ampliconnoise →
1.28-1 →
armhf → 2013-08-10 06:58:03
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on testbuildd.raspbian.org
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║ ampliconnoise 1.28-1 (armhf) 10 Aug 2013 06:50 ║
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Package: ampliconnoise
Version: 1.28-1
Source Version: 1.28-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/ampliconnoise-jckfs1/ampliconnoise-1.28' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/ampliconnoise-jckfs1' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-79752941-7577-422c-8dc2-93464ae954c2' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
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Get:1 http://172.17.0.1 jessie-staging Release.gpg [490 B]
Get:2 http://172.17.0.1 jessie-staging Release [10.8 kB]
Get:3 http://172.17.0.1 jessie-staging/main Sources [6695 kB]
Get:4 http://172.17.0.1 jessie-staging/main armhf Packages [7864 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 1390 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main ampliconnoise 1.28-1 (dsc) [1429 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main ampliconnoise 1.28-1 (tar) [1380 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main ampliconnoise 1.28-1 (diff) [8085 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-fFq0Ie/apt_archive/sbuild-build-depends-core-dummy.deb'.
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
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Installing build dependencies
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The following NEW packages will be installed:
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debconf: delaying package configuration, since apt-utils is not 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-iW0BAd/apt_archive/sbuild-build-depends-ampliconnoise-dummy.deb'.
OK
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install ampliconnoise build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
adduser bsdmainutils debhelper file gcc-4.8-base gettext gettext-base
groff-base intltool-debian libasprintf0c2 libcroco3 libffi6 libgcc1
libgfortran3 libglib2.0-0 libgomp1 libgsl0-dev libgsl0ldbl libibverbs-dev
libibverbs1 libmagic1 libopenmpi-dev libopenmpi1.3 libpipeline1 libstdc++6
libtorque2 libunistring0 libxml2 man-db openmpi-common po-debconf
Suggested packages:
wamerican wordlist whois vacation dh-make gettext-doc groff gsl-ref-psdoc
gsl-doc-pdf gsl-doc-info gsl-ref-html less www-browser libmail-box-perl
Recommended packages:
curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl
The following NEW packages will be installed:
adduser bsdmainutils debhelper file gettext gettext-base groff-base
intltool-debian libasprintf0c2 libcroco3 libffi6 libgfortran3 libglib2.0-0
libgsl0-dev libgsl0ldbl libibverbs-dev libibverbs1 libmagic1 libopenmpi-dev
libopenmpi1.3 libpipeline1 libtorque2 libunistring0 libxml2 man-db
openmpi-common po-debconf sbuild-build-depends-ampliconnoise-dummy
The following packages will be upgraded:
gcc-4.8-base libgcc1 libgomp1 libstdc++6
4 upgraded, 28 newly installed, 0 to remove and 43 not upgraded.
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After this operation, 44.2 MB of additional disk space will be used.
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Get:5 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.2.4-1 [36.9 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-3 [666 kB]
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Get:14 http://172.17.0.1/private/ jessie-staging/main libcroco3 armhf 0.6.8-2 [119 kB]
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Get:16 http://172.17.0.1/private/ jessie-staging/main libunistring0 armhf 0.9.3-5 [408 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main adduser all 3.113+nmu3 [264 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main file armhf 1:5.14-2 [53.8 kB]
Get:19 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.18.3-1 [136 kB]
Get:20 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.18.3-1 [1837 kB]
Get:21 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:22 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu2 [223 kB]
Get:23 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20130630 [710 kB]
Get:24 http://172.17.0.1/private/ jessie-staging/main libgsl0ldbl armhf 1.16+dfsg-1 [901 kB]
Get:25 http://172.17.0.1/private/ jessie-staging/main libgsl0-dev armhf 1.16+dfsg-1 [1124 kB]
Get:26 http://172.17.0.1/private/ jessie-staging/main libtorque2 armhf 2.4.16+dfsg-1 [109 kB]
Get:27 http://172.17.0.1/private/ jessie-staging/main libibverbs1 armhf 1.1.7-1 [31.0 kB]
Get:28 http://172.17.0.1/private/ jessie-staging/main libibverbs-dev armhf 1.1.7-1 [82.3 kB]
Get:29 http://172.17.0.1/private/ jessie-staging/main libopenmpi1.3 armhf 1.4.5-1 [1206 kB]
Get:30 http://172.17.0.1/private/ jessie-staging/main openmpi-common all 1.4.5-1 [101 kB]
Get:31 http://172.17.0.1/private/ jessie-staging/main libopenmpi-dev armhf 1.4.5-1 [2363 kB]
debconf: delaying package configuration, since apt-utils is not installed
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
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Kernel: Linux 3.9.8-imx5 armhf (armv7l)
Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.10 g++-4.6_4.6.4-2+rpi1 gcc-4.6_4.6.4-2+rpi1 libc6-dev_2.17-3 libstdc++6_4.8.1-6+rpi1 libstdc++6-4.6-dev_4.6.4-2+rpi1 linux-libc-dev_3.2.41-2+rpi1
Package versions: adduser_3.113+nmu3 apt_0.9.7.8+rpi1 base-files_7.2 base-passwd_3.5.26 bash_4.2+dfsg-1 binutils_2.22-8 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.4 build-essential_11.6 bzip2_1.0.6-4 coreutils_8.13-3.5 cpio_2.11+dfsg-1 cpp_4:4.6.3-8 cpp-4.6_4.6.4-2+rpi1 dash_0.5.7-3 debconf_1.5.50 debconf-i18n_1.5.50 debfoster_2.7-1.2 debhelper_9.20130630 debianutils_4.3.4 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.5-1.1 e2fsprogs_1.42.5-1.1 fakeroot_1.18.4-2 file_1:5.14-2 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.4-2+rpi1 gcc_4:4.6.3-8 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.4-2+rpi1 gcc-4.6-base_4.6.4-2+rpi1 gcc-4.7-base_4.7.3-4+rpi1 gcc-4.8-base_4.8.1-6+rpi1 gettext_0.18.3-1 gettext-base_0.18.3-1 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.14-2 groff-base_1.22.2-3 gzip_1.5-1.1 hostname_3.12 initramfs-tools_0.112 initscripts_2.88dsf-41 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.1-3.1+rpi1 kmod_9-3 libacl1_2.2.52-1 libapt-pkg4.12_0.9.7.8+rpi1 libasprintf0c2_0.18.3-1 libattr1_1:2.4.47-1 libblkid1_2.20.1-5.4 libbz2-1.0_1.0.6-4 libc-bin_2.17-3 libc-dev-bin_2.17-3 libc6_2.17-3 libc6-dev_2.17-3 libcap2_1:2.22-1.2 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1.1 libcroco3_0.6.8-2 libdb5.1_5.1.29-5 libdbus-1-3_1.6.10-1 libdpkg-perl_1.16.10 libffi6_3.0.13-4 libgc1c2_1:7.1-9.1 libgcc1_1:4.8.1-6+rpi1 libgdbm3_1.8.3-12 libgfortran3_4.8.1-6+rpi1 libglib2.0-0_2.36.3-3 libgmp10_2:5.1.2+dfsg-1 libgomp1_4.8.1-6+rpi1 libgsl0-dev_1.16+dfsg-1 libgsl0ldbl_1.16+dfsg-1 libibverbs-dev_1.1.7-1 libibverbs1_1.1.7-1 libklibc_2.0.1-3.1+rpi1 libkmod2_9-3 liblocale-gettext-perl_1.05-7 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.14-2 libmount1_2.20.1-5.4 libmpc2_0.9-4 libmpc3_1.0.1-1 libmpfr4_3.1.1-1 libncurses5_5.9+20130504-1 libncursesw5_5.9+20130504-1 libopenmpi-dev_1.4.5-1 libopenmpi1.3_1.4.5-1 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpcre3_1:8.31-2 libpipeline1_1.2.4-1 libprocps0_1:3.3.4-2 libreadline6_6.2+dfsg-0.1 libselinux1_2.1.13-2 libsemanage-common_2.1.10-2 libsemanage1_2.1.10-2 libsepol1_2.1.9-2 libslang2_2.2.4-15 libss2_1.42.5-1.1 libstdc++6_4.8.1-6+rpi1 libstdc++6-4.6-dev_4.6.4-2+rpi1 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+20130504-1 libtorque2_2.4.16+dfsg-1 libudev0_175-7.2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.2 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.4 libxml2_2.9.1+dfsg1-2 linux-libc-dev_3.2.41-2+rpi1 login_1:4.1.5.1-1 lsb-base_4.1+Debian8+rpi1 make_3.81-8.2 makedev_2.3.1-93 man-db_2.6.5-2 mawk_1.3.3-17 mount_2.20.1-5.4 multiarch-support_2.17-3 ncurses-base_5.9+20130504-1 ncurses-bin_5.9+20130504-1 openmpi-common_1.4.5-1 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-21+rpi1 perl-base_5.14.2-21+rpi1 perl-modules_5.14.2-21+rpi1 plymouth_0.8.8-6 po-debconf_1.0.16+nmu2 procps_1:3.3.4-2 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_4.2.2-1 sensible-utils_0.0.7 sysv-rc_2.88dsf-41 sysvinit_2.88dsf-41 sysvinit-utils_2.88dsf-41 tar_1.26+dfsg-6 tzdata_2013c-2 udev_175-7.2 util-linux_2.20.1-5.4 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Tue Jul 30 10:08:57 2013 UTC using DSA key ID C09FD35A
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./ampliconnoise_1.28-1.dsc
dpkg-source: info: extracting ampliconnoise in ampliconnoise-1.28
dpkg-source: info: unpacking ampliconnoise_1.28.orig.tar.gz
dpkg-source: info: unpacking ampliconnoise_1.28-1.debian.tar.gz
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
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
LANG=en_US.UTF-8
LC_ALL=POSIX
LOGNAME=root
LS_OPTIONS=--color=auto
MAIL=/var/mail/root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/root
SCHROOT_ALIAS_NAME=jessie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=jessie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=111
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-79752941-7577-422c-8dc2-93464ae954c2
SCHROOT_UID=106
SCHROOT_USER=buildd
SHELL=/bin/sh
SHLVL=1
SSH_CLIENT=192.168.1.2 38704 22
SSH_CONNECTION=192.168.1.2 38704 192.168.1.45 22
SSH_TTY=/dev/pts/0
TERM=xterm
USER=root
XDG_SESSION_COOKIE=106ef489ba27ee071ab233f6518d3bce-1375903963.174676-1948290074
_=/etc/init.d/buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package ampliconnoise
dpkg-buildpackage: source version 1.28-1
dpkg-source --before-build ampliconnoise-1.28
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 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]
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]
linking...
mpicc -Wl,-z,relro -o PyroNoiseM PyroNoiseM.o -lm
make[2]: Leaving directory `/«PKGBUILDDIR»/PyroNoiseM'
(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]
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]
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]
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 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/SeqNoise debian/ampliconnoise/usr/bin/NDist debian/ampliconnoise/usr/bin/PyroNoiseM debian/ampliconnoise/usr/bin/PyroNoise debian/ampliconnoise/usr/bin/PyroDist debian/ampliconnoise/usr/bin/SeqDist were not linked against libdl.so.2 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/ampliconnoise/usr/bin/SeqNoise debian/ampliconnoise/usr/bin/NDist debian/ampliconnoise/usr/bin/PyroNoiseM debian/ampliconnoise/usr/bin/PyroNoise debian/ampliconnoise/usr/bin/PyroDist debian/ampliconnoise/usr/bin/SeqDist were not linked against libopen-pal.so.0 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/ampliconnoise/usr/bin/Perseus debian/ampliconnoise/usr/bin/PerseusD 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/SeqNoise debian/ampliconnoise/usr/bin/NDist debian/ampliconnoise/usr/bin/PyroNoiseM debian/ampliconnoise/usr/bin/PyroNoise debian/ampliconnoise/usr/bin/PyroDist debian/ampliconnoise/usr/bin/SeqDist were not linked against libutil.so.1 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/ampliconnoise/usr/bin/SeqNoise debian/ampliconnoise/usr/bin/NDist debian/ampliconnoise/usr/bin/PyroNoiseM debian/ampliconnoise/usr/bin/PyroNoise debian/ampliconnoise/usr/bin/PyroDist debian/ampliconnoise/usr/bin/SeqDist were not linked against libnsl.so.1 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/ampliconnoise/usr/bin/SeqNoise debian/ampliconnoise/usr/bin/NDist debian/ampliconnoise/usr/bin/PyroNoiseM debian/ampliconnoise/usr/bin/PyroNoise debian/ampliconnoise/usr/bin/PyroDist debian/ampliconnoise/usr/bin/SeqDist were not linked against libopen-rte.so.0 (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_1.28-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian nitrogen6x test autobuilder <root@raspbian.org> >../ampliconnoise_1.28-1_armhf.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build ampliconnoise-1.28
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20130810-0657
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
ampliconnoise_1.28-1_armhf.changes:
───────────────────────────────────
Format: 1.8
Date: Tue, 30 Jul 2013 09:49:02 +0200
Source: ampliconnoise
Binary: ampliconnoise
Architecture: armhf
Version: 1.28-1
Distribution: jessie-staging
Urgency: low
Maintainer: Raspbian nitrogen6x test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
ampliconnoise - Programs for the removal of noise from 454 sequenced PCR amplicon
Changes:
ampliconnoise (1.28-1) unstable; urgency=low
.
* New upstream version uploaded to Debian
* debian/control
- cme fix dpkg-control
- no need to Build-Depend from quilt
- debhelper 9
- Priority: optional
- Normalised Vcs fields
- Remove duplicated publication information from
long description
* debian/get-orig-source: Removed because upstream
stripped off their tarball
* debian/README.source: Removed because it became now
unneeded.
* debian/doc-base: created
* debian/rules:
- do not compress pdf files
* debian/patches/hardening.patch: Propagate hardening options
Checksums-Sha1:
65e32ee4b162fb70318c9457165faa3b396c3af0 527546 ampliconnoise_1.28-1_armhf.deb
Checksums-Sha256:
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Files:
ff66ac4206faaaa402f7ae3099ae3d39 527546 science optional ampliconnoise_1.28-1_armhf.deb
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ampliconnoise_1.28-1_armhf.deb
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new debian package, version 2.0.
size 527546 bytes: control archive=2364 bytes.
918 bytes, 22 lines control
4124 bytes, 57 lines md5sums
Package: ampliconnoise
Version: 1.28-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1100
Depends: libc6 (>= 2.4), libgsl0ldbl (>= 1.9), libopenmpi1.3, mafft
Recommends: openmpi-bin
Section: science
Priority: optional
Homepage: http://code.google.com/p/ampliconnoise/
Description: Programs for the 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 2013-08-10 06:56 ./
drwxr-xr-x root/root 0 2013-08-10 06:56 ./usr/
drwxr-xr-x root/root 0 2013-08-10 06:56 ./usr/bin/
-rwxr-xr-x root/root 17928 2013-08-10 06:56 ./usr/bin/FCluster
-rwxr-xr-x root/root 9752 2013-08-10 06:56 ./usr/bin/FastaUnique
-rwxr-xr-x root/root 13864 2013-08-10 06:56 ./usr/bin/NDist
-rwxr-xr-x root/root 26152 2013-08-10 06:56 ./usr/bin/Perseus
-rwxr-xr-x root/root 26160 2013-08-10 06:56 ./usr/bin/PerseusD
-rwxr-xr-x root/root 22060 2013-08-10 06:56 ./usr/bin/PyroDist
-rwxr-xr-x root/root 50756 2013-08-10 06:56 ./usr/bin/PyroNoise
-rwxr-xr-x root/root 54852 2013-08-10 06:56 ./usr/bin/PyroNoiseM
-rwxr-xr-x root/root 17968 2013-08-10 06:56 ./usr/bin/SeqDist
-rwxr-xr-x root/root 38480 2013-08-10 06:56 ./usr/bin/SeqNoise
-rwxr-xr-x root/root 9712 2013-08-10 06:56 ./usr/bin/SplitClusterClust
-rwxr-xr-x root/root 17924 2013-08-10 06:56 ./usr/bin/SplitClusterEven
drwxr-xr-x root/root 0 2013-08-10 06:56 ./usr/share/
drwxr-xr-x root/root 0 2013-08-10 06:56 ./usr/share/ampliconnoise/
drwxr-xr-x root/root 0 2013-08-10 06:56 ./usr/share/ampliconnoise/Data/
-rw-r--r-- root/root 140066 2013-03-10 22:45 ./usr/share/ampliconnoise/Data/LookUp.dat
-rw-r--r-- root/root 140432 2013-03-10 22:45 ./usr/share/ampliconnoise/Data/LookUp_E123.dat
-rw-r--r-- root/root 140348 2013-03-10 22:45 ./usr/share/ampliconnoise/Data/LookUp_Titanium.dat
-rw-r--r-- root/root 156 2013-03-10 22:45 ./usr/share/ampliconnoise/Data/Tran.dat
-rw-r--r-- root/root 44 2013-03-10 22:45 ./usr/share/ampliconnoise/Data/TranN.dat
-rw-r--r-- root/root 156 2013-03-10 22:45 ./usr/share/ampliconnoise/Data/Tran_D.dat
-rw-r--r-- root/root 150 2013-03-10 22:45 ./usr/share/ampliconnoise/Data/Tran_V6.dat
drwxr-xr-x root/root 0 2013-08-10 06:56 ./usr/share/ampliconnoise/Scripts/
-rwxr-xr-x root/root 1726 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/CSV.pl
-rwxr-xr-x root/root 645 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/Class.pl
-rwxr-xr-x root/root 130 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/Clean.sh
-rwxr-xr-x root/root 1954 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/Clean360.pl
-rwxr-xr-x root/root 2505 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/CleanMinMax.pl
-rwxr-xr-x root/root 133 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/CleanMinMax.sh
-rwxr-xr-x root/root 751 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/ConvertDatFasta.pl
-rwxr-xr-x root/root 268 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/CountFasta.pl
-rwxr-xr-x root/root 185 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/CountSequences.pl
-rwxr-xr-x root/root 1335 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/Diversity.pl
-rwxr-xr-x root/root 896 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/FilterGoodClass.pl
-rwxr-xr-x root/root 3001 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/FlowsFA.pl
-rwxr-xr-x root/root 3008 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/FlowsFA360.pl
-rwxr-xr-x root/root 3117 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/FlowsMinMax.pl
-rwxr-xr-x root/root 495 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/Join.pl
-rwxr-xr-x root/root 789 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/Map.pl
-rwxr-xr-x root/root 374 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/MedianS.sh
-rwxr-xr-x root/root 671 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/Parse.pl
-rwxr-xr-x root/root 1901 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/Qiime.pl
-rwxr-xr-x root/root 2772 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/Qiime_OTU.pl
-rwxr-xr-x root/root 1746 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/Qiime_Typical.pl
-rwxr-xr-x root/root 10591 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/RunFLX.sh
-rwxr-xr-x root/root 10646 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/RunTitanium.sh
-rwxr-xr-x root/root 14460 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/RunTitaniumFast.sh
-rwxr-xr-x root/root 13951 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/RunTitaniumWeb.sh
-rwxr-xr-x root/root 967 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/Split.pl
-rwxr-xr-x root/root 3059 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/SplitKeys.pl
-rwxr-xr-x root/root 2839 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/SplitKeysFlower.pl
-rwxr-xr-x root/root 538 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/Sub.pl
-rwxr-xr-x root/root 699 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/SubsampleDat.pl
-rwxr-xr-x root/root 225 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/Truncate.pl
-rwxr-xr-x root/root 1747 2013-03-10 22:45 ./usr/share/ampliconnoise/Scripts/Typical.pl
drwxr-xr-x root/root 0 2013-08-10 06:56 ./usr/share/doc/
drwxr-xr-x root/root 0 2013-08-10 06:56 ./usr/share/doc/ampliconnoise/
-rw-r--r-- root/root 301508 2013-03-10 22:45 ./usr/share/doc/ampliconnoise/Doc.pdf
-rw-r--r-- root/root 353 2011-04-28 06:20 ./usr/share/doc/ampliconnoise/README.Debian
-rw-r--r-- root/root 1411 2012-12-22 17:25 ./usr/share/doc/ampliconnoise/copyright
-rw-r--r-- root/root 1518 2013-07-30 09:49 ./usr/share/doc/ampliconnoise/changelog.Debian.gz
drwxr-xr-x root/root 0 2013-08-10 06:56 ./usr/share/doc-base/
-rw-r--r-- root/root 808 2013-07-30 08:23 ./usr/share/doc-base/ampliconnoise
drwxr-xr-x root/root 0 2013-08-10 06:56 ./usr/share/man/
drwxr-xr-x root/root 0 2013-08-10 06:56 ./usr/share/man/man1/
-rw-r--r-- root/root 2744 2013-08-10 06:56 ./usr/share/man/man1/ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2013-08-10 06:56 ./usr/share/man/man1/FastaUnique.1.gz -> ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2013-08-10 06:56 ./usr/share/man/man1/PerseusD.1.gz -> ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2013-08-10 06:56 ./usr/share/man/man1/PyroNoise.1.gz -> ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2013-08-10 06:56 ./usr/share/man/man1/Perseus.1.gz -> ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2013-08-10 06:56 ./usr/share/man/man1/NDist.1.gz -> ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2013-08-10 06:56 ./usr/share/man/man1/PyroNoiseM.1.gz -> ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2013-08-10 06:56 ./usr/share/man/man1/SeqDist.1.gz -> ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2013-08-10 06:56 ./usr/share/man/man1/PyroDist.1.gz -> ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2013-08-10 06:56 ./usr/share/man/man1/SplitClusterEven.1.gz -> ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2013-08-10 06:56 ./usr/share/man/man1/SplitClusterClust.1.gz -> ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2013-08-10 06:56 ./usr/share/man/man1/FCluster.1.gz -> ampliconnoise.1.gz
lrwxrwxrwx root/root 0 2013-08-10 06:56 ./usr/share/man/man1/SeqNoise.1.gz -> ampliconnoise.1.gz
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Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
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Build Architecture: armhf
Build-Space: 10148
Build-Time: 109
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 241
Job: ampliconnoise_1.28-1
Machine Architecture: armhf
Package: ampliconnoise
Package-Time: 419
Source-Version: 1.28-1
Space: 10148
Status: successful
Version: 1.28-1
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Finished at 20130810-0657
Build needed 00:06:59, 10148k disc space