ ~ ./hhhit-C.h:188:23: warning: when type is in parentheses, array cannot have dynamic size bMI[i]=new(char[Nt]); ~ ^~ ~ ./hhhit-C.h:189:23: warning: when type is in parentheses, array cannot have dynamic size bIM[i]=new(char[Nt]); ~ ^~ ~ ./hhhit-C.h:190:23: warning: when type is in parentheses, array cannot have dynamic size bGD[i]=new(char[Nt]); ~ ^~ ~ ./hhhit-C.h:191:23: warning: when type is in parentheses, array cannot have dynamic size bDG[i]=new(char[Nt]); ~ ^~ ~ ./hhhit-C.h:192:28: warning: when type is in parentheses, array cannot have dynamic size cell_off[i]=new(char[Nt]); ~ ^~ ~ ./hhhit-C.h:239:20: warning: when type is in parentheses, array cannot have dynamic size F_MM=new(double*[Nq]); ~ ^~ ~ ./hhhit-C.h:240:20: warning: when type is in parentheses, array cannot have dynamic size F_MI=new(double*[Nq]); ~ ^~ ~ ./hhhit-C.h:241:20: warning: when type is in parentheses, array cannot have dynamic size F_DG=new(double*[Nq]); ~ ^~ ~ ./hhhit-C.h:242:20: warning: when type is in parentheses, array cannot have dynamic size F_IM=new(double*[Nq]); ~ ^~ ~ ./hhhit-C.h:243:20: warning: when type is in parentheses, array cannot have dynamic size F_GD=new(double*[Nq]); ~ ^~ ~ ./hhhit-C.h:244:20: warning: when type is in parentheses, array cannot have dynamic size scale=new(double[Nq+1]); // need Nq+3? ~ ^~~~ ~ ./hhhit-C.h:247:28: warning: when type is in parentheses, array cannot have dynamic size F_MM[i] = new(double[Nt]); ~ ^~ ~ ./hhhit-C.h:248:28: warning: when type is in parentheses, array cannot have dynamic size F_MI[i] = new(double[Nt]); ~ ^~ ~ ./hhhit-C.h:249:28: warning: when type is in parentheses, array cannot have dynamic size F_DG[i] = new(double[Nt]); ~ ^~ ~ ./hhhit-C.h:250:28: warning: when type is in parentheses, array cannot have dynamic size F_IM[i] = new(double[Nt]); ~ ^~ ~ ./hhhit-C.h:251:28: warning: when type is in parentheses, array cannot have dynamic size F_GD[i] = new(double[Nt]); ~ ^~ ~ ./hhhit-C.h:296:20: warning: when type is in parentheses, array cannot have dynamic size B_MM=new(double*[Nq]); ~ ^~ ~ ./hhhit-C.h:303:28: warning: when type is in parentheses, array cannot have dynamic size B_MM[i] = new(double[Nt]); ~ ^~ ~ ./hhhit-C.h:376:28: warning: when type is in parentheses, array cannot have dynamic size float *sMM = new(float[par.maxResLen]); // sMM[i][j] = score of best alignment up to indices (i,j) ending in (Match,Match) ~ ^~~~~~~~~~~~~ ~ ./hhhit-C.h:377:28: warning: when type is in parentheses, array cannot have dynamic size float *sGD = new(float[par.maxResLen]); // sGD[i][j] = score of best alignment up to indices (i,j) ending in (Gap,Delete) ~ ^~~~~~~~~~~~~ ~ ./hhhit-C.h:378:28: warning: when type is in parentheses, array cannot have dynamic size float *sDG = new(float[par.maxResLen]); // sDG[i][j] = score of best alignment up to indices (i,j) ending in (Delete,Gap) ~ ^~~~~~~~~~~~~ ~ ./hhhit-C.h:379:28: warning: when type is in parentheses, array cannot have dynamic size float *sIM = new(float[par.maxResLen]); // sIM[i][j] = score of best alignment up to indices (i,j) ending in (Ins,Match) ~ ^~~~~~~~~~~~~ ~ ./hhhit-C.h:380:28: warning: when type is in parentheses, array cannot have dynamic size float *sMI = new(float[par.maxResLen]); // sMI[i][j] = score of best alignment up to indices (i,j) ending in (Match,Ins) ~ ^~~~~~~~~~~~~ ~ ./hhhit-C.h:1126:34: warning: when type is in parentheses, array cannot have dynamic size if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query ~ ^~~~~ ~ ./hhhit-C.h:1127:21: warning: when type is in parentheses, array cannot have dynamic size S = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit-C.h:1128:21: warning: when type is in parentheses, array cannot have dynamic size S_ss = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit-C.h:1228:34: warning: when type is in parentheses, array cannot have dynamic size double* scale_cum = new(double[q.L+2]); ~ ^~~~~ ~ ./hhhit-C.h:1247:31: warning: when type is in parentheses, array cannot have dynamic size double* sumF=new(double[q.L+t.L]); ~ ^~~~~~~ ~ ./hhhit-C.h:1371:34: warning: when type is in parentheses, array cannot have dynamic size if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query ~ ^~~~~ ~ ./hhhit-C.h:1372:21: warning: when type is in parentheses, array cannot have dynamic size S = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit-C.h:1373:21: warning: when type is in parentheses, array cannot have dynamic size S_ss = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit-C.h:1475:34: warning: when type is in parentheses, array cannot have dynamic size if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query ~ ^~~~~ ~ ./hhhit-C.h:1476:21: warning: when type is in parentheses, array cannot have dynamic size S = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit-C.h:1477:21: warning: when type is in parentheses, array cannot have dynamic size S_ss = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit-C.h:1478:28: warning: when type is in parentheses, array cannot have dynamic size P_posterior = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit-C.h:1683:31: warning: when type is in parentheses, array cannot have dynamic size longname=new(char[strlen(t.longname)+1])(); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhhit-C.h:1684:31: warning: when type is in parentheses, array cannot have dynamic size name =new(char[strlen(t.name)+1])(); ~ ^~~~~~~~~~~~~~~~ ~ ./hhhit-C.h:1685:31: warning: when type is in parentheses, array cannot have dynamic size file =new(char[strlen(t.file)+1])(); ~ ^~~~~~~~~~~~~~~~ ~ ./hhhit-C.h:1696:29: warning: when type is in parentheses, array cannot have dynamic size sname=new(char*[t.n_display])(); // Call Compare only once with irep=1 ~ ^~~~~~~~~~~ ~ ./hhhit-C.h:1697:29: warning: when type is in parentheses, array cannot have dynamic size seq =new(char*[t.n_display])(); // Call Compare only once with irep=1 ~ ^~~~~~~~~~~ ~ ./hhhit-C.h:1730:24: warning: when type is in parentheses, array cannot have dynamic size this->i = new( int[i2+j2+2])(); ~ ^~~~~~~ ~ ./hhhit-C.h:1731:24: warning: when type is in parentheses, array cannot have dynamic size this->j = new( int[i2+j2+2])(); ~ ^~~~~~~ ~ ./hhhit-C.h:1732:25: warning: when type is in parentheses, array cannot have dynamic size states = new( char[i2+j2+2])(); ~ ^~~~~~~ ~ In file included from hhalign.cpp:73: ./hhhalfalignment-C.h:66:15: warning: when type is in parentheses, array cannot have dynamic size h = new(int[maxseqdis]); //h[k] = next position of sequence k to be written ~ ^~~~~~~~~ ~ ./hhhalfalignment-C.h:67:17: warning: when type is in parentheses, array cannot have dynamic size s = new(char*[maxseqdis]); //s[k][h] = character in column h, sequence k of output alignment ~ ^~~~~~~~~ ~ ./hhhalfalignment-C.h:68:16: warning: when type is in parentheses, array cannot have dynamic size l = new(int*[maxseqdis]); //counts non-gap residues: l[k][i] = index of last residue AT OR BEFORE match state i in seq k ~ ^~~~~~~~~ ~ ./hhhalfalignment-C.h:69:16: warning: when type is in parentheses, array cannot have dynamic size m = new(int*[maxseqdis]); //counts positions: m[k][i] = position of match state i in string seq[k] ~ ^~~~~~~~~ ~ In file included from hhalign.cpp:74: ./hhfullalignment-C.h:359:31: warning: when type is in parentheses, array cannot have dynamic size lq = new(short unsigned int[qa->n+2]); ~ ^~~~~~~ ~ ./hhfullalignment-C.h:360:31: warning: when type is in parentheses, array cannot have dynamic size lt = new(short unsigned int[ta->n+2]); ~ ^~~~~~~ ~ In file included from hhalign.cpp:75: ./hhhitlist-C.h:1285:18: warning: when type is in parentheses, array cannot have dynamic size Z = new(float*[N]); ~ ^ ~ ./hhhitlist-C.h:1288:24: warning: when type is in parentheses, array cannot have dynamic size Z[k] = new(float[N]); ~ ^ ~ ./hhhitlist-C.h:1293:18: warning: when type is in parentheses, array cannot have dynamic size C = new(float*[N]); ~ ^ ~ ./hhhitlist-C.h:1296:24: warning: when type is in parentheses, array cannot have dynamic size C[k] = new(float[N]); ~ ^ ~ ./hhhitlist-C.h:1303:18: warning: when type is in parentheses, array cannot have dynamic size Zq = new(float[N]); ~ ^ ~ ./hhhitlist-C.h:1304:19: warning: when type is in parentheses, array cannot have dynamic size Ztq = new(float[N]); ~ ^ ~ ./hhhitlist-C.h:1305:19: warning: when type is in parentheses, array cannot have dynamic size Zrq = new(float[N]); ~ ^ ~ ./hhhitlist-C.h:1306:20: warning: when type is in parentheses, array cannot have dynamic size fold = new(char*[N]); ~ ^ ~ ./hhhitlist-C.h:1307:19: warning: when type is in parentheses, array cannot have dynamic size fam = new(char*[N]); ~ ^ ~ ./hhhitlist-C.h:1308:20: warning: when type is in parentheses, array cannot have dynamic size Prob = new(float[N]); ~ ^ ~ ./hhhitlist-C.h:1309:16: warning: when type is in parentheses, array cannot have dynamic size ll = new(int[N]); ~ ^ ~ ./hhhitlist-C.h:1310:17: warning: when type is in parentheses, array cannot have dynamic size w = new(float[N]); ~ ^ ~ ./hhhitlist-C.h:1373:35: warning: when type is in parentheses, array cannot have dynamic size double** Csub = new(double*[M]); ~ ^ ~ ./hhhitlist-C.h:1374:35: warning: when type is in parentheses, array cannot have dynamic size double** Cinv = new(double*[M]); ~ ^ ~ ./hhhitlist-C.h:1377:25: warning: when type is in parentheses, array cannot have dynamic size Csub[m] = new(double[M]); ~ ^ ~ ./hhhitlist-C.h:1378:25: warning: when type is in parentheses, array cannot have dynamic size Cinv[m] = new(double[M]); ~ ^ ~ ./hhhitlist-C.h:1453:32: warning: when type is in parentheses, array cannot have dynamic size double** Csub = new(double*[M]); ~ ^ ~ ./hhhitlist-C.h:1456:29: warning: when type is in parentheses, array cannot have dynamic size Csub[m] = new(double[M]); ~ ^ ~ ./hhhitlist-C.h:1470:36: warning: when type is in parentheses, array cannot have dynamic size double** Cinv = new(double*[M]); ~ ^ ~ ./hhhitlist-C.h:1471:49: warning: when type is in parentheses, array cannot have dynamic size for (m=0; m/dev/null 2>&1 /bin/bash ../../libtool --tag=CXX --mode=link g++ -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -o libhhalign.la hhalign.lo -largtable2 -lm libtool: link: ar cru .libs/libhhalign.a .libs/hhalign.o libtool: link: ranlib .libs/libhhalign.a libtool: link: ( cd ".libs" && rm -f "libhhalign.la" && ln -s "../libhhalign.la" "libhhalign.la" ) make[4]: Leaving directory `/«PKGBUILDDIR»/src/hhalign' Making all in squid make[4]: Entering directory `/«PKGBUILDDIR»/src/squid' /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o a2m.lo a2m.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c a2m.c -fPIC -DPIC -o .libs/a2m.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c a2m.c -o a2m.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o aligneval.lo aligneval.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c aligneval.c -fPIC -DPIC -o .libs/aligneval.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO 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-c -o clustal.lo clustal.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c clustal.c -fPIC -DPIC -o .libs/clustal.o clustal.c:395:15: warning: extra tokens at end of #ifdef directive [-Wextra-tokens] #ifdef CLUSTAL) ^ // 1 warning generated. libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c clustal.c -o clustal.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cluster.lo cluster.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c cluster.c -fPIC -DPIC -o .libs/cluster.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c cluster.c -o cluster.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o dayhoff.lo dayhoff.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c dayhoff.c -fPIC -DPIC -o .libs/dayhoff.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c dayhoff.c -o dayhoff.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o eps.lo eps.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c eps.c -fPIC -DPIC -o .libs/eps.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c eps.c -o eps.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o file.lo file.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c file.c -fPIC -DPIC -o .libs/file.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c file.c -o file.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o getopt.lo getopt.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c getopt.c -fPIC -DPIC -o .libs/getopt.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c getopt.c -o getopt.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gki.lo gki.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c gki.c -fPIC -DPIC -o .libs/gki.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c gki.c -o gki.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsi.lo gsi.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c gsi.c -fPIC -DPIC -o .libs/gsi.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c gsi.c -o gsi.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsi64.lo gsi64.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c gsi64.c -fPIC -DPIC -o .libs/gsi64.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c gsi64.c -o gsi64.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o hsregex.lo hsregex.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c hsregex.c -fPIC -DPIC -o .libs/hsregex.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c hsregex.c -o hsregex.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iupac.lo iupac.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c iupac.c -fPIC -DPIC -o .libs/iupac.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 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-DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c KmTree.cpp -o KmTree.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o KmUtils.lo KmUtils.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c KmUtils.cpp -fPIC -DPIC -o .libs/KmUtils.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c KmUtils.cpp -o KmUtils.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CXX --mode=link g++ -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -o libkmpp.la KMeans.lo KmTree.lo KmUtils.lo -largtable2 -lm libtool: link: ar cru .libs/libkmpp.a .libs/KMeans.o .libs/KmTree.o .libs/KmUtils.o libtool: link: ranlib .libs/libkmpp.a libtool: link: ( cd ".libs" && rm -f "libkmpp.la" && ln -s "../libkmpp.la" "libkmpp.la" ) make[4]: Leaving directory `/«PKGBUILDDIR»/src/kmpp' Making all in clustal make[4]: Entering directory `/«PKGBUILDDIR»/src/clustal' /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o hhalign_wrapper.lo hhalign_wrapper.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c hhalign_wrapper.c -fPIC -DPIC -o .libs/hhalign_wrapper.o clang: warning: argument unused during compilation: '-fopenmp' libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c hhalign_wrapper.c -o hhalign_wrapper.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o ktuple_pair.lo ktuple_pair.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c ktuple_pair.c -fPIC -DPIC -o .libs/ktuple_pair.o clang: warning: argument unused during compilation: '-fopenmp' ktuple_pair.c:41:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. make[4]: *** [ktuple_pair.lo] Error 1 make[4]: Leaving directory `/«PKGBUILDDIR»/src/clustal' make[3]: *** [all-recursive] Error 1 make[2]: *** [all] Error 2 make[1]: *** [all-recursive] Error 1 dh_auto_build: make -j1 returned exit code 2 make[3]: Leaving directory `/«PKGBUILDDIR»/src' make[2]: Leaving directory `/«PKGBUILDDIR»/src' make[1]: Leaving directory `/«PKGBUILDDIR»' make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20130717-0345 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: amd64 Build-Space: 15576 Build-Time: 50 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 17 Job: clustalo_1.2.0-1 Machine Architecture: amd64 Package: clustalo Package-Time: 139 Source-Version: 1.2.0-1 Space: 15576 Status: attempted Version: 1.2.0-1clang1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20130717-0345 Build needed 00:02:19, 15576k disc space DC-Status: Failed 139.914137615s