sbuild (Debian sbuild) 0.62.6 (07 Dec 2011) on build01.raspbian.lan ╔══════════════════════════════════════════════════════════════════════════════╗ ║ infernal 1.0.2-2 (armhf) 04 May 2012 21:25 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: infernal Version: 1.0.2-2 Source Version: 1.0.2-2 Distribution: testing Architecture: armhf I: NOTICE: Log filtering will replace 'build/infernal-W43qnz/infernal-1.0.2' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/infernal-W43qnz' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/testing-armhf-sbuild-5fc9ef62-945a-42ce-8302-14026101c144' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Hit http://repo.raspbian.lan testing InRelease Hit http://repo.raspbian.lan testing/main Sources Hit http://repo.raspbian.lan testing/main armhf Packages Ign http://repo.raspbian.lan testing/main TranslationIndex Ign http://repo.raspbian.lan testing/main Translation-en 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: 'infernal' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/svn/debian-med/trunk/packages/infernal/trunk/ Need to get 15.2 MB of source archives. Get:1 http://repo.raspbian.lan/raspbian/ testing/main infernal 1.0.2-2 (dsc) [1503 B] Get:2 http://repo.raspbian.lan/raspbian/ testing/main infernal 1.0.2-2 (tar) [15.2 MB] Get:3 http://repo.raspbian.lan/raspbian/ testing/main infernal 1.0.2-2 (diff) [6680 B] Fetched 15.2 MB in 1s (10.6 MB/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-WuClPx/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/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 ... 10678 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), cdbs, debhelper (>= 7), autotools-dev, quilt Filtered Build-Depends: libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 7), autotools-dev, quilt dpkg-deb: building package `sbuild-build-depends-infernal-dummy' in `/«BUILDDIR»/resolver-4AR6LX/apt_archive/sbuild-build-depends-infernal-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install infernal build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: autotools-dev bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base html2text intltool-debian libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt Suggested packages: wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less www-browser libmail-box-perl procmail graphviz default-mta mail-transport-agent Recommended packages: curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: autotools-dev bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base html2text intltool-debian libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt sbuild-build-depends-infernal-dummy debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 23 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/9907 kB of archives. After this operation, 25.6 MB of additional disk space will be used. Selecting previously unselected package libpcre3:armhf. (Reading database ... 10678 files and directories currently installed.) Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.30-4_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) ... Selecting previously unselected package libxml2:armhf. Unpacking libxml2:armhf (from .../libxml2_2.7.8.dfsg-9_armhf.deb) ... Selecting previously unselected package libffi5:armhf. Unpacking libffi5:armhf (from .../libffi5_3.0.10-3+b3_armhf.deb) ... Selecting previously unselected package libglib2.0-0:armhf. Unpacking libglib2.0-0:armhf (from .../libglib2.0-0_2.32.0-4_armhf.deb) ... Selecting previously unselected package libcroco3:armhf. Unpacking libcroco3:armhf (from .../libcroco3_0.6.5-1_armhf.deb) ... Selecting previously unselected package libunistring0:armhf. Unpacking libunistring0:armhf (from .../libunistring0_0.9.3-5_armhf.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_armhf.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-7_armhf.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.1-2_armhf.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.11-1_armhf.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-5+rpi1_armhf.deb) ... Selecting previously unselected package autotools-dev. Unpacking autotools-dev (from .../autotools-dev_20120210.1_all.deb) ... Selecting previously unselected package cdbs. Unpacking cdbs (from .../archives/cdbs_0.4.111_all.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_armhf.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-5+rpi1_armhf.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_9.20120419_all.deb) ... Selecting previously unselected package diffstat. Unpacking diffstat (from .../diffstat_1.55-2_armhf.deb) ... Selecting previously unselected package quilt. Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ... Selecting previously unselected package sbuild-build-depends-infernal-dummy. Unpacking sbuild-build-depends-infernal-dummy (from .../sbuild-build-depends-infernal-dummy.deb) ... Setting up libpcre3:armhf (1:8.30-4) ... Setting up libpipeline1:armhf (1.2.1-1) ... Setting up libmagic1:armhf (5.11-1) ... Setting up libxml2:armhf (2.7.8.dfsg-9) ... Setting up libffi5:armhf (3.0.10-3+b3) ... Setting up libglib2.0-0:armhf (2.32.0-4) ... No schema files found: doing nothing. Setting up libcroco3:armhf (0.6.5-1) ... Setting up libunistring0:armhf (0.9.3-5) ... 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 autotools-dev (20120210.1) ... Setting up cdbs (0.4.111) ... 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 diffstat (1.55-2) ... Setting up quilt (0.60-2) ... Setting up sbuild-build-depends-infernal-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 autotools-dev_20120210.1 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 cdbs_0.4.111 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 diffstat_1.55-2 diffutils_1:3.2-2 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 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 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 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 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 libclass-isa-perl_0.36-3 libcomerr2_1.42.2-2 libcroco3_0.6.5-1 libdb5.1_5.1.29-1 libdpkg-perl_1.16.2 libffi5_3.0.10-3+b3 libfile-fcntllock-perl_0.14-1 libgc1c2_1:7.1-8 libgcc1_1:4.7.0-1.1+rpi libgdbm3_1.8.3-10 libglib2.0-0_2.32.0-4 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.7.0-1.1+rpi 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_5.9-6 libncursesw5_5.9-6 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7 libpcre3_1:8.30-4 libpipeline1_1.2.1-1 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_2.2.4-7 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 libtimedate-perl_1.2000-1 libtinfo5_5.9-6 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 libxml2_2.7.8.dfsg-9 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_5.9-6 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 quilt_0.60-2 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-infernal-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 tzdata_2012b-1 ucf_3.0025+nmu3 util-linux_2.20.1-4 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Tue Sep 27 15:45:12 2011 UTC using DSA key ID BE9D5339 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./infernal_1.0.2-2.dsc dpkg-source: info: extracting infernal in infernal-1.0.2 dpkg-source: info: unpacking infernal_1.0.2.orig.tar.gz dpkg-source: info: applying infernal_1.0.2-2.diff.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-5fc9ef62-945a-42ce-8302-14026101c144 SCHROOT_UID=106 SCHROOT_USER=buildd SHELL=/bin/sh TERM=xterm USER=buildd dpkg-buildpackage ───────────────── dpkg-buildpackage: source package infernal dpkg-buildpackage: source version 1.0.2-2 dpkg-source --before-build infernal-1.0.2 dpkg-buildpackage: host architecture armhf fakeroot debian/rules clean dh clean --with quilt dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory `/«PKGBUILDDIR»' if [ -r Makefile ]; then /usr/bin/make distclean; fi cd documentation/userguide; make distclean make[2]: Entering directory `/«PKGBUILDDIR»/documentation/userguide' rm -f *~ main.aux main.bbl main.blg main.dvi main.log main.out main.toc rm -f main.pdf rm -f manpages.tex make[2]: Leaving directory `/«PKGBUILDDIR»/documentation/userguide' cd easel/documentation; make distclean make[2]: Entering directory `/«PKGBUILDDIR»/easel/documentation' rm -rf cexcerpts rm -rf autotext make clean make[3]: Entering directory `/«PKGBUILDDIR»/easel/documentation' rm *~ TAGS rm: cannot remove `*~': No such file or directory rm: cannot remove `TAGS': No such file or directory make[3]: [clean] Error 1 (ignored) rm main.log main.out main.pdf main.aux main.toc rm: cannot remove `main.log': No such file or directory rm: cannot remove `main.out': No such file or directory rm: cannot remove `main.pdf': No such file or directory rm: cannot remove `main.aux': No such file or directory rm: cannot remove `main.toc': No such file or directory make[3]: [clean] Error 1 (ignored) rm main.bbl main.blg main.brf rm: cannot remove `main.bbl': No such file or directory rm: cannot remove `main.blg': No such file or directory rm: cannot remove `main.brf': No such file or directory make[3]: [clean] Error 1 (ignored) rm typography.log typography.aux typography.out rm: cannot remove `typography.log': No such file or directory rm: cannot remove `typography.aux': No such file or directory rm: cannot remove `typography.out': No such file or directory make[3]: [clean] Error 1 (ignored) rm autotext/*.tex rm: cannot remove `autotext/*.tex': No such file or directory make[3]: [clean] Error 1 (ignored) make[3]: Leaving directory `/«PKGBUILDDIR»/easel/documentation' make[2]: Leaving directory `/«PKGBUILDDIR»/easel/documentation' dh_clean *.1 */*.log *.log */Makefile Makefile documentation/manpages/*.1 make[1]: Leaving directory `/«PKGBUILDDIR»' dh_quilt_unpatch No patch removed dh_clean debian/rules build-arch dh build-arch --with quilt dh_testdir -a dh_quilt_patch -a Applying patch format_security.patch patching file easel/esl_getopts.c patching file easel/esl_msa.c patching file easel/esl_tree.c Now at patch format_security.patch dh_auto_configure -a configure: WARNING: unrecognized options: --disable-maintainer-mode, --disable-dependency-tracking configure: Configuring Infernal for your system. checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf configure: Full Infernal source distribution - using full configuration 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 how to run the C preprocessor... gcc -E checking for C compiler vendor... gnu checking for gcc option to accept ISO C99... -std=gnu99 checking for gcc -std=gnu99 option to accept ISO Standard C... (cached) -std=gnu99 checking for ranlib... ranlib checking for ar... /usr/bin/ar checking whether your make is GNU make... yes, it is. checking whether C compiler accepts -malign-double... no checking whether C compiler accepts -fstrict-aliasing... yes checking for gcc architecture flag... checking for gcc architecture flag... unknown checking whether C compiler accepts -O3 -fomit-frame-pointer -fstrict-aliasing... yes 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 emmintrin.h usability... no checking emmintrin.h presence... no checking for emmintrin.h... no checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking for stdint.h... (cached) yes checking for inttypes.h... (cached) yes checking whether byte ordering is bigendian... no checking for int8_t... yes checking for int16_t... yes checking for int32_t... yes checking for int64_t... yes checking for uint8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for off_t... yes checking for mkstemp... yes checking for popen... yes checking for strcasecmp... yes checking for times... yes checking for _LARGEFILE_SOURCE value needed for large files... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 configure: creating ./config.status config.status: creating src/Makefile config.status: creating testsuite/Makefile config.status: creating easel/miniapps/Makefile config.status: creating easel/testsuite/Makefile config.status: creating easel/Makefile config.status: creating Makefile config.status: creating src/config.h config.status: creating easel/esl_config.h configure: WARNING: unrecognized options: --disable-maintainer-mode, --disable-dependency-tracking dh_auto_build -a make[1]: Entering directory `/«PKGBUILDDIR»' (cd easel; make CC="gcc -std=gnu99" CFLAGS="-O3 -fomit-frame-pointer -fstrict-aliasing"; make) make[2]: Entering directory `/«PKGBUILDDIR»/easel' gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c easel.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_alphabet.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_cluster.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_dirichlet.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_distance.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_dmatrix.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_exponential.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_fileparser.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_gamma.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_getopts.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_gev.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_gumbel.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_histogram.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_hyperexp.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_keyhash.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_minimizer.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_mixgev.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_mpi.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_msa.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_msacluster.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_msashuffle.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_msaweight.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_normal.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_paml.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_random.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_randomseq.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_ratematrix.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_regexp.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_rootfinder.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_scorematrix.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_sq.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_sqio.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_sse.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_ssi.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_stack.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_stats.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_stopwatch.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_stretchexp.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_swat.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_tree.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_vectorops.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_vmx.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_weibull.c gcc -std=gnu99 -I. -O3 -fomit-frame-pointer -fstrict-aliasing -c esl_wuss.c /usr/bin/ar rcv libeasel.a easel.o esl_alphabet.o esl_cluster.o esl_dirichlet.o esl_distance.o esl_dmatrix.o esl_exponential.o esl_fileparser.o esl_gamma.o esl_getopts.o esl_gev.o esl_gumbel.o esl_histogram.o esl_hyperexp.o esl_keyhash.o esl_minimizer.o esl_mixgev.o esl_mpi.o esl_msa.o esl_msacluster.o esl_msashuffle.o esl_msaweight.o esl_normal.o esl_paml.o esl_random.o esl_randomseq.o esl_ratematrix.o esl_regexp.o esl_rootfinder.o esl_scorematrix.o esl_sq.o esl_sqio.o esl_sse.o esl_ssi.o esl_stack.o esl_stats.o esl_stopwatch.o esl_stretchexp.o esl_swat.o esl_tree.o esl_vectorops.o esl_vmx.o esl_weibull.o esl_wuss.o a - easel.o a - esl_alphabet.o a - esl_cluster.o a - esl_dirichlet.o a - esl_distance.o a - esl_dmatrix.o a - esl_exponential.o a - esl_fileparser.o a - esl_gamma.o a - esl_getopts.o a - esl_gev.o a - esl_gumbel.o a - esl_histogram.o a - esl_hyperexp.o a - esl_keyhash.o a - esl_minimizer.o a - esl_mixgev.o a - esl_mpi.o a - esl_msa.o a - esl_msacluster.o a - esl_msashuffle.o a - esl_msaweight.o a - esl_normal.o a - esl_paml.o a - esl_random.o a - esl_randomseq.o a - esl_ratematrix.o a - esl_regexp.o a - esl_rootfinder.o a - esl_scorematrix.o a - esl_sq.o a - esl_sqio.o a - esl_sse.o a - esl_ssi.o a - esl_stack.o a - esl_stats.o a - esl_stopwatch.o a - esl_stretchexp.o a - esl_swat.o a - esl_tree.o a - esl_vectorops.o a - esl_vmx.o a - esl_weibull.o a - esl_wuss.o ranlib libeasel.a chmod 644 libeasel.a (cd miniapps; make) make[3]: Entering directory `/«PKGBUILDDIR»/easel/miniapps' gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I.. -c esl-afetch.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L.. -o esl-afetch esl-afetch.o -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I.. -c esl-alimanip.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L.. -o esl-alimanip esl-alimanip.o -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I.. -c esl-alimap.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L.. -o esl-alimap esl-alimap.o -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I.. -c esl-alistat.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L.. -o esl-alistat esl-alistat.o -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I.. -c esl-compalign.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L.. -o esl-compalign esl-compalign.o -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I.. -c esl-compstruct.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L.. -o esl-compstruct esl-compstruct.o -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I.. -c esl-construct.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L.. -o esl-construct esl-construct.o -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I.. -c esl-histplot.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L.. -o esl-histplot esl-histplot.o -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I.. -c esl-reformat.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L.. -o esl-reformat esl-reformat.o -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I.. -c esl-selectn.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L.. -o esl-selectn esl-selectn.o -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I.. -c esl-seqstat.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L.. -o esl-seqstat esl-seqstat.o -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I.. -c esl-sfetch.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L.. -o esl-sfetch esl-sfetch.o -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I.. -c esl-shuffle.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L.. -o esl-shuffle esl-shuffle.o -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I.. -c esl-ssdraw.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L.. -o esl-ssdraw esl-ssdraw.o -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I.. -c esl-weight.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L.. -o esl-weight esl-weight.o -leasel -lm make[3]: Leaving directory `/«PKGBUILDDIR»/easel/miniapps' make[2]: Leaving directory `/«PKGBUILDDIR»/easel' make[2]: Entering directory `/«PKGBUILDDIR»/easel' (cd miniapps; make) make[3]: Entering directory `/«PKGBUILDDIR»/easel/miniapps' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/«PKGBUILDDIR»/easel/miniapps' make[2]: Leaving directory `/«PKGBUILDDIR»/easel' (cd src; make CC="gcc -std=gnu99" CFLAGS="-O3 -fomit-frame-pointer -fstrict-aliasing"; make module) make[2]: Entering directory `/«PKGBUILDDIR»/src' gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c cmalign.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c cm.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c cm_dpalign.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c cm_dpsearch.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c cm_dpsmall.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c cm_io.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c cm_modelconfig.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c cm_modelmaker.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c cm_mx.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c cm_parsetree.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c cm_qdband.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c cm_submodel.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c cp9.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c cp9_dp.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c cp9_modelconfig.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c cp9_modelmaker.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c cp9_mx.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c cp9_trace.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c alphabet.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c dispatch.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c display.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c eweight.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c errors.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c hmmband.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c hybridsearch.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c logsum.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c mpisupport.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c prior.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c rnamat.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c searchinfo.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c seqstoaln.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c stats.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c truncyk.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L../easel -o cmalign cmalign.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c cmbuild.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L../easel -o cmbuild cmbuild.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c cmcalibrate.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L../easel -o cmcalibrate cmcalibrate.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c cmemit.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L../easel -o cmemit cmemit.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c cmscore.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L../easel -o cmscore cmscore.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c cmsearch.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L../easel -o cmsearch cmsearch.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c cmstat.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L../easel -o cmstat cmstat.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c trcyk.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L../easel -o trcyk trcyk.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel -c truncyk_check.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L../easel -o truncyk_check truncyk_check.o cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o -leasel -lm make[2]: Leaving directory `/«PKGBUILDDIR»/src' make[2]: Entering directory `/«PKGBUILDDIR»/src' /usr/bin/ar rcv libinfernal.a cm.o cm_dpalign.o cm_dpsearch.o cm_dpsmall.o cm_io.o cm_modelconfig.o cm_modelmaker.o cm_mx.o cm_parsetree.o cm_qdband.o cm_submodel.o cp9.o cp9_dp.o cp9_modelconfig.o cp9_modelmaker.o cp9_mx.o cp9_trace.o alphabet.o dispatch.o display.o eweight.o errors.o hmmband.o hybridsearch.o logsum.o mpisupport.o prior.o rnamat.o searchinfo.o seqstoaln.o stats.o truncyk.o a - cm.o a - cm_dpalign.o a - cm_dpsearch.o a - cm_dpsmall.o a - cm_io.o a - cm_modelconfig.o a - cm_modelmaker.o a - cm_mx.o a - cm_parsetree.o a - cm_qdband.o a - cm_submodel.o a - cp9.o a - cp9_dp.o a - cp9_modelconfig.o a - cp9_modelmaker.o a - cp9_mx.o a - cp9_trace.o a - alphabet.o a - dispatch.o a - display.o a - eweight.o a - errors.o a - hmmband.o a - hybridsearch.o a - logsum.o a - mpisupport.o a - prior.o a - rnamat.o a - searchinfo.o a - seqstoaln.o a - stats.o a - truncyk.o ranlib libinfernal.a chmod 644 libinfernal.a make[2]: Leaving directory `/«PKGBUILDDIR»/src' (cd testsuite; make CC="gcc -std=gnu99" CFLAGS="-O3 -fomit-frame-pointer -fstrict-aliasing") make[2]: Entering directory `/«PKGBUILDDIR»/testsuite' gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel/ -I../src -c bandcyk-montecarlo-test.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L../easel/ -L../src -o bandcyk-montecarlo-test bandcyk-montecarlo-test.o -linfernal -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel/ -I../src -c bandcyk-truncation-test.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L../easel/ -L../src -o bandcyk-truncation-test bandcyk-truncation-test.o -linfernal -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel/ -I../src -c cp9-test.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L../easel/ -L../src -o cp9-test cp9-test.o -linfernal -leasel -lm gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -I../easel/ -I../src -c sub_cm-test.c gcc -std=gnu99 -O3 -fomit-frame-pointer -fstrict-aliasing -DHAVE_CONFIG_H -L../easel/ -L../src -o sub_cm-test sub_cm-test.o -linfernal -leasel -lm make[2]: Leaving directory `/«PKGBUILDDIR»/testsuite' make[1]: Leaving directory `/«PKGBUILDDIR»' dh_auto_test -a make[1]: Entering directory `/«PKGBUILDDIR»' (cd testsuite; ./sqc -p ../easel/miniapps 4 exercises.sqc . ../src) Legacy library getopts.pl will be removed from the Perl core distribution in the next major release. Please install the separate libperl4-corelibs-perl package. It is being used at ./sqc, line 179. Legacy library importenv.pl will be removed from the Perl core distribution in the next major release. Please install the separate libperl4-corelibs-perl package. It is being used at ./sqc, line 180. exercise 1 [ cmalign:help/1] ... ok. exercise 2 [ cmalign:help/2] ... ok. exercise 3 [ cmalign:trna/1] ... ok. exercise 4 [ cmalign:trna/2] ... ok. exercise 5 [ cmalign:vault/1] ... ok. exercise 6 [ cmalign:vault/2] ... ok. exercise 7 [ cmbuild:help/1] ... ok. exercise 8 [ cmbuild:help/2] ... ok. exercise 9 [ cmbuild/rf/trna] ... ok. exercise 10 [ cmbuild/trna] ... ok. exercise 11 [ cmbuild/rf/RNaseP] ... ok. exercise 12 [ cmbuild/RNaseP] ... ok. exercise 13 [ cmbuild/SRP] ... ok. exercise 14 [ cmcalibrate:help/1] ... ok. exercise 15 [ cmcalibrate:help/2] ... ok. exercise 16 [ cmcalibrate:trna] ... ok. exercise 17 [ cmscore:help/1] ... ok. exercise 18 [ cmscore:help/2] ... ok. exercise 19 [ cmscore/trna1] ... ok. exercise 20 [ cmscore/trna2] ... ok. exercise 21 [ cmscore/local/trna1] ... ok. exercise 22 [ cmscore/local/trna2] ... ok. exercise 23 [ trna1/rand50] ... ok. exercise 24 [ trna2/rand50] ... ok. exercise 25 [ trna1/rand50/local] ... ok. exercise 26 [ trna2/rand50/local] ... ok. exercise 27 [ rnaseP/bsu] ... ok. exercise 28 [ rnaseP/bsu/local] ... ok. exercise 29 [ srp/ffs] ... ok. exercise 30 [ rnaseP/rand] ... ok. exercise 31 [ rnaseP/rand/local] ... ok. exercise 32 [ cmsearch:help/1] ... ok. exercise 33 [ cmsearch:help/2] ... ok. exercise 34 [ trna/search] ... ok. exercise 35 [ rnaseP/search] ... ok. exercise 36 [ srp/search] ... ok. exercise 37 [ cmemit:help/1] ... ok. exercise 38 [ cmemit:help/2] ... ok. exercise 39 [ trna/emit] ... ok. exercise 40 [ rnaseP/emit] ... ok. exercise 41 [ srp/emit] ... ok. exercise 42 [ cmstat:help/1] ... ok. exercise 43 [ trna/stat] ... ok. exercise 44 [ rnaseP/stat] ... ok. exercise 45 [ srp/stat] ... ok. exercise 46 [ bandcyk/mc/trna] ... ok. exercise 47 [ bandcyk/mc/rp] ... ok. exercise 48 [ bandcyk/mc/ssu] ... ok. exercise 49 [ bandcyk/trunc/trna] ... ok. exercise 50 [ bandcyk/trunc/rp] ... ok. exercise 51 [ bandcyk/trunc/ssu] ... ok. exercise 52 [ cp9/trna] ... ok. exercise 53 [ cp9/trna] ... ok. exercise 54 [ cp9/rp] ... ok. exercise 55 [ cp9/ssu] ... ok. exercise 56 [ sub/trna1] ... ok. exercise 57 [ sub/rp] ... ok. exercise 58 [ sub/ssu] ... ok. exercise 59 [ sub/trna2] ... ok. All 59 exercises at level <= 4 passed. System information: Sat May 5 04:58:47 UTC 2012 Linux build01.raspbian.lan 3.2.0-2-mx5 #1 Sun Apr 15 19:59:08 UTC 2012 armv7l GNU/Linux make[1]: Leaving directory `/«PKGBUILDDIR»' fakeroot debian/rules binary-arch dh binary-arch --with quilt dh_testroot -a dh_prep -a dh_installdirs -a debian/rules override_dh_auto_install make[1]: Entering directory `/«PKGBUILDDIR»' /usr/bin/make install prefix=/«PKGBUILDDIR»/debian/tmp make[2]: Entering directory `/«PKGBUILDDIR»' mkdir -p /«PKGBUILDDIR»/debian/tmp/bin for file in cmalign cmbuild cmcalibrate cmemit cmscore cmsearch cmstat; do\ cp src/$file /«PKGBUILDDIR»/debian/tmp/bin/;\ done make[2]: Leaving directory `/«PKGBUILDDIR»' make[1]: Leaving directory `/«PKGBUILDDIR»' dh_install -a 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 debian/rules override_dh_compress make[1]: Entering directory `/«PKGBUILDDIR»' dh_compress -X.pdf make[1]: Leaving directory `/«PKGBUILDDIR»' dh_fixperms -a debian/rules override_dh_strip make[1]: Entering directory `/«PKGBUILDDIR»' dh_strip --dbg-package=infernal-dbg make[1]: Leaving directory `/«PKGBUILDDIR»' dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package `infernal' in `../infernal_1.0.2-2_armhf.deb'. dpkg-deb: building package `infernal-dbg' in `../infernal-dbg_1.0.2-2_armhf.deb'. dpkg-genchanges -B -mbuildd >../infernal_1.0.2-2_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 infernal-1.0.2 dpkg-buildpackage: binary only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120504-2159 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ infernal_1.0.2-2_armhf.changes: ─────────────────────────────── Format: 1.8 Date: Tue, 27 Sep 2011 15:48:27 +0200 Source: infernal Binary: infernal infernal-doc infernal-dbg Architecture: armhf Version: 1.0.2-2 Distribution: testing Urgency: low Maintainer: buildd Changed-By: Steffen Moeller Description: infernal - inference of RNA secondary structural alignments infernal-dbg - debug information for infernal infernal-doc - inference of RNA secondary structural alignments – documentation Closes: 643407 Changes: infernal (1.0.2-2) unstable; urgency=low . * Series of mall fixes (Closes: #643407). * source/format 3.0 * Policy to 3.9.2 * added infernal-dbg * corrected upstream's email address Checksums-Sha1: 6dae65ae3a0903cc3120efd64bebd0e711fcb766 4217168 infernal_1.0.2-2_armhf.deb c29ea111c7261c7206f5c67a518f0c36111d9586 230460 infernal-dbg_1.0.2-2_armhf.deb Checksums-Sha256: 4727fbd4ec2e2dec0d6f17df054f0b575a81d0f12e28ec5b311dbd16d62939c7 4217168 infernal_1.0.2-2_armhf.deb fc5be17043e2cc211da4e731fae67cdf71f4e638651f0738984b0c1cc1f9ae77 230460 infernal-dbg_1.0.2-2_armhf.deb Files: 86d96951de5645fae06fe77a5ff1a15a 4217168 science optional infernal_1.0.2-2_armhf.deb 09a62f27018aa403d40c10745d3b755e 230460 debug optional infernal-dbg_1.0.2-2_armhf.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ infernal_1.0.2-2_armhf.deb ────────────────────────── new debian package, version 2.0. size 4217168 bytes: control archive= 1466 bytes. 920 bytes, 20 lines control 1617 bytes, 26 lines md5sums Package: infernal Version: 1.0.2-2 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 8252 Depends: libc6 (>= 2.13-28), libgcc1 (>= 1:4.4.0) Section: science Priority: optional Homepage: http://infernal.janelia.org/ Description: inference of RNA secondary structural alignments Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence. . The tool is an integral component of the Rfam database. drwxr-xr-x root/root 0 2012-05-04 21:58 ./ drwxr-xr-x root/root 0 2012-05-04 21:58 ./usr/ drwxr-xr-x root/root 0 2012-05-04 21:58 ./usr/share/ drwxr-xr-x root/root 0 2012-05-04 21:58 ./usr/share/man/ drwxr-xr-x root/root 0 2012-05-04 21:59 ./usr/share/man/man1/ -rw-r--r-- root/root 6111 2012-05-04 21:58 ./usr/share/man/man1/cmbuild.1.gz -rw-r--r-- root/root 1108 2012-05-04 21:58 ./usr/share/man/man1/cm2hmm.1.gz -rw-r--r-- root/root 4756 2012-05-04 21:58 ./usr/share/man/man1/cmscore.1.gz -rw-r--r-- root/root 573 2012-05-04 21:58 ./usr/share/man/man1/truncyk_check.1.gz -rw-r--r-- root/root 2033 2012-05-04 21:58 ./usr/share/man/man1/cmemit.1.gz -rw-r--r-- root/root 2722 2012-05-04 21:58 ./usr/share/man/man1/cmstat.1.gz -rw-r--r-- root/root 1020 2012-05-04 21:58 ./usr/share/man/man1/cm2hmmsearch.1.gz -rw-r--r-- root/root 7270 2012-05-04 21:58 ./usr/share/man/man1/cmsearch.1.gz -rw-r--r-- root/root 335 2012-05-04 21:58 ./usr/share/man/man1/trcyk.1.gz -rw-r--r-- root/root 5992 2012-05-04 21:58 ./usr/share/man/man1/cmalign.1.gz -rw-r--r-- root/root 5046 2012-05-04 21:58 ./usr/share/man/man1/cmcalibrate.1.gz drwxr-xr-x root/root 0 2012-05-04 21:58 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-05-04 21:59 ./usr/share/doc/infernal/ -rw-r--r-- root/root 3088 2009-10-30 10:31 ./usr/share/doc/infernal/00README -rw-r--r-- root/root 1089 2012-05-04 21:26 ./usr/share/doc/infernal/changelog.Debian.gz -rw-r--r-- root/root 6532 2012-05-04 21:26 ./usr/share/doc/infernal/copyright -rw-r--r-- root/root 1375 2012-05-04 21:26 ./usr/share/doc/infernal/README.Debian -rw-r--r-- root/root 2204 2009-10-30 10:30 ./usr/share/doc/infernal/RELEASE-1.0.gz -rw-r--r-- root/root 1460 2009-10-30 10:30 ./usr/share/doc/infernal/00README-MPI drwxr-xr-x root/root 0 2012-05-04 21:59 ./usr/bin/ -rwxr-xr-x root/root 920856 2012-05-04 21:59 ./usr/bin/cmstat -rwxr-xr-x root/root 942764 2012-05-04 21:59 ./usr/bin/cmsearch -rwxr-xr-x root/root 904856 2012-05-04 21:59 ./usr/bin/truncyk_check -rwxr-xr-x root/root 929832 2012-05-04 21:59 ./usr/bin/cmalign -rwxr-xr-x root/root 958420 2012-05-04 21:59 ./usr/bin/cmcalibrate -rwxr-xr-x root/root 976100 2012-05-04 21:59 ./usr/bin/cmbuild -rwxr-xr-x root/root 922104 2012-05-04 21:59 ./usr/bin/cmscore -rwxr-xr-x root/root 913340 2012-05-04 21:59 ./usr/bin/cmemit -rwxr-xr-x root/root 891716 2012-05-04 21:59 ./usr/bin/trcyk infernal-dbg_1.0.2-2_armhf.deb ────────────────────────────── new debian package, version 2.0. size 230460 bytes: control archive= 850 bytes. 556 bytes, 15 lines control 735 bytes, 11 lines md5sums Package: infernal-dbg Source: infernal Version: 1.0.2-2 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 710 Depends: infernal (= 1.0.2-2) Section: debug Priority: optional Homepage: http://infernal.janelia.org/ Description: debug information for infernal This package contains extra information to help the debugging of the infernal suite. The package is auto-generated. You may be asked by the upstream developer to install it to help the identification of a technical problem. drwxr-xr-x root/root 0 2012-05-04 21:58 ./ drwxr-xr-x root/root 0 2012-05-04 21:59 ./usr/ drwxr-xr-x root/root 0 2012-05-04 21:58 ./usr/share/ drwxr-xr-x root/root 0 2012-05-04 21:58 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-05-04 21:59 ./usr/share/doc/infernal-dbg/ -rw-r--r-- root/root 1089 2012-05-04 21:26 ./usr/share/doc/infernal-dbg/changelog.Debian.gz -rw-r--r-- root/root 6532 2012-05-04 21:26 ./usr/share/doc/infernal-dbg/copyright drwxr-xr-x root/root 0 2012-05-04 21:59 ./usr/lib/ drwxr-xr-x root/root 0 2012-05-04 21:59 ./usr/lib/debug/ drwxr-xr-x root/root 0 2012-05-04 21:59 ./usr/lib/debug/usr/ drwxr-xr-x root/root 0 2012-05-04 21:59 ./usr/lib/debug/usr/bin/ -rw-r--r-- root/root 74338 2012-05-04 21:59 ./usr/lib/debug/usr/bin/cmstat -rw-r--r-- root/root 75163 2012-05-04 21:59 ./usr/lib/debug/usr/bin/cmsearch -rw-r--r-- root/root 74134 2012-05-04 21:59 ./usr/lib/debug/usr/bin/truncyk_check -rw-r--r-- root/root 74739 2012-05-04 21:59 ./usr/lib/debug/usr/bin/cmalign -rw-r--r-- root/root 77770 2012-05-04 21:59 ./usr/lib/debug/usr/bin/cmcalibrate -rw-r--r-- root/root 80314 2012-05-04 21:59 ./usr/lib/debug/usr/bin/cmbuild -rw-r--r-- root/root 74644 2012-05-04 21:59 ./usr/lib/debug/usr/bin/cmscore -rw-r--r-- root/root 74305 2012-05-04 21:59 ./usr/lib/debug/usr/bin/cmemit -rw-r--r-- root/root 72628 2012-05-04 21:59 ./usr/lib/debug/usr/bin/trcyk ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: autotools-dev* bsdmainutils* cdbs* debhelper* diffstat* file* gettext* gettext-base* groff-base* html2text* intltool-debian* libcroco3* libffi5* libglib2.0-0* libmagic1* libpcre3* libpipeline1* libunistring0* libxml2* man-db* po-debconf* quilt* sbuild-build-depends-core-dummy* sbuild-build-depends-infernal-dummy* 0 upgraded, 0 newly installed, 24 to remove and 0 not upgraded. After this operation, 25.6 MB disk space will be freed. (Reading database ... 12217 files and directories currently installed.) Removing sbuild-build-depends-infernal-dummy ... Removing autotools-dev ... Removing quilt ... Purging configuration files for quilt ... Removing debhelper ... Removing man-db ... Purging configuration files for man-db ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing cdbs ... Removing diffstat ... Removing file ... Removing po-debconf ... Removing intltool-debian ... Removing gettext ... Removing gettext-base ... Removing groff-base ... Purging configuration files for groff-base ... Removing html2text ... Purging configuration files for html2text ... Removing libcroco3:armhf ... Purging configuration files for libcroco3:armhf ... Removing libglib2.0-0:armhf ... Purging configuration files for libglib2.0-0:armhf ... Removing libffi5:armhf ... Purging configuration files for libffi5:armhf ... Removing libmagic1:armhf ... Purging configuration files for libmagic1:armhf ... Removing libpcre3:armhf ... Purging configuration files for libpcre3:armhf ... Removing libpipeline1:armhf ... Purging configuration files for libpipeline1:armhf ... Removing libunistring0:armhf ... Purging configuration files for libunistring0:armhf ... Removing libxml2:armhf ... Purging configuration files for libxml2:armhf ... Removing sbuild-build-depends-core-dummy ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: armhf Build-Space: 81096 Build-Time: 1980 Distribution: testing Install-Time: 54 Job: infernal_1.0.2-2 Package: infernal Package-Time: 2055 Source-Version: 1.0.2-2 Space: 81096 Status: successful Version: 1.0.2-2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120504-2159 Build needed 00:34:15, 81096k disc space