debian/changelog

+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@debian.org>  Mon, 09 Sep 2019 14:08:17 +0200
+
 fastqtl (2.184+dfsg-6) unstable; urgency=medium
 
   * Team upload

debian/compat

-11

debian/control

@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Dylan Aïssi <bob.dybian@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

+Author: Helmut Grohne <helmut@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

 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

-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
+- 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