[med-svn] [Git][med-team/rnahybrid][master] 9 commits: debhelper 11

Tue Oct 30 10:33:18 GMT 2018

Andreas Tille pushed to branch master at Debian Med / rnahybrid


Commits:
19a4d12e by Andreas Tille at 2018-10-30T09:35:59Z
debhelper 11

- - - - -
7a7fcf30 by Andreas Tille at 2018-10-30T09:36:01Z
Point Vcs fields to salsa.debian.org

- - - - -
dfc52fb8 by Andreas Tille at 2018-10-30T09:36:01Z
Standards-Version: 4.2.1

- - - - -
e5d66511 by Andreas Tille at 2018-10-30T09:36:02Z
Secure URI in copyright format

- - - - -
7bf0e221 by Andreas Tille at 2018-10-30T09:38:26Z
Respect DEB_BUILD_OPTIONS in override_dh_auto_test target

- - - - -
c90af2c6 by Andreas Tille at 2018-10-30T09:38:26Z
Remove trailing whitespace in debian/changelog

- - - - -
f23930dd by Andreas Tille at 2018-10-30T09:38:26Z
Remove trailing whitespace in debian/copyright

- - - - -
e155c1cc by Andreas Tille at 2018-10-30T10:29:31Z
Spelling

- - - - -
6a2870d3 by Andreas Tille at 2018-10-30T10:32:44Z
Upload to unstable

- - - - -


6 changed files:

- debian/changelog
- debian/compat
- debian/control
- debian/copyright
- debian/patches/fix_loop_index.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+rnahybrid (2.1.2-5) unstable; urgency=medium
+
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+  * Secure URI in copyright format
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+  * Remove trailing whitespace in debian/changelog
+  * Remove trailing whitespace in debian/copyright
+
+ -- Andreas Tille <tille at debian.org>  Tue, 30 Oct 2018 11:29:39 +0100
+
 rnahybrid (2.1.2-4) unstable; urgency=medium
 
   * Exclude armel from Architectures
@@ -46,7 +58,7 @@ rnahybrid (2.1.2-1) unstable; urgency=medium
 rnahybrid (2.1.1-2) unstable; urgency=low
 
   * debian/upstream: Make author field BibTeX compliant
-  * debian/control: 
+  * debian/control:
      - cme fix dpkg-control
      - use anonscm in VCS fields
   * debian/patches/gcc-4.8.patch: Fix build error with gcc-4.8 by adding


=====================================
debian/compat
=====================================
@@ -1 +1 @@
-10
+11


=====================================
debian/control
=====================================
@@ -4,11 +4,11 @@ Uploaders: Charles Plessy <plessy at debian.org>,
            Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                libg2-dev
-Standards-Version: 4.1.2
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/rnahybrid.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/rnahybrid.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/rnahybrid
+Vcs-Git: https://salsa.debian.org/med-team/rnahybrid.git
 Homepage: http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/submission.html
 
 Package: rnahybrid


=====================================
debian/copyright
=====================================
@@ -1,5 +1,5 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: RNAhybrid 
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: RNAhybrid
 Upstream-Contact: Marc Rehmsmeier <marc at techfak.uni-bielefeld.de>
                   Peter Steffen <psteffen at techfak.uni-bielefeld.de>
                   Matthias Hoechsmann <mhoechsm at techfak.uni-bielefeld.de>


=====================================
debian/patches/fix_loop_index.patch
=====================================
@@ -8,7 +8,7 @@ Description: Fix issues that are becoming visible on arm but might be
  energy.c:539:53: note: within this loop
    for(i=0;i<ALPHASIZE;i++) for(j=0;j<ALPHASIZE;j++) for(k=0;k<=ALPHASIZE;k++) dr_dangle_dg_ar[i][j][k] = 0;
  .
- Perhaps that that k<= in the k loop should be < like in the i and j loops so it doesn't go beyond the end of the array.
+ Perhaps that k<= in the k loop should be < like in the i and j loops so it doesn't go beyond the end of the array.
  .
  ALPHASIZE is 6, so the k loop would try go one too far.  Every array allocated with ALPHASIZE certainly don't add one anywhere, so any look going from 0 to ALPHASIZE must use < not <= so there are two places in the file that are wrong.
 


=====================================
debian/rules
=====================================
@@ -13,6 +13,7 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 	dh $@
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	src/RNAhybrid -s 3utr_worm -t examples/cel-hbl-1.fasta -q examples/cel-let-7.fasta
 	src/RNAcalibrate -d examples/3UTR_worm.freq -k 50 -l 50,30 -q examples/cel-let-7.fasta
 	src/RNAhybrid -d 1.9,0.28 -t examples/cel-hbl-1.fasta -q examples/cel-let-7.fasta
@@ -20,3 +21,4 @@ override_dh_auto_test:
 	src/RNAcalibrate -f 2,7 -d examples/3UTR_worm.freq -k 50 -l 50,30 -q examples/cel-let-7.fasta
 	src/RNAhybrid -s 3utr_worm -t examples/cbr-hbl-1.fasta -q examples/cel-let-7.fasta
 	-src/RNAeffective -k 30 -s -t examples/hbl-1.fasta -q examples/cel-let-7.fasta
+endif



View it on GitLab: https://salsa.debian.org/med-team/rnahybrid/compare/d7ce6c32eb76f093fff9125d40ceb48c7c5d2e16...6a2870d358b2b380f8b20106423eb59f1cbf4bfa

-- 
View it on GitLab: https://salsa.debian.org/med-team/rnahybrid/compare/d7ce6c32eb76f093fff9125d40ceb48c7c5d2e16...6a2870d358b2b380f8b20106423eb59f1cbf4bfa
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