debian/changelog

+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@debian.org>  Tue, 30 Oct 2018 11:29:39 +0100
+
 rnahybrid (2.1.2-4) unstable; urgency=medium
 
   * Exclude armel from Architectures

debian/compat

-10
+11

debian/control

@@ -4,11 +4,11 @@ Uploaders: Charles Plessy <plessy@debian.org>,
            Andreas Tille <tille@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

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