stacks →
1.37-1 →
armhf → 2016-04-06 17:07:04
sbuild (Debian sbuild) 0.68.0 (15 Jan 2016) on bm-wb-01
+==============================================================================+
| stacks 1.37-1 (armhf) 06 Apr 2016 16:25 |
+==============================================================================+
Package: stacks
Version: 1.37-1
Source Version: 1.37-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/stacks-8sGrts/stacks-1.37' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/stacks-8sGrts' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/stretch-staging-armhf-sbuild-4619cf74-8d7e-47cc-9efd-ca36e3ad7e95' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [8882 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [10.9 MB]
Fetched 19.8 MB in 22s (898 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'stacks' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/stacks.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/stacks.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 515 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main stacks 1.37-1 (dsc) [2024 B]
Get:2 http://172.17.0.1/private stretch-staging/main stacks 1.37-1 (tar) [505 kB]
Get:3 http://172.17.0.1/private stretch-staging/main stacks 1.37-1 (diff) [7928 B]
Fetched 515 kB in 0s (6348 kB/s)
Download complete and in download only mode
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-ywAaj4/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-ywAaj4/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-ywAaj4/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-ywAaj4/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-ywAaj4/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-ywAaj4/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-ywAaj4/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-ywAaj4/apt_archive ./ Sources [214 B]
Get:5 file:/<<BUILDDIR>>/resolver-ywAaj4/apt_archive ./ Packages [525 B]
Ign:4 file:/<<BUILDDIR>>/resolver-ywAaj4/apt_archive ./ Sources
Ign:5 file:/<<BUILDDIR>>/resolver-ywAaj4/apt_archive ./ Packages
Get:4 file:/<<BUILDDIR>>/resolver-ywAaj4/apt_archive ./ Sources [214 B]
Get:5 file:/<<BUILDDIR>>/resolver-ywAaj4/apt_archive ./ Packages [525 B]
Reading package lists...
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
manpages
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 45 not upgraded.
Need to get 0 B/764 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-ywAaj4/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [764 B]
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sbuild-build-depends-core-dummy.
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Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 9), zlib1g-dev, libbam-dev, libsparsehash-dev (>= 2.0)
Filtered Build-Depends: debhelper (>= 9), zlib1g-dev, libbam-dev, libsparsehash-dev (>= 2.0)
dpkg-deb: building package 'sbuild-build-depends-stacks-dummy' in '/<<BUILDDIR>>/resolver-o17VKz/apt_archive/sbuild-build-depends-stacks-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-o17VKz/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-o17VKz/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-o17VKz/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-o17VKz/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-o17VKz/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-o17VKz/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-o17VKz/apt_archive ./ Sources [237 B]
Get:5 file:/<<BUILDDIR>>/resolver-o17VKz/apt_archive ./ Packages [551 B]
Ign:4 file:/<<BUILDDIR>>/resolver-o17VKz/apt_archive ./ Sources
Ign:5 file:/<<BUILDDIR>>/resolver-o17VKz/apt_archive ./ Packages
Get:4 file:/<<BUILDDIR>>/resolver-o17VKz/apt_archive ./ Sources [237 B]
Get:5 file:/<<BUILDDIR>>/resolver-o17VKz/apt_archive ./ Packages [551 B]
Reading package lists...
Reading package lists...
Install stacks build dependencies (apt-based resolver)
------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
manpages
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autotools-dev bsdmainutils debhelper dh-strip-nondeterminism file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libbam-dev
libbsd0 libcroco3 libffi6 libfile-stripnondeterminism-perl libglib2.0-0
libicu55 libmagic1 libpipeline1 libsparsehash-dev libtimedate-perl
libunistring0 libxml2 man-db po-debconf zlib1g-dev
Suggested packages:
wamerican | wordlist whois vacation dh-make gettext-doc autopoint
libasprintf-dev libgettextpo-dev groff less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx-cur 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 dh-strip-nondeterminism file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libbam-dev
libbsd0 libcroco3 libffi6 libfile-stripnondeterminism-perl libglib2.0-0
libicu55 libmagic1 libpipeline1 libsparsehash-dev libtimedate-perl
libunistring0 libxml2 man-db po-debconf sbuild-build-depends-stacks-dummy
zlib1g-dev
0 upgraded, 27 newly installed, 0 to remove and 45 not upgraded.
Need to get 17.0 MB/17.0 MB of archives.
After this operation, 59.3 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-o17VKz/apt_archive ./ sbuild-build-depends-stacks-dummy 0.invalid.0 [794 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-7 [1083 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.2-1 [88.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.10 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.25-2 [250 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.25-2 [61.2 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.7-2 [111 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libicu55 armhf 55.1-7 [7380 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.3+dfsg1-1 [800 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20150820.1 [71.7 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libffi6 armhf 3.2.1-4 [18.5 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.48.0-1 [2540 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.7-2 [1400 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.56-2 [94.9 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.016-1 [6998 B]
Get:24 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160313 [808 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libbam-dev armhf 0.1.19-2 [109 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libsparsehash-dev all 2.0.2-1 [76.9 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Preparing to unpack .../libffi6_3.2.1-4_armhf.deb ...
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Unpacking sbuild-build-depends-stacks-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.22-3) ...
Setting up groff-base (1.22.3-7) ...
Setting up libbsd0:armhf (0.8.2-1) ...
Setting up bsdmainutils (9.0.10) ...
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 libpipeline1:armhf (1.4.1-2) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up libmagic1:armhf (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.7-2) ...
Setting up libicu55:armhf (55.1-7) ...
Setting up libxml2:armhf (2.9.3+dfsg1-1) ...
Setting up autotools-dev (20150820.1) ...
Setting up libffi6:armhf (3.2.1-4) ...
Setting up libglib2.0-0:armhf (2.48.0-1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.11-1) ...
Setting up gettext (0.19.7-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.19) ...
Setting up libarchive-zip-perl (1.56-2) ...
Setting up libfile-stripnondeterminism-perl (0.016-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libbam-dev (0.1.19-2) ...
Setting up libsparsehash-dev (2.0.2-1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up debhelper (9.20160313) ...
Setting up sbuild-build-depends-stacks-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.016-1) ...
Processing triggers for libc-bin (2.22-3) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26-5 dpkg-dev_1.18.4 g++-5_5.3.1-11 gcc-5_5.3.1-11 libc6-dev_2.22-3 libstdc++-5-dev_5.3.1-11 libstdc++6_5.3.1-11 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.114 apt_1.2.6 autotools-dev_20150820.1 base-files_9.5+rpi1 base-passwd_3.5.39 bash_4.3-14 binutils_2.26-5 bsdmainutils_9.0.10 bsdutils_1:2.27.1-6 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:5.3.1-1+rpi1 cpp-5_5.3.1-11 dash_0.5.8-2.1 debconf_1.5.59 debfoster_2.7-2 debhelper_9.20160313 debianutils_4.7 dh-strip-nondeterminism_0.016-1 diffutils_1:3.3-3 dmsetup_2:1.02.116-1 dpkg_1.18.4 dpkg-dev_1.18.4 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.6.0+git+20160126-2 g++_4:5.3.1-1+rpi1 g++-5_5.3.1-11 gcc_4:5.3.1-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-12 gcc-5_5.3.1-11 gcc-5-base_5.3.1-11 gettext_0.19.7-2 gettext-base_0.19.7-2 gnupg_1.4.20-4 gpgv_1.4.20-4 grep_2.22-1 groff-base_1.22.3-7 gzip_1.6-4 hostname_3.17 init_1.29 init-system-helpers_1.29 initscripts_2.88dsf-59.3 insserv_1.14.0-5.3 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-8+rpi1 kmod_22-1 libacl1_2.2.52-3 libapparmor1_2.10-3 libapt-pkg5.0_1.2.6 libarchive-zip-perl_1.56-2 libasan2_5.3.1-11 libatomic1_5.3.1-11 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1 libaudit1_1:2.4.5-1 libbam-dev_0.1.19-2 libblkid1_2.27.1-6 libbsd0_0.8.2-1 libbz2-1.0_1.0.6-8 libc-bin_2.22-3 libc-dev-bin_2.22-3 libc6_2.22-3 libc6-dev_2.22-3 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-11 libcomerr2_1.42.13-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.8-1 libdebconfclient0_0.207 libdevmapper1.02.1_2:1.02.116-1 libdpkg-perl_1.18.4 libdrm2_2.4.67-1 libfakeroot_1.20.2-1 libfdisk1_2.27.1-6 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.016-1 libgc1c2_1:7.4.2-7.3 libgcc-5-dev_5.3.1-11 libgcc1_1:5.3.1-11 libgcrypt20_1.6.5-2 libgdbm3_1.8.3-13.1 libglib2.0-0_2.48.0-1 libgmp10_2:6.1.0+dfsg-2 libgomp1_5.3.1-11 libgpg-error0_1.21-2 libicu55_55.1-7 libisl15_0.16.1-1 libklibc_2.0.4-8+rpi1 libkmod2_22-1 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.27.1-6 libmpc3_1.0.3-1 libmpfr4_3.1.4-1 libncurses5_6.0+20160213-1 libncursesw5_6.0+20160213-1 libpam-modules_1.1.8-3.2 libpam-modules-bin_1.1.8-3.2 libpam-runtime_1.1.8-3.2 libpam0g_1.1.8-3.2 libpcre3_2:8.38-3 libperl5.22_5.22.1-9 libpipeline1_1.4.1-2 libpng12-0_1.2.54-4 libprocps5_2:3.3.11-3 libreadline6_6.3-8+b3 libseccomp2_2.2.3-3 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libsmartcols1_2.27.1-6 libsparsehash-dev_2.0.2-1 libss2_1.42.13-1 libstdc++-5-dev_5.3.1-11 libstdc++6_5.3.1-11 libsystemd0_229-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160213-1 libubsan0_5.3.1-11 libudev1_229-2 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-28 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-6 libxml2_2.9.3+dfsg1-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160110+rpi1 make_4.1-6 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.04-2 mawk_1.3.3-17 mount_2.27.1-6 multiarch-support_2.22-3 nano_2.5.3-2 ncurses-base_6.0+20160213-1 ncurses-bin_6.0+20160213-1 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.1-9 perl-base_5.22.1-9 perl-modules-5.22_5.22.1-9 po-debconf_1.0.19 procps_2:3.3.11-3 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-stacks-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_229-2 systemd-sysv_229-2 sysv-rc_2.88dsf-59.3 sysvinit-utils_2.88dsf-59.3 tar_1.28-2.1 tzdata_2016a-1 udev_229-2 util-linux_2.27.1-6 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Thu Mar 10 22:42:35 2016 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./stacks_1.37-1.dsc
dpkg-source: info: extracting stacks in stacks-1.37
dpkg-source: info: unpacking stacks_1.37.orig.tar.gz
dpkg-source: info: unpacking stacks_1.37-1.debian.tar.xz
dpkg-source: info: applying constants.php.patch
dpkg-source: info: applying email-settings.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=root
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-4619cf74-8d7e-47cc-9efd-ca36e3ad7e95
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: source package stacks
dpkg-buildpackage: source version 1.37-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build stacks-1.37
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
debian/rules override_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_clean
rm -f ./constants.php
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_update_autotools_config -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- --enable-sparsehash --enable-bam \
--with-bam-include-path=/usr/include/samtools \
--with-bam-lib-path=/usr/lib
./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-sparsehash --enable-bam --with-bam-include-path=/usr/include/samtools --with-bam-lib-path=/usr/lib
configure: WARNING: unrecognized options: --disable-maintainer-mode
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for g++... g++
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 g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... none
checking for gcc... gcc
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 whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking whether g++ supports C++11 features by default... no
checking whether g++ supports C++11 features with -std=gnu++11... yes
checking for omp_set_num_threads in -lgomp... yes
checking for gzread in -lz... yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking how to run the C preprocessor... gcc -E
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 float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for gcc option to support OpenMP... -fopenmp
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking whether closedir returns void... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for floor... no
checking for memset... yes
checking for pow... no
checking for sqrt... no
checking for gawk... (cached) mawk
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -a
make -j1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make all-am
make[2]: Entering directory '/<<PKGBUILDDIR>>'
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/ustacks-ustacks.o `test -f 'src/ustacks.cc' || echo './'`src/ustacks.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/ustacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/ustacks-mstack.o `test -f 'src/mstack.cc' || echo './'`src/mstack.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/ustacks-mst.o `test -f 'src/mst.cc' || echo './'`src/mst.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/ustacks-cmb.o `test -f 'src/cmb.cc' || echo './'`src/cmb.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/ustacks-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/ustacks-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/ustacks-models.o `test -f 'src/models.cc' || echo './'`src/models.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/ustacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/ustacks-kmers.o `test -f 'src/kmers.cc' || echo './'`src/kmers.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/ustacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
g++ -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -fopenmp -Wl,-z,relro -o ustacks src/ustacks-ustacks.o src/ustacks-stacks.o src/ustacks-mstack.o src/ustacks-mst.o src/ustacks-cmb.o src/ustacks-DNASeq.o src/ustacks-DNANSeq.o src/ustacks-models.o src/ustacks-utils.o src/ustacks-kmers.o src/ustacks-input.o -lz -lgomp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/pstacks-pstacks.o `test -f 'src/pstacks.cc' || echo './'`src/pstacks.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/pstacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/pstacks-mstack.o `test -f 'src/mstack.cc' || echo './'`src/mstack.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/pstacks-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/pstacks-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/pstacks-models.o `test -f 'src/models.cc' || echo './'`src/models.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/pstacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/pstacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
g++ -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -fopenmp -Wl,-z,relro -o pstacks src/pstacks-pstacks.o src/pstacks-stacks.o src/pstacks-mstack.o src/pstacks-DNANSeq.o src/pstacks-DNASeq.o src/pstacks-models.o src/pstacks-utils.o src/pstacks-input.o /usr/lib/libbam.a -lz -lgomp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/estacks-estacks.o `test -f 'src/estacks.cc' || echo './'`src/estacks.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/estacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/estacks-mstack.o `test -f 'src/mstack.cc' || echo './'`src/mstack.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/estacks-models.o `test -f 'src/models.cc' || echo './'`src/models.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/estacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/estacks-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/estacks-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/estacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
g++ -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -fopenmp -Wl,-z,relro -o estacks src/estacks-estacks.o src/estacks-stacks.o src/estacks-mstack.o src/estacks-models.o src/estacks-utils.o src/estacks-DNASeq.o src/estacks-DNANSeq.o src/estacks-input.o -lz -lgomp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/cstacks-cstacks.o `test -f 'src/cstacks.cc' || echo './'`src/cstacks.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/cstacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/cstacks-locus.o `test -f 'src/locus.cc' || echo './'`src/locus.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/cstacks-kmers.o `test -f 'src/kmers.cc' || echo './'`src/kmers.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/cstacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/cstacks-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/cstacks-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/cstacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
g++ -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -fopenmp -Wl,-z,relro -o cstacks src/cstacks-cstacks.o src/cstacks-stacks.o src/cstacks-locus.o src/cstacks-kmers.o src/cstacks-utils.o src/cstacks-DNASeq.o src/cstacks-DNANSeq.o src/cstacks-input.o -lz -lgomp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/sstacks-sstacks.o `test -f 'src/sstacks.cc' || echo './'`src/sstacks.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/sstacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/sstacks-locus.o `test -f 'src/locus.cc' || echo './'`src/locus.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/sstacks-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/sstacks-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/sstacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/sstacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
g++ -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -fopenmp -Wl,-z,relro -o sstacks src/sstacks-sstacks.o src/sstacks-stacks.o src/sstacks-locus.o src/sstacks-DNASeq.o src/sstacks-DNANSeq.o src/sstacks-utils.o src/sstacks-input.o -lz -lgomp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/rxstacks-rxstacks.o `test -f 'src/rxstacks.cc' || echo './'`src/rxstacks.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/rxstacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/rxstacks-locus.o `test -f 'src/locus.cc' || echo './'`src/locus.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/rxstacks-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/rxstacks-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/rxstacks-mst.o `test -f 'src/mst.cc' || echo './'`src/mst.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/rxstacks-models.o `test -f 'src/models.cc' || echo './'`src/models.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/rxstacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/rxstacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
g++ -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -fopenmp -Wl,-z,relro -o rxstacks src/rxstacks-rxstacks.o src/rxstacks-stacks.o src/rxstacks-locus.o src/rxstacks-DNANSeq.o src/rxstacks-DNASeq.o src/rxstacks-mst.o src/rxstacks-models.o src/rxstacks-utils.o src/rxstacks-input.o -lz -lgomp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/hstacks-hstacks.o `test -f 'src/hstacks.cc' || echo './'`src/hstacks.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/hstacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/hstacks-locus.o `test -f 'src/locus.cc' || echo './'`src/locus.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/hstacks-kmers.o `test -f 'src/kmers.cc' || echo './'`src/kmers.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/hstacks-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/hstacks-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/hstacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/hstacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
g++ -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -fopenmp -Wl,-z,relro -o hstacks src/hstacks-hstacks.o src/hstacks-stacks.o src/hstacks-locus.o src/hstacks-kmers.o src/hstacks-DNASeq.o src/hstacks-DNANSeq.o src/hstacks-utils.o src/hstacks-input.o -lz -lgomp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/process_radtags-process_radtags.o `test -f 'src/process_radtags.cc' || echo './'`src/process_radtags.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/process_radtags-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/process_radtags-log_utils.o `test -f 'src/log_utils.cc' || echo './'`src/log_utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/process_radtags-write.o `test -f 'src/write.cc' || echo './'`src/write.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/process_radtags-clean.o `test -f 'src/clean.cc' || echo './'`src/clean.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/process_radtags-file_io.o `test -f 'src/file_io.cc' || echo './'`src/file_io.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/process_radtags-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
g++ -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -fopenmp -Wl,-z,relro -o process_radtags src/process_radtags-process_radtags.o src/process_radtags-utils.o src/process_radtags-log_utils.o src/process_radtags-write.o src/process_radtags-clean.o src/process_radtags-file_io.o src/process_radtags-input.o /usr/lib/libbam.a -lz -lgomp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/process_shortreads-process_shortreads.o `test -f 'src/process_shortreads.cc' || echo './'`src/process_shortreads.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/process_shortreads-clean.o `test -f 'src/clean.cc' || echo './'`src/clean.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/process_shortreads-file_io.o `test -f 'src/file_io.cc' || echo './'`src/file_io.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/process_shortreads-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/process_shortreads-log_utils.o `test -f 'src/log_utils.cc' || echo './'`src/log_utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/process_shortreads-write.o `test -f 'src/write.cc' || echo './'`src/write.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/process_shortreads-kmers.o `test -f 'src/kmers.cc' || echo './'`src/kmers.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/process_shortreads-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
g++ -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -fopenmp -Wl,-z,relro -o process_shortreads src/process_shortreads-process_shortreads.o src/process_shortreads-clean.o src/process_shortreads-file_io.o src/process_shortreads-utils.o src/process_shortreads-log_utils.o src/process_shortreads-write.o src/process_shortreads-kmers.o src/process_shortreads-input.o /usr/lib/libbam.a -lz -lgomp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/kmer_filter-kmer_filter.o `test -f 'src/kmer_filter.cc' || echo './'`src/kmer_filter.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/kmer_filter-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/kmer_filter-write.o `test -f 'src/write.cc' || echo './'`src/write.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/kmer_filter-kmers.o `test -f 'src/kmers.cc' || echo './'`src/kmers.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/kmer_filter-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
g++ -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -fopenmp -Wl,-z,relro -o kmer_filter src/kmer_filter-kmer_filter.o src/kmer_filter-utils.o src/kmer_filter-write.o src/kmer_filter-kmers.o src/kmer_filter-input.o -lz -lgomp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/clone_filter-clone_filter.o `test -f 'src/clone_filter.cc' || echo './'`src/clone_filter.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/clone_filter-kmers.o `test -f 'src/kmers.cc' || echo './'`src/kmers.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/clone_filter-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/clone_filter-write.o `test -f 'src/write.cc' || echo './'`src/write.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/clone_filter-clean.o `test -f 'src/clean.cc' || echo './'`src/clean.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/clone_filter-file_io.o `test -f 'src/file_io.cc' || echo './'`src/file_io.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/clone_filter-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
g++ -fopenmp -I/usr/include/samtools -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -fopenmp -Wl,-z,relro -o clone_filter src/clone_filter-clone_filter.o src/clone_filter-kmers.o src/clone_filter-utils.o src/clone_filter-write.o src/clone_filter-clean.o src/clone_filter-file_io.o src/clone_filter-input.o /usr/lib/libbam.a -lz -lgomp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/genotypes-genotypes.o `test -f 'src/genotypes.cc' || echo './'`src/genotypes.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/genotypes-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/genotypes-catalog_utils.o `test -f 'src/catalog_utils.cc' || echo './'`src/catalog_utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/genotypes-log_utils.o `test -f 'src/log_utils.cc' || echo './'`src/log_utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/genotypes-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/genotypes-locus.o `test -f 'src/locus.cc' || echo './'`src/locus.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/genotypes-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/genotypes-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/genotypes-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
g++ -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -fopenmp -Wl,-z,relro -o genotypes src/genotypes-genotypes.o src/genotypes-utils.o src/genotypes-catalog_utils.o src/genotypes-log_utils.o src/genotypes-stacks.o src/genotypes-locus.o src/genotypes-DNASeq.o src/genotypes-DNANSeq.o src/genotypes-input.o -lz -lgomp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/populations-populations.o `test -f 'src/populations.cc' || echo './'`src/populations.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/populations-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/populations-catalog_utils.o `test -f 'src/catalog_utils.cc' || echo './'`src/catalog_utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/populations-log_utils.o `test -f 'src/log_utils.cc' || echo './'`src/log_utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/populations-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/populations-locus.o `test -f 'src/locus.cc' || echo './'`src/locus.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/populations-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/populations-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/populations-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
g++ -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -fopenmp -Wl,-z,relro -o populations src/populations-populations.o src/populations-utils.o src/populations-catalog_utils.o src/populations-log_utils.o src/populations-stacks.o src/populations-locus.o src/populations-DNASeq.o src/populations-DNANSeq.o src/populations-input.o -lz -lgomp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/phasedstacks-phasedstacks.o `test -f 'src/phasedstacks.cc' || echo './'`src/phasedstacks.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/phasedstacks-locus.o `test -f 'src/locus.cc' || echo './'`src/locus.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/phasedstacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/phasedstacks-log_utils.o `test -f 'src/log_utils.cc' || echo './'`src/log_utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/phasedstacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -c -o src/phasedstacks-catalog_utils.o `test -f 'src/catalog_utils.cc' || echo './'`src/catalog_utils.cc
g++ -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -fopenmp -Wl,-z,relro -o phasedstacks src/phasedstacks-phasedstacks.o src/phasedstacks-locus.o src/phasedstacks-input.o src/phasedstacks-log_utils.o src/phasedstacks-utils.o src/phasedstacks-catalog_utils.o -lz -lgomp
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
#ln -s /usr/share/automake-1.14/tap-driver.sh tests/tap-driver.sh
#dh_auto_test
# Does not work even after this trick. See
# https://groups.google.com/forum/#!msg/stacks-users/TA2tMEqb4Mg/pQy4fUCYi9kJ
true
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
fakeroot debian/rules binary-arch
dh binary-arch
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>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c ustacks pstacks estacks cstacks sstacks rxstacks hstacks process_radtags process_shortreads kmer_filter clone_filter genotypes populations phasedstacks '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c scripts/denovo_map.pl scripts/ref_map.pl scripts/export_sql.pl scripts/sort_read_pairs.pl scripts/exec_velvet.pl scripts/load_sequences.pl scripts/index_radtags.pl scripts/load_radtags.pl scripts/stacks_export_notify.pl '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/stacks'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/stacks/sql'
/usr/bin/install -c -m 644 sql/mysql.cnf.dist sql/catalog_index.sql sql/stacks.sql sql/tag_index.sql sql/chr_index.sql '/<<PKGBUILDDIR>>/debian/tmp/usr/share/stacks/sql'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/stacks/php'
/usr/bin/install -c -m 644 php/CatalogClass.php php/annotate_marker.php php/constants.php.dist php/index.php php/tags.php php/tag.php php/Locus.php php/catalog.php php/correct_genotypes.php php/correct_genotype.php php/export_batch.php php/last_modified.php php/version.php php/catalog_genotypes.php php/db_functions.php php/header.php php/samples.php php/stacks_functions.php php/view_sequence.php php/sequence_blast.php php/pop_view.php php/sumstat_view.php php/hapstat_view.php php/fst_view.php php/phist_view.php php/stack_view.php php/population_view.js php/ajax.js php/annotate.js php/stacks.js php/export.js php/stacks.css '/<<PKGBUILDDIR>>/debian/tmp/usr/share/stacks/php'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/stacks/php/images'
/usr/bin/install -c -m 644 php/images/caret-d.png php/images/caret-u.png php/images/excel_icon.png php/images/l-arrow-disabled.png php/images/l-arrow.png php/images/r-arrow-disabled.png php/images/r-arrow.png php/images/stacks_bg.png php/images/stacks_logo_rev_small.png '/<<PKGBUILDDIR>>/debian/tmp/usr/share/stacks/php/images'
make install-data-hook
make[3]: Entering directory '/<<PKGBUILDDIR>>'
sed -e 's,_VERSION_,1.37,' -e 's,_BINDIR_,/usr/bin/,g' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /<<PKGBUILDDIR>>/debian/tmp/usr/bin/denovo_map.pl > /<<PKGBUILDDIR>>/debian/tmp/usr/bin/denovo_map.pl.subst
mv /<<PKGBUILDDIR>>/debian/tmp/usr/bin/denovo_map.pl.subst /<<PKGBUILDDIR>>/debian/tmp/usr/bin/denovo_map.pl
chmod +x /<<PKGBUILDDIR>>/debian/tmp/usr/bin/denovo_map.pl
sed -e 's,_VERSION_,1.37,' -e 's,_BINDIR_,/usr/bin/,g' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /<<PKGBUILDDIR>>/debian/tmp/usr/bin/ref_map.pl > /<<PKGBUILDDIR>>/debian/tmp/usr/bin/ref_map.pl.subst
mv /<<PKGBUILDDIR>>/debian/tmp/usr/bin/ref_map.pl.subst /<<PKGBUILDDIR>>/debian/tmp/usr/bin/ref_map.pl
chmod +x /<<PKGBUILDDIR>>/debian/tmp/usr/bin/ref_map.pl
sed -e 's,_VERSION_,1.37,' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /<<PKGBUILDDIR>>/debian/tmp/usr/bin/export_sql.pl > /<<PKGBUILDDIR>>/debian/tmp/usr/bin/export_sql.pl.subst
mv /<<PKGBUILDDIR>>/debian/tmp/usr/bin/export_sql.pl.subst /<<PKGBUILDDIR>>/debian/tmp/usr/bin/export_sql.pl
chmod +x /<<PKGBUILDDIR>>/debian/tmp/usr/bin/export_sql.pl
sed -e 's,_VERSION_,1.37,' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /<<PKGBUILDDIR>>/debian/tmp/usr/bin/index_radtags.pl > /<<PKGBUILDDIR>>/debian/tmp/usr/bin/index_radtags.pl.subst
mv /<<PKGBUILDDIR>>/debian/tmp/usr/bin/index_radtags.pl.subst /<<PKGBUILDDIR>>/debian/tmp/usr/bin/index_radtags.pl
chmod +x /<<PKGBUILDDIR>>/debian/tmp/usr/bin/index_radtags.pl
sed -e 's,_VERSION_,1.37,' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /<<PKGBUILDDIR>>/debian/tmp/usr/bin/load_radtags.pl > /<<PKGBUILDDIR>>/debian/tmp/usr/bin/load_radtags.pl.subst
mv /<<PKGBUILDDIR>>/debian/tmp/usr/bin/load_radtags.pl.subst /<<PKGBUILDDIR>>/debian/tmp/usr/bin/load_radtags.pl
chmod +x /<<PKGBUILDDIR>>/debian/tmp/usr/bin/load_radtags.pl
sed -e 's,_VERSION_,1.37,' /<<PKGBUILDDIR>>/debian/tmp/usr/bin/sort_read_pairs.pl > /<<PKGBUILDDIR>>/debian/tmp/usr/bin/sort_read_pairs.pl.subst
mv /<<PKGBUILDDIR>>/debian/tmp/usr/bin/sort_read_pairs.pl.subst /<<PKGBUILDDIR>>/debian/tmp/usr/bin/sort_read_pairs.pl
chmod +x /<<PKGBUILDDIR>>/debian/tmp/usr/bin/sort_read_pairs.pl
sed -e 's,_VERSION_,1.37,' /<<PKGBUILDDIR>>/debian/tmp/usr/bin/exec_velvet.pl > /<<PKGBUILDDIR>>/debian/tmp/usr/bin/exec_velvet.pl.subst
mv /<<PKGBUILDDIR>>/debian/tmp/usr/bin/exec_velvet.pl.subst /<<PKGBUILDDIR>>/debian/tmp/usr/bin/exec_velvet.pl
chmod +x /<<PKGBUILDDIR>>/debian/tmp/usr/bin/exec_velvet.pl
sed -e 's,_VERSION_,1.37,' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /<<PKGBUILDDIR>>/debian/tmp/usr/bin/load_sequences.pl > /<<PKGBUILDDIR>>/debian/tmp/usr/bin/load_sequences.pl.subst
mv /<<PKGBUILDDIR>>/debian/tmp/usr/bin/load_sequences.pl.subst /<<PKGBUILDDIR>>/debian/tmp/usr/bin/load_sequences.pl
chmod +x /<<PKGBUILDDIR>>/debian/tmp/usr/bin/load_sequences.pl
sed -e 's,_VERSION_,1.37,' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' -e 's,_BINDIR_,/usr/bin/,g' \
/<<PKGBUILDDIR>>/debian/tmp/usr/bin/stacks_export_notify.pl > /<<PKGBUILDDIR>>/debian/tmp/usr/bin/stacks_export_notify.pl.subst
mv /<<PKGBUILDDIR>>/debian/tmp/usr/bin/stacks_export_notify.pl.subst /<<PKGBUILDDIR>>/debian/tmp/usr/bin/stacks_export_notify.pl
chmod +x /<<PKGBUILDDIR>>/debian/tmp/usr/bin/stacks_export_notify.pl
sed -e 's,_PKGDATADIR_,/usr/share/stacks/,g' -e 's,_BINDIR_,/usr/bin/,g' \
/<<PKGBUILDDIR>>/debian/tmp/usr/share/stacks/php/constants.php.dist > /<<PKGBUILDDIR>>/debian/tmp/usr/share/stacks/php/constants.php.dist.subst
mv /<<PKGBUILDDIR>>/debian/tmp/usr/share/stacks/php/constants.php.dist.subst /<<PKGBUILDDIR>>/debian/tmp/usr/share/stacks/php/constants.php.dist
echo 1.37 > /<<PKGBUILDDIR>>/debian/tmp/usr/share/stacks/php/version.php
/bin/bash /<<PKGBUILDDIR>>/config/install-sh -d -m 755 /<<PKGBUILDDIR>>/debian/tmp/usr/share/stacks/php/export
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cp php/constants.php.dist ./constants.php
dh_install
# Skip this bit if not building stacks
! cd debian/stacks/usr/lib/stacks/bin || \
for f in *.pl ; do \
ln -s "$f" "`basename $f .pl`" ; \
done
# Skip this bit if not building stacks-web
# Note - directory perms will be set in postinst
dh_installdirs -pstacks-web /var/lib/stacks/export
dh_installdirs: No packages to build.
if [ -e debian/stacks-web/usr/share/stacks/php ] ; then \
rmdir debian/stacks-web/usr/share/stacks/php/export ; \
ln -s /var/lib/stacks/export \
debian/stacks-web/usr/share/stacks/php/export ; \
fi
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_perl -a
debian/rules override_dh_link
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_link
mkdir -p debian/stacks/usr/lib/debian-med/bin
cd debian/stacks/usr/lib/debian-med/bin && \
for f in `ls /<<PKGBUILDDIR>>/debian/stacks/usr/lib/stacks/bin` ; do \
ln -s ../../stacks/bin/$f ; \
done
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/kmer_filter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/cstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/genotypes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/clone_filter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/process_shortreads contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/sstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/pstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/hstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/estacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/rxstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/ustacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/process_radtags contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/phasedstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/populations contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/stacks/usr/lib/stacks/bin/kmer_filter debian/stacks/usr/lib/stacks/bin/cstacks debian/stacks/usr/lib/stacks/bin/genotypes debian/stacks/usr/lib/stacks/bin/clone_filter debian/stacks/usr/lib/stacks/bin/process_shortreads debian/stacks/usr/lib/stacks/bin/sstacks debian/stacks/usr/lib/stacks/bin/pstacks debian/stacks/usr/lib/stacks/bin/hstacks debian/stacks/usr/lib/stacks/bin/estacks debian/stacks/usr/lib/stacks/bin/rxstacks debian/stacks/usr/lib/stacks/bin/ustacks debian/stacks/usr/lib/stacks/bin/process_radtags debian/stacks/usr/lib/stacks/bin/phasedstacks debian/stacks/usr/lib/stacks/bin/populations were not linked against ld-linux-armhf.so.3 (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 stacks: unused substitution variable ${perl:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package stacks: unused substitution variable ${perl:Depends}
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'stacks-dbgsym' in '../stacks-dbgsym_1.37-1_armhf.deb'.
dpkg-deb: building package 'stacks' in '../stacks_1.37-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../stacks_1.37-1_armhf.changes
dpkg-genchanges: warning: package stacks-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build stacks-1.37
dpkg-buildpackage: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160406-1706
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
stacks_1.37-1_armhf.changes:
----------------------------
Format: 1.8
Date: Thu, 10 Mar 2016 23:31:22 +0100
Source: stacks
Binary: stacks stacks-web
Architecture: armhf
Version: 1.37-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
stacks - pipeline for building loci from short-read DNA sequences
stacks-web - web interface for displaying loci from short-read sequences
Changes:
stacks (1.37-1) unstable; urgency=medium
.
* New upstream version
* Moved from SVN to Git
* cme fix dpkg-control
Checksums-Sha1:
d48f50714b06fba287b9dd39fdeb81830dda31c7 11447520 stacks-dbgsym_1.37-1_armhf.deb
8b09d33f44b739e1e68645de975b0b3b556035d3 620836 stacks_1.37-1_armhf.deb
Checksums-Sha256:
c3977cdd70d8484ab496d30353292cbf2d62f92714c91037c606ce21692f9f71 11447520 stacks-dbgsym_1.37-1_armhf.deb
598934fb71b674e328340c06baca2474a6d6c358e5f0667f8b472e477116d68c 620836 stacks_1.37-1_armhf.deb
Files:
fed77c969af99e748d0f8427899c4289 11447520 debug extra stacks-dbgsym_1.37-1_armhf.deb
9ec5d3eadde6e1565bd02ed3c2cdb9c6 620836 science optional stacks_1.37-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
stacks-dbgsym_1.37-1_armhf.deb
------------------------------
new debian package, version 2.0.
size 11447520 bytes: control archive=1191 bytes.
943 bytes, 13 lines control
1484 bytes, 14 lines md5sums
Package: stacks-dbgsym
Source: stacks
Version: 1.37-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 12027
Depends: stacks (= 1.37-1)
Section: debug
Priority: extra
Homepage: http://creskolab.uoregon.edu/stacks/
Description: Debug symbols for stacks
Auto-Built-Package: debug-symbols
Build-Ids: 07767e9edfbdaed48e352e26ce5b0e4bc0291286 0e041e7f5c3b4131c9bbecde11281ae82a0ed005 1f7e1db01ba75dbc0e69628f42d9a69da5990628 30d32d15d5137c3699ca39c026d9479c8b337fbf 3e07d33ad5149f5bcc5efc16e3f2a9b40a4856c7 4390edbfb8861593a55a8542e13af023c294e6e1 4e8091b37b597577f8d55875b612a2f0a95b5c61 60e2838335332f6c5bdfff48857dbc608e92839b 60fab87bc17307f3e965fd4d40482f2dd89d3365 772879b659451c62eb9dd4b33c5d3997ecddee82 9df03455d5322736a59a802816d6d43dc32ba031 9fff741e180cd634296e05ea6162c38227a9e7f5 dc6e02d95b5879809f57426a982292a318867faa ef1500066dcb41f8fb651e0b01b2606c5de2f988
drwxr-xr-x root/root 0 2016-04-06 17:05 ./
drwxr-xr-x root/root 0 2016-04-06 17:05 ./usr/
drwxr-xr-x root/root 0 2016-04-06 17:04 ./usr/lib/
drwxr-xr-x root/root 0 2016-04-06 17:04 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-04-06 17:05 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-04-06 17:04 ./usr/lib/debug/.build-id/07/
-rw-r--r-- root/root 1200900 2016-04-06 17:04 ./usr/lib/debug/.build-id/07/767e9edfbdaed48e352e26ce5b0e4bc0291286.debug
drwxr-xr-x root/root 0 2016-04-06 17:05 ./usr/lib/debug/.build-id/0e/
-rw-r--r-- root/root 1077964 2016-04-06 17:05 ./usr/lib/debug/.build-id/0e/041e7f5c3b4131c9bbecde11281ae82a0ed005.debug
drwxr-xr-x root/root 0 2016-04-06 17:05 ./usr/lib/debug/.build-id/1f/
-rw-r--r-- root/root 575240 2016-04-06 17:05 ./usr/lib/debug/.build-id/1f/7e1db01ba75dbc0e69628f42d9a69da5990628.debug
drwxr-xr-x root/root 0 2016-04-06 17:04 ./usr/lib/debug/.build-id/30/
-rw-r--r-- root/root 594336 2016-04-06 17:04 ./usr/lib/debug/.build-id/30/d32d15d5137c3699ca39c026d9479c8b337fbf.debug
drwxr-xr-x root/root 0 2016-04-06 17:04 ./usr/lib/debug/.build-id/3e/
-rw-r--r-- root/root 861076 2016-04-06 17:04 ./usr/lib/debug/.build-id/3e/07d33ad5149f5bcc5efc16e3f2a9b40a4856c7.debug
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drwxr-xr-x root/root 0 2016-04-06 17:05 ./usr/lib/debug/.build-id/dc/
-rw-r--r-- root/root 775052 2016-04-06 17:05 ./usr/lib/debug/.build-id/dc/6e02d95b5879809f57426a982292a318867faa.debug
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drwxr-xr-x root/root 0 2016-04-06 17:05 ./usr/share/
drwxr-xr-x root/root 0 2016-04-06 17:05 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-04-06 17:05 ./usr/share/doc/stacks-dbgsym -> stacks
stacks_1.37-1_armhf.deb
-----------------------
new debian package, version 2.0.
size 620836 bytes: control archive=1548 bytes.
899 bytes, 18 lines control
1845 bytes, 28 lines md5sums
Package: stacks
Version: 1.37-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3244
Depends: libc6 (>= 2.15), libgcc1 (>= 1:3.5), libgomp1 (>= 4.9), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.6), samtools, libdbi-perl
Recommends: libspreadsheet-writeexcel-perl
Section: science
Priority: optional
Homepage: http://creskolab.uoregon.edu/stacks/
Description: pipeline for building loci from short-read DNA sequences
Stacks is a software pipeline for building loci from short-read sequences,
such as those generated on the Illumina platform. Stacks was developed to work
with restriction enzyme-based data, such as RAD-seq, for the purpose of
building genetic maps and conducting population genomics and phylogeography.
.
Note that this package installs Stacks such that all commands must be run as:
$ stacks <cmdname> <args>
drwxr-xr-x root/root 0 2016-04-06 17:05 ./
drwxr-xr-x root/root 0 2016-04-06 17:04 ./usr/
drwxr-xr-x root/root 0 2016-04-06 17:04 ./usr/bin/
-rwxr-xr-x root/root 771 2016-03-10 22:40 ./usr/bin/stacks
drwxr-xr-x root/root 0 2016-04-06 17:04 ./usr/lib/
drwxr-xr-x root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/
drwxr-xr-x root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/clone_filter -> ../../stacks/bin/clone_filter
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/cstacks -> ../../stacks/bin/cstacks
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/denovo_map -> ../../stacks/bin/denovo_map
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/denovo_map.pl -> ../../stacks/bin/denovo_map.pl
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/estacks -> ../../stacks/bin/estacks
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/exec_velvet -> ../../stacks/bin/exec_velvet
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/exec_velvet.pl -> ../../stacks/bin/exec_velvet.pl
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/export_sql -> ../../stacks/bin/export_sql
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/export_sql.pl -> ../../stacks/bin/export_sql.pl
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/genotypes -> ../../stacks/bin/genotypes
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/hstacks -> ../../stacks/bin/hstacks
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/index_radtags -> ../../stacks/bin/index_radtags
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/index_radtags.pl -> ../../stacks/bin/index_radtags.pl
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/kmer_filter -> ../../stacks/bin/kmer_filter
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/load_radtags -> ../../stacks/bin/load_radtags
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/load_radtags.pl -> ../../stacks/bin/load_radtags.pl
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/load_sequences -> ../../stacks/bin/load_sequences
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/load_sequences.pl -> ../../stacks/bin/load_sequences.pl
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/phasedstacks -> ../../stacks/bin/phasedstacks
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/populations -> ../../stacks/bin/populations
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/process_radtags -> ../../stacks/bin/process_radtags
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/process_shortreads -> ../../stacks/bin/process_shortreads
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/pstacks -> ../../stacks/bin/pstacks
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/ref_map -> ../../stacks/bin/ref_map
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/ref_map.pl -> ../../stacks/bin/ref_map.pl
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/rxstacks -> ../../stacks/bin/rxstacks
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/sort_read_pairs -> ../../stacks/bin/sort_read_pairs
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/sort_read_pairs.pl -> ../../stacks/bin/sort_read_pairs.pl
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/sstacks -> ../../stacks/bin/sstacks
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/stacks_export_notify -> ../../stacks/bin/stacks_export_notify
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/stacks_export_notify.pl -> ../../stacks/bin/stacks_export_notify.pl
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/debian-med/bin/ustacks -> ../../stacks/bin/ustacks
drwxr-xr-x root/root 0 2016-04-06 17:04 ./usr/lib/stacks/
drwxr-xr-x root/root 0 2016-04-06 17:05 ./usr/lib/stacks/bin/
-rwxr-xr-x root/root 360056 2016-04-06 17:05 ./usr/lib/stacks/bin/clone_filter
-rwxr-xr-x root/root 194780 2016-04-06 17:04 ./usr/lib/stacks/bin/cstacks
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/stacks/bin/denovo_map -> denovo_map.pl
-rwxr-xr-x root/root 24480 2016-04-06 17:04 ./usr/lib/stacks/bin/denovo_map.pl
-rwxr-xr-x root/root 108664 2016-04-06 17:04 ./usr/lib/stacks/bin/estacks
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/stacks/bin/exec_velvet -> exec_velvet.pl
-rwxr-xr-x root/root 8919 2016-04-06 17:04 ./usr/lib/stacks/bin/exec_velvet.pl
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/stacks/bin/export_sql -> export_sql.pl
-rwxr-xr-x root/root 31818 2016-04-06 17:04 ./usr/lib/stacks/bin/export_sql.pl
-rwxr-xr-x root/root 240388 2016-04-06 17:05 ./usr/lib/stacks/bin/genotypes
-rwxr-xr-x root/root 170084 2016-04-06 17:05 ./usr/lib/stacks/bin/hstacks
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/stacks/bin/index_radtags -> index_radtags.pl
-rwxr-xr-x root/root 20389 2016-04-06 17:04 ./usr/lib/stacks/bin/index_radtags.pl
-rwxr-xr-x root/root 215368 2016-04-06 17:05 ./usr/lib/stacks/bin/kmer_filter
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/stacks/bin/load_radtags -> load_radtags.pl
-rwxr-xr-x root/root 15091 2016-04-06 17:04 ./usr/lib/stacks/bin/load_radtags.pl
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/stacks/bin/load_sequences -> load_sequences.pl
-rwxr-xr-x root/root 6241 2016-04-06 17:04 ./usr/lib/stacks/bin/load_sequences.pl
-rwxr-xr-x root/root 100608 2016-04-06 17:05 ./usr/lib/stacks/bin/phasedstacks
-rwxr-xr-x root/root 445808 2016-04-06 17:05 ./usr/lib/stacks/bin/populations
-rwxr-xr-x root/root 246056 2016-04-06 17:05 ./usr/lib/stacks/bin/process_radtags
-rwxr-xr-x root/root 307132 2016-04-06 17:05 ./usr/lib/stacks/bin/process_shortreads
-rwxr-xr-x root/root 175656 2016-04-06 17:04 ./usr/lib/stacks/bin/pstacks
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/stacks/bin/ref_map -> ref_map.pl
-rwxr-xr-x root/root 22729 2016-04-06 17:04 ./usr/lib/stacks/bin/ref_map.pl
-rwxr-xr-x root/root 141640 2016-04-06 17:04 ./usr/lib/stacks/bin/rxstacks
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/stacks/bin/sort_read_pairs -> sort_read_pairs.pl
-rwxr-xr-x root/root 14915 2016-04-06 17:04 ./usr/lib/stacks/bin/sort_read_pairs.pl
-rwxr-xr-x root/root 120996 2016-04-06 17:04 ./usr/lib/stacks/bin/sstacks
lrwxrwxrwx root/root 0 2016-04-06 17:04 ./usr/lib/stacks/bin/stacks_export_notify -> stacks_export_notify.pl
-rwxr-xr-x root/root 6443 2016-04-06 17:04 ./usr/lib/stacks/bin/stacks_export_notify.pl
-rwxr-xr-x root/root 248356 2016-04-06 17:04 ./usr/lib/stacks/bin/ustacks
drwxr-xr-x root/root 0 2016-04-06 17:04 ./usr/share/
drwxr-xr-x root/root 0 2016-04-06 17:04 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-04-06 17:04 ./usr/share/doc/stacks/
-rw-r--r-- root/root 1451 2016-03-10 22:40 ./usr/share/doc/stacks/README.Debian
-rw-r--r-- root/root 705 2016-03-10 22:40 ./usr/share/doc/stacks/changelog.Debian.gz
-rw-r--r-- root/root 21382 2016-02-24 16:41 ./usr/share/doc/stacks/changelog.gz
-rw-r--r-- root/root 1335 2016-03-10 22:40 ./usr/share/doc/stacks/copyright
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 180148
Build-Time: 2239
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 181
Job: stacks_1.37-1
Machine Architecture: armhf
Package: stacks
Package-Time: 2462
Source-Version: 1.37-1
Space: 180148
Status: successful
Version: 1.37-1
--------------------------------------------------------------------------------
Finished at 20160406-1706
Build needed 00:41:02, 180148k disc space