[med-svn] [Git][med-team/fastqtl][master] 6 commits: pass cross tools to make

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / fastqtl


Commits:
36297498 by Andreas Tille at 2019-09-09T12:07:55Z
pass cross tools to make

- - - - -
d2c7fd26 by Andreas Tille at 2019-09-09T12:08:08Z
debhelper-compat 12

- - - - -
f5609344 by Andreas Tille at 2019-09-09T12:08:12Z
Standards-Version: 4.4.0

- - - - -
63aa10a6 by Andreas Tille at 2019-09-09T12:08:13Z
Trim trailing whitespace.

Fixes lintian: file-contains-trailing-whitespace
See https://lintian.debian.org/tags/file-contains-trailing-whitespace.html for more details.

- - - - -
24c1e90a by Andreas Tille at 2019-09-09T12:08:16Z
Remove obsolete fields Name, Contact from debian/upstream/metadata.
- - - - -
d0cfb623 by Andreas Tille at 2019-09-09T12:35:53Z
Upload to unstable

- - - - -


7 changed files:

- debian/changelog
- − debian/compat
- debian/control
- + debian/patches/cross.patch
- debian/patches/series
- debian/rules
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,20 @@
+fastqtl (2.184+dfsg-7) unstable; urgency=medium
+
+  * Team upload
+
+  [ Helmut Grohne ]
+  * Fix FTCBFS: (Closes: #939811)
+    + Let dh_auto_build pass cross tools to make.
+    + cross.patch: Fix Makefile dependencies.
+
+  [ Andreas Tille ]
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * Trim trailing whitespace.
+  * Remove obsolete fields Name, Contact from debian/upstream/metadata.
+
+ -- Andreas Tille <tille at debian.org>  Mon, 09 Sep 2019 14:08:17 +0200
+
 fastqtl (2.184+dfsg-6) unstable; urgency=medium
 
   * Team upload


=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11


=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Dylan Aïssi <bob.dybian at gmail.com>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                libboost-dev,
                libboost-iostreams-dev,
                libboost-program-options-dev,
@@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 11~),
                libblas-dev,
                libeigen3-dev,
                libhts-dev
-Standards-Version: 4.1.5
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/fastqtl
 Vcs-Git: https://salsa.debian.org/med-team/fastqtl.git
 Homepage: http://fastqtl.sourceforge.net/


=====================================
debian/patches/cross.patch
=====================================
@@ -0,0 +1,16 @@
+Author: Helmut Grohne <helmut at subdivi.de>
+Last-Update: Mon, 9 Sep 2019 06:18:33 +0200
+Description: pass cross tools to make
+Bug-Debian: https://bugs.debian.org/939811
+
+--- fastqtl-2.184+dfsg.orig/Makefile
++++ fastqtl-2.184+dfsg/Makefile
+@@ -90,7 +90,7 @@
+ $(LIB_TABX):
+ 	cd $(PATH_TABX) && make && cd ../..
+ 
+-$(FILE_BIN): $(FILE_O) $(LIB_TABX)
++$(FILE_BIN): $(FILE_O) $(if $(DYNAMIC_LINK),,$(LIB_TABX))
+ 	$(CXX) $(LDFLAG) $^ $(LIB) -o $@
+ 
+ obj/%.o: %.cpp $(FILE_H)


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 01_Makefile_dynamic_hardenings.patch
 02_Replace_libtabix_by_libhts.patch
 03_Reproducible_builds.patch
+cross.patch


=====================================
debian/rules
=====================================
@@ -11,7 +11,6 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 override_dh_auto_build:
 	mkdir -p $(CURDIR)/obj/
 	mkdir -p $(CURDIR)/bin/
-	$(MAKE) CXXFLAGS='$(CXXFLAGS)'
+	dh_auto_build -- CXXFLAGS='$(CXXFLAGS)'
 	cd $(CURDIR)/example/ && \
 		tar Jcvf examples.tar.xz * --sort=name --mode=go=rX,u+rw,a-s --owner=root --group=root --numeric-owner
-


=====================================
debian/upstream/metadata
=====================================
@@ -1,17 +1,16 @@
-Contact: Olivier Delaneau <olivier.delaneau at gmail.com>
-Name: FastQTL
 Reference:
-  - Author: Halit Ongen and Alfonso Buil and Andrew Anand Brown and Emmanouil T. Dermitzakis and and Olivier Delaneau
-    Title: "Fast and efficient QTL mapper for thousands of molecular phenotypes"
-    Journal: Bioinformatics
-    Year: 2015
-    DOI: 10.1093/bioinformatics/btv722
-    URL: https://bioinformatics.oxfordjournals.org/content/32/10/1479.full
-    eprint: https://bioinformatics.oxfordjournals.org/content/32/10/1479.full.pdf+html
+- Author: Halit Ongen and Alfonso Buil and Andrew Anand Brown and Emmanouil T. Dermitzakis
+    and and Olivier Delaneau
+  Title: "Fast and efficient QTL mapper for thousands of molecular phenotypes"
+  Journal: Bioinformatics
+  Year: 2015
+  DOI: 10.1093/bioinformatics/btv722
+  URL: https://bioinformatics.oxfordjournals.org/content/32/10/1479.full
+  eprint: https://bioinformatics.oxfordjournals.org/content/32/10/1479.full.pdf+html
 Registry:
-  - Name: SciCrunch
-    Entry: NA
-  - Name: OMICtools
-    Entry: OMICS_10934
-  - Name: bio.tools
-    Entry: NA
+- Name: SciCrunch
+  Entry: NA
+- Name: OMICtools
+  Entry: OMICS_10934
+- Name: bio.tools
+  Entry: NA



View it on GitLab: https://salsa.debian.org/med-team/fastqtl/compare/360336124ab3ea8dccef84edbdacfbbc994c5543...d0cfb6231b828ba2d74001d2c239d131382c5ba7

-- 
View it on GitLab: https://salsa.debian.org/med-team/fastqtl/compare/360336124ab3ea8dccef84edbdacfbbc994c5543...d0cfb6231b828ba2d74001d2c239d131382c5ba7
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