[med-svn] [Git][med-team/phyx][master] 5 commits: Fix linking

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / phyx


Commits:
2171679e by Andreas Tille at 2018-09-08T20:20:49Z
Fix linking

- - - - -
db665cb4 by Andreas Tille at 2018-09-08T20:22:01Z
Respect DEB_BUILD_OPTIONS in override_dh_auto_test

- - - - -
61cf7af7 by Andreas Tille at 2018-09-08T20:22:33Z
Upload to unstable

- - - - -
33487a46 by Andreas Tille at 2018-09-08T20:26:11Z
Standards-Version: 4.2.1

- - - - -
09ddc840 by Andreas Tille at 2018-09-08T20:26:52Z
Add myself to Uploaders

- - - - -


5 changed files:

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


Changes:

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


=====================================
debian/control
=====================================
@@ -1,6 +1,7 @@
 Source: phyx
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Afif Elghraoui <afif at debian.org>
+Uploaders: Afif Elghraoui <afif at debian.org>,
+           Andreas Tille <tille at 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
=====================================
@@ -0,0 +1,33 @@
+Author: Andreas Tille <tille at 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
=====================================
@@ -0,0 +1 @@
+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



View it on GitLab: https://salsa.debian.org/med-team/phyx/compare/08d24ff6d2a69cc83c8237562f5834935c3ddfc4...09ddc84098b1894368f5cc12673bc21be001799a

-- 
View it on GitLab: https://salsa.debian.org/med-team/phyx/compare/08d24ff6d2a69cc83c8237562f5834935c3ddfc4...09ddc84098b1894368f5cc12673bc21be001799a
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