[med-svn] [Git][med-team/primer3][master] 14 commits: Also skip autopkgtests that fail on big endian
Andreas Tille
gitlab at salsa.debian.org
Thu Jun 4 13:15:37 BST 2020
Andreas Tille pushed to branch master at Debian Med / primer3
Commits:
29f7bc9a by Andreas Tille at 2020-06-04T13:20:43+02:00
Also skip autopkgtests that fail on big endian
- - - - -
48950b35 by Andreas Tille at 2020-06-04T13:21:15+02:00
routine-update: Standards-Version: 4.5.0
- - - - -
ab0a470c by Andreas Tille at 2020-06-04T13:21:15+02:00
routine-update: debhelper-compat 13
- - - - -
53d50d54 by Andreas Tille at 2020-06-04T13:21:25+02:00
routine-update: Secure URI in copyright format
- - - - -
07d8f4f6 by Andreas Tille at 2020-06-04T13:41:23+02:00
routine-update: Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
- - - - -
47036b4e by Andreas Tille at 2020-06-04T13:41:23+02:00
routine-update: Remove trailing whitespace in debian/changelog
- - - - -
20407d13 by Andreas Tille at 2020-06-04T13:41:23+02:00
routine-update: Add salsa-ci file
- - - - -
3cc778f7 by Andreas Tille at 2020-06-04T13:41:23+02:00
routine-update: Rules-Requires-Root: no
- - - - -
b8412225 by Andreas Tille at 2020-06-04T13:41:27+02:00
Trim trailing whitespace.
Fixes: lintian: file-contains-trailing-whitespace
See-also: https://lintian.debian.org/tags/file-contains-trailing-whitespace.html
- - - - -
72519c2e by Andreas Tille at 2020-06-04T13:41:29+02:00
debian/copyright: use spaces rather than tabs to start continuation lines..
Fixes: lintian: tab-in-license-text
See-also: https://lintian.debian.org/tags/tab-in-license-text.html
- - - - -
965e2ae2 by Andreas Tille at 2020-06-04T13:41:39+02:00
Set fields Upstream-Name, Upstream-Contact in debian/copyright.
- - - - -
b3b78d82 by Andreas Tille at 2020-06-04T13:41:47+02:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
- - - - -
218a18cd by Andreas Tille at 2020-06-04T13:41:49+02:00
Remove obsolete fields Contact, Name from debian/upstream/metadata (already present in machine-readable debian/copyright).
- - - - -
6b6246ba by Andreas Tille at 2020-06-04T13:41:50+02:00
Fix day-of-week for changelog entry 0.9-0.2.
Fixes: lintian: debian-changelog-has-wrong-day-of-week
See-also: https://lintian.debian.org/tags/debian-changelog-has-wrong-day-of-week.html
- - - - -
8 changed files:
- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- debian/rules
- + debian/salsa-ci.yml
- debian/tests/run-unit-test
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,29 @@
+primer3 (2.4.0-3) UNRELEASED; urgency=medium
+
+ [ Gianfranco Costamagna ]
+ * Also skip autopkgtests that fail on big endian (see: 890993)
+ Closes: #962190
+
+ [ Andreas Tille ]
+ * Standards-Version: 4.5.0 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * Secure URI in copyright format (routine-update)
+ * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target (routine-
+ update)
+ * Remove trailing whitespace in debian/changelog (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * Trim trailing whitespace.
+ * debian/copyright: use spaces rather than tabs to start continuation lines.
+ * Set fields Upstream-Name, Upstream-Contact in debian/copyright.
+ * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
+ Repository-Browse.
+ * Remove obsolete fields Contact, Name from debian/upstream/metadata (already
+ present in machine-readable debian/copyright).
+ * Fix day-of-week for changelog entry 0.9-0.2.
+
+ -- Gianfranco Costamagna <locutusofborg at debian.org> Thu, 04 Jun 2020 11:47:04 +0200
+
primer3 (2.4.0-2) unstable; urgency=medium
[ Liubov Chuprikova ]
@@ -67,7 +93,7 @@ primer3 (2.3.7-2) unstable; urgency=medium
* debian/rules:
- added dh_clean to override_dh_auto_test section
- sed perl interpreter path
-
+
-- Canberk Koç <canberkkoc at gmail.com> Mon, 27 Jun 2016 04:28:31 +0300
primer3 (2.3.7-1) unstable; urgency=medium
@@ -96,7 +122,7 @@ primer3 (2.3.6-1) unstable; urgency=low
instead of /opt/primer3_config/
Closes: #702693
* Verified that new upstream
- Closes: #716151, #716213
+ Closes: #716151, #716213
* New executable: ntthal (including manpage)
* Removed *.xml variants of manpages to reduce redundancy
@@ -231,14 +257,13 @@ primer3 (1.0b-1) unstable; urgency=low
-- Charles Plessy <charles-debian-nospam at plessy.org> Thu, 28 Sep 2006 20:18:54 +0900
primer3 (0.9-0.2) unstable; urgency=low
-
+
* Contacted upstream author, change of section to non-free/optional.
- -- Steffen Moeller <moeller at pzr.uni-rostock.de> Wed, 1 Apr 2004 15:07:10 +0200
-
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Thu, 01 Apr 2004 15:07:10 +0200
+
primer3 (0.9-0.1) unstable; urgency=low
* Pre-Release.
-- Steffen Moeller <moeller at pzr.uni-rostock.de> Wed, 31 Mar 2004 15:07:10 +0200
-
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -5,11 +5,12 @@ Uploaders: Steffen Moeller <moeller at debian.org>,
Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~)
-Standards-Version: 4.1.4
+Build-Depends: debhelper-compat (= 13)
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/primer3
Vcs-Git: https://salsa.debian.org/med-team/primer3.git
Homepage: http://primer3.sourceforge.net
+Rules-Requires-Root: no
Package: primer3
Architecture: any
=====================================
debian/copyright
=====================================
@@ -1,5 +1,7 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Source: http://qa.debian.org/watch/sf.php/primer3/primer3-2.3.6.tar.gz
+Upstream-Name: Primer3
+Upstream-Contact: Steve Rozen (http://purl.com/STEVEROZEN/)
Files: *
Copyright: © 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008,2009,2010,2011,2012
@@ -16,7 +18,7 @@ Files: debian/*
Copyright: © 2004 Steffen Möller <moeller at debian.org>
© 2006-2008 Charles Plessy <plessy at debian.org>
© 2008 David Paleino <d.paleino at gmail.com>
- © 2012-2013 Andreas Tille <tille at debian.org>
+ © 2012-2013 Andreas Tille <tille at debian.org>
License: GPL-2+
License: GPL-2+
@@ -51,4 +53,3 @@ License: GPL-2+
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Comment: On Debian systems, the complete text of the GNU General
Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'.
-
=====================================
debian/rules
=====================================
@@ -20,6 +20,7 @@ override_dh_auto_build:
dh_auto_build -- 'CPP=$$(CXX)'
override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
ifneq ($(BUILDARCH),little)
cp -a test/p3test.pl test/p3test.pl~
cp -a test/Makefile test/Makefile~
@@ -36,7 +37,7 @@ ifneq ($(BUILDARCH),little)
mv test/Makefile~ test/Makefile
endif
dh clean --sourcedirectory=test
-
+endif
override_dh_installexamples:
dh_installexamples
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/tests/run-unit-test
=====================================
@@ -8,6 +8,13 @@ if [ "$AUTOPKGTEST_TMP" = "" ] ; then
AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
fi
+BUILDARCH=$(dpkg-architecture -q DEB_BUILD_ARCH_ENDIAN)
+
+P3CORE_FAILED_TESTS='primer_masker' \
+ 'primer_masker_formatted'
+
+FAILED_TESTS=testmasker
+
cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
cd $AUTOPKGTEST_TMP
@@ -19,6 +26,16 @@ ln -s /usr/bin/ntdpal ./src/ntdpal
ln -s /usr/bin/ntthal ./src/ntthal
ln -s /usr/bin/oligotm ./src/oligotm
+if [ $BUILDARCH = big ]; then
+ cp -a test/p3test.pl test/p3test.pl~
+ cp -a test/Makefile test/Makefile~
+ # exclude tests known to fail on big endian
+ # See README.source for further explanation.
+ for tst in $(P3CORE_FAILED_TESTS) ; do sed -i "/$${tst}/d" test/p3test.pl ; done
+ sed -i "0,/$(FAILED_TESTS)/s///" test/Makefile
+ sed -i "/$(FAILED_TESTS)/,/endif/d" test/Makefile
+fi
+
cd test/;
echo "testcmdline:"
@@ -36,4 +53,12 @@ echo; echo; echo 'TESTING THERMODYNAMIC ALIGNMENT CALCS'; echo; perl thal_test.p
echo "testtm:"
perl oligotm_test.pl ${TESTOPTS}
+cd ..
+
+if [ $BUILDARCH = big ]; then
+ # restore original test file
+ mv test/p3test.pl~ test/p3test.pl
+ mv test/Makefile~ test/Makefile
+fi
+
echo "PASS"
=====================================
debian/upstream/metadata
=====================================
@@ -1,5 +1,5 @@
-Contact: Steve Rozen (http://purl.com/STEVEROZEN/)
-Name: Primer3
+Bug-Database: https://github.com/primer3-org/primer3/issues
+Bug-Submit: https://github.com/primer3-org/primer3/issues/new
Reference:
Author: Steve Rozen and Helen J. Skaletsky
Year: 2000
@@ -25,6 +25,8 @@ Registry:
Entry: SCR_003139
- Name: conda:bioconda
Entry: primer3
+Repository: https://github.com/primer3-org/primer3.git
+Repository-Browse: https://github.com/primer3-org/primer3
Webservice:
- http://frodo.wi.mit.edu/primer3/
- http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi
View it on GitLab: https://salsa.debian.org/med-team/primer3/-/compare/ebf07a00547a15df534c7375f07eae146024ca87...6b6246ba43555a46ef66b5c9d8afb29633c09772
--
View it on GitLab: https://salsa.debian.org/med-team/primer3/-/compare/ebf07a00547a15df534c7375f07eae146024ca87...6b6246ba43555a46ef66b5c9d8afb29633c09772
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