debian/changelog

@@ -2,4 +2,4 @@ phyx (0.99+ds-1) unstable; urgency=medium
 
   * Initial release (Closes: #855597)
 
- -- Afif Elghraoui <afif@debian.org>  Fri, 01 Jun 2018 11:30:27 +0200
+ -- Andreas Tille <tille@debian.org>  Sat, 08 Sep 2018 22:16:39 +0200

debian/control

 Source: phyx
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
-Uploaders: Afif Elghraoui <afif@debian.org>
+Uploaders: Afif Elghraoui <afif@debian.org>,
+           Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 11~),
@@ -10,7 +11,7 @@ Build-Depends: debhelper (>= 11~),
                libnlopt-dev,
                libatlas-cpp-0.6-dev,
                libarmadillo-dev
-Standards-Version: 4.1.4
+Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/phyx
 Vcs-Git: https://salsa.debian.org/med-team/phyx.git
 Homepage: https://github.com/FePhyFoFum/phyx

debian/patches/link_lnlopt.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Sat, 08 Sep 2018 22:16:39 +0200
+Description: Somehow nlopt library needs to be added
+
+--- a/src/Makefile.in
++++ b/src/Makefile.in
+@@ -317,7 +317,7 @@ all: pxmrca pxmrcacut pxmrcaname pxconsq
+ 
+ pxstrec: $(CPP_OBJS) $(RATE_OBJS) $(STREC_OBJ) #$(FORT_OBJS)
+ 	@echo 'building pxstrec'
+-	$(CXX) -o "pxstrec" $(OPT_FLAGS) $(STREC_OBJ) $(CPP_OBJS) $(RATE_OBJS) $(CPP_LIBS) #$(FORT_OBJS) -lgfortran
++	$(CXX) -o "pxstrec" $(OPT_FLAGS) $(STREC_OBJ) $(CPP_OBJS) $(RATE_OBJS) $(CPP_LIBS) -lnlopt_cxx -lnlopt #$(FORT_OBJS) -lgfortran
+ 
+ pxmrca: $(CPP_OBJS) $(MRCA_OBJ)
+ 	@echo 'building pxmrca'
+@@ -417,7 +417,7 @@ pxboot: $(CPP_OBJS) $(SEQSAMP_OBJ)
+ 
+ pxseqgen: $(CPP_OBJS) $(RATE_OBJS) $(SEQGEN_OBJ) $(FORT_OBJS)
+ 	@echo 'building pxseqgen'
+-	$(CXX) -o "pxseqgen" $(OPT_FLAGS) $(SEQGEN_OBJ) $(CPP_OBJS) $(RATE_OBJS) $(CPP_LIBS) #$(FORT_OBJS)  -lgfortran
++	$(CXX) -o "pxseqgen" $(OPT_FLAGS) $(SEQGEN_OBJ) $(CPP_OBJS) $(RATE_OBJS) $(CPP_LIBS) -lnlopt_cxx -lnlopt #$(FORT_OBJS)  -lgfortran
+ 
+ pxcat: $(CPP_OBJS) $(CONCAT_OBJ)
+ 	@echo 'building pxcat'
+@@ -433,7 +433,7 @@ pxvcf2fa: $(CPP_OBJS) $(VCF2FA_OBJ)
+ 
+ pxcontrates: $(CPP_OBJS) $(CONTRATES_OBJ) $(RATE_OBJS) $(FORT_OBJS)
+ 	@echo 'building pxcontrates'
+-	$(CXX) -o "pxcontrates" $(OPT_FLAGS) $(CONTRATES_OBJ) $(RATE_OBJS) $(CPP_OBJS) $(CPP_LIBS) #$(FORT_OBJS) -lgfortran
++	$(CXX) -o "pxcontrates" $(OPT_FLAGS) $(CONTRATES_OBJ) $(RATE_OBJS) $(CPP_OBJS) $(CPP_LIBS) -lnlopt_cxx -lnlopt #$(FORT_OBJS) -lgfortran
+ 
+ pxrecode: $(CPP_OBJS) $(SEQRECODE_OBJ)
+ 	@echo 'building pxrecode'

debian/patches/series

+link_lnlopt.patch

debian/rules

@@ -9,7 +9,9 @@ include /usr/share/dpkg/default.mk
 	dh $@ --sourcedirectory=src
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	cd src && python run_tests.py
+endif
 
 override_dh_auto_install:
 	mkdir -p $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin