hmmer →
3.1b2-1 →
armhf → 2015-07-11 06:12:42
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bm-wb-02
╔══════════════════════════════════════════════════════════════════════════════╗
║ hmmer 3.1b2-1 (armhf) 11 Jul 2015 05:47 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: hmmer
Version: 3.1b2-1
Source Version: 3.1b2-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/hmmer-S9l3Lq/hmmer-3.1b2' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/hmmer-S9l3Lq' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-69c1c3b6-b139-4233-8401-8d06c27e612e' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 stretch-staging/main Sources [8075 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [9924 kB]
Ign http://172.17.0.1 stretch-staging/main Translation-en
Fetched 18.0 MB in 35s (502 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...
NOTICE: 'hmmer' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/hmmer/trunk/
Need to get 5974 kB of source archives.
Get:1 http://172.17.0.1/private/ stretch-staging/main hmmer 3.1b2-1 (dsc) [2110 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main hmmer 3.1b2-1 (tar) [5965 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main hmmer 3.1b2-1 (diff) [6280 B]
Fetched 5974 kB in 1s (4354 kB/s)
Download complete and in download only mode
Check architectures
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Check dependencies
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-bHqwIb/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
Get:2 file: ./ Release [2119 B]
Ign file: ./ Translation-en
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
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 79 not upgraded.
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Selecting previously unselected package sbuild-build-depends-core-dummy.
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(Reading database ... 11998 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), autotools-dev
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), autotools-dev
dpkg-deb: building package `sbuild-build-depends-hmmer-dummy' in `/«BUILDDIR»/resolver-XeTjRg/apt_archive/sbuild-build-depends-hmmer-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
Get:2 file: ./ Release [2119 B]
Ign file: ./ Translation-en
Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install hmmer 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 debhelper file gettext gettext-base groff-base
intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libmagic1
libpipeline1 libunistring0 libxml2 man-db po-debconf
Suggested packages:
wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser
libmail-box-perl
Recommended packages:
curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libglib2.0-data shared-mime-info xdg-user-dirs xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
autotools-dev bsdmainutils debhelper file gettext gettext-base groff-base
intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libmagic1
libpipeline1 libunistring0 libxml2 man-db po-debconf
sbuild-build-depends-hmmer-dummy
0 upgraded, 19 newly installed, 0 to remove and 79 not upgraded.
Need to get 8447 kB/8448 kB of archives.
After this operation, 24.3 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ stretch-staging/main libpipeline1 armhf 1.4.0-1 [24.0 kB]
Get:2 http://172.17.0.1/private/ stretch-staging/main groff-base armhf 1.22.3-1 [1085 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main bsdmainutils armhf 9.0.6 [177 kB]
Get:4 http://172.17.0.1/private/ stretch-staging/main man-db armhf 2.7.0.2-5 [972 kB]
Get:5 http://172.17.0.1/private/ stretch-staging/main libasprintf0c2 armhf 0.19.4-1 [31.5 kB]
Get:6 http://172.17.0.1/private/ stretch-staging/main libmagic1 armhf 1:5.22+15-2 [244 kB]
Get:7 http://172.17.0.1/private/ stretch-staging/main libxml2 armhf 2.9.1+dfsg1-5 [703 kB]
Get:8 http://172.17.0.1/private/ stretch-staging/main libffi6 armhf 3.1-2 [18.1 kB]
Get:9 http://172.17.0.1/private/ stretch-staging/main libglib2.0-0 armhf 2.44.1-1.1 [2312 kB]
Get:10 http://172.17.0.1/private/ stretch-staging/main libcroco3 armhf 0.6.8-3 [121 kB]
Get:11 http://172.17.0.1/private/ stretch-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:12 http://172.17.0.1/private/ stretch-staging/main file armhf 1:5.22+15-2 [59.9 kB]
Get:13 http://172.17.0.1/private/ stretch-staging/main gettext-base armhf 0.19.4-1 [117 kB]
Get:14 http://172.17.0.1/private/ stretch-staging/main autotools-dev all 20140911.1 [70.5 kB]
Get:15 http://172.17.0.1/private/ stretch-staging/main gettext armhf 0.19.4-1 [1168 kB]
Get:16 http://172.17.0.1/private/ stretch-staging/main intltool-debian all 0.35.0+20060710.2 [25.9 kB]
Get:17 http://172.17.0.1/private/ stretch-staging/main po-debconf all 1.0.18 [248 kB]
Get:18 http://172.17.0.1/private/ stretch-staging/main debhelper all 9.20150628 [817 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 8447 kB in 2s (3960 kB/s)
Selecting previously unselected package libpipeline1:armhf.
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Preparing to unpack .../libpipeline1_1.4.0-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.4.0-1) ...
Selecting previously unselected package groff-base.
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Preparing to unpack .../bsdmainutils_9.0.6_armhf.deb ...
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Selecting previously unselected package libcroco3:armhf.
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Unpacking sbuild-build-depends-hmmer-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.4.0-1) ...
Setting up groff-base (1.22.3-1) ...
Setting up bsdmainutils (9.0.6) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up man-db (2.7.0.2-5) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasprintf0c2:armhf (0.19.4-1) ...
Setting up libmagic1:armhf (1:5.22+15-2) ...
Setting up libxml2:armhf (2.9.1+dfsg1-5) ...
Setting up libffi6:armhf (3.1-2) ...
Setting up libglib2.0-0:armhf (2.44.1-1.1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.8-3) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up file (1:5.22+15-2) ...
Setting up gettext-base (0.19.4-1) ...
Setting up autotools-dev (20140911.1) ...
Setting up gettext (0.19.4-1) ...
Setting up intltool-debian (0.35.0+20060710.2) ...
Setting up po-debconf (1.0.18) ...
Setting up debhelper (9.20150628) ...
Setting up sbuild-build-depends-hmmer-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-18) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25-5 dpkg-dev_1.17.25 g++-4.9_4.9.2-10 gcc-4.9_4.9.2-10 libc6-dev_2.19-18 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 linux-libc-dev_3.16.7-ckt4-1+rpi1
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.9.8 autotools-dev_20140911.1 base-files_8+rpi1 base-passwd_3.5.37 bash_4.3-11 binutils_2.25-5 bsdmainutils_9.0.6 bsdutils_1:2.25.2-6 build-essential_11.7 bzip2_1.0.6-7 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:4.9.2-2 cpp-4.9_4.9.2-10 dash_0.5.7-4 debconf_1.5.56 debconf-i18n_1.5.56 debfoster_2.7-2 debhelper_9.20150628 debianutils_4.4 diffutils_1:3.3-1 dmsetup_2:1.02.90-2.2 dpkg_1.17.25 dpkg-dev_1.17.25 e2fslibs_1.42.12-1.1 e2fsprogs_1.42.12-1.1 fakeroot_1.20.2-1 file_1:5.22+15-2 findutils_4.4.2-9 g++_4:4.9.2-2 g++-4.9_4.9.2-10 gcc_4:4.9.2-2 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.4-1 gcc-4.9_4.9.2-10 gcc-4.9-base_4.9.2-10 gettext_0.19.4-1 gettext-base_0.19.4-1 gnupg_1.4.18-7 gpgv_1.4.18-7 grep_2.20-4.1 groff-base_1.22.3-1 gzip_1.6-4 hostname_3.15 init_1.22 init-system-helpers_1.22 initramfs-tools_0.120 initscripts_2.88dsf-59 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.2 klibc-utils_2.0.4-2+rpi1 kmod_18-3 libacl1_2.2.52-2 libapt-pkg4.12_1.0.9.8 libasan1_4.9.2-10 libasprintf0c2_0.19.4-1 libatomic1_4.9.2-10 libattr1_1:2.4.47-2 libaudit-common_1:2.4-1 libaudit1_1:2.4-1 libblkid1_2.25.2-6 libbz2-1.0_1.0.6-7 libc-bin_2.19-18 libc-dev-bin_2.19-18 libc6_2.19-18 libc6-dev_2.19-18 libcap2_1:2.24-8 libcap2-bin_1:2.24-8 libcloog-isl4_0.18.2-1 libcomerr2_1.42.12-1.1 libcroco3_0.6.8-3 libcryptsetup4_2:1.6.6-5 libdb5.3_5.3.28-9 libdbus-1-3_1.8.16-1 libdebconfclient0_0.192 libdevmapper1.02.1_2:1.02.90-2.2 libdpkg-perl_1.17.25 libdrm2_2.4.58-2 libfakeroot_1.20.2-1 libffi6_3.1-2 libgc1c2_1:7.2d-6.4 libgcc-4.9-dev_4.9.2-10 libgcc1_1:4.9.2-10 libgcrypt20_1.6.3-2 libgdbm3_1.8.3-13.1 libglib2.0-0_2.44.1-1.1 libgmp10_2:6.0.0+dfsg-6+rpi1 libgomp1_4.9.2-10 libgpg-error0_1.17-3 libisl10_0.12.2-2 libklibc_2.0.4-2+rpi1 libkmod2_18-3 liblocale-gettext-perl_1.05-8+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.22+15-2 libmount1_2.25.2-6 libmpc3_1.0.2-1 libmpfr4_3.1.2-2 libncurses5_5.9+20140913-1 libncursesw5_5.9+20140913-1 libnih-dbus1_1.0.3-4.3 libnih1_1.0.3-4.3 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpcre3_2:8.35-3.3 libpipeline1_1.4.0-1 libpng12-0_1.2.50-2 libprocps3_2:3.3.9-9 libreadline6_6.3-8 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libslang2_2.3.0-2 libsmartcols1_2.25.2-6 libss2_1.42.12-1.1 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 libsystemd0_215-17 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140913-1 libubsan0_4.9.2-10 libudev1_215-17 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-25 libustr-1.0-1_1.0.4-3 libuuid1_2.25.2-6 libxml2_2.9.1+dfsg1-5 linux-libc-dev_3.16.7-ckt4-1+rpi1 login_1:4.2-3 lsb-base_4.1+Debian13+rpi1+nmu1 make_4.0-8.1 makedev_2.3.1-93 man-db_2.7.0.2-5 mawk_1.3.3-17 mount_2.25.2-6 mountall_2.54 multiarch-support_2.19-18 ncurses-base_5.9+20140913-1 ncurses-bin_5.9+20140913-1 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-3 perl-base_5.20.2-3 perl-modules_5.20.2-3 plymouth_0.9.0-9 po-debconf_1.0.18 procps_2:3.3.9-9 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-hmmer-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 startpar_0.59-3 systemd_215-17 systemd-sysv_215-17 sysv-rc_2.88dsf-59 sysvinit-utils_2.88dsf-59 tar_1.27.1-2 tzdata_2015c-1 udev_215-17 util-linux_2.25.2-6 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sun Jul 5 20:48:14 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./hmmer_3.1b2-1.dsc
dpkg-source: info: extracting hmmer in hmmer-3.1b2
dpkg-source: info: unpacking hmmer_3.1b2.orig.tar.gz
dpkg-source: info: unpacking hmmer_3.1b2-1.debian.tar.xz
dpkg-source: info: applying debian-changes-3.0-1
dpkg-source: info: applying debian-changes-3.0-2.1
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-69c1c3b6-b139-4233-8401-8d06c27e612e
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package hmmer
dpkg-buildpackage: source version 3.1b2-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build hmmer-3.1b2
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean --with autotools_dev
dh_testdir
debian/rules override_dh_auto_clean
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_clean
rm -f testsuite/esltmp*
rm -f easel/testsuite/esltmp*
rm -f tutorial/MADE1.hmm.h3?
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_autotools-dev_restoreconfig
dh_clean
debian/rules build-arch
dh build-arch --with autotools_dev
dh_testdir -a
dh_autotools-dev_updateconfig -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_configure -- --enable-threads
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --disable-maintainer-mode --disable-dependency-tracking --enable-threads
configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking
configure: Configuring HMMER for your system.
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
configure: Full HMMER source distribution - using full configuration
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether 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 for C compiler vendor... gnu
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for cc_r... gcc
configure: WARNING: It appears your platform will not fully support H3.
configure: WARNING: We'll use the 'dummy' implementation, a slow reference implementation.
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking for a BSD-compatible install... /usr/bin/install -c
checking how to run the C preprocessor... gcc -E
checking for C compiler vendor... (cached) 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 you have a GNU make... yes, you do; and we assume you will use it!
checking for a sed that does not truncate output... /bin/sed
checking for gcc -std=gnu99 option to produce PIC... -fPIC
configure: Activating "dummy" implementation
checking compiler support --start-group... yes
checking for gzip... /bin/gzip
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 endian.h usability... yes
checking endian.h presence... yes
checking for endian.h... yes
checking for inttypes.h... (cached) yes
checking for stdint.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/types.h... (cached) yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking for sys/sysctl.h... yes
checking whether byte ordering is bigendian... no
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 getpid... yes
checking for sysctl... yes
checking for sysconf... yes
checking for getcwd... yes
checking for stat... yes
checking for fstat... yes
checking for ntohs... yes
checking for ntohl... yes
checking for htons... yes
checking for htonl... 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 documentation/Makefile
config.status: creating documentation/man/Makefile
config.status: creating src/Makefile
config.status: creating testsuite/Makefile
config.status: creating profmark/Makefile
config.status: creating src/impl_dummy/Makefile
config.status: creating easel/miniapps/Makefile
config.status: creating easel/testsuite/Makefile
config.status: creating easel/Makefile
config.status: creating libdivsufsort/Makefile
config.status: creating Makefile
config.status: creating src/p7_config.h
config.status: creating easel/esl_config.h
config.status: creating libdivsufsort/divsufsort.h
config.status: linking src/impl_dummy to src/impl
configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking
configure: WARNING: We will compile the "dummy", a portable ANSI C reference implementation.
configure: WARNING: It is slow, about 100x slower than real H3, and is NOT intended for production use!
configure: WARNING: It only intended to show the basics of how HMMER3 works, portably.
HMMER configuration:
compiler: gcc -std=gnu99 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -pthread -fPIC
host: arm-unknown-linux-gnueabihf
linker: -Wl,-z,relro
libraries:
DP implementation: dummy
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_auto_build -a
make -j1
make[1]: Entering directory '/«PKGBUILDDIR»'
SUBDIR easel
make[2]: Entering directory '/«PKGBUILDDIR»/easel'
CC easel.o
CC esl_alphabet.o
CC esl_buffer.o
CC esl_cluster.o
CC esl_composition.o
CC esl_dirichlet.o
CC esl_distance.o
CC esl_dmatrix.o
CC esl_exponential.o
CC esl_fileparser.o
CC esl_gamma.o
CC esl_getopts.o
CC esl_gev.o
CC esl_gumbel.o
CC esl_histogram.o
CC esl_hmm.o
CC esl_hyperexp.o
CC esl_keyhash.o
CC esl_mem.o
CC esl_minimizer.o
CC esl_mixgev.o
CC esl_mpi.o
CC esl_msa.o
CC esl_msacluster.o
CC esl_msafile.o
CC esl_msafile2.o
CC esl_msafile_a2m.o
CC esl_msafile_afa.o
CC esl_msafile_clustal.o
CC esl_msafile_phylip.o
CC esl_msafile_psiblast.o
CC esl_msafile_selex.o
CC esl_msafile_stockholm.o
CC esl_msashuffle.o
CC esl_msaweight.o
CC esl_normal.o
CC esl_paml.o
CC esl_random.o
CC esl_randomseq.o
CC esl_ratematrix.o
CC esl_recorder.o
CC esl_regexp.o
CC esl_rootfinder.o
CC esl_scorematrix.o
CC esl_sq.o
CC esl_sqio.o
CC esl_sqio_ascii.o
CC esl_sqio_ncbi.o
CC esl_sse.o
CC esl_ssi.o
CC esl_stack.o
CC esl_stats.o
CC esl_stopwatch.o
CC esl_stretchexp.o
CC esl_threads.o
CC esl_translate.o
CC esl_tree.o
CC esl_vectorops.o
CC esl_vmx.o
CC esl_weibull.o
CC esl_workqueue.o
CC esl_wuss.o
AR libeasel.a
SUBDIR miniapps
make[3]: Entering directory '/«PKGBUILDDIR»/easel/miniapps'
CC esl-afetch.o
GEN esl-afetch
CC esl-alimanip.o
GEN esl-alimanip
CC esl-alimap.o
GEN esl-alimap
CC esl-alimask.o
GEN esl-alimask
CC esl-alimerge.o
GEN esl-alimerge
CC esl-alipid.o
GEN esl-alipid
CC esl-alistat.o
GEN esl-alistat
CC esl-cluster.o
GEN esl-cluster
CC esl-compalign.o
GEN esl-compalign
CC esl-compstruct.o
GEN esl-compstruct
CC esl-construct.o
GEN esl-construct
CC esl-histplot.o
GEN esl-histplot
CC esl-mask.o
GEN esl-mask
CC esl-reformat.o
GEN esl-reformat
CC esl-selectn.o
GEN esl-selectn
CC esl-seqrange.o
GEN esl-seqrange
CC esl-seqstat.o
GEN esl-seqstat
CC esl-sfetch.o
GEN esl-sfetch
CC esl-shuffle.o
GEN esl-shuffle
CC esl-ssdraw.o
GEN esl-ssdraw
CC esl-stranslate.o
GEN esl-stranslate
CC esl-weight.o
GEN esl-weight
make[3]: Leaving directory '/«PKGBUILDDIR»/easel/miniapps'
make[2]: Leaving directory '/«PKGBUILDDIR»/easel'
SUBDIR libdivsufsort
make[2]: Entering directory '/«PKGBUILDDIR»/libdivsufsort'
CC divsufsort.o
AR libdivsufsort.a
make[2]: Leaving directory '/«PKGBUILDDIR»/libdivsufsort'
SUBDIR src
make[2]: Entering directory '/«PKGBUILDDIR»/src'
CC alimask.o
CC build.o
CC cachedb.o
CC emit.o
CC errors.o
CC evalues.o
CC eweight.o
CC generic_decoding.o
CC generic_fwdback.o
CC generic_fwdback_chk.o
CC generic_fwdback_banded.o
CC generic_null2.o
CC generic_msv.o
CC generic_optacc.o
CC generic_stotrace.o
CC generic_viterbi.o
CC generic_vtrace.o
CC h2_io.o
CC heatmap.o
CC hmmlogo.o
CC hmmdmstr.o
In file included from /usr/include/string.h:640:0,
from hmmdmstr.c:13:
In function 'strncat',
inlined from 'clientside_loop' at hmmdmstr.c:1405:5:
/usr/include/arm-linux-gnueabihf/bits/string3.h:150:3: warning: call to __builtin___strncat_chk might overflow destination buffer
return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
^
CC hmmdwrkr.o
CC hmmdutils.o
CC hmmer.o
CC logsum.o
CC modelconfig.o
CC modelstats.o
CC mpisupport.o
CC seqmodel.o
CC tracealign.o
CC p7_alidisplay.o
CC p7_bg.o
CC p7_builder.o
CC p7_domaindef.o
CC p7_gbands.o
CC p7_gmx.o
CC p7_gmxb.o
CC p7_gmxchk.o
CC p7_hmm.o
CC p7_hmmcache.o
CC p7_hmmfile.o
CC p7_hmmwindow.o
CC p7_null3.o
CC p7_pipeline.o
CC p7_prior.o
CC p7_profile.o
CC p7_spensemble.o
CC p7_tophits.o
CC p7_trace.o
CC p7_scoredata.o
CC hmmpgmd2msa.o
CC fm_alphabet.o
CC fm_general.o
CC fm_sse.o
CC fm_ssv.o
AR libhmmer-src.stamp
SUBDIR impl_dummy
make[3]: Entering directory '/«PKGBUILDDIR»/src/impl_dummy'
CC decoding.o
CC fwdback.o
CC io.o
CC msvfilter.o
CC null2.o
CC optacc.o
CC stotrace.o
CC vitfilter.o
CC p7_omx.o
CC p7_oprofile.o
CC mpi.o
AR libhmmer-impl.stamp
make[3]: Leaving directory '/«PKGBUILDDIR»/src/impl_dummy'
GEN alimask
CC hmmalign.o
GEN hmmalign
CC hmmbuild.o
GEN hmmbuild
CC hmmconvert.o
GEN hmmconvert
CC hmmemit.o
GEN hmmemit
CC hmmfetch.o
GEN hmmfetch
GEN hmmlogo
CC hmmpress.o
GEN hmmpress
CC hmmscan.o
GEN hmmscan
CC hmmsearch.o
GEN hmmsearch
CC hmmsim.o
GEN hmmsim
CC hmmstat.o
GEN hmmstat
CC jackhmmer.o
GEN jackhmmer
CC phmmer.o
GEN phmmer
CC nhmmer.o
GEN nhmmer
CC nhmmscan.o
nhmmscan.c: In function 'serial_loop':
nhmmscan.c:671:9: warning: implicit declaration of function 'p7_oprofile_UpdateVitEmissionScores' [-Wimplicit-function-declaration]
p7_oprofile_UpdateVitEmissionScores(om, info->bg, info->fwd_emissions, info->scores);
^
nhmmscan.c:672:9: warning: implicit declaration of function 'p7_oprofile_UpdateMSVEmissionScores' [-Wimplicit-function-declaration]
p7_oprofile_UpdateMSVEmissionScores(om, info->bg, info->fwd_emissions, info->scores);
^
GEN nhmmscan
CC hmmpgmd.o
GEN hmmpgmd
CC hmmc2.o
In file included from /usr/include/string.h:640:0,
from hmmc2.c:10:
In function 'strncat',
inlined from 'main' at hmmc2.c:364:7:
/usr/include/arm-linux-gnueabihf/bits/string3.h:150:3: warning: call to __builtin___strncat_chk might overflow destination buffer
return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
^
GEN hmmc2
CC makehmmerdb.o
GEN makehmmerdb
CC hmmerfm-exactmatch.o
GEN hmmerfm-exactmatch
make[2]: Leaving directory '/«PKGBUILDDIR»/src'
SUBDIR profmark
make[2]: Entering directory '/«PKGBUILDDIR»/profmark'
CC create-profmark.o
GEN create-profmark
CC rocplot.o
GEN rocplot
make[2]: Leaving directory '/«PKGBUILDDIR»/profmark'
make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_auto_test
make[1]: Entering directory '/«PKGBUILDDIR»'
make check
make[2]: Entering directory '/«PKGBUILDDIR»'
SUBDIR easel
make[3]: Entering directory '/«PKGBUILDDIR»/easel'
GEN easel_utest
GEN esl_alphabet_utest
GEN esl_buffer_utest
GEN esl_cluster_utest
GEN esl_dirichlet_utest
GEN esl_distance_utest
GEN esl_dmatrix_utest
GEN esl_exponential_utest
GEN esl_fileparser_utest
GEN esl_gamma_utest
GEN esl_getopts_utest
GEN esl_gumbel_utest
GEN esl_histogram_utest
GEN esl_hyperexp_utest
GEN esl_keyhash_utest
GEN esl_mem_utest
GEN esl_msa_utest
GEN esl_msacluster_utest
GEN esl_msafile_utest
GEN esl_msafile2_utest
GEN esl_msafile_a2m_utest
GEN esl_msafile_afa_utest
GEN esl_msafile_clustal_utest
GEN esl_msafile_phylip_utest
GEN esl_msafile_psiblast_utest
GEN esl_msafile_selex_utest
GEN esl_msafile_stockholm_utest
GEN esl_msaweight_utest
GEN esl_random_utest
GEN esl_randomseq_utest
GEN esl_ratematrix_utest
GEN esl_recorder_utest
GEN esl_regexp_utest
GEN esl_rootfinder_utest
GEN esl_scorematrix_utest
GEN esl_sq_utest
GEN esl_sqio_utest
GEN esl_sse_utest
GEN esl_ssi_utest
GEN esl_stack_utest
GEN esl_stats_utest
GEN esl_stretchexp_utest
GEN esl_tree_utest
GEN esl_vectorops_utest
GEN esl_weibull_utest
GEN esl_wuss_utest
SUBDIR miniapps
make[4]: Entering directory '/«PKGBUILDDIR»/easel/miniapps'
make[4]: Nothing to be done for 'tests'.
make[4]: Leaving directory '/«PKGBUILDDIR»/easel/miniapps'
make[3]: Leaving directory '/«PKGBUILDDIR»/easel'
SUBDIR libdivsufsort
make[3]: Entering directory '/«PKGBUILDDIR»/libdivsufsort'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/«PKGBUILDDIR»/libdivsufsort'
SUBDIR src
make[3]: Entering directory '/«PKGBUILDDIR»/src'
SUBDIR impl_dummy
make[4]: Entering directory '/«PKGBUILDDIR»/src/impl_dummy'
make[4]: 'libhmmer-impl.stamp' is up to date.
make[4]: Leaving directory '/«PKGBUILDDIR»/src/impl_dummy'
GEN build_utest
GEN generic_fwdback_utest
GEN generic_fwdback_chk_utest
GEN generic_msv_utest
GEN generic_stotrace_utest
GEN generic_viterbi_utest
GEN hmmer_utest
GEN logsum_utest
GEN modelconfig_utest
GEN seqmodel_utest
GEN p7_alidisplay_utest
GEN p7_bg_utest
GEN p7_gmx_utest
GEN p7_gmxchk_utest
GEN p7_hmm_utest
GEN p7_hmmfile_utest
GEN p7_profile_utest
GEN p7_tophits_utest
GEN p7_trace_utest
GEN p7_scoredata_utest
GEN hmmpgmd2msa_utest
CC itest_brute.o
GEN itest_brute
SUBDIR impl_dummy
make[4]: Entering directory '/«PKGBUILDDIR»/src/impl_dummy'
GEN decoding_utest
GEN fwdback_utest
GEN io_utest
GEN msvfilter_utest
GEN null2_utest
GEN optacc_utest
GEN stotrace_utest
GEN vitfilter_utest
make[4]: Leaving directory '/«PKGBUILDDIR»/src/impl_dummy'
make[3]: Leaving directory '/«PKGBUILDDIR»/src'
SUBDIR easel
make[3]: Entering directory '/«PKGBUILDDIR»/easel'
SUBDIR miniapps
make[4]: Entering directory '/«PKGBUILDDIR»/easel/miniapps'
make[4]: Nothing to be done for 'check'.
make[4]: Leaving directory '/«PKGBUILDDIR»/easel/miniapps'
SUBDIR testsuite
make[4]: Entering directory '/«PKGBUILDDIR»/easel/testsuite'
Running Easel test suite...
exercise 1 [ alphabet-utest] ... ok.
exercise 2 [ buffer-utest] ... ok.
exercise 3 [ cluster-utest] ... ok.
exercise 4 [ dirichlet-utest] ... ok.
exercise 5 [ distance-utest] ... ok.
exercise 6 [ dmatrix-utest] ... ok.
exercise 7 [ easel-utest] ... ok.
exercise 8 [ exponential-utest] ... ok.
exercise 9 [ fileparser-utest] ... ok.
exercise 10 [ gamma-utest] ... ok.
exercise 11 [ getopts-utest] ... ok.
exercise 12 [ gumbel-utest] ... ok.
exercise 13 [ histogram-utest] ... ok.
exercise 14 [ hyperexp-utest] ... ok.
exercise 15 [ keyhash-utest] ... ok.
exercise 16 [ mem-utest] ... ok.
exercise 17 [ msa-utest] ... ok.
exercise 18 [ msafile] ... ok.
exercise 19 [ msafile2] ... ok.
exercise 20 [ msafile-a2m] ... ok.
exercise 21 [ msafile-afa] ... ok.
exercise 22 [ msafile-clustal] ... ok.
exercise 23 [ msafile-phylip] ... ok.
exercise 24 [ msafile-psiblast] ... ok.
exercise 25 [ msafile-selex] ... ok.
exercise 26 [ msafile-stockholm] ... ok.
exercise 27 [ msacluster-utest] ... ok.
exercise 28 [ msaweight-utest] ... ok.
exercise 29 [ random-utest] ... ok.
exercise 30 [ randomseq-utest] ... ok.
exercise 31 [ ratematrix-utest] ... ok.
exercise 32 [ recorder-utest] ... ok.
exercise 33 [ regexp-utest] ... ok.
exercise 34 [ rootfinder-utest] ... ok.
exercise 35 [ scorematrix-utest] ... ok.
exercise 36 [ sq-utest] ... ok.
exercise 37 [ sqio-utest] ... ok.
exercise 38 [ sse-utest] ... ok.
exercise 39 [ ssi-utest] ... ok.
exercise 40 [ stack-utest] ... ok.
exercise 41 [ stats-utest] ... ok.
exercise 42 [ stretchexp-utest] ... ok.
exercise 43 [ tree-utest] ... ok.
exercise 44 [ vectorops-utest] ... ok.
exercise 45 [ weibull-utest] ... ok.
exercise 46 [ wuss-utest] ... ok.
exercise 47 [ e2] ... ok.
exercise 48 [ degen-residues] ... ok.
exercise 49 [ ncbi-indices] ... ok.
exercise 50 [ blank-gf] ... ok.
exercise 51 [ esl-afetch] ... ok.
exercise 52 [ esl-alimanip] ... ok.
exercise 53 [ esl-alimap] ... ok.
exercise 54 [ esl-alimask] ... ok.
exercise 55 [ esl-alimerge] ... ok.
exercise 56 [ esl-alistat] ... ok.
exercise 57 [ esl-compalign] ... ok.
exercise 58 [ esl-construct] ... ok.
exercise 59 [ esl-mask] ... ok.
exercise 60 [ esl-seqrange] ... ok.
exercise 61 [ esl-shuffle] ... ok.
exercise 62 [ esl-ssdraw] ... ok.
All 62 exercises at level <= 2 passed.
System information:
Sat Jul 11 06:07:31 UTC 2015
Linux bm-wb-02 3.19.0-trunk-armmp #1 SMP Debian 3.19.1-1~exp1+plugwash1 (2015-03-28) armv7l GNU/Linux
make[4]: Leaving directory '/«PKGBUILDDIR»/easel/testsuite'
make[3]: Leaving directory '/«PKGBUILDDIR»/easel'
SUBDIR testsuite
make[3]: Entering directory '/«PKGBUILDDIR»/testsuite'
Running HMMER test suite...
exercise 1 [ hmmer] ... ok.
exercise 2 [ build] ... ok.
exercise 3 [ generic_fwdback] ... ok.
exercise 4 [ generic_msv] ... ok.
exercise 5 [ generic_stotrace] ... ok.
exercise 6 [ generic_viterbi] ... ok.
exercise 7 [ logsum] ... ok.
exercise 8 [ modelconfig] ... ok.
exercise 9 [ seqmodel] ... ok.
exercise 10 [ p7_alidisplay] ... ok.
exercise 11 [ p7_bg] ... ok.
exercise 12 [ p7_gmx] ... ok.
exercise 13 [ p7_hmm] ... ok.
exercise 14 [ p7_hmmfile] ... ok.
exercise 15 [ p7_profile] ... ok.
exercise 16 [ p7_tophits] ... ok.
exercise 17 [ p7_trace] ... ok.
exercise 18 [ p7_scoredata] ... ok.
exercise 19 [ decoding] ... ok.
exercise 20 [ fwdback] ... ok.
exercise 21 [ io] ... ok.
exercise 22 [ msvfilter] ... ok.
exercise 23 [ null2] ... ok.
exercise 24 [ optacc] ... ok.
exercise 25 [ stotrace] ... ok.
exercise 26 [ vitfilter] ... ok.
exercise 27 [ hmmalign] ... ok.
exercise 28 [ hmmalign/-h] ... ok.
exercise 29 [ hmmalign/-o] ... ok.
exercise 30 [ hmmalign/--mapali] ... ok.
exercise 31 [ hmmalign/--trim] ... ok.
exercise 32 [ hmmalign/--amino] ... ok.
exercise 33 [ hmmalign/--informat] ... ok.
exercise 34 [ hmmalign/--outformat] ... ok.
exercise 35 [ build] ... ok.
exercise 36 [ build/-h] ... ok.
exercise 37 [ build/-n] ... ok.
exercise 38 [ build/-o] ... ok.
exercise 39 [ build/-O] ... ok.
exercise 40 [ build/--amino] ... ok.
exercise 41 [ build/--dna] ... ok.
exercise 42 [ build/--rna] ... ok.
exercise 43 [ build/--fast] ... ok.
exercise 44 [ build/--hand] ... ok.
exercise 45 [ build/--symfrac] ... ok.
exercise 46 [ build/--fragthresh] ... ok.
exercise 47 [ build/--wpb] ... ok.
exercise 48 [ build/--wgsc] ... ok.
exercise 49 [ build/--wblosum] ... ok.
exercise 50 [ build/--wnone] ... ok.
exercise 51 [ build/--wid] ... ok.
exercise 52 [ build/--eent] ... ok.
exercise 53 [ build/--eclust] ... ok.
exercise 54 [ build/--enone] ... ok.
exercise 55 [ build/--eset] ... ok.
exercise 56 [ build/--ere] ... ok.
exercise 57 [ build/--esigma] ... ok.
exercise 58 [ build/--eid] ... ok.
exercise 59 [ build/--pnone] ... ok.
exercise 60 [ build/--plaplace] ... ok.
exercise 61 [ build/--EmL] ... ok.
exercise 62 [ build/--EmN] ... ok.
exercise 63 [ build/--EvL] ... ok.
exercise 64 [ build/--EvN] ... ok.
exercise 65 [ build/--EfL] ... ok.
exercise 66 [ build/--EfN] ... ok.
exercise 67 [ build/--Eft] ... ok.
exercise 68 [ build/--informat] ... ok.
exercise 69 [ build/--seed] ... ok.
exercise 70 [ hmmemit] ... ok.
exercise 71 [ hmmemit/-h] ... ok.
exercise 72 [ hmmemit/-c] ... ok.
exercise 73 [ hmmemit/-o] ... ok.
exercise 74 [ hmmemit/-p] ... ok.
exercise 75 [ hmmemit/-N] ... ok.
exercise 76 [ hmmemit/-L] ... ok.
exercise 77 [ hmmemit/--local] ... ok.
exercise 78 [ hmmemit/--unilocal] ... ok.
exercise 79 [ hmmemit/--glocal] ... ok.
exercise 80 [ hmmemit/--uniglocal] ... ok.
exercise 81 [ search] ... ok.
exercise 82 [ search/-h] ... ok.
exercise 83 [ search/-o] ... ok.
exercise 84 [ search/-A] ... ok.
exercise 85 [ search/--tblout] ... ok.
exercise 86 [ search/--domtblout] ... ok.
exercise 87 [ search/--pfamtblout] ... ok.
exercise 88 [ search/--acc] ... ok.
exercise 89 [ search/--noali] ... ok.
exercise 90 [ search/--notextw] ... ok.
exercise 91 [ search/--textw] ... ok.
exercise 92 [ search/-E] ... ok.
exercise 93 [ search/-T] ... ok.
exercise 94 [ search/--domE] ... ok.
exercise 95 [ search/--domT] ... ok.
exercise 96 [ search/--incE] ... ok.
exercise 97 [ search/--incT] ... ok.
exercise 98 [ search/--incdomE] ... ok.
exercise 99 [ search/--incdomT] ... ok.
exercise 100 [ search/--cut_ga] ... ok.
exercise 101 [ search/--cut_nc] ... ok.
exercise 102 [ search/--cut_tc] ... ok.
exercise 103 [ search/--max] ... ok.
exercise 104 [ search/--F1] ... ok.
exercise 105 [ search/--F2] ... ok.
exercise 106 [ search/--F3] ... ok.
exercise 107 [ search/--nobias] ... ok.
exercise 108 [ search/--nonull2] ... ok.
exercise 109 [ search/-Z] ... ok.
exercise 110 [ search/--domZ] ... ok.
exercise 111 [ search/--seed] ... ok.
exercise 112 [ search/--tformat] ... ok.
exercise 113 [ jackhmmer] ... ok.
exercise 114 [ j/-h] ... ok.
exercise 115 [ j/-N] ... ok.
exercise 116 [ j/-o] ... ok.
exercise 117 [ j/-A] ... ok.
exercise 118 [ j/--tblout] ... ok.
exercise 119 [ j/--domtblout] ... ok.
exercise 120 [ j/--chkhmm] ... ok.
exercise 121 [ j/--chkali] ... ok.
exercise 122 [ j/--acc] ... ok.
exercise 123 [ j/--noali] ... ok.
exercise 124 [ j/--notextw] ... ok.
exercise 125 [ j/--textw] ... ok.
exercise 126 [ j/--popen] ... ok.
exercise 127 [ j/--pextend] ... ok.
exercise 128 [ j/--mxfile] ... ok.
exercise 129 [ j/-E] ... ok.
exercise 130 [ j/-T] ... ok.
exercise 131 [ j/--domE] ... ok.
exercise 132 [ j/--domT] ... ok.
exercise 133 [ j/--incE] ... ok.
exercise 134 [ j/--incT] ... ok.
exercise 135 [ j/--incdomE] ... ok.
exercise 136 [ j/--incdomT] ... ok.
exercise 137 [ j/--max] ... ok.
exercise 138 [ j/--F1] ... ok.
exercise 139 [ j/--F2] ... ok.
exercise 140 [ j/--F3] ... ok.
exercise 141 [ j/--nobias] ... ok.
exercise 142 [ j/--EmL] ... ok.
exercise 143 [ j/--EmN] ... ok.
exercise 144 [ j/--EvL] ... ok.
exercise 145 [ j/--EvN] ... ok.
exercise 146 [ j/--EfL] ... ok.
exercise 147 [ j/--EfN] ... ok.
exercise 148 [ j/--Eft] ... ok.
exercise 149 [ j/--nonull2] ... ok.
exercise 150 [ j/-Z] ... ok.
exercise 151 [ j/--domZ] ... ok.
exercise 152 [ j/--seed] ... ok.
exercise 153 [ j/--qformat] ... ok.
exercise 154 [ j/--tformat] ... ok.
exercise 155 [ phmmer] ... ok.
exercise 156 [ phmmer/-h] ... ok.
exercise 157 [ phmmer/-o] ... ok.
exercise 158 [ phmmer/-A] ... ok.
exercise 159 [ phmmer/--tblout] ... ok.
exercise 160 [ phmmer/--domtblout] ... ok.
exercise 161 [ phmmer/--pfamtblout] ... ok.
exercise 162 [ phmmer/--acc] ... ok.
exercise 163 [ phmmer/--noali] ... ok.
exercise 164 [ phmmer/--notextw] ... ok.
exercise 165 [ phmmer/--textw] ... ok.
exercise 166 [ phmmer/--popen] ... ok.
exercise 167 [ phmmer/--pextend] ... ok.
exercise 168 [ phmmer/--mxfile] ... ok.
exercise 169 [ phmmer/-E] ... ok.
exercise 170 [ phmmer/-T] ... ok.
exercise 171 [ phmmer/--domE] ... ok.
exercise 172 [ phmmer/--domT] ... ok.
exercise 173 [ phmmer/--incE] ... ok.
exercise 174 [ phmmer/--incT] ... ok.
exercise 175 [ phmmer/--incdomE] ... ok.
exercise 176 [ phmmer/--incdomT] ... ok.
exercise 177 [ phmmer/--max] ... ok.
exercise 178 [ phmmer/--F1] ... ok.
exercise 179 [ phmmer/--F2] ... ok.
exercise 180 [ phmmer/--F3] ... ok.
exercise 181 [ phmmer/--nobias] ... ok.
exercise 182 [ phmmer/--EmL] ... ok.
exercise 183 [ phmmer/--EmN] ... ok.
exercise 184 [ phmmer/--EvL] ... ok.
exercise 185 [ phmmer/--EvN] ... ok.
exercise 186 [ phmmer/--EfL] ... ok.
exercise 187 [ phmmer/--EfN] ... ok.
exercise 188 [ phmmer/--Eft] ... ok.
exercise 189 [ phmmer/--nonull2] ... ok.
exercise 190 [ phmmer/-Z] ... ok.
exercise 191 [ phmmer/--domZ] ... ok.
exercise 192 [ phmmer/--seed] ... ok.
exercise 193 [ phmmer/--qformat] ... ok.
exercise 194 [ phmmer/--tformat] ... ok.
exercise 195 [ nhmmer] ... ok.
exercise 196 [ nhmmer/-h] ... ok.
exercise 197 [ nhmmer/-o] ... ok.
exercise 198 [ nhmmer/-A] ... ok.
exercise 199 [ nhmmer/--tblout] ... ok.
exercise 200 [ nhmmer/--dfamtblout] ... ok.
exercise 201 [ nhmmer/--acc] ... ok.
exercise 202 [ nhmmer/--noali] ... ok.
exercise 203 [ nhmmer/--notextw] ... ok.
exercise 204 [ nhmmer/--textw] ... ok.
exercise 205 [ nhmmer/-E] ... ok.
exercise 206 [ nhmmer/-T] ... ok.
exercise 207 [ nhmmer/--incE] ... ok.
exercise 208 [ nhmmer/--incT] ... ok.
exercise 209 [ nhmmer/--max] ... ok.
exercise 210 [ nhmmer/--F1] ... ok.
exercise 211 [ nhmmer/--F2] ... ok.
exercise 212 [ nhmmer/--F3] ... ok.
exercise 213 [ nhmmer/--nobias] ... ok.
exercise 214 [ nhmmer/--nonull2] ... ok.
exercise 215 [ nhmmer/-Z] ... ok.
exercise 216 [ nhmmer/--seed] ... ok.
exercise 217 [ nhmmscan] ... ok.
exercise 218 [ nhmmscan/-h] ... ok.
exercise 219 [ nhmmscan/-o] ... ok.
exercise 220 [ nhmmscan/--tblout] ... ok.
exercise 221 [nhmmscan/--dfamtblout] ... ok.
exercise 222 [ nhmmscan/--acc] ... ok.
exercise 223 [ nhmmscan/--noali] ... ok.
exercise 224 [ nhmmscan/--notextw] ... ok.
exercise 225 [ nhmmscan/--textw] ... ok.
exercise 226 [ nhmmscan/-E] ... ok.
exercise 227 [ nhmmscan/-T] ... ok.
exercise 228 [ nhmmscan/--incE] ... ok.
exercise 229 [ nhmmscan/--incT] ... ok.
exercise 230 [ nhmmscan/--max] ... ok.
exercise 231 [ nhmmscan/--F1] ... ok.
exercise 232 [ nhmmscan/--F2] ... ok.
exercise 233 [ nhmmscan/--F3] ... ok.
exercise 234 [ nhmmscan/--nobias] ... ok.
exercise 235 [ nhmmscan/--nonull2] ... ok.
exercise 236 [ nhmmscan/-Z] ... ok.
exercise 237 [ nhmmscan/--seed] ... ok.
exercise 238 [ hmmbuild_variation] ... ok.
exercise 239 [ hmmscan_variation] ... ok.
exercise 240 [ hmmsearch_variation] ... ok.
exercise 241 [ phmmer_variation] ... ok.
exercise 242 [ mapali] ... ok.
exercise 243 [ fragments] ... ok.
exercise 244 [ nonresidues] ... FAILED [command failed]
exercise 245 [ opt-annotation] ... ok.
exercise 246 [ dup-names] ... ok.
exercise 247 [ mapali-again] ... ok.
exercise 248 [ delete-corruption] ... ok.
exercise 249 [ msa-integrity] ... ok.
exercise 250 [ hmmemit-consensus] ... ok.
exercise 251 [ hmmconvert] ... ok.
exercise 252 [ stdin_pipes] ... FAILED [command failed]
exercise 253 [ nhmmer_generic] ... FAILED [command failed]
exercise 254 [ hmmpgmd_ga] ... ok.
exercise 255 [ brute-itest] ... ok.
exercise 256 [ hmmpress-itest] ... ok.
exercise 257 [ h39] ... ok.
exercise 258 [ h45] ... ok.
exercise 259 [ h50] ... ok.
exercise 260 [ h82] ... ok.
3 of 260 exercises at level <= 2 FAILED.
System information:
Sat Jul 11 06:11:19 UTC 2015
Linux bm-wb-02 3.19.0-trunk-armmp #1 SMP Debian 3.19.1-1~exp1+plugwash1 (2015-03-28) armv7l GNU/Linux
make[3]: Leaving directory '/«PKGBUILDDIR»/testsuite'
make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
fakeroot debian/rules binary-arch
dh binary-arch --with autotools_dev
dh_testroot -a
dh_prep -a
dh_auto_install -a
make -j1 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/«PKGBUILDDIR»'
/usr/bin/install -c -d /«PKGBUILDDIR»/debian/tmp/usr/bin
/usr/bin/install -c -d /«PKGBUILDDIR»/debian/tmp/usr/lib/arm-linux-gnueabihf
/usr/bin/install -c -d /«PKGBUILDDIR»/debian/tmp/usr/include
/usr/bin/install -c -d /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
/usr/bin/install -c -d /«PKGBUILDDIR»/debian/tmp/usr/share/doc/hmmer
SUBDIR src
make[2]: Entering directory '/«PKGBUILDDIR»/src'
SUBDIR impl_dummy
make[3]: Entering directory '/«PKGBUILDDIR»/src/impl_dummy'
for file in impl_dummy.h; do \
/usr/bin/install -c -m 0644 ./$file /«PKGBUILDDIR»/debian/tmp/usr/include/ ;\
done
make[3]: Leaving directory '/«PKGBUILDDIR»/src/impl_dummy'
for file in alimask hmmalign hmmbuild hmmconvert hmmemit hmmfetch hmmlogo hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer phmmer nhmmer nhmmscan hmmpgmd hmmc2 makehmmerdb hmmerfm-exactmatch; do \
/usr/bin/install -c -m 0755 $file /«PKGBUILDDIR»/debian/tmp/usr/bin/ ;\
done
/usr/bin/install -c -m 0755 libhmmer.a /«PKGBUILDDIR»/debian/tmp/usr/lib/arm-linux-gnueabihf/
for file in hmmer.h cachedb.h p7_gbands.h p7_gmxb.h p7_gmxchk.h p7_hmmcache.h; do \
/usr/bin/install -c -m 0644 ./$file /«PKGBUILDDIR»/debian/tmp/usr/include/ ;\
done
/usr/bin/install -c -m 0644 p7_config.h /«PKGBUILDDIR»/debian/tmp/usr/include/ ;\
make[2]: Leaving directory '/«PKGBUILDDIR»/src'
SUBDIR documentation
make[2]: Entering directory '/«PKGBUILDDIR»/documentation'
SUBDIR man
make[3]: Entering directory '/«PKGBUILDDIR»/documentation/man'
for file in hmmer hmmalign hmmbuild hmmconvert hmmemit hmmfetch hmmlogo hmmpgmd hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer makehmmerdb phmmer nhmmer nhmmscan alimask; do \
/usr/bin/install -c -m 0755 ./$file.man /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1/${file}.1 ;\
done
make[3]: Leaving directory '/«PKGBUILDDIR»/documentation/man'
make[2]: Leaving directory '/«PKGBUILDDIR»/documentation'
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
debian/rules override_dh_compress
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_compress -Xtutorial/
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package `hmmer' in `../hmmer_3.1b2-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../hmmer_3.1b2-1_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build hmmer-3.1b2
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20150711-0612
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
hmmer_3.1b2-1_armhf.changes:
────────────────────────────
Format: 1.8
Date: Sun, 05 Jul 2015 22:45:41 +0200
Source: hmmer
Binary: hmmer hmmer-doc
Architecture: armhf
Version: 3.1b2-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
hmmer - profile hidden Markov models for protein sequence analysis
hmmer-doc - profile hidden Markov models for protein sequence analysis (docs)
Changes:
hmmer (3.1b2-1) unstable; urgency=medium
.
* New upstream version (adapted patches)
* Moved debian/upstream to debian/upstream/metadata
* cme fix dpkg-control
Checksums-Sha1:
619dd93500cab4bb31da42585d8c163292a414c2 838960 hmmer_3.1b2-1_armhf.deb
Checksums-Sha256:
fa91faa6de63c03c51d456b5641ca635c407ec58d222ee78ec6cfde1561064f4 838960 hmmer_3.1b2-1_armhf.deb
Files:
edf13ed9185c9a4c869aabeaf4047994 838960 science optional hmmer_3.1b2-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
hmmer_3.1b2-1_armhf.deb
───────────────────────
new debian package, version 2.0.
size 838960 bytes: control archive=1859 bytes.
777 bytes, 19 lines control
2493 bytes, 42 lines md5sums
Package: hmmer
Version: 3.1b2-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 9006
Depends: libc6 (>= 2.15)
Suggests: hmmer-doc (>= 3.1b2-1)
Section: science
Priority: optional
Homepage: http://hmmer.janelia.org/
Description: profile hidden Markov models for protein sequence analysis
HMMER is an implementation of profile hidden Markov model methods for
sensitive searches of biological sequence databases using multiple sequence
alignments as queries.
.
Given a multiple sequence alignment as input, HMMER builds a statistical
model called a "hidden Markov model" which can then be used as a query into
a sequence database to find (and/or align) additional homologues of the
sequence family.
drwxr-xr-x root/root 0 2015-07-11 06:11 ./
drwxr-xr-x root/root 0 2015-07-11 06:11 ./usr/
drwxr-xr-x root/root 0 2015-07-11 06:11 ./usr/bin/
-rwxr-xr-x root/root 289592 2015-07-11 06:11 ./usr/bin/alimask
-rwxr-xr-x root/root 485672 2015-07-11 06:11 ./usr/bin/hmmalign
-rwxr-xr-x root/root 570692 2015-07-11 06:11 ./usr/bin/hmmbuild
-rwxr-xr-x root/root 545656 2015-07-11 06:11 ./usr/bin/hmmc2
-rwxr-xr-x root/root 260160 2015-07-11 06:11 ./usr/bin/hmmconvert
-rwxr-xr-x root/root 490012 2015-07-11 06:11 ./usr/bin/hmmemit
-rwxr-xr-x root/root 87972 2015-07-11 06:11 ./usr/bin/hmmerfm-exactmatch
-rwxr-xr-x root/root 264420 2015-07-11 06:11 ./usr/bin/hmmfetch
-rwxr-xr-x root/root 256084 2015-07-11 06:11 ./usr/bin/hmmlogo
-rwxr-xr-x root/root 755280 2015-07-11 06:11 ./usr/bin/hmmpgmd
-rwxr-xr-x root/root 264164 2015-07-11 06:11 ./usr/bin/hmmpress
-rwxr-xr-x root/root 601328 2015-07-11 06:11 ./usr/bin/hmmscan
-rwxr-xr-x root/root 601444 2015-07-11 06:11 ./usr/bin/hmmsearch
-rwxr-xr-x root/root 282000 2015-07-11 06:11 ./usr/bin/hmmsim
-rwxr-xr-x root/root 260292 2015-07-11 06:11 ./usr/bin/hmmstat
-rwxr-xr-x root/root 727176 2015-07-11 06:11 ./usr/bin/jackhmmer
-rwxr-xr-x root/root 350384 2015-07-11 06:11 ./usr/bin/makehmmerdb
-rwxr-xr-x root/root 730808 2015-07-11 06:11 ./usr/bin/nhmmer
-rwxr-xr-x root/root 605712 2015-07-11 06:11 ./usr/bin/nhmmscan
-rwxr-xr-x root/root 722392 2015-07-11 06:11 ./usr/bin/phmmer
drwxr-xr-x root/root 0 2015-07-11 06:11 ./usr/share/
drwxr-xr-x root/root 0 2015-07-11 06:11 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-07-11 06:11 ./usr/share/doc/hmmer/
-rw-r--r-- root/root 491 2013-09-12 09:00 ./usr/share/doc/hmmer/README.Debian
-rw-r--r-- root/root 2582 2015-07-05 20:45 ./usr/share/doc/hmmer/changelog.Debian.gz
-rw-r--r-- root/root 3390 2013-09-12 09:00 ./usr/share/doc/hmmer/copyright
drwxr-xr-x root/root 0 2015-07-11 06:11 ./usr/share/man/
drwxr-xr-x root/root 0 2015-07-11 06:11 ./usr/share/man/man1/
-rw-r--r-- root/root 3560 2015-07-11 06:11 ./usr/share/man/man1/alimask.1.gz
-rw-r--r-- root/root 1577 2015-07-11 06:11 ./usr/share/man/man1/hmmalign.1.gz
-rw-r--r-- root/root 5121 2015-07-11 06:11 ./usr/share/man/man1/hmmbuild.1.gz
-rw-r--r-- root/root 1044 2015-07-11 06:11 ./usr/share/man/man1/hmmconvert.1.gz
-rw-r--r-- root/root 2272 2015-07-11 06:11 ./usr/share/man/man1/hmmemit.1.gz
-rw-r--r-- root/root 2234 2015-07-11 06:11 ./usr/share/man/man1/hmmer.1.gz
-rw-r--r-- root/root 1768 2015-07-11 06:11 ./usr/share/man/man1/hmmfetch.1.gz
-rw-r--r-- root/root 1146 2015-07-11 06:11 ./usr/share/man/man1/hmmlogo.1.gz
-rw-r--r-- root/root 2312 2015-07-11 06:11 ./usr/share/man/man1/hmmpgmd.1.gz
-rw-r--r-- root/root 997 2015-07-11 06:11 ./usr/share/man/man1/hmmpress.1.gz
-rw-r--r-- root/root 4559 2015-07-11 06:11 ./usr/share/man/man1/hmmscan.1.gz
-rw-r--r-- root/root 4482 2015-07-11 06:11 ./usr/share/man/man1/hmmsearch.1.gz
-rw-r--r-- root/root 5264 2015-07-11 06:11 ./usr/share/man/man1/hmmsim.1.gz
-rw-r--r-- root/root 1419 2015-07-11 06:11 ./usr/share/man/man1/hmmstat.1.gz
-rw-r--r-- root/root 7695 2015-07-11 06:11 ./usr/share/man/man1/jackhmmer.1.gz
-rw-r--r-- root/root 1843 2015-07-11 06:11 ./usr/share/man/man1/makehmmerdb.1.gz
-rw-r--r-- root/root 6398 2015-07-11 06:11 ./usr/share/man/man1/nhmmer.1.gz
-rw-r--r-- root/root 4845 2015-07-11 06:11 ./usr/share/man/man1/nhmmscan.1.gz
-rw-r--r-- root/root 4907 2015-07-11 06:11 ./usr/share/man/man1/phmmer.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 174528
Build-Time: 1274
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 148
Job: hmmer_3.1b2-1
Machine Architecture: armhf
Package: hmmer
Package-Time: 1485
Source-Version: 3.1b2-1
Space: 174528
Status: successful
Version: 3.1b2-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20150711-0612
Build needed 00:24:45, 174528k disc space