[med-svn] [Git][med-team/proteinortho][master] 3 commits: Fix baseline violation

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / proteinortho


Commits:
f7423924 by Andreas Tille at 2020-11-15T20:15:02+01:00
Fix baseline violation

- - - - -
5ea52480 by Andreas Tille at 2020-11-15T20:15:39+01:00
routine-update: No tab in license text

- - - - -
ff006171 by Andreas Tille at 2020-11-15T20:48:36+01:00
Lintian override for script-with-language-extension

- - - - -


5 changed files:

- debian/changelog
- debian/copyright
- + debian/lintian-overrides
- + debian/patches/baseline.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+proteinortho (6.0.24+dfsg-2) unstable; urgency=medium
+
+  * Fix baseline violation
+    Closes: #974850
+  * No tab in license text (routine-update)
+  * Lintian override for script-with-language-extension
+
+ -- Andreas Tille <tille at debian.org>  Sun, 15 Nov 2020 20:15:41 +0100
+
 proteinortho (6.0.24+dfsg-1) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/copyright
=====================================
@@ -3,7 +3,7 @@ Upstream-Name: Proteinortho
 Upstream-Contact: Marcus Lechner <lechner at staff.uni-marburg.de>
 Source: https://www.bioinf.uni-leipzig.de/Software/proteinortho/
 Files-Excluded: */BUILD
- 		*/lapack-*.tar.gz
+                 */lapack-*.tar.gz
 
 Files: *
 Copyright: 2009-2014 Marcus Lechner <lechner at staff.uni-marburg.de>


=====================================
debian/lintian-overrides
=====================================
@@ -0,0 +1,3 @@
+# see https://lists.debian.org/debian-med/2018/06/msg00043.html
+proteinortho: script-with-language-extension usr/bin/proteinortho*.pl
+proteinortho: script-with-language-extension usr/bin/proteinortho_ffadj_mcs.py


=====================================
debian/patches/baseline.patch
=====================================
@@ -0,0 +1,32 @@
+Description: Fix baseline violation
+Bug-Debian: https://bugs.debian.org/974850
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sun, 15 Nov 2020 20:11:22 +0100
+
+--- a/Makefile
++++ b/Makefile
+@@ -158,10 +158,10 @@ ifeq ($(USELAPACK),TRUE)
+ ifeq ($(USEPRECOMPILEDLAPACK),TRUE)
+ ifeq ($(STATIC),TRUE)
+ 	@echo "[ 20%] Building **proteinortho_clustering** with LAPACK (static linking)";
+-	@echo "$(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -march=native -mtune=native -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath" && $(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -march=native -mtune=native -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] ) || ( \
++	@echo "$(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath" && $(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] ) || ( \
+ 		echo "......$(ORANGE)dynamic linking failed too, now I try dynamic linking without -WL,-whole-archive... (this should now work for OSX).$(NC)"; \
+-			echo "$(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -march=native -mtune=native -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread" && $(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -march=native -mtune=native -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
+-			echo "......$(ORANGE)-march=native -mtune=native failed, I try without them again.$(NC)"; \
++			echo "$(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread" && $(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
++			echo "......$(ORANGE) failed, I try without them again.$(NC)"; \
+ 			echo "$(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath" && $(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] ) || ( \
+ 				echo "......$(ORANGE)static linking failed, now I try dynamic linking.$(NC)"; \
+ 				echo "$(CXX) -O2  $(CPPFLAGS) $(CXXFLAGS) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive" && $(CXX) -O2  $(CPPFLAGS) $(CXXFLAGS) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
+@@ -178,8 +178,8 @@ ifeq ($(STATIC),TRUE)
+ 							echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran && echo "......OK dynamic linking was successful for proteinortho_clustering!" || ( echo "" ) ; ) ) ) ) ) )
+ else
+ 	@echo "[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking)";
+-	@echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -march=native -mtune=native -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -march=native -mtune=native -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
+-		echo "......$(ORANGE)-march=native -mtune=native failed, I try without them again.$(NC)"; \
++	@echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
++		echo "......$(ORANGE) failed, I try without them again.$(NC)"; \
+ 		echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
+ 			echo "......$(ORANGE)dynamic linking failed too, now I try dynamic linking without -WL,-whole-archive (this should now work for OSX).$(NC)"; \
+ 			echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \


=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
 deb_diamond
+baseline.patch



View it on GitLab: https://salsa.debian.org/med-team/proteinortho/-/compare/af2d491e9b7426efc8a261bc270d27896b821bef...ff006171fa68e37ec21dfef0cd1c5b9e53bc93f9

-- 
View it on GitLab: https://salsa.debian.org/med-team/proteinortho/-/compare/af2d491e9b7426efc8a261bc270d27896b821bef...ff006171fa68e37ec21dfef0cd1c5b9e53bc93f9
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