[med-svn] [Git][med-team/transdecoder][master] 9 commits: Point Vcs fields to salsa.debian.org

Tue Oct 30 13:42:54 GMT 2018

Andreas Tille pushed to branch master at Debian Med / transdecoder


Commits:
43407e09 by Andreas Tille at 2018-10-30T11:54:04Z
Point Vcs fields to salsa.debian.org

- - - - -
c2f12ce3 by Andreas Tille at 2018-10-30T11:54:04Z
Standards-Version: 4.2.1

- - - - -
bc8205e3 by Andreas Tille at 2018-10-30T11:54:48Z
Respect DEB_BUILD_OPTIONS in override_dh_auto_test target

- - - - -
1cbad50d by Andreas Tille at 2018-10-30T11:54:49Z
Remove trailing whitespace in debian/changelog

- - - - -
2c573049 by Andreas Tille at 2018-10-30T11:54:49Z
Remove trailing whitespace in debian/copyright

- - - - -
e355f30b by Andreas Tille at 2018-10-30T13:23:25Z
Fix Perl path

- - - - -
e82ac8a8 by Andreas Tille at 2018-10-30T13:24:09Z
Remove unused patch

- - - - -
3eeef9ba by Andreas Tille at 2018-10-30T13:25:10Z
May be broken Perl pathes are also in docs - fix path after doc is installed

- - - - -
079ee4b0 by Andreas Tille at 2018-10-30T13:41:32Z
Upload to unstable

- - - - -


5 changed files:

- debian/changelog
- debian/control
- debian/copyright
- − debian/patches/fix-test
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+transdecoder (5.0.1-2) unstable; urgency=medium
+
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+  * Remove trailing whitespace in debian/changelog
+  * Remove trailing whitespace in debian/copyright
+  * Fix Perl path
+
+ -- Andreas Tille <tille at debian.org>  Tue, 30 Oct 2018 14:25:40 +0100
+
 transdecoder (5.0.1-1) unstable; urgency=medium
 
   * New upstream version (no need to repackage since binary files are now
@@ -82,4 +93,4 @@ transdecoder (2.0.1+dfsg-1) unstable; urgency=low
 
   * Initial release (Closes: #778300)
 
- -- Michael R. Crusoe <mcrusoe at msu.edu>  Fri, 13 Feb 2015 06:26:24 -0500 
+ -- Michael R. Crusoe <mcrusoe at msu.edu>  Fri, 13 Feb 2015 06:26:24 -0500


=====================================
debian/control
=====================================
@@ -6,9 +6,9 @@ Section: science
 Priority: optional
 Build-Depends: debhelper (>= 11~),
                liburi-perl
-Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/transdecoder.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/transdecoder.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/transdecoder
+Vcs-Git: https://salsa.debian.org/med-team/transdecoder.git
 Homepage: https://transdecoder.github.io/
 
 Package: transdecoder


=====================================
debian/copyright
=====================================
@@ -20,9 +20,9 @@ License: BSD-3-clause
  .
  ·         Neither the name of the Broad Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.**
  .
- THIS SOFTWARE IS PROVIDED BY THE BROAD INSTITUTE  ''AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE BROAD INSTITUTE 
- BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES(INCLUDING, BUT NOT LIMITED TO, 
+ THIS SOFTWARE IS PROVIDED BY THE BROAD INSTITUTE  ''AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+ THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE BROAD INSTITUTE
+ BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES(INCLUDING, BUT NOT LIMITED TO,
  PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, 
+ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
  EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.


=====================================
debian/patches/fix-test deleted
=====================================
@@ -1,14 +0,0 @@
-Author: Michael R. Crusoe <michael.crusoe at gmail.com>
-Description: Fix tests
---- transdecoder.orig/Makefile
-+++ transdecoder/Makefile
-@@ -8,6 +8,7 @@
- 	cd ./sample_data && ./cleanme.pl
- 
- test:
--	cd ./sample_data/ && ./runMe.sh
--
-+	cd sample_data/cufflinks_example && ./runMe.sh
-+	cd sample_data/pasa_example && ./runMe.sh
-+	cd sample_data/simple_transcriptome_target && ./runMe.sh
- 


=====================================
debian/rules
=====================================
@@ -13,8 +13,10 @@ override_dh_auto_clean:
 override_dh_auto_build:
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	dh_auto_test
 	cd ./sample_data && for script in ./*/cleanme.pl; do $$($$script); done
+endif
 
 override_dh_install:
 	dh_install
@@ -39,3 +41,9 @@ override_dh_fixperms:
 override_dh_clean:
 	# generated man pages
 	dh_clean debian/TransDecoder.LongOrfs.1 debian/TransDecoder.Predict.1
+
+override_dh_installdocs:
+	dh_installdocs
+	for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
+	    sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \
+	done



View it on GitLab: https://salsa.debian.org/med-team/transdecoder/compare/786e4524851fc18eb6f44d685acac7e5564e822a...079ee4b070931c3eb4f8210c4cf1acb8f64debfc

-- 
View it on GitLab: https://salsa.debian.org/med-team/transdecoder/compare/786e4524851fc18eb6f44d685acac7e5564e822a...079ee4b070931c3eb4f8210c4cf1acb8f64debfc
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