[med-svn] [Git][med-team/bowtie][master] 5 commits: Add patch fixing FTBFS #906341

[Alexandre Mestiashvili]

Alexandre Mestiashvili pushed to branch master at Debian Med / bowtie


Commits:
9130118e by Alexandre Mestiashvili at 2018-09-05T11:50:09Z
Add patch fixing FTBFS #906341

- - - - -
856f986e by Alexandre Mestiashvili at 2018-09-05T13:27:36Z
Check for DEB_BUILD_OPTIONS and nocheck option

- - - - -
bfcc2330 by Alexandre Mestiashvili at 2018-09-05T14:31:45Z
Print DEB_BUILD_OPTIONS

Gbp-Dch: Ignore

- - - - -
64216a44 by Alexandre Mestiashvili at 2018-09-05T14:34:50Z
Bump policy to 4.2.1, update Uploader's email

- - - - -
5c093e5d by Alexandre Mestiashvili at 2018-09-05T14:36:59Z
Update changelog, prepare for release

Gbp-Dch: Ignore

- - - - -


5 changed files:

- debian/changelog
- debian/control
- + debian/patches/fix_isa_return.patch
- debian/patches/series
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,19 @@
+bowtie (1.2.2+dfsg-4) unstable; urgency=medium
+
+  [ Andreas Tille ]
+  * spelling
+  * Upload to unstable
+
+  [ Dylan Aïssi ]
+  * Update metadata: Add bio.tools ref
+
+  [ Alexandre Mestiashvili ]
+  * Add patch fixing FTBFS, thanks to ch4rr0 at github.com
+    Closes: #906341
+  * Check for DEB_BUILD_OPTIONS and nocheck
+
+ -- Alexandre Mestiashvili <mestia at debian.org>  Wed, 05 Sep 2018 14:34:56 +0000
+
 bowtie (1.2.2+dfsg-3) unstable; urgency=medium
 
   * Fix watch file to not detect beta versions


=====================================
debian/control
=====================================
@@ -4,7 +4,7 @@ Uploaders: Steffen Moeller <moeller at debian.org>,
            Andreas Tille <tille at debian.org>,
            Ognyan Kulev <ogi at debian.org>,
            Stephan Struckmann <stephan.struckmann at gmail.com>,
-           Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
+           Alexandre Mestiashvili <mestia at debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 11),
@@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 11),
                python,
                seqan-dev (>= 1.4),
                zlib1g-dev
-Standards-Version: 4.1.4
+Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/bowtie
 Vcs-Git: https://salsa.debian.org/med-team/bowtie.git
 Homepage: http://bowtie-bio.sourceforge.net/


=====================================
debian/patches/fix_isa_return.patch
=====================================
@@ -0,0 +1,15 @@
+Subject: Fix isa return type
+From: ch4rr0
+Comment:
+ see https://github.com/BenLangmead/bowtie/commit/58c6ac97b1938909881877ef83167f5eff0e8ab1
+--- bowtie.orig/ebwt.h
++++ bowtie/ebwt.h
+@@ -862,7 +862,7 @@
+ 	TIndexOffU*   ftab() const         { return _ftab; }
+ 	TIndexOffU*   eftab() const        { return _eftab; }
+ 	TIndexOffU*   offs() const         { return _offs; }
+-	uint32_t*   isa() const          { return _isa; } /* check */
++	TIndexOffU*   isa() const          { return _isa; } /* check */
+ 	TIndexOffU*   plen() const         { return _plen; }
+ 	TIndexOffU*   rstarts() const      { return _rstarts; }
+ 	uint8_t*    ebwt() const         { return _ebwt; }


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
+fix_isa_return.patch
 no_hash_style_both_for_mips.patch
 use-dpkg-buildflags.patch
 use_debian_seqan.patch


=====================================
debian/rules
=====================================
@@ -44,6 +44,10 @@ override_dh_auto_clean:
 	dh_auto_clean
 
 override_dh_auto_test:
+	# print DEB_BUILD_OPTIONS
+	$(info $$DEB_BUILD_OPTIONS is [${DEB_BUILD_OPTIONS}])
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	ln -s debian/tests
 	sh debian/tests/run-unit-test test_at_build_time
 	rm -f tests examples[0-9].out
+endif



View it on GitLab: https://salsa.debian.org/med-team/bowtie/compare/64ec87f2e7baba2a5c255abcd1eb32b6501847e8...5c093e5db47c129a0e9b1fbd6c8d6b97b6d827f7

-- 
View it on GitLab: https://salsa.debian.org/med-team/bowtie/compare/64ec87f2e7baba2a5c255abcd1eb32b6501847e8...5c093e5db47c129a0e9b1fbd6c8d6b97b6d827f7
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