stacks →
1.44-1 →
armhf → 2016-10-29 19:05:11
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| stacks 1.44-1 (armhf) Sat, 29 Oct 2016 18:06:27 +0000 |
+==============================================================================+
Package: stacks
Version: 1.44-1
Source Version: 1.44-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-0a45722b-4fa6-43c9-b5b6-82da8fd54458' 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 [9411 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.4 MB]
Fetched 20.8 MB in 23s (874 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| 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 915 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main stacks 1.44-1 (dsc) [2048 B]
Get:2 http://172.17.0.1/private stretch-staging/main stacks 1.44-1 (tar) [904 kB]
Get:3 http://172.17.0.1/private stretch-staging/main stacks 1.44-1 (diff) [8688 B]
Fetched 915 kB in 0s (5473 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/stacks-uWee2M/stacks-1.44' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/stacks-uWee2M' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| 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-68LJxq/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-68LJxq/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-68LJxq/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-68LJxq/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-68LJxq/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-68LJxq/apt_archive ./ Release.gpg [342 B]
Get:4 copy:/<<BUILDDIR>>/resolver-68LJxq/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-68LJxq/apt_archive ./ Packages [432 B]
Fetched 2080 B in 0s (3582 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
dirmngr fuse2fs gnupg-l10n kbd libffi6 libfuse2 libgnutls30 libhogweed4
libldap-2.4-2 libnettle6 libp11-kit0 libsasl2-2 libsasl2-modules
libsasl2-modules-db libssl1.0.2 libtasn1-6 manpages netbase psmisc
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 766 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-68LJxq/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [766 B]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13408 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 9), python, zlib1g-dev, libbam-dev, libsparsehash-dev (>= 2.0), samtools
Filtered Build-Depends: debhelper (>= 9), python, zlib1g-dev, libbam-dev, libsparsehash-dev (>= 2.0), samtools
dpkg-deb: building package 'sbuild-build-depends-stacks-dummy' in '/<<BUILDDIR>>/resolver-68LJxq/apt_archive/sbuild-build-depends-stacks-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-stacks-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-68LJxq/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-68LJxq/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-68LJxq/apt_archive ./ Release.gpg [342 B]
Get:4 copy:/<<BUILDDIR>>/resolver-68LJxq/apt_archive ./ Sources [525 B]
Get:5 copy:/<<BUILDDIR>>/resolver-68LJxq/apt_archive ./ Packages [605 B]
Fetched 2435 B in 0s (4133 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install stacks build dependencies (apt-based resolver)
------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
dirmngr fuse2fs gnupg-l10n kbd libfuse2 libsasl2-modules manpages netbase
psmisc
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbam-dev libbsd0 libcroco3
libcurl3-gnutls libexpat1 libfile-stripnondeterminism-perl libglib2.0-0
libgssapi-krb5-2 libhts1 libicu57 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 libmagic-mgc libmagic1 libnghttp2-14 libpipeline1
libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline6
librtmp1 libsigsegv2 libsparsehash-dev libssh2-1 libtimedate-perl libtool
libunistring0 libxml2 m4 man-db mime-support po-debconf python
python-minimal python2.7 python2.7-minimal samtools zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc
krb5-user libtool-doc gfortran | fortran95-compiler gcj-jdk less www-browser
libmail-box-perl python-doc python-tk python2.7-doc binfmt-support
Recommended packages:
curl | wget | lynx-cur ca-certificates libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales libltdl-dev xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbam-dev libbsd0 libcroco3
libcurl3-gnutls libexpat1 libfile-stripnondeterminism-perl libglib2.0-0
libgssapi-krb5-2 libhts1 libicu57 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 libmagic-mgc libmagic1 libnghttp2-14 libpipeline1
libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline6
librtmp1 libsigsegv2 libsparsehash-dev libssh2-1 libtimedate-perl libtool
libunistring0 libxml2 m4 man-db mime-support po-debconf python
python-minimal python2.7 python2.7-minimal samtools
sbuild-build-depends-stacks-dummy zlib1g-dev
0 upgraded, 55 newly installed, 0 to remove and 0 not upgraded.
Need to get 25.0 MB/25.1 MB of archives.
After this operation, 86.3 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-68LJxq/apt_archive ./ sbuild-build-depends-stacks-dummy 0.invalid.0 [802 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-8 [1087 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.11 [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 libpython2.7-minimal armhf 2.7.12-3 [388 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.12-3 [1174 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf python-minimal armhf 2.7.11-2 [40.3 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.2.0-1 [61.7 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-stdlib armhf 2.7.12-3 [1843 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf python2.7 armhf 2.7.12-3 [279 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libpython-stdlib armhf 2.7.11-2 [19.8 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf python armhf 2.7.11-2 [153 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.28-4 [210 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.28-4 [104 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.28-4 [62.7 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libkrb5support0 armhf 1.14.3+dfsg-2 [57.5 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libk5crypto3 armhf 1.14.3+dfsg-2 [110 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libkrb5-3 armhf 1.14.3+dfsg-2 [262 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libgssapi-krb5-2 armhf 1.14.3+dfsg-2 [131 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-4 [7407 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2 [805 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.028-1 [14.6 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.028-1 [9020 B]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.0-2+rpi1 [2523 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.2 [826 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libbam-dev armhf 0.1.19-2 [109 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libnghttp2-14 armhf 1.15.0-1 [72.6 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libssh2-1 armhf 1.7.0-1 [125 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libcurl3-gnutls armhf 7.50.1-1 [248 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libhts1 armhf 1.3.1-3+rpi1 [216 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libsparsehash-dev all 2.0.2-1 [76.9 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf samtools armhf 1.3.1-2 [219 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
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Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../24-libglib2.0-0_2.50.0-2+rpi1_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.50.0-2+rpi1) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../25-libcroco3_0.6.11-2_armhf.deb ...
Unpacking libcroco3:armhf (0.6.11-2) ...
Selecting previously unselected package libunistring0:armhf.
Preparing to unpack .../26-libunistring0_0.9.6+really0.9.3-0.1_armhf.deb ...
Unpacking libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../27-gettext_0.19.8.1-1_armhf.deb ...
Unpacking gettext (0.19.8.1-1) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../28-intltool-debian_0.35.0+20060710.4_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.4) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../29-po-debconf_1.0.20_all.deb ...
Unpacking po-debconf (1.0.20) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../30-debhelper_10.2.2_all.deb ...
Unpacking debhelper (10.2.2) ...
Selecting previously unselected package libbam-dev.
Preparing to unpack .../31-libbam-dev_0.1.19-2_armhf.deb ...
Unpacking libbam-dev (0.1.19-2) ...
Selecting previously unselected package libnghttp2-14:armhf.
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Unpacking libnghttp2-14:armhf (1.15.0-1) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../33-librtmp1_2.4+20151223.gitfa8646d.1-1_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../34-libssh2-1_1.7.0-1_armhf.deb ...
Unpacking libssh2-1:armhf (1.7.0-1) ...
Selecting previously unselected package libcurl3-gnutls:armhf.
Preparing to unpack .../35-libcurl3-gnutls_7.50.1-1_armhf.deb ...
Unpacking libcurl3-gnutls:armhf (7.50.1-1) ...
Selecting previously unselected package libhts1:armhf.
Preparing to unpack .../36-libhts1_1.3.1-3+rpi1_armhf.deb ...
Unpacking libhts1:armhf (1.3.1-3+rpi1) ...
Selecting previously unselected package libsparsehash-dev.
Preparing to unpack .../37-libsparsehash-dev_2.0.2-1_all.deb ...
Unpacking libsparsehash-dev (2.0.2-1) ...
Selecting previously unselected package samtools.
Preparing to unpack .../38-samtools_1.3.1-2_armhf.deb ...
Unpacking samtools (1.3.1-2) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../39-zlib1g-dev_1%3a1.2.8.dfsg-2+b1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Selecting previously unselected package sbuild-build-depends-stacks-dummy.
Preparing to unpack .../40-sbuild-build-depends-stacks-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-stacks-dummy (0.invalid.0) ...
Setting up libsparsehash-dev (2.0.2-1) ...
Setting up libexpat1:armhf (2.2.0-1) ...
Setting up libarchive-zip-perl (1.59-1) ...
Setting up libnghttp2-14:armhf (1.15.0-1) ...
Setting up mime-support (3.60) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up groff-base (1.22.3-8) ...
Setting up libglib2.0-0:armhf (2.50.0-2+rpi1) ...
No schema files found: doing nothing.
Setting up gettext-base (0.19.8.1-1) ...
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up m4 (1.4.17-5) ...
Setting up libicu57:armhf (57.1-4) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-2) ...
Setting up libmagic-mgc (1:5.28-4) ...
Setting up libmagic1:armhf (1:5.28-4) ...
Setting up libcroco3:armhf (0.6.11-2) ...
Setting up libssh2-1:armhf (1.7.0-1) ...
Processing triggers for libc-bin (2.24-5+rpi1) ...
Setting up autotools-dev (20160430.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up libbam-dev (0.1.19-2) ...
Setting up libkeyutils1:armhf (1.5.9-9) ...
Setting up bsdmainutils (9.0.11) ...
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 autopoint (0.19.8.1-1) ...
Setting up libreadline6:armhf (6.3-9) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up libfile-stripnondeterminism-perl (0.028-1) ...
Setting up gettext (0.19.8.1-1) ...
Setting up autoconf (2.69-10) ...
Setting up file (1:5.28-4) ...
Setting up libkrb5support0:armhf (1.14.3+dfsg-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up automake (1:1.15-4) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libpython2.7-stdlib:armhf (2.7.12-3) ...
Setting up libtool (2.4.6-2) ...
Setting up libk5crypto3:armhf (1.14.3+dfsg-2) ...
Setting up po-debconf (1.0.20) ...
Setting up python2.7 (2.7.12-3) ...
Setting up libpython-stdlib:armhf (2.7.11-2) ...
Setting up libkrb5-3:armhf (1.14.3+dfsg-2) ...
Setting up python (2.7.11-2) ...
Setting up libgssapi-krb5-2:armhf (1.14.3+dfsg-2) ...
Setting up libcurl3-gnutls:armhf (7.50.1-1) ...
Setting up libhts1:armhf (1.3.1-3+rpi1) ...
Setting up samtools (1.3.1-2) ...
Setting up dh-strip-nondeterminism (0.028-1) ...
Setting up debhelper (10.2.2) ...
Setting up dh-autoreconf (12) ...
Setting up sbuild-build-depends-stacks-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-5+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.27-9 dpkg-dev_1.18.10 g++-6_6.2.0-6+rpi1 gcc-6_6.2.0-6+rpi1 libc6-dev_2.24-5+rpi1 libstdc++-6-dev_6.2.0-6+rpi1 libstdc++6_6.2.0-6+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.3.1 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.40 bash_4.4-1 binutils_2.27-9 bsdmainutils_9.0.11 bsdutils_1:2.28.2-1 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:6.1.1-1 cpp-6_6.2.0-6+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10.2.2 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.028-1 diffutils_1:3.5-1 dirmngr_2.1.15-4 dmsetup_2:1.02.133-1 dpkg_1.18.10 dpkg-dev_1.18.10 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-2 file_1:5.28-4 findutils_4.6.0+git+20160703-2 fuse2fs_1.43.3-1 g++_4:6.1.1-1 g++-6_6.2.0-6+rpi1 gcc_4:6.1.1-1 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_4.9.3-14 gcc-6_6.2.0-6+rpi1 gcc-6-base_6.2.0-6+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gnupg_2.1.15-4 gnupg-agent_2.1.15-4 gnupg-l10n_2.1.15-4 gpgv_2.1.15-4 grep_2.26-1 groff-base_1.22.3-8 gzip_1.6-5 hostname_3.18 init_1.45 init-system-helpers_1.45 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 kbd_2.0.3-2 klibc-utils_2.0.4-9+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libapparmor1_2.10.95-5 libapt-pkg5.0_1.3.1 libarchive-zip-perl_1.59-1 libasan3_6.2.0-6+rpi1 libassuan0_2.4.3-1 libatomic1_6.2.0-6+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-1 libaudit1_1:2.6.7-1 libbam-dev_0.1.19-2 libblkid1_2.28.2-1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.24-5+rpi1 libc-dev-bin_2.24-5+rpi1 libc6_2.24-5+rpi1 libc6-dev_2.24-5+rpi1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.2.0-6+rpi1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.2-5 libcurl3-gnutls_7.50.1-1 libdb5.3_5.3.28-12 libdbus-1-3_1.10.12-1 libdebconfclient0_0.218 libdevmapper1.02.1_2:1.02.133-1 libdpkg-perl_1.18.10 libdrm2_2.4.71-1 libexpat1_2.2.0-1 libfakeroot_1.21-2 libfdisk1_2.28.2-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.028-1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.2.0-6+rpi1 libgcc1_1:6.2.0-6+rpi1 libgcrypt20_1.7.3-2 libgdbm3_1.8.3-14 libglib2.0-0_2.50.0-2+rpi1 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.5-2 libgomp1_6.2.0-6+rpi1 libgpg-error0_1.24-1 libgssapi-krb5-2_1.14.3+dfsg-2 libhogweed4_3.3-1 libhts1_1.3.1-3+rpi1 libicu57_57.1-4 libidn11_1.33-1 libip4tc0_1.6.0-4 libisl15_0.17.1-1 libk5crypto3_1.14.3+dfsg-2 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_22-1.1 libkrb5-3_1.14.3+dfsg-2 libkrb5support0_1.14.3+dfsg-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.42+dfsg-2+rpi1+b3 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.28-4 libmagic1_1:5.28-4 libmount1_2.28.2-1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160917-1 libncursesw5_6.0+20160917-1 libnettle6_3.3-1 libnghttp2-14_1.15.0-1 libnpth0_1.2-3 libp11-kit0_0.23.2-5 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpcre3_2:8.39-2 libperl5.24_5.24.1~rc3-3 libpipeline1_1.4.1-2 libplymouth4_0.9.2-3 libpng12-0_1.2.54-6 libprocps6_2:3.3.12-2 libpython-stdlib_2.7.11-2 libpython2.7-minimal_2.7.12-3 libpython2.7-stdlib_2.7.12-3 libreadline6_6.3-9 libreadline7_7.0-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.3.1-2 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsmartcols1_2.28.2-1 libsparsehash-dev_2.0.2-1 libsqlite3-0_3.14.2-1 libss2_1.43.3-1 libssh2-1_1.7.0-1 libssl1.0.2_1.0.2j-1 libstdc++-6-dev_6.2.0-6+rpi1 libstdc++6_6.2.0-6+rpi1 libsystemd0_231-9 libtasn1-6_4.9-4 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160917-1 libtool_2.4.6-2 libubsan0_6.2.0-6+rpi1 libudev1_231-9 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28.2-1 libxml2_2.9.4+dfsg1-2 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.2 lsb-base_9.20160629+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.08-1 mawk_1.3.3-17 mime-support_3.60 mount_2.28.2-1 multiarch-support_2.24-5+rpi1 ncurses-base_6.0+20160917-1 ncurses-bin_6.0+20160917-1 netbase_5.3 passwd_1:4.2-3.2 patch_2.7.5-1 perl_5.24.1~rc3-3 perl-base_5.24.1~rc3-3 perl-modules-5.24_5.24.1~rc3-3 pinentry-curses_0.9.7-6 po-debconf_1.0.20 procps_2:3.3.12-2 psmisc_22.21-2.1 python_2.7.11-2 python-minimal_2.7.11-2 python2.7_2.7.12-3 python2.7-minimal_2.7.12-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-1 samtools_1.3.1-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-stacks-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_231-9 systemd-sysv_231-9 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1 tzdata_2016h-1 udev_231-9 util-linux_2.28.2-1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sat Oct 22 19:20:27 2016 UTC
gpgv: using RSA key 578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./stacks_1.44-1.dsc
dpkg-source: info: extracting stacks in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking stacks_1.44.orig.tar.gz
dpkg-source: info: unpacking stacks_1.44-1.debian.tar.xz
dpkg-source: info: applying constants.php.patch
dpkg-source: info: applying email-settings.patch
dpkg-source: info: applying script-exe-paths
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-0a45722b-4fa6-43c9-b5b6-82da8fd54458
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package stacks
dpkg-buildpackage: info: source version 1.44-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build stacks-1.44
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --with python2
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 --with python2
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, --with-bam-include-path, --with-bam-lib-path
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... 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, --with-bam-include-path, --with-bam-lib-path
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -a
make -j1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd . && /bin/bash /<<PKGBUILDDIR>>/config/missing automake-1.15 --foreign Makefile
cd . && /bin/bash ./config.status Makefile depfiles
config.status: creating Makefile
config.status: executing depfiles commands
make all-recursive
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making all in htslib
make[3]: Entering directory '/<<PKGBUILDDIR>>/htslib'
echo '/* Empty config.h generated by Makefile */' > config.h
gcc -g -Wall -O2 -I. -c -o kfunc.o kfunc.c
gcc -g -Wall -O2 -I. -c -o knetfile.o knetfile.c
gcc -g -Wall -O2 -I. -c -o kstring.o kstring.c
gcc -g -Wall -O2 -I. -c -o bgzf.o bgzf.c
gcc -g -Wall -O2 -I. -c -o faidx.o faidx.c
gcc -g -Wall -O2 -I. -c -o hfile.o hfile.c
gcc -g -Wall -O2 -I. -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.3.1"' > version.h
gcc -g -Wall -O2 -I. -c -o hts.o hts.c
gcc -g -Wall -O2 -I. -c -o md5.o md5.c
gcc -g -Wall -O2 -I. -c -o regidx.o regidx.c
gcc -g -Wall -O2 -I. -c -o sam.o sam.c
gcc -g -Wall -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -Wall -O2 -I. -c -o vcf_sweep.o vcf_sweep.c
gcc -g -Wall -O2 -I. -c -o tbx.o tbx.c
gcc -g -Wall -O2 -I. -c -o vcf.o vcf.c
gcc -g -Wall -O2 -I. -c -o vcfutils.o vcfutils.c
gcc -g -Wall -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -Wall -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -Wall -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -Wall -O2 -I. -c -o cram/cram_external.o cram/cram_external.c
gcc -g -Wall -O2 -I. -c -o cram/cram_index.o cram/cram_index.c
gcc -g -Wall -O2 -I. -c -o cram/cram_io.o cram/cram_io.c
gcc -g -Wall -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -Wall -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -Wall -O2 -I. -c -o cram/files.o cram/files.c
gcc -g -Wall -O2 -I. -c -o cram/mFILE.o cram/mFILE.c
gcc -g -Wall -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -Wall -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -Wall -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -Wall -O2 -I. -c -o cram/sam_header.o cram/sam_header.c
gcc -g -Wall -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -Wall -O2 -I. -c -o cram/thread_pool.o cram/thread_pool.c
gcc -g -Wall -O2 -I. -c -o cram/vlen.o cram/vlen.c
gcc -g -Wall -O2 -I. -c -o cram/zfio.o cram/zfio.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o
ranlib libhts.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/htslib'
Making all in .
make[3]: Entering directory '/<<PKGBUILDDIR>>'
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ustacks-aln_utils.o `test -f 'src/aln_utils.cc' || echo './'`src/aln_utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ustacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
g++ -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -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-aln_utils.o src/ustacks-input.o -lz -lgomp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/pstacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
g++ -fopenmp -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -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 ./htslib/libhts.a -lz -lgomp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/estacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
g++ -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cstacks-aln_utils.o `test -f 'src/aln_utils.cc' || echo './'`src/aln_utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cstacks-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo './'`src/sql_utilities.cc
g++ -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o cstacks src/cstacks-cstacks.o src/cstacks-stacks.o src/cstacks-locus.o src/cstacks-kmers.o src/cstacks-utils.o src/cstacks-aln_utils.o src/cstacks-DNASeq.o src/cstacks-DNANSeq.o src/cstacks-input.o src/cstacks-sql_utilities.o -lz -lgomp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks-aln_utils.o `test -f 'src/aln_utils.cc' || echo './'`src/aln_utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo './'`src/sql_utilities.cc
g++ -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o sstacks src/sstacks-sstacks.o src/sstacks-stacks.o src/sstacks-locus.o src/sstacks-kmers.o src/sstacks-aln_utils.o src/sstacks-DNASeq.o src/sstacks-DNANSeq.o src/sstacks-utils.o src/sstacks-input.o src/sstacks-sql_utilities.o -lz -lgomp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/rxstacks-aln_utils.o `test -f 'src/aln_utils.cc' || echo './'`src/aln_utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/rxstacks-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/rxstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo './'`src/sql_utilities.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/rxstacks-MetaPopInfo.o `test -f 'src/MetaPopInfo.cc' || echo './'`src/MetaPopInfo.cc
g++ -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -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-aln_utils.o src/rxstacks-utils.o src/rxstacks-input.o src/rxstacks-sql_utilities.o src/rxstacks-MetaPopInfo.o -lz -lgomp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/hstacks-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/hstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo './'`src/sql_utilities.cc
g++ -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -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 src/hstacks-sql_utilities.o -lz -lgomp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_radtags-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_radtags-renz.o `test -f 'src/renz.cc' || echo './'`src/renz.cc
g++ -fopenmp -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -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 src/process_radtags-renz.o ./htslib/libhts.a -lz -lgomp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_shortreads-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
g++ -fopenmp -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -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 ./htslib/libhts.a -lz -lgomp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/kmer_filter-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
g++ -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/clone_filter-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
g++ -fopenmp -I./htslib/htslib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -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 ./htslib/libhts.a -lz -lgomp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotypes-aln_utils.o `test -f 'src/aln_utils.cc' || echo './'`src/aln_utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotypes-genotype_dictionaries.o `test -f 'src/genotype_dictionaries.cc' || echo './'`src/genotype_dictionaries.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotypes-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotypes-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo './'`src/sql_utilities.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotypes-renz.o `test -f 'src/renz.cc' || echo './'`src/renz.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotypes-MetaPopInfo.o `test -f 'src/MetaPopInfo.cc' || echo './'`src/MetaPopInfo.cc
g++ -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -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-aln_utils.o src/genotypes-genotype_dictionaries.o src/genotypes-input.o src/genotypes-sql_utilities.o src/genotypes-renz.o src/genotypes-MetaPopInfo.o -lz -lgomp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-aln_utils.o `test -f 'src/aln_utils.cc' || echo './'`src/aln_utils.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-genotype_dictionaries.o `test -f 'src/genotype_dictionaries.cc' || echo './'`src/genotype_dictionaries.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo './'`src/sql_utilities.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-renz.o `test -f 'src/renz.cc' || echo './'`src/renz.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-export_formats.o `test -f 'src/export_formats.cc' || echo './'`src/export_formats.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-MetaPopInfo.o `test -f 'src/MetaPopInfo.cc' || echo './'`src/MetaPopInfo.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations-Vcf.o `test -f 'src/Vcf.cc' || echo './'`src/Vcf.cc
g++ -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -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-aln_utils.o src/populations-genotype_dictionaries.o src/populations-input.o src/populations-sql_utilities.o src/populations-renz.o src/populations-export_formats.o src/populations-MetaPopInfo.o src/populations-Vcf.o -lz -lgomp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/phasedstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo './'`src/sql_utilities.cc
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/phasedstacks-catalog_utils.o `test -f 'src/catalog_utils.cc' || echo './'`src/catalog_utils.cc
g++ -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o phasedstacks src/phasedstacks-phasedstacks.o src/phasedstacks-locus.o src/phasedstacks-input.o src/phasedstacks-sql_utilities.o src/phasedstacks-log_utils.o src/phasedstacks-utils.o src/phasedstacks-catalog_utils.o -lz -lgomp
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
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 --with python2
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>>'
Making install in htslib
make[2]: Entering directory '/<<PKGBUILDDIR>>/htslib'
make[2]: Nothing to be done for 'install'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/htslib'
Making install in .
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: 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 scripts/integrate_alignments.py '/<<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[4]: Entering directory '/<<PKGBUILDDIR>>'
sed -e 's,_VERSION_,1.44,' -e 's,_BINDIR_,/usr/lib/stacks/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_,1.44,' -e 's,_BINDIR_,/usr/lib/stacks/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_,1.44,' -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_,1.44,' -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_,1.44,' -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_,1.44,' /<<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_,1.44,' /<<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_,1.44,' -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_,1.44,' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' -e 's,_BINDIR_,/usr/lib/stacks/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/lib/stacks/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 1.44 > /<<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[4]: Leaving directory '/<<PKGBUILDDIR>>'
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 $f .pl`" ; \
done
# Skip this bit if not building stacks-web
# Note - directory perms will be set in postinst
dh_installdirs -pstacks-web /var/lib/stacks/export
dh_installdirs: No packages to build.
if [ -e debian/stacks-web/usr/share/stacks/php ] ; then \
rmdir debian/stacks-web/usr/share/stacks/php/export ; \
ln -s /var/lib/stacks/export \
debian/stacks-web/usr/share/stacks/php/export ; \
fi
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_python2 -a
W: dh_python2:479: Please add dh-python package to Build-Depends
dh_perl -a
debian/rules override_dh_link
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_link
mkdir -p debian/stacks/usr/lib/debian-med/bin
cd debian/stacks/usr/lib/debian-med/bin && \
for f in `ls /<<PKGBUILDDIR>>/debian/stacks/usr/lib/stacks/bin` ; do \
ln -s ../../stacks/bin/$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/populations 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/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/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/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/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/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/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/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/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/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/genotypes 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/populations debian/stacks/usr/lib/stacks/bin/sstacks debian/stacks/usr/lib/stacks/bin/estacks debian/stacks/usr/lib/stacks/bin/ustacks debian/stacks/usr/lib/stacks/bin/process_radtags debian/stacks/usr/lib/stacks/bin/rxstacks debian/stacks/usr/lib/stacks/bin/clone_filter debian/stacks/usr/lib/stacks/bin/kmer_filter debian/stacks/usr/lib/stacks/bin/process_shortreads debian/stacks/usr/lib/stacks/bin/phasedstacks debian/stacks/usr/lib/stacks/bin/cstacks debian/stacks/usr/lib/stacks/bin/pstacks debian/stacks/usr/lib/stacks/bin/hstacks debian/stacks/usr/lib/stacks/bin/genotypes 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_1.44-1_armhf.deb'.
dpkg-deb: building package 'stacks' in '../stacks_1.44-1_armhf.deb'.
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../stacks_1.44-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build stacks-1.44
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2016-10-29T19:02:23Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
stacks_1.44-1_armhf.changes:
----------------------------
Format: 1.8
Date: Sat, 22 Oct 2016 21:04:24 +0200
Source: stacks
Binary: stacks stacks-web
Architecture: armhf
Version: 1.44-1
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 (1.44-1) unstable; urgency=medium
.
[ Kevin Murray ]
* Fix script executable paths to reflect debian install directory
.
[ Andreas Tille ]
* New upstream version
* stacks-web Depends: default-mysql-server | mysql-server
Checksums-Sha1:
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Checksums-Sha256:
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Files:
7eb553d497671e3fe84e4fab5516c379 16477694 debug extra stacks-dbgsym_1.44-1_armhf.deb
0c262d233caacb5218744f9a262d190d 825446 science optional stacks_1.44-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
stacks-dbgsym_1.44-1_armhf.deb
------------------------------
new debian package, version 2.0.
size 16477694 bytes: control archive=1193 bytes.
943 bytes, 13 lines control
1484 bytes, 14 lines md5sums
Package: stacks-dbgsym
Source: stacks
Version: 1.44-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 17039
Depends: stacks (= 1.44-1)
Section: debug
Priority: extra
Homepage: http://creskolab.uoregon.edu/stacks/
Description: Debug symbols for stacks
Auto-Built-Package: debug-symbols
Build-Ids: 00ae422edea47a919665bb6cdbf66a6c2568cca7 06f554678614b193b45f9912e6b6af82558246fd 10d60ac58425259512a267f987485100d3e7c2b8 21d6cc323358463fa7bb984e0b3e2e658ac8f084 3e636d5fad3534e3bc18cccbcd2255a7747b1ee2 96dff97f894a6798ec90ec39829eaab06401bf95 9dba1ed97b5cb10bc831fbe87b2c000e386e69c1 d2fe31b71ecc34ac8ea10de9e617d3cd86d4b616 d53801117c9a8dc6b86a6e9aaf610b2793f0fa6f da91fe4c62e841f861bdae977e7b15e9bb6fb38f ec8ceebb05f8b82c90b97d7f4872ec67085c8d32 f55e4174da40d6c248dd0a80a5430d50cf500462 f989ae1ceb16f2576bcde113524b3827738b1f91 faa9cdbd42b51c81da66abad4fff54d765272224
drwxr-xr-x root/root 0 2016-10-22 19:04 ./
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/lib/
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/lib/debug/.build-id/00/
-rw-r--r-- root/root 1573220 2016-10-22 19:04 ./usr/lib/debug/.build-id/00/ae422edea47a919665bb6cdbf66a6c2568cca7.debug
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/lib/debug/.build-id/06/
-rw-r--r-- root/root 771948 2016-10-22 19:04 ./usr/lib/debug/.build-id/06/f554678614b193b45f9912e6b6af82558246fd.debug
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/lib/debug/.build-id/10/
-rw-r--r-- root/root 1439380 2016-10-22 19:04 ./usr/lib/debug/.build-id/10/d60ac58425259512a267f987485100d3e7c2b8.debug
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/lib/debug/.build-id/21/
-rw-r--r-- root/root 600872 2016-10-22 19:04 ./usr/lib/debug/.build-id/21/d6cc323358463fa7bb984e0b3e2e658ac8f084.debug
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/lib/debug/.build-id/3e/
-rw-r--r-- root/root 882664 2016-10-22 19:04 ./usr/lib/debug/.build-id/3e/636d5fad3534e3bc18cccbcd2255a7747b1ee2.debug
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/lib/debug/.build-id/96/
-rw-r--r-- root/root 1297052 2016-10-22 19:04 ./usr/lib/debug/.build-id/96/dff97f894a6798ec90ec39829eaab06401bf95.debug
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/lib/debug/.build-id/9d/
-rw-r--r-- root/root 1048192 2016-10-22 19:04 ./usr/lib/debug/.build-id/9d/ba1ed97b5cb10bc831fbe87b2c000e386e69c1.debug
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/lib/debug/.build-id/d2/
-rw-r--r-- root/root 713472 2016-10-22 19:04 ./usr/lib/debug/.build-id/d2/fe31b71ecc34ac8ea10de9e617d3cd86d4b616.debug
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/lib/debug/.build-id/d5/
-rw-r--r-- root/root 1103652 2016-10-22 19:04 ./usr/lib/debug/.build-id/d5/3801117c9a8dc6b86a6e9aaf610b2793f0fa6f.debug
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/lib/debug/.build-id/da/
-rw-r--r-- root/root 1182816 2016-10-22 19:04 ./usr/lib/debug/.build-id/da/91fe4c62e841f861bdae977e7b15e9bb6fb38f.debug
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/lib/debug/.build-id/ec/
-rw-r--r-- root/root 1162408 2016-10-22 19:04 ./usr/lib/debug/.build-id/ec/8ceebb05f8b82c90b97d7f4872ec67085c8d32.debug
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/lib/debug/.build-id/f5/
-rw-r--r-- root/root 1464368 2016-10-22 19:04 ./usr/lib/debug/.build-id/f5/5e4174da40d6c248dd0a80a5430d50cf500462.debug
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/lib/debug/.build-id/f9/
-rw-r--r-- root/root 2602220 2016-10-22 19:04 ./usr/lib/debug/.build-id/f9/89ae1ceb16f2576bcde113524b3827738b1f91.debug
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/lib/debug/.build-id/fa/
-rw-r--r-- root/root 1575248 2016-10-22 19:04 ./usr/lib/debug/.build-id/fa/a9cdbd42b51c81da66abad4fff54d765272224.debug
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/share/
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/share/doc/stacks-dbgsym -> stacks
stacks_1.44-1_armhf.deb
-----------------------
new debian package, version 2.0.
size 825446 bytes: control archive=1869 bytes.
924 bytes, 18 lines control
1999 bytes, 30 lines md5sums
171 bytes, 9 lines * postinst #!/bin/sh
249 bytes, 14 lines * prerm #!/bin/sh
Package: stacks
Version: 1.44-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4761
Depends: libc6 (>= 2.7), libgcc1 (>= 1:3.5), libgomp1 (>= 4.9), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.6), python:any (>= 2.6.6-7~), 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 2016-10-22 19:04 ./
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/bin/
-rwxr-xr-x root/root 771 2016-10-22 19:04 ./usr/bin/stacks
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/lib/
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/clone_filter -> ../../stacks/bin/clone_filter
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/cstacks -> ../../stacks/bin/cstacks
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/denovo_map -> ../../stacks/bin/denovo_map
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/denovo_map.pl -> ../../stacks/bin/denovo_map.pl
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/estacks -> ../../stacks/bin/estacks
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/exec_velvet -> ../../stacks/bin/exec_velvet
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/exec_velvet.pl -> ../../stacks/bin/exec_velvet.pl
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/export_sql -> ../../stacks/bin/export_sql
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/export_sql.pl -> ../../stacks/bin/export_sql.pl
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/genotypes -> ../../stacks/bin/genotypes
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/hstacks -> ../../stacks/bin/hstacks
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/index_radtags -> ../../stacks/bin/index_radtags
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/index_radtags.pl -> ../../stacks/bin/index_radtags.pl
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/integrate_alignments.py -> ../../stacks/bin/integrate_alignments.py
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/kmer_filter -> ../../stacks/bin/kmer_filter
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/load_radtags -> ../../stacks/bin/load_radtags
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/load_radtags.pl -> ../../stacks/bin/load_radtags.pl
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/load_sequences -> ../../stacks/bin/load_sequences
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/load_sequences.pl -> ../../stacks/bin/load_sequences.pl
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/phasedstacks -> ../../stacks/bin/phasedstacks
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/populations -> ../../stacks/bin/populations
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/process_radtags -> ../../stacks/bin/process_radtags
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/process_shortreads -> ../../stacks/bin/process_shortreads
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/pstacks -> ../../stacks/bin/pstacks
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/ref_map -> ../../stacks/bin/ref_map
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/ref_map.pl -> ../../stacks/bin/ref_map.pl
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/rxstacks -> ../../stacks/bin/rxstacks
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/sort_read_pairs -> ../../stacks/bin/sort_read_pairs
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/sort_read_pairs.pl -> ../../stacks/bin/sort_read_pairs.pl
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/sstacks -> ../../stacks/bin/sstacks
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/stacks_export_notify -> ../../stacks/bin/stacks_export_notify
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/stacks_export_notify.pl -> ../../stacks/bin/stacks_export_notify.pl
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/debian-med/bin/ustacks -> ../../stacks/bin/ustacks
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/lib/stacks/
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/lib/stacks/bin/
-rwxr-xr-x root/root 640868 2016-10-22 19:04 ./usr/lib/stacks/bin/clone_filter
-rwxr-xr-x root/root 235316 2016-10-22 19:04 ./usr/lib/stacks/bin/cstacks
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/stacks/bin/denovo_map -> denovo_map.pl
-rwxr-xr-x root/root 33716 2016-10-22 19:04 ./usr/lib/stacks/bin/denovo_map.pl
-rwxr-xr-x root/root 108272 2016-10-22 19:04 ./usr/lib/stacks/bin/estacks
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/stacks/bin/exec_velvet -> exec_velvet.pl
-rwxr-xr-x root/root 8919 2016-10-22 19:04 ./usr/lib/stacks/bin/exec_velvet.pl
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/stacks/bin/export_sql -> export_sql.pl
-rwxr-xr-x root/root 31818 2016-10-22 19:04 ./usr/lib/stacks/bin/export_sql.pl
-rwxr-xr-x root/root 276844 2016-10-22 19:04 ./usr/lib/stacks/bin/genotypes
-rwxr-xr-x root/root 173724 2016-10-22 19:04 ./usr/lib/stacks/bin/hstacks
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/stacks/bin/index_radtags -> index_radtags.pl
-rwxr-xr-x root/root 20389 2016-10-22 19:04 ./usr/lib/stacks/bin/index_radtags.pl
-rwxr-xr-x root/root 10799 2016-10-22 19:04 ./usr/lib/stacks/bin/integrate_alignments.py
-rwxr-xr-x root/root 219016 2016-10-22 19:04 ./usr/lib/stacks/bin/kmer_filter
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/stacks/bin/load_radtags -> load_radtags.pl
-rwxr-xr-x root/root 15091 2016-10-22 19:04 ./usr/lib/stacks/bin/load_radtags.pl
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/stacks/bin/load_sequences -> load_sequences.pl
-rwxr-xr-x root/root 6245 2016-10-22 19:04 ./usr/lib/stacks/bin/load_sequences.pl
-rwxr-xr-x root/root 116520 2016-10-22 19:04 ./usr/lib/stacks/bin/phasedstacks
-rwxr-xr-x root/root 531388 2016-10-22 19:04 ./usr/lib/stacks/bin/populations
-rwxr-xr-x root/root 543332 2016-10-22 19:04 ./usr/lib/stacks/bin/process_radtags
-rwxr-xr-x root/root 596144 2016-10-22 19:04 ./usr/lib/stacks/bin/process_shortreads
-rwxr-xr-x root/root 456540 2016-10-22 19:04 ./usr/lib/stacks/bin/pstacks
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/stacks/bin/ref_map -> ref_map.pl
-rwxr-xr-x root/root 31285 2016-10-22 19:04 ./usr/lib/stacks/bin/ref_map.pl
-rwxr-xr-x root/root 182128 2016-10-22 19:04 ./usr/lib/stacks/bin/rxstacks
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/stacks/bin/sort_read_pairs -> sort_read_pairs.pl
-rwxr-xr-x root/root 14915 2016-10-22 19:04 ./usr/lib/stacks/bin/sort_read_pairs.pl
-rwxr-xr-x root/root 239336 2016-10-22 19:04 ./usr/lib/stacks/bin/sstacks
lrwxrwxrwx root/root 0 2016-10-22 19:04 ./usr/lib/stacks/bin/stacks_export_notify -> stacks_export_notify.pl
-rwxr-xr-x root/root 6454 2016-10-22 19:04 ./usr/lib/stacks/bin/stacks_export_notify.pl
-rwxr-xr-x root/root 276484 2016-10-22 19:04 ./usr/lib/stacks/bin/ustacks
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/share/
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/share/doc/stacks/
-rw-r--r-- root/root 1451 2016-10-22 19:04 ./usr/share/doc/stacks/README.Debian
-rw-r--r-- root/root 984 2016-10-22 19:04 ./usr/share/doc/stacks/changelog.Debian.gz
-rw-r--r-- root/root 22990 2016-10-16 23:25 ./usr/share/doc/stacks/changelog.gz
-rw-r--r-- root/root 1335 2016-10-22 19:04 ./usr/share/doc/stacks/copyright
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/share/python/
drwxr-xr-x root/root 0 2016-10-22 19:04 ./usr/share/python/runtime.d/
-rwxr-xr-x root/root 122 2016-10-22 19:04 ./usr/share/python/runtime.d/stacks.rtupdate
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 250520
Build-Time: 2996
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 311
Job: stacks_1.44-1
Machine Architecture: armhf
Package: stacks
Package-Time: 3356
Source-Version: 1.44-1
Space: 250520
Status: successful
Version: 1.44-1
--------------------------------------------------------------------------------
Finished at 2016-10-29T19:02:23Z
Build needed 00:55:56, 250520k disc space