sbuild (Debian sbuild) 0.62.6 (07 Dec 2011) on build02.raspbian.lan ╔══════════════════════════════════════════════════════════════════════════════╗ ║ clustalo 1.1.0-1 (armhf) 17 May 2012 12:52 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: clustalo Version: 1.1.0-1 Source Version: 1.1.0-1 Distribution: testing Architecture: armhf I: NOTICE: Log filtering will replace 'build/clustalo-fIK4Vt/clustalo-1.1.0' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/clustalo-fIK4Vt' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/testing-armhf-sbuild-6618d512-c82c-4845-ba5d-b7b30b6dc63e' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Get:1 http://repo.raspbian.lan testing InRelease [3588 B] Get:2 http://repo.raspbian.lan testing/main Sources [5943 kB] Get:3 http://repo.raspbian.lan testing/main armhf Packages [5919 kB] Ign http://repo.raspbian.lan testing/main TranslationIndex Ign http://repo.raspbian.lan testing/main Translation-en Fetched 11.9 MB in 26s (454 kB/s) Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ 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://svn.debian.org/debian-med/trunk/packages/clustalo/trunk/ Need to get 1156 kB of source archives. Get:1 http://repo.raspbian.lan/raspbian/ testing/main clustalo 1.1.0-1 (dsc) [2120 B] Get:2 http://repo.raspbian.lan/raspbian/ testing/main clustalo 1.1.0-1 (tar) [1150 kB] Get:3 http://repo.raspbian.lan/raspbian/ testing/main clustalo 1.1.0-1 (diff) [3592 B] Fetched 1156 kB in 0s (8511 kB/s) Download complete and in download only mode Check arch ────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-toHxiY/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 18 not upgraded. Need to get 0 B/704 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 ... 10670 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: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8.0.0), libargtable2-dev, doxygen, graphviz Filtered Build-Depends: libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8.0.0), libargtable2-dev, doxygen, graphviz dpkg-deb: building package `sbuild-build-depends-clustalo-dummy' in `/«BUILDDIR»/resolver-INElo9/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 gettext gettext-base graphviz groff-base html2text intltool-debian libargtable2-0 libargtable2-dev libargtable2-docs libcairo2 libcdt4 libcgraph5 libcroco3 libdatrie1 libexpat1 libffi5 libfontconfig1 libfreetype6 libgd2-noxpm libglib2.0-0 libgraph4 libgvc5 libgvpr1 libice6 libjpeg8 libmagic1 libpango1.0-0 libpathplan4 libpcre3 libpipeline1 libpixman-1-0 libpng12-0 libsm6 libthai-data libthai0 libunistring0 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxdot4 libxext6 libxft2 libxml2 libxmu6 libxpm4 libxrender1 libxt6 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 ttf-liberation 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 gettext gettext-base graphviz groff-base html2text intltool-debian libargtable2-0 libargtable2-dev libargtable2-docs libcairo2 libcdt4 libcgraph5 libcroco3 libdatrie1 libexpat1 libffi5 libfontconfig1 libfreetype6 libgd2-noxpm libglib2.0-0 libgraph4 libgvc5 libgvpr1 libice6 libjpeg8 libmagic1 libpango1.0-0 libpathplan4 libpcre3 libpipeline1 libpixman-1-0 libpng12-0 libsm6 libthai-data libthai0 libunistring0 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxdot4 libxext6 libxft2 libxml2 libxmu6 libxpm4 libxrender1 libxt6 man-db po-debconf sbuild-build-depends-clustalo-dummy ttf-dejavu-core x11-common 0 upgraded, 63 newly installed, 0 to remove and 18 not upgraded. Need to get 3033 kB/23.4 MB of archives. After this operation, 51.7 MB of additional disk space will be used. Get:1 http://repo.raspbian.lan/raspbian/ testing/main libargtable2-0 armhf 12-1 [17.0 kB] Get:2 http://repo.raspbian.lan/raspbian/ testing/main libargtable2-docs all 12-1 [2958 kB] Get:3 http://repo.raspbian.lan/raspbian/ testing/main libargtable2-dev armhf 12-1 [57.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3033 kB in 0s (9489 kB/s) Selecting previously unselected package libpcre3:armhf. (Reading database ... 10670 files and directories currently installed.) Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.30-5_armhf.deb) ... Selecting previously unselected package libpipeline1:armhf. Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.1-1_armhf.deb) ... Selecting previously unselected package libmagic1:armhf. Unpacking libmagic1:armhf (from .../libmagic1_5.11-1_armhf.deb) ... 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Setting up libfreetype6:armhf (2.4.9-1) ... Setting up ttf-dejavu-core (2.33-2) ... Setting up fontconfig-config (2.9.0-3) ... Setting up libfontconfig1:armhf (2.9.0-3) ... Setting up libpixman-1-0:armhf (0.24.4-1) ... Setting up libpng12-0:armhf (1.2.49-1) ... Setting up libxau6:armhf (1:1.0.7-1) ... Setting up libxdmcp6:armhf (1:1.1.1-1) ... Setting up libxcb1:armhf (1.8.1-1) ... Setting up libx11-data (2:1.4.99.901-2) ... Setting up libx11-6:armhf (2:1.4.99.901-2) ... Setting up libxcb-render0:armhf (1.8.1-1) ... Setting up libxcb-shm0:armhf (1.8.1-1) ... Setting up libxrender1:armhf (1:0.9.7-1) ... Setting up libcairo2:armhf (1.12.2-1) ... Setting up libffi5:armhf (3.0.10-3+b3) ... Setting up libglib2.0-0:armhf (2.32.2-1) ... No schema files found: doing nothing. Setting up libcroco3:armhf (0.6.5-1) ... Setting up libdatrie1:armhf (0.2.5-3) ... Setting up x11-common (1:7.6+13) ... All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of start. Setting up libice6:armhf (2:1.0.8-2) ... Setting up libjpeg8:armhf (8d-1) ... Setting up libthai-data (0.1.17-1) ... Setting up libthai0:armhf (0.1.17-1) ... Setting up libxft2:armhf (2.2.0-3) ... Setting up fontconfig (2.9.0-3) ... Cleaning up old fontconfig caches... done. Regenerating fonts cache... done. Setting up libpango1.0-0:armhf (1.30.0-1) ... Setting up libsm6:armhf (2:1.2.1-2) ... Setting up libunistring0:armhf (0.9.3-5) ... Setting up libxext6:armhf (2:1.3.1-2) ... Setting up libxt6:armhf (1:1.1.3-1) ... Setting up libxmu6:armhf (2:1.1.1-1) ... Setting up libxpm4:armhf (1:3.5.10-1) ... Setting up libxaw7:armhf (2:1.0.10-2) ... Setting up bsdmainutils (9.0.1) ... 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 groff-base (1.21-7) ... Setting up man-db (2.6.1-2) ... Building database of manual pages ... Setting up file (5.11-1) ... Setting up gettext-base (0.18.1.1-5+rpi1) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5+rpi1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120419) ... Setting up doxygen (1.7.6.1-2.1) ... Setting up libcdt4 (2.26.3-10+rpi1) ... Setting up libcgraph5 (2.26.3-10+rpi1) ... Setting up libgd2-noxpm (2.0.36~rc1~dfsg-6) ... Setting up libgraph4 (2.26.3-10+rpi1) ... Setting up libpathplan4 (2.26.3-10+rpi1) ... Setting up libxdot4 (2.26.3-10+rpi1) ... Setting up libgvc5 (2.26.3-10+rpi1) ... Setting up libgvpr1 (2.26.3-10+rpi1) ... Setting up graphviz (2.26.3-10+rpi1) ... 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) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.2.0-2-mx5 armhf (armv7l) Toolchain package versions: binutils_2.22-6 dpkg-dev_1.16.2 g++-4.6_4.6.3-1.1+rpi2 gcc-4.6_4.6.3-1.1+rpi2 libc6-dev_2.13-30 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 linux-libc-dev_3.2.12-1 Package versions: apt_0.8.15.10 base-files_6.7 base-passwd_3.5.24 bash_4.2-2 binutils_2.22-6 bsdmainutils_9.0.1 bsdutils_1:2.20.1-4 build-essential_11.5+b1 bzip2_1.0.6-1 coreutils_8.13-3.1 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1.1+rpi2 dash_0.5.7-3 debconf_1.5.42 debfoster_2.7-1.1 debhelper_9.20120419 debian-archive-keyring_2010.08.28 debianutils_4.3 diffutils_1:3.2-2 doxygen_1.7.6.1-2.1 dpkg_1.16.2 dpkg-dev_1.16.2 e2fslibs_1.42.2-2 e2fsprogs_1.42.2-2 fakeroot_1.18.3-1 file_5.11-1 findutils_4.4.2-4 fontconfig_2.9.0-3 fontconfig-config_2.9.0-3 g++_4:4.6.2-4 g++-4.6_4.6.3-1.1+rpi2 gcc_4:4.6.2-4 gcc-4.4-base_4.4.7-1.1+rpi1 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.3-1.1+rpi2 gcc-4.6-base_4.6.3-1.1+rpi2 gcc-4.7-base_4.7.0-1.1+rpi gettext_0.18.1.1-5+rpi1 gettext-base_0.18.1.1-5+rpi1 gnupg_1.4.12-4 gpgv_1.4.12-4 graphviz_2.26.3-10+rpi1 grep_2.11-3 groff-base_1.21-7 gzip_1.4-5 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-22.1 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libargtable2-0_12-1 libargtable2-dev_12-1 libargtable2-docs_12-1 libattr1_1:2.4.46-5 libblkid1_2.20.1-4 libbz2-1.0_1.0.6-1 libc-bin_2.13-30 libc-dev-bin_2.13-30 libc6_2.13-30 libc6-dev_2.13-30 libcairo2_1.12.2-1 libcdt4_2.26.3-10+rpi1 libcgraph5_2.26.3-10+rpi1 libclass-isa-perl_0.36-3 libcomerr2_1.42.2-2 libcroco3_0.6.5-1 libdatrie1_0.2.5-3 libdb5.1_5.1.29-1 libdpkg-perl_1.16.2 libexpat1_2.1.0-1 libffi5_3.0.10-3+b3 libfile-fcntllock-perl_0.14-1 libfontconfig1_2.9.0-3 libfreetype6_2.4.9-1 libgc1c2_1:7.1-8 libgcc1_1:4.7.0-1.1+rpi libgd2-noxpm_2.0.36~rc1~dfsg-6 libgdbm3_1.8.3-10 libglib2.0-0_2.32.2-1 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.7.0-1.1+rpi libgraph4_2.26.3-10+rpi1 libgvc5_2.26.3-10+rpi1 libgvpr1_2.26.3-10+rpi1 libice6_2:1.0.8-2 libjpeg8_8d-1 liblocale-gettext-perl_1.05-7 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.11-1 libmount1_2.20.1-4 libmpc2_0.9-4 libmpfr4_3.1.0-4 libncurses5_5.9-7 libncursesw5_5.9-7 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7 libpango1.0-0_1.30.0-1 libpathplan4_2.26.3-10+rpi1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libpixman-1-0_0.24.4-1 libpng12-0_1.2.49-1 libreadline6_6.2-8 libselinux1_2.1.9-2 libsemanage-common_2.1.6-2 libsemanage1_2.1.6-2 libsepol1_2.1.4-1 libslang2_2.2.4-10 libsm6_2:1.2.1-2 libss2_1.42.2-2 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libthai-data_0.1.17-1 libthai0_0.1.17-1 libtimedate-perl_1.2000-1 libtinfo5_5.9-7 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-2 libuuid1_2.20.1-4 libx11-6_2:1.4.99.901-2 libx11-data_2:1.4.99.901-2 libxau6_1:1.0.7-1 libxaw7_2:1.0.10-2 libxcb-render0_1.8.1-1 libxcb-shm0_1.8.1-1 libxcb1_1.8.1-1 libxdmcp6_1:1.1.1-1 libxdot4_2.26.3-10+rpi1 libxext6_2:1.3.1-2 libxft2_2.2.0-3 libxml2_2.7.8.dfsg-9 libxmu6_2:1.1.1-1 libxpm4_1:3.5.10-1 libxrender1_1:0.9.7-1 libxt6_1:1.1.3-1 linux-libc-dev_3.2.12-1 login_1:4.1.5-1 lsb-base_4.1+Debian0 make_3.81-8.1 man-db_2.6.1-2 mawk_1.3.3-17 mount_2.20.1-4 multiarch-support_2.13-30 ncurses-base_5.9-6 ncurses-bin_5.9-7 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-9 perl-base_5.14.2-9 perl-modules_5.14.2-9 po-debconf_1.0.16+nmu2 readline-common_6.2-8 sbuild-build-depends-clustalo-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-22.1 sysvinit_2.88dsf-22.1 sysvinit-utils_2.88dsf-22.1 tar_1.26-4 ttf-dejavu-core_2.33-2 tzdata_2012c-1 ucf_3.0025+nmu3 util-linux_2.20.1-4 x11-common_1:7.6+13 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.7.dfsg-1 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Wed May 2 09:07:46 2012 UTC using RSA key ID 326D8438 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./clustalo_1.1.0-1.dsc dpkg-source: info: extracting clustalo in clustalo-1.1.0 dpkg-source: info: unpacking clustalo_1.1.0.orig.tar.gz dpkg-source: info: unpacking clustalo_1.1.0-1.debian.tar.gz Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=buildd PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/usr/games SCHROOT_CHROOT_NAME=testing-armhf-sbuild SCHROOT_COMMAND=env SCHROOT_GID=108 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=testing-armhf-sbuild-6618d512-c82c-4845-ba5d-b7b30b6dc63e SCHROOT_UID=106 SCHROOT_USER=buildd SHELL=/bin/sh TERM=xterm USER=buildd dpkg-buildpackage ───────────────── dpkg-buildpackage: source package clustalo dpkg-buildpackage: source version 1.1.0-1 dpkg-source --before-build clustalo-1.1.0 dpkg-buildpackage: host architecture armhf 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 1.1.0 (FilumVitae) +NMMMMMMMMMS= MMMMM? :MMMMM8 IMMMMS MMMMM, ~MMMMN ,MMMMM 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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... 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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: 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 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -c -o hhalign.lo hhalign.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -c hhalign.cpp -fPIC -DPIC -o .libs/hhalign.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -c hhalign.cpp -o hhalign.o >/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 -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 -DCLUSTALO -O3 -g -O2 -c -o a2m.lo a2m.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O3 -g -O2 -c a2m.c -fPIC -DPIC -o .libs/a2m.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O3 -g -O2 -c a2m.c -o a2m.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O3 -g -O2 -c -o aligneval.lo aligneval.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O3 -g -O2 -c aligneval.c -fPIC -DPIC -o .libs/aligneval.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O3 -g -O2 -c aligneval.c -o aligneval.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O3 -g -O2 -c -o alignio.lo alignio.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O3 -g -O2 -c alignio.c -fPIC -DPIC -o .libs/alignio.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O3 -g -O2 -c alignio.c -o alignio.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O3 -g -O2 -c -o clustal.lo clustal.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O3 -g -O2 -c clustal.c -fPIC -DPIC -o .libs/clustal.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O3 -g -O2 -c clustal.c -o clustal.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O3 -g -O2 -c -o cluster.lo cluster.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O3 -g -O2 -c cluster.c -fPIC -DPIC -o .libs/cluster.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O3 -g -O2 -c cluster.c -o cluster.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O3 -g -O2 -c -o dayhoff.lo dayhoff.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O3 -g -O2 -c dayhoff.c -fPIC -DPIC -o .libs/dayhoff.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O3 -g -O2 -c dayhoff.c -o dayhoff.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O3 -g -O2 -c -o eps.lo eps.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O3 -g -O2 -c eps.c -fPIC -DPIC -o .libs/eps.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O3 -g -O2 -c eps.c -o eps.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O3 -g -O2 -c -o file.lo file.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O3 -g -O2 -c file.c -fPIC -DPIC -o .libs/file.o libtool: compile: gcc -DHAVE_CONFIG_H -I. 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-DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -g -O2 -c progress.c -o progress.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -g -O2 -c -o seq.lo seq.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -g -O2 -c seq.c -fPIC -DPIC -o .libs/seq.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -g -O2 -c seq.c -o seq.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -g -O2 -c -o symmatrix.lo symmatrix.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -g -O2 -c symmatrix.c -fPIC -DPIC -o .libs/symmatrix.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -g -O2 -c symmatrix.c -o symmatrix.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -g -O2 -c -o tree.lo tree.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -g -O2 -c tree.c -fPIC -DPIC -o .libs/tree.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -g -O2 -c tree.c -o tree.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -g -O2 -c -o util.lo util.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -g -O2 -c util.c -fPIC -DPIC -o .libs/util.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -g -O2 -c util.c -o util.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -g -O2 -c -o weights.lo weights.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -g -O2 -c weights.c -fPIC -DPIC -o .libs/weights.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -g -O2 -c weights.c -o weights.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=link gcc -fopenmp -O3 -g -O2 -o libclustal.la hhalign_wrapper.lo ktuple_pair.lo list.lo log.lo muscle_upgma.lo muscle_tree.lo mbed.lo pair_dist.lo progress.lo seq.lo symmatrix.lo tree.lo util.lo weights.lo -largtable2 -lm libtool: link: ar cru .libs/libclustal.a .libs/hhalign_wrapper.o .libs/ktuple_pair.o .libs/list.o .libs/log.o .libs/muscle_upgma.o .libs/muscle_tree.o .libs/mbed.o .libs/pair_dist.o .libs/progress.o .libs/seq.o .libs/symmatrix.o .libs/tree.o .libs/util.o .libs/weights.o libtool: link: ranlib .libs/libclustal.a libtool: link: ( cd ".libs" && rm -f "libclustal.la" && ln -s "../libclustal.la" "libclustal.la" ) make[4]: Leaving directory `/«PKGBUILDDIR»/src/clustal' make[4]: Entering directory `/«PKGBUILDDIR»/src' /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -O3 -fopenmp -g -O2 -c -o clustal-omega.lo clustal-omega.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -O3 -fopenmp -g -O2 -c clustal-omega.c -fPIC -DPIC -o .libs/clustal-omega.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -O3 -fopenmp -g -O2 -c clustal-omega.c -o clustal-omega.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=link gcc -O3 -fopenmp -g -O2 -static -o libclustalo.la -rpath /usr/lib clustal-omega.lo clustal/libclustal.la hhalign/libhhalign.la squid/libsquid.la kmpp/libkmpp.la -largtable2 -lm libtool: link: (cd .libs/libclustalo.lax/libclustal.a && ar x "/«PKGBUILDDIR»/src/clustal/.libs/libclustal.a") libtool: link: (cd .libs/libclustalo.lax/libhhalign.a && ar x "/«PKGBUILDDIR»/src/hhalign/.libs/libhhalign.a") libtool: link: (cd .libs/libclustalo.lax/libsquid.a && ar x "/«PKGBUILDDIR»/src/squid/.libs/libsquid.a") libtool: link: (cd .libs/libclustalo.lax/libkmpp.a && ar x "/«PKGBUILDDIR»/src/kmpp/.libs/libkmpp.a") libtool: link: ar cru .libs/libclustalo.a clustal-omega.o .libs/libclustalo.lax/libclustal.a/muscle_tree.o .libs/libclustalo.lax/libclustal.a/weights.o .libs/libclustalo.lax/libclustal.a/log.o .libs/libclustalo.lax/libclustal.a/ktuple_pair.o .libs/libclustalo.lax/libclustal.a/mbed.o .libs/libclustalo.lax/libclustal.a/tree.o .libs/libclustalo.lax/libclustal.a/muscle_upgma.o .libs/libclustalo.lax/libclustal.a/progress.o .libs/libclustalo.lax/libclustal.a/list.o .libs/libclustalo.lax/libclustal.a/util.o .libs/libclustalo.lax/libclustal.a/symmatrix.o .libs/libclustalo.lax/libclustal.a/pair_dist.o .libs/libclustalo.lax/libclustal.a/seq.o .libs/libclustalo.lax/libclustal.a/hhalign_wrapper.o .libs/libclustalo.lax/libhhalign.a/hhalign.o .libs/libclustalo.lax/libsquid.a/hsregex.o .libs/libclustalo.lax/libsquid.a/sqerror.o .libs/libclustalo.lax/libsquid.a/file.o .libs/libclustalo.lax/libsquid.a/stack.o .libs/libclustalo.lax/libsquid.a/alignio.o .libs/libclustalo.lax/libsquid.a/gsi64.o .libs/libclustalo.lax/libsquid.a/aligneval.o .libs/libclustalo.lax/libsquid.a/gki.o .libs/libclustalo.lax/libsquid.a/sre_ctype.o .libs/libclustalo.lax/libsquid.a/eps.o .libs/libclustalo.lax/libsquid.a/dayhoff.o .libs/libclustalo.lax/libsquid.a/vectorops.o .libs/libclustalo.lax/libsquid.a/sqio.o .libs/libclustalo.lax/libsquid.a/rk.o .libs/libclustalo.lax/libsquid.a/translate.o .libs/libclustalo.lax/libsquid.a/stockholm.o .libs/libclustalo.lax/libsquid.a/cluster.o .libs/libclustalo.lax/libsquid.a/iupac.o .libs/libclustalo.lax/libsquid.a/shuffle.o .libs/libclustalo.lax/libsquid.a/clustal.o .libs/libclustalo.lax/libsquid.a/msa.o .libs/libclustalo.lax/libsquid.a/getopt.o .libs/libclustalo.lax/libsquid.a/sre_math.o .libs/libclustalo.lax/libsquid.a/weight.o .libs/libclustalo.lax/libsquid.a/phylip.o .libs/libclustalo.lax/libsquid.a/types.o .libs/libclustalo.lax/libsquid.a/a2m.o .libs/libclustalo.lax/libsquid.a/msf.o .libs/libclustalo.lax/libsquid.a/sre_random.o .libs/libclustalo.lax/libsquid.a/selex.o .libs/libclustalo.lax/libsquid.a/squidcore.o .libs/libclustalo.lax/libsquid.a/seqencode.o .libs/libclustalo.lax/libsquid.a/ssi.o .libs/libclustalo.lax/libsquid.a/gsi.o .libs/libclustalo.lax/libsquid.a/revcomp.o .libs/libclustalo.lax/libsquid.a/sre_string.o .libs/libclustalo.lax/libsquid.a/stopwatch.o .libs/libclustalo.lax/libkmpp.a/KmTree.o .libs/libclustalo.lax/libkmpp.a/KmUtils.o .libs/libclustalo.lax/libkmpp.a/KMeans.o libtool: link: ranlib .libs/libclustalo.a libtool: link: rm -fr .libs/libclustalo.lax libtool: link: ( cd ".libs" && rm -f "libclustalo.la" && ln -s "../libclustalo.la" "libclustalo.la" ) g++ -DHAVE_CONFIG_H -I. -O3 -fopenmp -g -O2 -c -o main.o main.cpp gcc -DHAVE_CONFIG_H -I. -O3 -fopenmp -g -O2 -c mymain.c /bin/bash ../libtool --tag=CXX --mode=link g++ -O3 -fopenmp -g -O2 -o clustalo main.o mymain.o libclustalo.la -largtable2 -lm libtool: link: g++ -O3 -fopenmp -g -O2 -o clustalo main.o mymain.o ./.libs/libclustalo.a /usr/lib/libargtable2.so -lm make[4]: Leaving directory `/«PKGBUILDDIR»/src' make[3]: Leaving directory `/«PKGBUILDDIR»/src' make[2]: Leaving directory `/«PKGBUILDDIR»/src' make[2]: Entering directory `/«PKGBUILDDIR»' make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/«PKGBUILDDIR»' make[1]: Leaving directory `/«PKGBUILDDIR»' dh_auto_test -a make[1]: Entering directory `/«PKGBUILDDIR»' Making check in src make[2]: Entering directory `/«PKGBUILDDIR»/src' Making check in hhalign make[3]: Entering directory `/«PKGBUILDDIR»/src/hhalign' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/src/hhalign' Making check in squid make[3]: Entering directory `/«PKGBUILDDIR»/src/squid' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/src/squid' Making check in kmpp make[3]: Entering directory `/«PKGBUILDDIR»/src/kmpp' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/src/kmpp' Making check in clustal make[3]: Entering directory `/«PKGBUILDDIR»/src/clustal' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/src/clustal' make[3]: Entering directory `/«PKGBUILDDIR»/src' make[3]: Leaving directory `/«PKGBUILDDIR»/src' make[2]: Leaving directory `/«PKGBUILDDIR»/src' make[2]: Entering directory `/«PKGBUILDDIR»' make[2]: Nothing to be done for `check-am'. make[2]: Leaving directory `/«PKGBUILDDIR»' make[1]: Leaving directory `/«PKGBUILDDIR»' fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_installdirs -a dh_auto_install -a make[1]: Entering directory `/«PKGBUILDDIR»' Making install in src make[2]: Entering directory `/«PKGBUILDDIR»/src' Making install in hhalign make[3]: Entering directory `/«PKGBUILDDIR»/src/hhalign' make[4]: Entering directory `/«PKGBUILDDIR»/src/hhalign' make[4]: Nothing to be done for `install-exec-am'. test -z "/usr/include/clustalo/hhalign" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/tmp/usr/include/clustalo/hhalign" /usr/bin/install -c -m 644 general.h hhfunc.h '/«PKGBUILDDIR»/debian/tmp/usr/include/clustalo/hhalign' make[4]: Leaving directory `/«PKGBUILDDIR»/src/hhalign' make[3]: Leaving directory `/«PKGBUILDDIR»/src/hhalign' Making install in squid make[3]: Entering directory `/«PKGBUILDDIR»/src/squid' make[4]: Entering directory `/«PKGBUILDDIR»/src/squid' make[4]: Nothing to be done for `install-exec-am'. test -z "/usr/include/clustalo/squid" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/tmp/usr/include/clustalo/squid" /usr/bin/install -c -m 644 gki.h gsi64.h msa.h rk.h squid.h stopwatch.h sqfuncs.h sre_random.h ssi.h stockholm.h vectorops.h version.h '/«PKGBUILDDIR»/debian/tmp/usr/include/clustalo/squid' make[4]: Leaving directory `/«PKGBUILDDIR»/src/squid' make[3]: Leaving directory `/«PKGBUILDDIR»/src/squid' Making install in kmpp make[3]: Entering directory `/«PKGBUILDDIR»/src/kmpp' make[4]: Entering directory `/«PKGBUILDDIR»/src/kmpp' make[4]: Nothing to be done for `install-exec-am'. make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/src/kmpp' make[3]: Leaving directory `/«PKGBUILDDIR»/src/kmpp' Making install in clustal make[3]: Entering directory `/«PKGBUILDDIR»/src/clustal' make[4]: Entering directory `/«PKGBUILDDIR»/src/clustal' make[4]: Nothing to be done for `install-exec-am'. test -z "/usr/include/clustalo/clustal" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/tmp/usr/include/clustalo/clustal" /usr/bin/install -c -m 644 hhalign_wrapper.h ktuple_pair.h log.h mbed.h muscle_tree.h pair_dist.h progress.h seq.h symmatrix.h tree.h util.h weights.h '/«PKGBUILDDIR»/debian/tmp/usr/include/clustalo/clustal' make[4]: Leaving directory `/«PKGBUILDDIR»/src/clustal' make[3]: Leaving directory `/«PKGBUILDDIR»/src/clustal' make[3]: Entering directory `/«PKGBUILDDIR»/src' make[4]: Entering directory `/«PKGBUILDDIR»/src' test -z "/usr/lib" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/tmp/usr/lib" /bin/bash ../libtool --mode=install /usr/bin/install -c libclustalo.la '/«PKGBUILDDIR»/debian/tmp/usr/lib' libtool: install: /usr/bin/install -c .libs/libclustalo.lai /«PKGBUILDDIR»/debian/tmp/usr/lib/libclustalo.la libtool: install: /usr/bin/install -c .libs/libclustalo.a /«PKGBUILDDIR»/debian/tmp/usr/lib/libclustalo.a libtool: install: chmod 644 /«PKGBUILDDIR»/debian/tmp/usr/lib/libclustalo.a libtool: install: ranlib /«PKGBUILDDIR»/debian/tmp/usr/lib/libclustalo.a libtool: install: warning: remember to run `libtool --finish /usr/lib' test -z "/usr/bin" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/tmp/usr/bin" /bin/bash ../libtool --mode=install /usr/bin/install -c clustalo '/«PKGBUILDDIR»/debian/tmp/usr/bin' libtool: install: /usr/bin/install -c clustalo /«PKGBUILDDIR»/debian/tmp/usr/bin/clustalo test -z "/usr/include/clustalo/" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/tmp/usr/include/clustalo/" /usr/bin/install -c -m 644 clustal-omega-config.h clustal-omega.h '/«PKGBUILDDIR»/debian/tmp/usr/include/clustalo/' make[4]: Leaving directory `/«PKGBUILDDIR»/src' make[3]: Leaving directory `/«PKGBUILDDIR»/src' make[2]: Leaving directory `/«PKGBUILDDIR»/src' make[2]: Entering directory `/«PKGBUILDDIR»' make[3]: Entering directory `/«PKGBUILDDIR»' make[3]: Nothing to be done for `install-exec-am'. test -z "/usr/share/doc/clustal-omega" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/tmp/usr/share/doc/clustal-omega" /usr/bin/install -c -m 644 README '/«PKGBUILDDIR»/debian/tmp/usr/share/doc/clustal-omega' test -z "/usr/lib/pkgconfig" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/tmp/usr/lib/pkgconfig" /usr/bin/install -c -m 644 clustalo.pc '/«PKGBUILDDIR»/debian/tmp/usr/lib/pkgconfig' make[3]: Leaving directory `/«PKGBUILDDIR»' make[2]: Leaving directory `/«PKGBUILDDIR»' make[1]: Leaving directory `/«PKGBUILDDIR»' debian/rules override_dh_install make[1]: Entering directory `/«PKGBUILDDIR»' # Generate doxygen doc mkdir -p doc doxygen Doxyfile /«PKGBUILDDIR»/src/clustal/seq.c:396: warning: The following parameters of ReadSequences(mseq_t *prMSeq, char *seqfile, int iSeqType, int iSeqFmt, int iMaxNumSeq, int iMaxSeqLen) are not documented: parameter 'iSeqFmt' /«PKGBUILDDIR»/src/clustal/seq.c:396: warning: The following parameters of ReadSequences(mseq_t *prMSeq, char *seqfile, int iSeqType, int iSeqFmt, int iMaxNumSeq, int iMaxSeqLen) are not documented: parameter 'iSeqFmt' (process:9754): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9753): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9756): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9758): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9760): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9762): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9764): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9767): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9768): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9770): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9772): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9774): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9776): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9780): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9779): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9784): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9783): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9786): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9789): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9790): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9792): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9794): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9796): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9798): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9800): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9802): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9804): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9806): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9808): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9810): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9812): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9814): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9816): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9818): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9820): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9822): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9824): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9826): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9828): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9830): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9832): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9834): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9836): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9838): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9840): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9842): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9844): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9848): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9847): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9850): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9852): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9854): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9856): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9858): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9860): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9863): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9864): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9866): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9868): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9870): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9872): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9874): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9876): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9879): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9880): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9882): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9884): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9886): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9888): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9890): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9892): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9894): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9896): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9898): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9900): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9902): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9904): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9906): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9908): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9910): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9912): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9914): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9918): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9917): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9920): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9922): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9924): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9926): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9928): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9930): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9932): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9934): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9936): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9938): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9940): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9942): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9944): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9946): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9948): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9950): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9952): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9954): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:9956): Pango-WARNING **: error 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Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:10000): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:10002): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:10004): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:10006): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:10010): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:10009): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:10012): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:10014): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:10017): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:10018): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:10022): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:10021): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:10024): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:10026): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied (process:10028): Pango-WARNING **: error opening config file '/root/.pangorc': Permission denied dh_install rm -rf debian/tmp/usr/lib/pkgconfig rm -f debian/tmp/usr/lib/libclustalo.la mv debian/tmp/usr/include debian/libclustalo-dev/usr mv debian/tmp/usr/lib debian/libclustalo-dev/usr mv debian/tmp/usr/bin debian/clustalo/usr make[1]: Leaving directory `/«PKGBUILDDIR»' dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_installcatalogs -a dh_installcron -a dh_installdebconf -a dh_installemacsen -a dh_installifupdown -a dh_installinfo -a dh_installinit -a dh_installmenu -a dh_installmime -a dh_installmodules -a dh_installlogcheck -a dh_installlogrotate -a dh_installpam -a dh_installppp -a dh_installudev -a dh_installwm -a dh_installxfonts -a dh_installgsettings -a dh_bugfiles -a dh_ucf -a dh_lintian -a dh_gconf -a dh_icons -a dh_perl -a dh_usrlocal -a dh_link -a dh_compress -a dh_fixperms -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/clustalo/usr/bin/clustalo contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: Depends field of package libclustalo-dev: unknown substitution variable ${shlibs:Depends} dh_md5sums -a dh_builddeb -a dpkg-deb: building package `clustalo' in `../clustalo_1.1.0-1_armhf.deb'. dpkg-deb: building package `libclustalo-dev' in `../libclustalo-dev_1.1.0-1_armhf.deb'. dpkg-genchanges -B -mbuildd >../clustalo_1.1.0-1_armhf.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build clustalo-1.1.0 dpkg-buildpackage: binary only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120517-1305 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ clustalo_1.1.0-1_armhf.changes: ─────────────────────────────── Format: 1.8 Date: Wed, 02 May 2012 10:56:19 +0200 Source: clustalo Binary: clustalo libclustalo-dev libclustalo-doc Architecture: armhf Version: 1.1.0-1 Distribution: testing Urgency: low Maintainer: buildd Changed-By: Olivier Sallou Description: clustalo - General purpose multiple sequence alignment program for proteins libclustalo-dev - library to embed Clustal Omega libclustalo-doc - API documentation Changes: clustalo (1.1.0-1) unstable; urgency=low . * New upstream version (DNA/RNA support added) Checksums-Sha1: 27fdb32f06ec5e9ace6274b7e43c7109cabbc162 271588 clustalo_1.1.0-1_armhf.deb ac441ff1503714db756026a5a3c379c78290fca1 361990 libclustalo-dev_1.1.0-1_armhf.deb Checksums-Sha256: 77a5d552a5cc96ba09c20c5e0d4cd1b4ff6185f04293672de46ded747626e6d4 271588 clustalo_1.1.0-1_armhf.deb 76e901dcb9c0e8a84f81ce4c64a3586f8909e9b8b518e084daa0592506d6564e 361990 libclustalo-dev_1.1.0-1_armhf.deb Files: 2939ddf9d4135c4b9ed87fc8695d65ec 271588 science optional clustalo_1.1.0-1_armhf.deb c117b3040f05594356603258b87eb718 361990 libdevel optional libclustalo-dev_1.1.0-1_armhf.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ clustalo_1.1.0-1_armhf.deb ────────────────────────── new debian package, version 2.0. size 271588 bytes: control archive= 771 bytes. 651 bytes, 14 lines control 399 bytes, 6 lines md5sums Package: clustalo Version: 1.1.0-1 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 548 Depends: libargtable2-0 (>= 7), libc6 (>= 2.13-28), libgcc1 (>= 1:4.4.0), libgomp1 (>= 4.2.1), libstdc++6 (>= 4.4.0) Section: science Priority: optional Homepage: http://www.clustal.org/omega/ Description: General purpose multiple sequence alignment program for proteins Clustal-Omega is a general purpose multiple sequence alignment (MSA) program for proteins. It produces high quality MSAs and is capable of handling data-sets of hundreds of thousands of sequences in reasonable time. drwxr-xr-x root/root 0 2012-05-17 13:04 ./ drwxr-xr-x root/root 0 2012-05-17 13:04 ./usr/ drwxr-xr-x root/root 0 2012-05-17 13:04 ./usr/share/ drwxr-xr-x root/root 0 2012-05-17 13:04 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-05-17 13:04 ./usr/share/doc/clustalo/ -rw-r--r-- root/root 645 2012-01-19 06:39 ./usr/share/doc/clustalo/changelog.gz -rw-r--r-- root/root 232 2012-05-02 02:02 ./usr/share/doc/clustalo/changelog.Debian.gz -rw-r--r-- root/root 9035 2012-01-19 06:39 ./usr/share/doc/clustalo/README.gz -rw-r--r-- root/root 1178 2012-05-02 01:52 ./usr/share/doc/clustalo/copyright drwxr-xr-x root/root 0 2012-05-17 13:04 ./usr/share/man/ drwxr-xr-x root/root 0 2012-05-17 13:04 ./usr/share/man/man1/ -rw-r--r-- root/root 1083 2012-05-17 13:04 ./usr/share/man/man1/clustalo.1.gz drwxr-xr-x root/root 0 2012-05-17 13:04 ./usr/bin/ -rwxr-xr-x root/root 511212 2012-05-17 13:04 ./usr/bin/clustalo libclustalo-dev_1.1.0-1_armhf.deb ───────────────────────────────── new debian package, version 2.0. size 361990 bytes: control archive= 1437 bytes. 504 bytes, 15 lines control 2305 bytes, 32 lines md5sums Package: libclustalo-dev Source: clustalo Version: 1.1.0-1 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 914 Depends: libargtable2-dev, clustalo (= 1.1.0-1) Suggests: libclustalo-doc Section: libdevel Priority: optional Homepage: http://www.clustal.org/omega/ Description: library to embed Clustal Omega This package contains headers and libraries to include Clustal Omega in a program. It provides clustal usage with an API. drwxr-xr-x root/root 0 2012-05-17 13:04 ./ drwxr-xr-x root/root 0 2012-05-17 13:04 ./usr/ drwxr-xr-x root/root 0 2012-05-17 13:04 ./usr/lib/ -rw-r--r-- root/root 783332 2012-05-17 13:04 ./usr/lib/libclustalo.a drwxr-xr-x root/root 0 2012-05-17 13:04 ./usr/share/ drwxr-xr-x root/root 0 2012-05-17 13:04 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-05-17 13:04 ./usr/share/doc/libclustalo-dev/ -rw-r--r-- root/root 645 2012-01-19 06:39 ./usr/share/doc/libclustalo-dev/changelog.gz -rw-r--r-- root/root 232 2012-05-02 02:02 ./usr/share/doc/libclustalo-dev/changelog.Debian.gz -rw-r--r-- root/root 1178 2012-05-02 01:52 ./usr/share/doc/libclustalo-dev/copyright drwxr-xr-x root/root 0 2012-05-17 13:03 ./usr/include/ drwxr-xr-x root/root 0 2012-05-17 13:03 ./usr/include/clustalo/ -rw-r--r-- root/root 9526 2012-05-17 13:03 ./usr/include/clustalo/clustal-omega-config.h -rw-r--r-- root/root 3986 2012-05-17 13:03 ./usr/include/clustalo/clustal-omega.h drwxr-xr-x root/root 0 2012-05-17 13:03 ./usr/include/clustalo/clustal/ -rw-r--r-- root/root 816 2012-05-17 13:03 ./usr/include/clustalo/clustal/mbed.h -rw-r--r-- root/root 1251 2012-05-17 13:03 ./usr/include/clustalo/clustal/ktuple_pair.h -rw-r--r-- root/root 1257 2012-05-17 13:03 ./usr/include/clustalo/clustal/progress.h -rw-r--r-- root/root 1066 2012-05-17 13:03 ./usr/include/clustalo/clustal/tree.h -rw-r--r-- root/root 2184 2012-05-17 13:03 ./usr/include/clustalo/clustal/symmatrix.h -rw-r--r-- root/root 949 2012-05-17 13:03 ./usr/include/clustalo/clustal/hhalign_wrapper.h -rw-r--r-- root/root 4112 2012-05-17 13:03 ./usr/include/clustalo/clustal/muscle_tree.h -rw-r--r-- root/root 1261 2012-05-17 13:03 ./usr/include/clustalo/clustal/pair_dist.h -rw-r--r-- root/root 741 2012-05-17 13:03 ./usr/include/clustalo/clustal/weights.h -rw-r--r-- root/root 1787 2012-05-17 13:03 ./usr/include/clustalo/clustal/log.h -rw-r--r-- root/root 2308 2012-05-17 13:03 ./usr/include/clustalo/clustal/util.h -rw-r--r-- root/root 3752 2012-05-17 13:03 ./usr/include/clustalo/clustal/seq.h drwxr-xr-x root/root 0 2012-05-17 13:03 ./usr/include/clustalo/hhalign/ -rw-r--r-- root/root 2511 2012-05-17 13:03 ./usr/include/clustalo/hhalign/general.h -rw-r--r-- root/root 832 2012-05-17 13:03 ./usr/include/clustalo/hhalign/hhfunc.h drwxr-xr-x root/root 0 2012-05-17 13:03 ./usr/include/clustalo/squid/ -rw-r--r-- root/root 10390 2012-05-17 13:03 ./usr/include/clustalo/squid/sqfuncs.h -rw-r--r-- root/root 1381 2012-05-17 13:03 ./usr/include/clustalo/squid/gki.h -rw-r--r-- root/root 1868 2012-05-17 13:03 ./usr/include/clustalo/squid/stockholm.h -rw-r--r-- root/root 1434 2012-05-17 13:03 ./usr/include/clustalo/squid/vectorops.h -rw-r--r-- root/root 489 2012-05-17 13:03 ./usr/include/clustalo/squid/sre_random.h -rw-r--r-- root/root 333 2012-05-17 13:03 ./usr/include/clustalo/squid/version.h -rw-r--r-- root/root 19393 2012-05-17 13:03 ./usr/include/clustalo/squid/squid.h -rw-r--r-- root/root 3473 2012-05-17 13:03 ./usr/include/clustalo/squid/gsi64.h -rw-r--r-- root/root 1264 2012-05-17 13:03 ./usr/include/clustalo/squid/rk.h -rw-r--r-- root/root 12782 2012-05-17 13:03 ./usr/include/clustalo/squid/msa.h -rw-r--r-- root/root 7610 2012-05-17 13:03 ./usr/include/clustalo/squid/ssi.h -rw-r--r-- root/root 1937 2012-05-17 13:03 ./usr/include/clustalo/squid/stopwatch.h ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 18 not upgraded. Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bsdmainutils* debhelper* doxygen* file* fontconfig* fontconfig-config* gettext* gettext-base* graphviz* groff-base* html2text* intltool-debian* libargtable2-0* libargtable2-dev* libargtable2-docs* libcairo2* libcdt4* libcgraph5* libcroco3* libdatrie1* libexpat1* libffi5* libfontconfig1* libfreetype6* libgd2-noxpm* libglib2.0-0* libgraph4* libgvc5* libgvpr1* libice6* libjpeg8* libmagic1* libpango1.0-0* libpathplan4* libpcre3* libpipeline1* libpixman-1-0* libpng12-0* libsm6* libthai-data* libthai0* libunistring0* libx11-6* libx11-data* libxau6* libxaw7* libxcb-render0* libxcb-shm0* libxcb1* libxdmcp6* libxdot4* libxext6* libxft2* libxml2* libxmu6* libxpm4* libxrender1* libxt6* man-db* po-debconf* sbuild-build-depends-clustalo-dummy* sbuild-build-depends-core-dummy* ttf-dejavu-core* x11-common* 0 upgraded, 0 newly installed, 64 to remove and 18 not upgraded. After this operation, 51.7 MB disk space will be freed. (Reading database ... 12872 files and directories currently installed.) Removing sbuild-build-depends-clustalo-dummy ... Removing debhelper ... Removing man-db ... Purging configuration files for man-db ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing doxygen ... Removing file ... Removing graphviz ... Purging configuration files for graphviz ... Removing libgvc5 ... Purging configuration files for libgvc5 ... Removing libpango1.0-0:armhf ... Purging configuration files for libpango1.0-0:armhf ... Removing fontconfig ... Purging configuration files for fontconfig ... Removing libxft2:armhf ... Purging configuration files for libxft2:armhf ... Removing libcairo2:armhf ... Purging configuration files for libcairo2:armhf ... Removing libfontconfig1:armhf ... Purging configuration files for libfontconfig1:armhf ... Removing fontconfig-config ... Purging configuration files for fontconfig-config ... Removing po-debconf ... Removing intltool-debian ... 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Purging configuration files for x11-common ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: armhf Build-Space: 23624 Build-Time: 609 Distribution: testing Install-Time: 124 Job: clustalo_1.1.0-1 Package: clustalo Package-Time: 781 Source-Version: 1.1.0-1 Space: 23624 Status: successful Version: 1.1.0-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120517-1305 Build needed 00:13:01, 23624k disc space