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 <[email protected]> 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 <[email protected]> Source: https://www.bioinf.uni-leipzig.de/Software/proteinortho/ Files-Excluded: */BUILD - */lapack-*.tar.gz + */lapack-*.tar.gz Files: * Copyright: 2009-2014 Marcus Lechner <[email protected]> ===================================== 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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