ampliconnoise →
1.29-2 →
armhf → 2014-03-08 05:14:29
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on testwandboard
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║ ampliconnoise 1.29-2 (armhf) 08 Mar 2014 05:11 ║
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Package: ampliconnoise
Version: 1.29-2
Source Version: 1.29-2
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/ampliconnoise-LkiioX/ampliconnoise-1.29' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/ampliconnoise-LkiioX' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-bb1f613a-f949-4005-959f-fd42d611cf3d' with '«CHROOT»'
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Get:1 http://172.17.0.1 jessie-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 jessie-staging/main Sources [7299 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8459 kB]
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NOTICE: 'ampliconnoise' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/ampliconnoise/trunk/
Need to get 1413 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main ampliconnoise 1.29-2 (dsc) [2052 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main ampliconnoise 1.29-2 (tar) [1403 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main ampliconnoise 1.29-2 (diff) [7708 B]
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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-X4cAHv/apt_archive/sbuild-build-depends-core-dummy.deb'.
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The following NEW packages will be installed:
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Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), libgsl0-dev, libopenmpi-dev
Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), libgsl0-dev, libopenmpi-dev
dpkg-deb: building package `sbuild-build-depends-ampliconnoise-dummy' in `/«BUILDDIR»/resolver-Dk9GK0/apt_archive/sbuild-build-depends-ampliconnoise-dummy.deb'.
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install ampliconnoise build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
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The following extra packages will be installed:
adduser bsdmainutils debhelper file gettext gettext-base groff-base
intltool-debian libasprintf0c2 libcr0 libcroco3 libffi6 libgfortran3
libglib2.0-0 libgsl0-dev libgsl0ldbl libhwloc-dev libhwloc5 libibverbs-dev
libibverbs1 libltdl7 libmagic1 libopenmpi-dev libopenmpi1.6 libpci-dev
libpci3 libpipeline1 libsctp1 libtorque2 libunistring0 libxml2 libxml2-dev
man-db openmpi-common po-debconf zlib1g-dev
Suggested packages:
liblocale-gettext-perl wamerican wordlist whois vacation dh-make gettext-doc
groff blcr-dkms gsl-ref-psdoc gsl-doc-pdf gsl-doc-info gsl-ref-html
libhwloc-contrib-plugins pkg-config less www-browser libmail-box-perl
Recommended packages:
curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libglib2.0-data shared-mime-info libhwloc-plugins lksctp-tools xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
adduser bsdmainutils debhelper file gettext gettext-base groff-base
intltool-debian libasprintf0c2 libcr0 libcroco3 libffi6 libgfortran3
libglib2.0-0 libgsl0-dev libgsl0ldbl libhwloc-dev libhwloc5 libibverbs-dev
libibverbs1 libltdl7 libmagic1 libopenmpi-dev libopenmpi1.6 libpci-dev
libpci3 libpipeline1 libsctp1 libtorque2 libunistring0 libxml2 libxml2-dev
man-db openmpi-common po-debconf sbuild-build-depends-ampliconnoise-dummy
zlib1g-dev
0 upgraded, 37 newly installed, 0 to remove and 3 not upgraded.
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┌──────────────────────────────────────────────────────────────────────────────┐
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Kernel: Linux 3.13-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.24-3 dpkg-dev_1.17.6+rpi1 g++-4.6_4.6.4-5+rpi1 g++-4.8_4.8.2-16 gcc-4.6_4.6.4-5+rpi1 gcc-4.8_4.8.2-16 libc6-dev_2.18-4 libstdc++-4.8-dev_4.8.2-16 libstdc++6_4.8.2-16 libstdc++6-4.6-dev_4.6.4-5+rpi1 linux-libc-dev_3.12.6-2+rpi1
Package versions: adduser_3.113+nmu3 apt_0.9.15.4 base-files_7.2+rpi1 base-passwd_3.5.28 bash_4.2+dfsg-1 binutils_2.24-3 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.6 build-essential_11.6 bzip2_1.0.6-5 coreutils_8.21-1 cpio_2.11+dfsg-1 cpp_4:4.8.2-2 cpp-4.6_4.6.4-5+rpi1 cpp-4.8_4.8.2-16 dash_0.5.7-4 debconf_1.5.52 debfoster_2.7-1.2 debhelper_9.20140228 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.6+rpi1 dpkg-dev_1.17.6+rpi1 e2fslibs_1.42.9-3 e2fsprogs_1.42.9-3 fakeroot_1.18.4-2 file_1:5.17-0.1 findutils_4.4.2-7 g++_4:4.8.2-2 g++-4.6_4.6.4-5+rpi1 g++-4.8_4.8.2-16 gcc_4:4.8.2-2 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.4-5+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-10+rpi1 gcc-4.8_4.8.2-16 gcc-4.8-base_4.8.2-16 gettext_0.18.3.2-1 gettext-base_0.18.3.2-1 gnupg_1.4.16-1.1 gpgv_1.4.16-1.1 grep_2.16-1 groff-base_1.22.2-5 gzip_1.6-3 hostname_3.15 initramfs-tools_0.115 initscripts_2.88dsf-51 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.2-1+rpi1 kmod_16-2 libacl1_2.2.52-1 libapt-pkg4.12_0.9.15.4 libarchive-extract-perl_0.72-1 libasan0_4.8.2-16 libasprintf0c2_0.18.3.2-1 libatomic1_4.8.2-16 libattr1_1:2.4.47-1 libaudit-common_1:2.3.3-4 libaudit1_1:2.3.3-4 libblkid1_2.20.1-5.6 libbz2-1.0_1.0.6-5 libc-bin_2.18-4 libc-dev-bin_2.18-4 libc6_2.18-4 libc6-dev_2.18-4 libcap2_1:2.22-1.2 libclass-isa-perl_0.36-5 libcloog-isl4_0.18.2-1 libcomerr2_1.42.9-3 libcr0_0.8.5-2.1 libcroco3_0.6.8-2 libdb5.1_5.1.29-6 libdb5.3_5.3.28-3 libdbus-1-3_1.8.0-1 libdpkg-perl_1.17.6+rpi1 libffi6_3.0.13-12 libgc1c2_1:7.2d-6 libgcc-4.8-dev_4.8.2-16 libgcc1_1:4.8.2-16 libgdbm3_1.8.3-12 libgfortran3_4.8.2-16 libglib2.0-0_2.38.2-5 libgmp10_2:5.1.3+dfsg-1 libgomp1_4.8.2-16 libgsl0-dev_1.16+dfsg-1 libgsl0ldbl_1.16+dfsg-1 libhwloc-dev_1.8.1-1 libhwloc5_1.8.1-1 libibverbs-dev_1.1.7-1 libibverbs1_1.1.7-1 libisl10_0.12.2-1 libklibc_2.0.2-1+rpi1 libkmod2_16-2 liblog-message-simple-perl_0.10-1 libltdl7_2.4.2-1.7 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.17-0.1 libmodule-pluggable-perl_5.1-1 libmount1_2.20.1-5.6 libmpc3_1.0.1-1 libmpfr4_3.1.2-1 libncurses5_5.9+20140118-1 libncursesw5_5.9+20140118-1 libopenmpi-dev_1.6.5-8+rpi1 libopenmpi1.6_1.6.5-8+rpi1 libpam-modules_1.1.8-2 libpam-modules-bin_1.1.8-2 libpam-runtime_1.1.8-2 libpam0g_1.1.8-2 libpci-dev_1:3.2.1-2 libpci3_1:3.2.1-2 libpcre3_1:8.31-2 libpipeline1_1.2.6-2 libpod-latex-perl_0.61-1 libprocps0_1:3.3.4-2 libprocps3_1:3.3.9-2 libreadline6_6.2+dfsg-0.1 libsctp1_1.0.16+dfsg-1 libselinux1_2.2.2-1 libsemanage-common_2.2-1 libsemanage1_2.2-1 libsepol1_2.2-1 libslang2_2.2.4-16 libss2_1.42.9-3 libstdc++-4.8-dev_4.8.2-16 libstdc++6_4.8.2-16 libstdc++6-4.6-dev_4.6.4-5+rpi1 libswitch-perl_2.16-2 libterm-ui-perl_0.42-1 libtimedate-perl_2.3000-1 libtinfo5_5.9+20140118-1 libtorque2_2.4.16+dfsg-1.3 libudev0_175-7.2 libudev1_204-7 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.3 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.6 libxml2_2.9.1+dfsg1-3 libxml2-dev_2.9.1+dfsg1-3 linux-libc-dev_3.12.6-2+rpi1 login_1:4.1.5.1-1 lsb-base_4.1+Debian12+rpi1 make_3.81-8.3 makedev_2.3.1-93 man-db_2.6.6-1 mawk_1.3.3-17 mount_2.20.1-5.6 multiarch-support_2.18-4 nano_2.2.6-1 ncurses-base_5.9+20140118-1 ncurses-bin_5.9+20140118-1 openmpi-common_1.6.5-8+rpi1 passwd_1:4.1.5.1-1 patch_2.7.1-4 perl_5.18.2-2 perl-base_5.18.2-2 perl-modules_5.18.2-2 plymouth_0.8.8-6+deb8u3 po-debconf_1.0.16+nmu2 procps_1:3.3.9-2 raspbian-archive-keyring_20120528.2 readline-common_6.2+dfsg-0.1 sbuild-build-depends-ampliconnoise-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 sysv-rc_2.88dsf-51 sysvinit_2.88dsf-51 sysvinit-core_2.88dsf-51 sysvinit-utils_2.88dsf-51 tar_1.27.1-1 tzdata_2013i-1 udev_204-7 util-linux_2.20.1-5.6 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1 zlib1g-dev_1:1.2.8.dfsg-1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Tue Feb 25 08:03:44 2014 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./ampliconnoise_1.29-2.dsc
dpkg-source: info: extracting ampliconnoise in ampliconnoise-1.29
dpkg-source: info: unpacking ampliconnoise_1.29.orig.tar.gz
dpkg-source: info: unpacking ampliconnoise_1.29-2.debian.tar.xz
dpkg-source: info: applying fix-path-for-data.patch
dpkg-source: info: applying fix-segfault-on-non-fasta-input.patch
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying clang-ftbfs.patch
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/build/buildd
SCHROOT_ALIAS_NAME=jessie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=jessie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-bb1f613a-f949-4005-959f-fd42d611cf3d
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package ampliconnoise
dpkg-buildpackage: source version 1.29-2
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build ampliconnoise-1.29
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
make[1]: Entering directory `/«PKGBUILDDIR»'
(cd FCluster && make clean)
make[2]: Entering directory `/«PKGBUILDDIR»/FCluster'
rm -rf *o FCluster
make[2]: Leaving directory `/«PKGBUILDDIR»/FCluster'
(cd FastaUnique && make clean)
make[2]: Entering directory `/«PKGBUILDDIR»/FastaUnique'
rm -rf *.o FastaUnique
make[2]: Leaving directory `/«PKGBUILDDIR»/FastaUnique'
(cd NDist && make clean)
make[2]: Entering directory `/«PKGBUILDDIR»/NDist'
rm -rf *.o NDist
make[2]: Leaving directory `/«PKGBUILDDIR»/NDist'
(cd PyroDist && make clean)
make[2]: Entering directory `/«PKGBUILDDIR»/PyroDist'
rm -rf *.o PyroDist
make[2]: Leaving directory `/«PKGBUILDDIR»/PyroDist'
(cd PyroNoise && make clean)
make[2]: Entering directory `/«PKGBUILDDIR»/PyroNoise'
rm -rf *.o PyroNoise
make[2]: Leaving directory `/«PKGBUILDDIR»/PyroNoise'
(cd PyroNoiseM && make clean)
make[2]: Entering directory `/«PKGBUILDDIR»/PyroNoiseM'
rm -rf *.o PyroNoiseM
make[2]: Leaving directory `/«PKGBUILDDIR»/PyroNoiseM'
(cd PyroNoiseA && make clean)
make[2]: Entering directory `/«PKGBUILDDIR»/PyroNoiseA'
rm -rf *.o PyroNoiseA
make[2]: Leaving directory `/«PKGBUILDDIR»/PyroNoiseA'
(cd SeqDist && make clean)
make[2]: Entering directory `/«PKGBUILDDIR»/SeqDist'
rm -rf *.o SeqDist
make[2]: Leaving directory `/«PKGBUILDDIR»/SeqDist'
(cd SeqNoise && make clean)
make[2]: Entering directory `/«PKGBUILDDIR»/SeqNoise'
rm -rf *.o SeqNoise
make[2]: Leaving directory `/«PKGBUILDDIR»/SeqNoise'
(cd SplitClusterEven && make clean)
make[2]: Entering directory `/«PKGBUILDDIR»/SplitClusterEven'
rm -rf *.o SplitClusterEven
make[2]: Leaving directory `/«PKGBUILDDIR»/SplitClusterEven'
(cd SplitClusterClust && make clean)
make[2]: Entering directory `/«PKGBUILDDIR»/SplitClusterClust'
rm -rf *.o SplitClusterClust
make[2]: Leaving directory `/«PKGBUILDDIR»/SplitClusterClust'
(cd Perseus && make clean)
make[2]: Entering directory `/«PKGBUILDDIR»/Perseus'
rm -rf *.o Perseus
make[2]: Leaving directory `/«PKGBUILDDIR»/Perseus'
(cd PerseusD && make clean)
make[2]: Entering directory `/«PKGBUILDDIR»/PerseusD'
rm -rf *.o PerseusD
make[2]: Leaving directory `/«PKGBUILDDIR»/PerseusD'
(cd bin && rm -rf *)
make[1]: Leaving directory `/«PKGBUILDDIR»'
debian/rules override_dh_clean
make[1]: Entering directory `/«PKGBUILDDIR»'
dh_clean
rm -f *.o
rm -f *.1
make[1]: Leaving directory `/«PKGBUILDDIR»'
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_auto_configure -a
dh_auto_build -a
make[1]: Entering directory `/«PKGBUILDDIR»'
(cd FCluster && CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make)
make[2]: Entering directory `/«PKGBUILDDIR»/FCluster'
cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -c FCluster.c
linking...
cc -Wl,-z,relro -o FCluster FCluster.o -lm
make[2]: Leaving directory `/«PKGBUILDDIR»/FCluster'
(cd FastaUnique && CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make)
make[2]: Entering directory `/«PKGBUILDDIR»/FastaUnique'
cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -c FastaUnique.c
linking...
cc -Wl,-z,relro -o FastaUnique FastaUnique.o -lm
make[2]: Leaving directory `/«PKGBUILDDIR»/FastaUnique'
(cd NDist && CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make)
make[2]: Entering directory `/«PKGBUILDDIR»/NDist'
mpicc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -c NDist.c
linking...
mpicc -Wl,-z,relro -o NDist NDist.o -lm
make[2]: Leaving directory `/«PKGBUILDDIR»/NDist'
(cd PyroDist && CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make)
make[2]: Entering directory `/«PKGBUILDDIR»/PyroDist'
mpicc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -c PyroDist.c
linking...
mpicc -Wl,-z,relro -o PyroDist PyroDist.o -lm
make[2]: Leaving directory `/«PKGBUILDDIR»/PyroDist'
(cd PyroNoise && CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make)
make[2]: Entering directory `/«PKGBUILDDIR»/PyroNoise'
mpicc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -c PyroNoise.c
PyroNoise.c: In function 'writeCentroids':
PyroNoise.c:2073:5: warning: too many arguments for format [-Wformat-extra-args]
fprintf(stderr, "Can't open szCenFile for writing\n",szCenFile);
^
linking...
mpicc -Wl,-z,relro -o PyroNoise PyroNoise.o -lm
make[2]: Leaving directory `/«PKGBUILDDIR»/PyroNoise'
(cd SeqDist && CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make)
make[2]: Entering directory `/«PKGBUILDDIR»/SeqDist'
mpicc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -c SeqDist.c
linking...
mpicc -Wl,-z,relro -o SeqDist SeqDist.o -lm
make[2]: Leaving directory `/«PKGBUILDDIR»/SeqDist'
(cd PyroNoiseM && CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make)
make[2]: Entering directory `/«PKGBUILDDIR»/PyroNoiseM'
mpicc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -c PyroNoiseM.c
PyroNoiseM.c: In function 'writeCentroids':
PyroNoiseM.c:2139:5: warning: too many arguments for format [-Wformat-extra-args]
fprintf(stderr, "Can't open szCenFile for writing\n",szCenFile);
^
linking...
mpicc -Wl,-z,relro -o PyroNoiseM PyroNoiseM.o -lm
make[2]: Leaving directory `/«PKGBUILDDIR»/PyroNoiseM'
(cd PyroNoiseA && CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make)
make[2]: Entering directory `/«PKGBUILDDIR»/PyroNoiseA'
mpicc -O3 -c PyroNoiseA.c
linking...
mpicc -o PyroNoiseA PyroNoiseA.o -lm
make[2]: Leaving directory `/«PKGBUILDDIR»/PyroNoiseA'
(cd SeqNoise && CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make)
make[2]: Entering directory `/«PKGBUILDDIR»/SeqNoise'
mpicc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -c SeqNoise.c
SeqNoise.c: In function 'main':
SeqNoise.c:120:5: warning: too many arguments for format [-Wformat-extra-args]
if(bVerbose){printf("%d: Broadcast distance matrix\n", rank, nSize, nPacket); fflush(stdout);}
^
linking...
mpicc -Wl,-z,relro -o SeqNoise SeqNoise.o -lm
make[2]: Leaving directory `/«PKGBUILDDIR»/SeqNoise'
(cd SplitClusterEven && CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make)
make[2]: Entering directory `/«PKGBUILDDIR»/SplitClusterEven'
cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -c SplitClusterEven.c
SplitClusterEven.c: In function 'readMapFile':
SplitClusterEven.c:681:3: warning: too many arguments for format [-Wformat-extra-args]
fprintf(stderr, "Failed to open map file\n", szMapFile);
^
linking...
cc -Wl,-z,relro -o SplitClusterEven SplitClusterEven.o -lm
make[2]: Leaving directory `/«PKGBUILDDIR»/SplitClusterEven'
(cd SplitClusterClust && CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make)
make[2]: Entering directory `/«PKGBUILDDIR»/SplitClusterClust'
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -c SplitClusterClust.c
SplitClusterClust.c: In function 'readMapFile':
SplitClusterClust.c:316:3: warning: too many arguments for format [-Wformat-extra-args]
fprintf(stderr, "Failed to open map file\n", szMapFile);
^
linking...
gcc -Wl,-z,relro -o SplitClusterClust SplitClusterClust.o -lm
make[2]: Leaving directory `/«PKGBUILDDIR»/SplitClusterClust'
(cd Perseus && CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make)
make[2]: Entering directory `/«PKGBUILDDIR»/Perseus'
cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -c Perseus.c
linking...
cc -Wl,-z,relro -o Perseus Perseus.o -lm -lgsl -lgslcblas
make[2]: Leaving directory `/«PKGBUILDDIR»/Perseus'
(cd PerseusD && CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make)
make[2]: Entering directory `/«PKGBUILDDIR»/PerseusD'
cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -c PerseusD.c
linking...
cc -Wl,-z,relro -o PerseusD PerseusD.o -lm -lgsl -lgslcblas
make[2]: Leaving directory `/«PKGBUILDDIR»/PerseusD'
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_auto_test -a
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory `/«PKGBUILDDIR»'
make install
make[2]: Entering directory `/«PKGBUILDDIR»'
cp FCluster/FCluster bin
cp FastaUnique/FastaUnique bin
cp NDist/NDist bin
cp PyroDist/PyroDist bin
cp PyroNoise/PyroNoise bin
cp PyroNoiseM/PyroNoiseM bin
cp PyroNoiseA/PyroNoiseA bin
cp SeqDist/SeqDist bin
cp SeqNoise/SeqNoise bin
cp SplitClusterEven/SplitClusterEven bin
cp SplitClusterClust/SplitClusterClust bin
cp Perseus/Perseus bin
cp PerseusD/PerseusD bin
make[2]: Leaving directory `/«PKGBUILDDIR»'
dh_install bin/* /usr/bin
dh_install Data/* /usr/share/ampliconnoise/Data/
dh_install Scripts/* /usr/share/ampliconnoise/Scripts/
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_installdocs -a
dh_installchangelogs -a
debian/rules override_dh_installman
make[1]: Entering directory `/«PKGBUILDDIR»'
debian/ampliconnoise.pod
pod2man -c AmpliconNoise Documentation debian/ampliconnoise.pod > ampliconnoise.1
dh_installman ampliconnoise.1
( for f in bin/* ; do \
ln -s ampliconnoise.1 debian/ampliconnoise/usr/share/man/man1/`basename "$f"`.1 ; \
done )
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_perl -a
dh_link -a
debian/rules override_dh_compress
make[1]: Entering directory `/«PKGBUILDDIR»'
dh_compress --exclude=.pdf
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/ampliconnoise/usr/bin/NDist debian/ampliconnoise/usr/bin/SeqNoise debian/ampliconnoise/usr/bin/PyroDist debian/ampliconnoise/usr/bin/PyroNoiseM debian/ampliconnoise/usr/bin/SeqDist debian/ampliconnoise/usr/bin/PyroNoiseA debian/ampliconnoise/usr/bin/PyroNoise were not linked against libhwloc.so.5 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/ampliconnoise/usr/bin/PerseusD debian/ampliconnoise/usr/bin/Perseus were not linked against libgslcblas.so.0 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/ampliconnoise/usr/bin/NDist debian/ampliconnoise/usr/bin/SeqNoise debian/ampliconnoise/usr/bin/PyroDist debian/ampliconnoise/usr/bin/PyroNoiseM debian/ampliconnoise/usr/bin/SeqDist debian/ampliconnoise/usr/bin/PyroNoiseA debian/ampliconnoise/usr/bin/PyroNoise were not linked against libdl.so.2 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package ampliconnoise: unused substitution variable ${perl:Depends}
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package `ampliconnoise' in `../ampliconnoise_1.29-2_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../ampliconnoise_1.29-2_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 ampliconnoise-1.29
dpkg-buildpackage: binary-only upload (no source included)
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Build finished at 20140308-0517
Finished
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I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
ampliconnoise_1.29-2_armhf.changes:
───────────────────────────────────
Format: 1.8
Date: Tue, 25 Feb 2014 08:57:09 +0100
Source: ampliconnoise
Binary: ampliconnoise
Architecture: armhf
Version: 1.29-2
Distribution: jessie-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
ampliconnoise - removal of noise from 454 sequenced PCR amplicons
Closes: 740029
Changes:
ampliconnoise (1.29-2) unstable; urgency=low
.
[ Arthur Marble ]
* Fix the FTBFS with clang:
- Fixed the non-void function should return a value in
FCluster/FCluster.c
SplitClusterEven/SplitClusterEven.c
Closes: #740029
.
[ James McCoy ]
* Moved debian/upstream to debian/upstream/metadata
Checksums-Sha1:
99129324713c0a384e0b947ed98c49dd058c7289 441958 ampliconnoise_1.29-2_armhf.deb
Checksums-Sha256:
0a480c2ba3d8d4e86b8fd17aba08d9c0a8b76be0cf4447a68bd40217bfdbe3d4 441958 ampliconnoise_1.29-2_armhf.deb
Files:
040ccaba5a2288f397020047b18fd299 441958 science optional ampliconnoise_1.29-2_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
ampliconnoise_1.29-2_armhf.deb
──────────────────────────────
new debian package, version 2.0.
size 441958 bytes: control archive=2761 bytes.
912 bytes, 22 lines control
4898 bytes, 67 lines md5sums
Package: ampliconnoise
Version: 1.29-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1201
Depends: libc6 (>= 2.4), libgsl0ldbl (>= 1.9), libhwloc5, libopenmpi1.6, mafft
Recommends: openmpi-bin
Section: science
Priority: optional
Homepage: http://code.google.com/p/ampliconnoise/
Description: removal of noise from 454 sequenced PCR amplicons
AmpliconNoise is a package of applications to clean up high-throughput
sequence data. It consists of three main parts:
.
Pyronoise - does flowgram-based clustering to spot misreads
SeqNoise - removes PCR point mutations
Perseus - removes PCR chimeras without the need for a set of reference
sequences
.
Previously there was a standalone "Pyronoise" by the same authors and
this package includes an updated version. There is also a "Denoiser"
in Qiime which is related but distinct.
drwxr-xr-x root/root 0 2014-03-08 05:17 ./
drwxr-xr-x root/root 0 2014-03-08 05:17 ./usr/
drwxr-xr-x root/root 0 2014-03-08 05:17 ./usr/bin/
-rwxr-xr-x root/root 17896 2014-03-08 05:17 ./usr/bin/FCluster
-rwxr-xr-x root/root 9712 2014-03-08 05:17 ./usr/bin/FastaUnique
-rwxr-xr-x root/root 13828 2014-03-08 05:17 ./usr/bin/NDist
-rwxr-xr-x root/root 30212 2014-03-08 05:17 ./usr/bin/Perseus
-rwxr-xr-x root/root 30220 2014-03-08 05:17 ./usr/bin/PerseusD
-rwxr-xr-x root/root 17928 2014-03-08 05:17 ./usr/bin/PyroDist
-rwxr-xr-x root/root 50720 2014-03-08 05:17 ./usr/bin/PyroNoise
-rwxr-xr-x root/root 51008 2014-03-08 05:17 ./usr/bin/PyroNoiseA
-rwxr-xr-x root/root 50720 2014-03-08 05:17 ./usr/bin/PyroNoiseM
-rwxr-xr-x root/root 17932 2014-03-08 05:17 ./usr/bin/SeqDist
-rwxr-xr-x root/root 38444 2014-03-08 05:17 ./usr/bin/SeqNoise
-rwxr-xr-x root/root 9676 2014-03-08 05:17 ./usr/bin/SplitClusterClust
-rwxr-xr-x root/root 17884 2014-03-08 05:17 ./usr/bin/SplitClusterEven
drwxr-xr-x root/root 0 2014-03-08 05:17 ./usr/share/
drwxr-xr-x root/root 0 2014-03-08 05:17 ./usr/share/ampliconnoise/
drwxr-xr-x root/root 0 2014-03-08 05:17 ./usr/share/ampliconnoise/Data/
-rw-r--r-- root/root 140066 2013-08-01 14:37 ./usr/share/ampliconnoise/Data/LookUp.dat
-rw-r--r-- root/root 140432 2013-08-01 14:37 ./usr/share/ampliconnoise/Data/LookUp_E123.dat
-rw-r--r-- root/root 140348 2013-08-01 14:37 ./usr/share/ampliconnoise/Data/LookUp_Titanium.dat
-rw-r--r-- root/root 156 2013-08-01 14:37 ./usr/share/ampliconnoise/Data/Tran.dat
-rw-r--r-- root/root 44 2013-08-01 14:37 ./usr/share/ampliconnoise/Data/TranN.dat
-rw-r--r-- root/root 156 2013-08-01 14:37 ./usr/share/ampliconnoise/Data/Tran_D.dat
-rw-r--r-- root/root 150 2013-08-01 14:37 ./usr/share/ampliconnoise/Data/Tran_V6.dat
drwxr-xr-x root/root 0 2014-03-08 05:17 ./usr/share/ampliconnoise/Scripts/
-rwxr-xr-x root/root 1726 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/CSV.pl
-rwxr-xr-x root/root 645 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/Class.pl
-rwxr-xr-x root/root 130 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/Clean.sh
-rwxr-xr-x root/root 1954 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/Clean360.pl
-rwxr-xr-x root/root 2604 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/CleanAcyclic.pl
-rwxr-xr-x root/root 2554 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/CleanBoth.pl
-rwxr-xr-x root/root 2460 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/CleanBothM.pl
-rwxr-xr-x root/root 2468 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/CleanMinMax.pl
-rwxr-xr-x root/root 133 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/CleanMinMax.sh
-rwxr-xr-x root/root 751 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/ConvertDatFasta.pl
-rwxr-xr-x root/root 268 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/CountFasta.pl
-rwxr-xr-x root/root 185 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/CountSequences.pl
-rwxr-xr-x root/root 1335 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/Diversity.pl
-rwxr-xr-x root/root 896 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/FilterGoodClass.pl
-rwxr-xr-x root/root 3001 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/FlowsFA.pl
-rwxr-xr-x root/root 3008 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/FlowsFA360.pl
-rwxr-xr-x root/root 3117 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/FlowsMinMax.pl
-rwxr-xr-x root/root 495 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/Join.pl
-rwxr-xr-x root/root 789 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/Map.pl
-rwxr-xr-x root/root 374 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/MedianS.sh
-rwxr-xr-x root/root 671 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/Parse.pl
-rwxr-xr-x root/root 687 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/ParseBoth.pl
-rwxr-xr-x root/root 1901 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/Qiime.pl
-rwxr-xr-x root/root 2772 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/Qiime_OTU.pl
-rwxr-xr-x root/root 1746 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/Qiime_Typical.pl
-rwxr-xr-x root/root 11538 2013-08-01 14:50 ./usr/share/ampliconnoise/Scripts/RunBoth.sh
-rwxr-xr-x root/root 11534 2013-08-01 14:54 ./usr/share/ampliconnoise/Scripts/RunBothFLX.sh
-rwxr-xr-x root/root 11195 2013-08-01 14:40 ./usr/share/ampliconnoise/Scripts/RunFLX.sh
-rwxr-xr-x root/root 11259 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/RunTitanium.sh
-rwxr-xr-x root/root 11259 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/RunTitaniumA.sh
-rwxr-xr-x root/root 14461 2013-08-01 14:40 ./usr/share/ampliconnoise/Scripts/RunTitaniumFast.sh
-rwxr-xr-x root/root 13951 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/RunTitaniumWeb.sh
-rwxr-xr-x root/root 967 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/Split.pl
-rwxr-xr-x root/root 3580 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/SplitKeys.pl
-rwxr-xr-x root/root 3440 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/SplitKeysBoth.pl
-rwxr-xr-x root/root 2839 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/SplitKeysFlower.pl
-rwxr-xr-x root/root 538 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/Sub.pl
-rwxr-xr-x root/root 320 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/Subsample.sh
-rwxr-xr-x root/root 699 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/SubsampleDat.pl
-rwxr-xr-x root/root 225 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/Truncate.pl
-rwxr-xr-x root/root 1747 2013-08-01 14:37 ./usr/share/ampliconnoise/Scripts/Typical.pl
drwxr-xr-x root/root 0 2014-03-08 05:17 ./usr/share/doc/
drwxr-xr-x root/root 0 2014-03-08 05:17 ./usr/share/doc/ampliconnoise/
-rw-r--r-- root/root 306514 2013-08-01 14:53 ./usr/share/doc/ampliconnoise/Doc.pdf
-rw-r--r-- root/root 353 2013-09-12 08:57 ./usr/share/doc/ampliconnoise/README.Debian
-rw-r--r-- root/root 1411 2013-09-12 08:57 ./usr/share/doc/ampliconnoise/copyright
-rw-r--r-- root/root 1712 2014-02-25 07:58 ./usr/share/doc/ampliconnoise/changelog.Debian.gz
drwxr-xr-x root/root 0 2014-03-08 05:17 ./usr/share/doc-base/
-rw-r--r-- root/root 808 2013-09-12 08:57 ./usr/share/doc-base/ampliconnoise
drwxr-xr-x root/root 0 2014-03-08 05:17 ./usr/share/man/
drwxr-xr-x root/root 0 2014-03-08 05:17 ./usr/share/man/man1/
-rw-r--r-- root/root 2829 2014-03-08 05:17 ./usr/share/man/man1/ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2014-03-08 05:17 ./usr/share/man/man1/SplitClusterEven.1.gz -> ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2014-03-08 05:17 ./usr/share/man/man1/Perseus.1.gz -> ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2014-03-08 05:17 ./usr/share/man/man1/SeqDist.1.gz -> ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2014-03-08 05:17 ./usr/share/man/man1/PyroNoise.1.gz -> ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2014-03-08 05:17 ./usr/share/man/man1/PyroNoiseM.1.gz -> ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2014-03-08 05:17 ./usr/share/man/man1/FCluster.1.gz -> ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2014-03-08 05:17 ./usr/share/man/man1/PyroDist.1.gz -> ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2014-03-08 05:17 ./usr/share/man/man1/SplitClusterClust.1.gz -> ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2014-03-08 05:17 ./usr/share/man/man1/PyroNoiseA.1.gz -> ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2014-03-08 05:17 ./usr/share/man/man1/PerseusD.1.gz -> ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2014-03-08 05:17 ./usr/share/man/man1/SeqNoise.1.gz -> ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2014-03-08 05:17 ./usr/share/man/man1/FastaUnique.1.gz -> ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2014-03-08 05:17 ./usr/share/man/man1/NDist.1.gz -> ampliconnoise.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 11080
Build-Time: 137
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 184
Job: ampliconnoise_1.29-2
Machine Architecture: armhf
Package: ampliconnoise
Package-Time: 382
Source-Version: 1.29-2
Space: 11080
Status: successful
Version: 1.29-2
────────────────────────────────────────────────────────────────────────────────
Finished at 20140308-0517
Build needed 00:06:22, 11080k disc space