[med-svn] [Git][med-team/proteinortho][master] 5 commits: New upstream version 6.0.24+dfsg
Nilesh Patra
gitlab at salsa.debian.org
Tue Oct 20 20:41:47 BST 2020
Nilesh Patra pushed to branch master at Debian Med / proteinortho
Commits:
3c35c1d7 by Nilesh Patra at 2020-10-21T01:02:27+05:30
New upstream version 6.0.24+dfsg
- - - - -
9986291d by Nilesh Patra at 2020-10-21T01:02:27+05:30
routine-update: New upstream version
- - - - -
e889399e by Nilesh Patra at 2020-10-21T01:02:29+05:30
Update upstream source from tag 'upstream/6.0.24+dfsg'
Update to upstream version '6.0.24+dfsg'
with Debian dir 526e63e794044617c57b90dee4b78384d76c57fd
- - - - -
d7481e05 by Nilesh Patra at 2020-10-21T01:06:08+05:30
Remove merged patches, refresh rest with new upstream release
- - - - -
af2d491e by Nilesh Patra at 2020-10-21T01:06:59+05:30
Update changelog
- - - - -
12 changed files:
- CHANGELOG
- CHANGEUID
- Makefile
- README.md
- debian/changelog
- debian/patches/deb_diamond
- − debian/patches/hardening
- debian/patches/series
- − debian/patches/spelling
- proteinortho6.pl
- src/proteinortho_clustering.cpp
- src/proteinortho_clustering_nolapack.cpp
Changes:
=====================================
CHANGELOG
=====================================
@@ -271,3 +271,5 @@
31. Aug (5110)
fixed a bug that the html version prints out ids encapsuled with parenthesis, while the proteinortho_grab_proteins.pl does not understand such queries.
refined the Makefile for proteinortho_clustering, now it additionally tests if the program is executable with the -test option
+ 12. Oct (5122)
+ enhancement of the Makefile (more verbose, added standard compiler flags, cleanup)
=====================================
CHANGEUID
=====================================
@@ -1 +1 @@
-5110
+5122
=====================================
Makefile
=====================================
@@ -148,71 +148,66 @@ echoENV:
$(BUILDDIR)/proteinortho_clustering: src/proteinortho_clustering.cpp
$(dir_guard)
-ifeq ($(MTUNEARCH),TRUE)
- @echo "using the -mtune and -march compiler options. WARNING: this can lead to runtime errors (code 33792) on some machines."
-else
- @echo "the compiler options -mtune and -march are disabled. If you want to add these use MTUNEARCH=TRUE."
-endif
@echo "[ 10%] Prepare proteinortho_clustering ..."
ifeq ($(DEPLOY),TRUE)
@echo "[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking, no mtune,march , for gitlab)";
- @$(CXX) -static $(CXXFLAGS) $(CXXFLAGS_PO) -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 "$(CXX) -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) -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 ] )
else
ifeq ($(USELAPACK),TRUE)
ifeq ($(USEPRECOMPILEDLAPACK),TRUE)
ifeq ($(STATIC),TRUE)
@echo "[ 20%] Building **proteinortho_clustering** with LAPACK (static linking)";
- @$(CXX) -static $(CXXFLAGS) $(CXXFLAGS_PO) -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 -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 "......$(ORANGE)dynamic linking failed too, now I try dynamic linking without -WL,-whole-archive... (this should now work for OSX).$(NC)"; \
- $(CXX) -static $(CXXFLAGS) $(CXXFLAGS_PO) -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 "$(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)"; \
- @$(CXX) -static $(CXXFLAGS) $(CXXFLAGS_PO) -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 "$(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)"; \
- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -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 "$(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)"; \
- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
+ 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!";) || ( \
echo "......$(ORANGE)dynamic linking failed (without -WL,-whole-archive) too too, now I try to openblas.$(NC)"; \
- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
+ echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
echo "......$(ORANGE)last linking failed too too too, now I try to recompile lapack (v.3.8.0) and then compile proteinortho_clustering with dynamic linking.$(NC)"; \
echo "......[ 33%] Extracting the LAPACK library"; \
- if [ ! -d src/lapack-3.8.0 ]; then cd src; tar -xzvf lapack-3.8.0.tar.gz > /dev/null 2>&1; cd ..; fi; \
+ if [ ! -d src/lapack-3.8.0 ]; then echo "cd src; tar -xzvf lapack-3.8.0.tar.gz"; cd src; tar -xzvf lapack-3.8.0.tar.gz > /dev/null 2>&1; cd ..; fi; \
echo "......[ 66%] Compiling the LAPACK library (using cmake + make)"; \
- if [ ! -f src/lapack-3.8.0/build/lib/liblapack.a ]; then mkdir src/lapack-3.8.0/build 2> /dev/null; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=$(CXX) > /dev/null; make all -j4 > /dev/null 2>&1; cd ../../.. ; fi; \
+ if [ ! -f src/lapack-3.8.0/build/lib/liblapack.a ]; then echo " mkdir src/lapack-3.8.0/build; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=$(CXX) > /dev/null; make all -j4 "; mkdir src/lapack-3.8.0/build 2> /dev/null; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=$(CXX) > /dev/null; make all -j4 > /dev/null 2>&1; cd ../../.. ; fi; \
echo "......[ 99%] Building **proteinortho_clustering** with LAPACK (dynamic linking)"; \
- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran && echo "......OK dynamic linking was successful for proteinortho_clustering!" || ( echo "" ) ; ) ) ) ) ) )
+ echo "$(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) $(LDLIBS) -lgfortran && echo "......OK dynamic linking was successful for proteinortho_clustering!" || ( echo "" ) ; ) ) ) ) ) )
else
@echo "[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking)";
- @$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -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 "$(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)"; \
- @$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -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 "$(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)"; \
- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
+ 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!";) || ( \
echo "......$(ORANGE)dynamic linking failed (without -WL,-whole-archive) too too, now I try to openblas.$(NC)"; \
- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
+ echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
echo "......$(ORANGE)last linking failed too too too, now I try to recompile lapack (v.3.8.0) and then compile proteinortho_clustering with dynamic linking.$(NC)"; \
echo "......[ 33%] Extracting the LAPACK library"; \
- if [ ! -d src/lapack-3.8.0 ]; then cd src; tar -xzvf lapack-3.8.0.tar.gz > /dev/null 2>&1; cd ..; fi; \
+ if [ ! -d src/lapack-3.8.0 ]; then echo "cd src; tar -xzvf lapack-3.8.0.tar.gz"; cd src; tar -xzvf lapack-3.8.0.tar.gz > /dev/null 2>&1; cd ..; fi; \
echo "......[ 66%] Compiling the LAPACK library (using cmake + make)"; \
- if [ ! -f src/lapack-3.8.0/build/lib/liblapack.a ]; then mkdir src/lapack-3.8.0/build 2> /dev/null; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=$(CXX) > /dev/null; make all -j4 > /dev/null 2>&1; cd ../../.. ; fi; \
+ if [ ! -f src/lapack-3.8.0/build/lib/liblapack.a ]; then echo "mkdir src/lapack-3.8.0/build; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=$(CXX) > /dev/null; make all -j4"; mkdir src/lapack-3.8.0/build 2> /dev/null; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=$(CXX) > /dev/null; make all -j4 > /dev/null 2>&1; cd ../../.. ; fi; \
echo "......[ 99%] Building **proteinortho_clustering** with LAPACK (dynamic linking)"; \
- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran && echo "......OK dynamic linking was successful for proteinortho_clustering!" || ( echo "" ) ; ) ) ) )
+ echo "$(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 "" ) ; ) ) ) )
endif
@if [ ! -e $(BUILDDIR)/proteinortho_clustering ]; then echo "proteinortho_clustering compilation failed. Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes"; false; fi
else
@echo "[ 15%] Extracting the LAPACK library";
- @if [ ! -d src/lapack-3.8.0 ]; then cd src; tar -xzvf lapack-3.8.0.tar.gz > /dev/null 2>&1; cd ..; fi;
+ @if [ ! -d src/lapack-3.8.0 ]; then echo "cd src; tar -xzvf lapack-3.8.0.tar.gz"; cd src; tar -xzvf lapack-3.8.0.tar.gz > /dev/null 2>&1; cd ..; fi;
@echo "[ 18%] Compiling the LAPACK library (using cmake + make)";
- @if [ ! -f src/lapack-3.8.0/build/lib/liblapack.a ]; then mkdir src/lapack-3.8.0/build; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=$(CXX) > /dev/null 2>&1; make all -j4 > /dev/null 2>&1; cd ../../.. ; fi;
+ @if [ ! -f src/lapack-3.8.0/build/lib/liblapack.a ]; then echo "mkdir src/lapack-3.8.0/build; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=$(CXX); make all -j4"; mkdir src/lapack-3.8.0/build; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=$(CXX) > /dev/null 2>&1; make all -j4 > /dev/null 2>&1; cd ../../.. ; fi;
@echo "[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking)";
- @$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran;
+ @echo "$(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) $(LDLIBS) -lgfortran;
endif
endif
ifeq ($(USELAPACK),FALSE)
@echo "[ 20%] Building **proteinortho_clustering** WITHOUT(!) LAPACK";
- @$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
+ @echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS) -static" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
echo "......$(ORANGE)static linking failed of proteinortho_clustering_nolapack, now i switch to dynamic linking.$(NC)"; \
- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS) && echo "......OK dynamic linking was successful for proteinortho_clustering_nolapack!"; )
+ echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS)" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS) && echo "......OK dynamic linking was successful for proteinortho_clustering_nolapack!"; )
endif
endif
@@ -220,33 +215,33 @@ $(BUILDDIR)/proteinortho_cleanupblastgraph: src/cleanupblastgraph.cpp
$(dir_guard)
@echo "[ 50%] Building **cleanupblastgraph**"
ifeq ($(STATIC),TRUE)
- @$(CXX) -std=c++11 $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
+ @echo "$(CXX) -std=c++11 $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) -static" && $(CXX) -std=c++11 $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
echo "......$(ORANGE)static linking failed of cleanupblastgraph, now i switch to dynamic linking.$(NC)"; \
- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< && echo "......OK dynamic linking was successful of cleanupblastgraph!"; )
+ echo "$(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS)" && $(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) && echo "......OK dynamic linking was successful of cleanupblastgraph!"; )
else
- @$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS)
+ @echo "$(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS)" && $(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS)
endif
$(BUILDDIR)/proteinortho_graphMinusRemovegraph: src/graphMinusRemovegraph.cpp
$(dir_guard)
@echo "[ 25%] Building **graphMinusRemovegraph**"
ifeq ($(STATIC),TRUE)
- @$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
+ @echo "$(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) -static" && $(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
echo "......$(ORANGE)static linking failed of graphMinusRemovegraph, now i switch to dynamic linking.$(NC)"; \
- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< && echo "......OK dynamic linking was successful of graphMinusRemovegraph!"; )
+ echo "$(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $@ $<" && $(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $@ $< && echo "......OK dynamic linking was successful of graphMinusRemovegraph!"; )
else
- @$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS)
+ @echo "$(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS)" && $(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS)
endif
$(BUILDDIR)/proteinortho_treeBuilderCore: src/po_tree.c
$(dir_guard)
@echo "[ 75%] Building **po_tree**"
ifeq ($(STATIC),TRUE)
- @$(CC) $(CCFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
+ @echo "$(CC) $(CPPFLAGS) $(CCFLAGS) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) -static" && $(CC) $(CPPFLAGS) $(CCFLAGS) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
echo "......$(ORANGE)static linking failed of po_tree, now i switch to dynamic linking.$(NC)"; \
- $(CC) $(CCFLAGS) -o $@ $< && echo "......OK dynamic linking was successful of po_tree!"; )
+ echo "$(CC) $(CPPFLAGS) $(CCFLAGS) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS)" && $(CC) $(CPPFLAGS) $(CCFLAGS) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) && echo "......OK dynamic linking was successful of po_tree!"; )
else
- @$(CC) $(CCFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS)
+ $(CC) $(CPPFLAGS) $(CCFLAGS) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS)
endif
.PHONY: install
=====================================
README.md
=====================================
@@ -77,31 +77,29 @@ If you cannot execute the src/BUILD/Linux_x86_64/proteinortho_clustering, then y
<br>
-#### Easy installation with (bio)conda (for Linux + OSX)
+#### Easy installation with (bio)conda (for Linux + OSX) [](http://bioconda.github.io/recipes/proteinortho/README.html) [](https://bioconda.github.io/recipes/proteinortho/README.html)
conda install proteinortho
If you need conda (see [here](https://docs.anaconda.com/anaconda/install/)) and the bioconda channel: `conda config --add channels defaults && conda config --add channels bioconda && conda config --add channels conda-forge`.
-[](http://bioconda.github.io/recipes/proteinortho/README.html) [](https://bioconda.github.io/recipes/proteinortho/README.html)
-
<br>
-#### Easy installation with brew (for OSX)
+#### Easy installation with brew (for OSX) [](https://formulae.brew.sh/formula/proteinortho) [](https://formulae.brew.sh/formula/proteinortho)
brew install proteinortho
If you need brew (see [here](https://brew.sh/index_de))
-[](https://formulae.brew.sh/formula/proteinortho) [](https://formulae.brew.sh/formula/proteinortho)
-
<br>
-#### Easy installation with docker
+#### Easy installation with docker [](https://quay.io/repository/biocontainers/proteinortho)
+
+ docker pull quay.io/biocontainers/proteinortho:TAG
+
+with TAG specified [here](https://quay.io/repository/biocontainers/proteinortho?tab=tags) (e.g. 6.0.23--hfd40d39_0).
- docker pull quay.io/biocontainers/proteinortho
-[](https://quay.io/repository/biocontainers/proteinortho)
<details>
@@ -111,7 +109,7 @@ If you need brew (see [here](https://brew.sh/index_de))
To start a bash shell
- ```sudo docker run --rm -it quay.io/biocontainers/proteinortho:6.0.22--hfd40d39_0 bash ```
+ ```docker run --rm -it quay.io/biocontainers/proteinortho:6.0.22--hfd40d39_0 bash ```
Here you can start/use proteinortho.
You can change "6.0.22--hfd40d39_0" with any tag/version that is available [here](https://quay.io/repository/biocontainers/proteinortho?tab=tags). Sadly there is no ":latest" tag available ...
@@ -120,9 +118,9 @@ If you need brew (see [here](https://brew.sh/index_de))
This is neccessary if you want to access your local files:
- ```sudo docker run --rm --mount "type=bind,src=/home/$(id -un),dst=/home/$(id -un)" -u $(id -u):$(id -g) -it quay.io/biocontainers/proteinortho:6.0.22--hfd40d39_0 bash```
+ ```docker run --rm --mount "type=bind,src=/home/$(id -un),dst=/home/$(id -un)" -u $(id -u):$(id -g) -it quay.io/biocontainers/proteinortho:6.0.22--hfd40d39_0 bash```
- now you have your home directory mounted to /home/YOURNAME. (load your bashrc with ```source ~/.bashrc```)
+ now you have your home directory mounted to /home/YOURNAME. (load your bashrc within docker : ```source /home/YOURNAME/.bashrc```)
</details>
@@ -149,13 +147,13 @@ Afterwards the deb package can be installed with `sudo dpkg -i proteinortho*deb`
#### *(Easy installation with apt-get)*
**! Disclamer: Work in progress !**
-*proteinortho will be released to stable with Debian 11 (~2021), then proteinortho can be installed with `sudo apt-get install proteinortho` (currently this installes the outdated version v5.16b)*
+*proteinortho will be released to stable with Debian 11 (~2021), then proteinortho can be installed with `apt-get install proteinortho` (currently this installes the outdated version v5.16b)*
<br>
#### Prerequisites for compiling proteinortho from source
-Proteinortho uses standard software which is often installed already or is part of then package repositories and can thus easily be installed. The sources come with a precompiled version of Proteinortho for 64bit Linux..
+Proteinortho uses standard software which is often installed already or is part of then package repositories and can thus easily be installed. The sources come with a precompiled version of Proteinortho for 64bit Linux x86.
<details>
<summary>To <b>run</b> Proteinortho, you need: (Click to expand)</summary>
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+proteinortho (6.0.24+dfsg-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version 6.0.24+dfsg
+ * Remove merged patches, refresh rest with new upstream release
+
+ -- Nilesh Patra <npatra974 at gmail.com> Wed, 21 Oct 2020 01:06:33 +0530
+
proteinortho (6.0.23+dfsg-1) unstable; urgency=medium
* Team upload.
=====================================
debian/patches/deb_diamond
=====================================
@@ -2,8 +2,8 @@ Author: Michael R. Crusoe <crusoe at debian.org>
Description: Find some Debian packaged software under their original names
Forwarded: not-needed
---- proteinortho.orig/proteinortho6.pl
-+++ proteinortho/proteinortho6.pl
+--- a/proteinortho6.pl
++++ b/proteinortho6.pl
@@ -548,6 +548,9 @@
$NC="";
}
@@ -14,9 +14,9 @@ Forwarded: not-needed
##########################################################################################
# Parameters
##########################################################################################
---- proteinortho.orig/Makefile
-+++ proteinortho/Makefile
-@@ -283,7 +283,7 @@
+--- a/Makefile
++++ b/Makefile
+@@ -278,7 +278,7 @@
fi
@echo -n " [3/12] -p=diamond test: "
@@ -25,7 +25,7 @@ Forwarded: not-needed
echo "$(ORANGE)diamond missing, skipping...$(NC)"; \
else \
./proteinortho6.pl -silent -force -project=test_diamond -p=diamond test/*.faa; \
-@@ -292,7 +292,7 @@
+@@ -287,7 +287,7 @@
fi
@echo -n " [4/12] -p=diamond (--moresensitive) test (subparaBlast): "
=====================================
debian/patches/hardening deleted
=====================================
@@ -1,128 +0,0 @@
-From: Michael R. Crusoe <crusoe at debian.org>
-Subject: Add CPPFLAGS & CFLAGS
-Forwarded: https://gitlab.com/paulklemm_PHD/proteinortho/-/merge_requests/5
-
-And make the build more verbose so we can confirm this.
---- proteinortho.orig/Makefile
-+++ proteinortho/Makefile
-@@ -157,46 +157,46 @@
-
- ifeq ($(DEPLOY),TRUE)
- @echo "[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking, no mtune,march , for gitlab)";
-- @$(CXX) -static $(CXXFLAGS) $(CXXFLAGS_PO) -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 ] )
-+ $(CXX) -static $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -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 ] )
- else
- ifeq ($(USELAPACK),TRUE)
- ifeq ($(USEPRECOMPILEDLAPACK),TRUE)
- ifeq ($(STATIC),TRUE)
- @echo "[ 20%] Building **proteinortho_clustering** with LAPACK (static linking)";
-- @$(CXX) -static $(CXXFLAGS) $(CXXFLAGS_PO) -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 ] ) || ( \
-+ $(CXX) -static $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -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 "......$(ORANGE)dynamic linking failed too, now I try dynamic linking without -WL,-whole-archive... (this should now work for OSX).$(NC)"; \
-- $(CXX) -static $(CXXFLAGS) $(CXXFLAGS_PO) -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!";) || ( \
-+ $(CXX) -static $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -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)"; \
-- @$(CXX) -static $(CXXFLAGS) $(CXXFLAGS_PO) -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 ] ) || ( \
-+ $(CXX) -static $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -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)"; \
-- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -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!";) || ( \
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -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)"; \
-- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
- echo "......$(ORANGE)dynamic linking failed (without -WL,-whole-archive) too too, now I try to openblas.$(NC)"; \
-- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
- echo "......$(ORANGE)last linking failed too too too, now I try to recompile lapack (v.3.8.0) and then compile proteinortho_clustering with dynamic linking.$(NC)"; \
- echo "......[ 33%] Extracting the LAPACK library"; \
- if [ ! -d src/lapack-3.8.0 ]; then cd src; tar -xzvf lapack-3.8.0.tar.gz > /dev/null 2>&1; cd ..; fi; \
- echo "......[ 66%] Compiling the LAPACK library (using cmake + make)"; \
- if [ ! -f src/lapack-3.8.0/build/lib/liblapack.a ]; then mkdir src/lapack-3.8.0/build 2> /dev/null; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=$(CXX) > /dev/null; make all -j4 > /dev/null 2>&1; cd ../../.. ; fi; \
- echo "......[ 99%] Building **proteinortho_clustering** with LAPACK (dynamic linking)"; \
-- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -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 "" ) ; ) ) ) ) ) )
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran && echo "......OK dynamic linking was successful for proteinortho_clustering!" || ( echo "" ) ; ) ) ) ) ) )
- else
- @echo "[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking)";
-- @$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -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!";) || ( \
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -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)"; \
-- @$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -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!";) || ( \
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -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)"; \
-- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
- echo "......$(ORANGE)dynamic linking failed (without -WL,-whole-archive) too too, now I try to openblas.$(NC)"; \
-- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
- echo "......$(ORANGE)last linking failed too too too, now I try to recompile lapack (v.3.8.0) and then compile proteinortho_clustering with dynamic linking.$(NC)"; \
- echo "......[ 33%] Extracting the LAPACK library"; \
- if [ ! -d src/lapack-3.8.0 ]; then cd src; tar -xzvf lapack-3.8.0.tar.gz > /dev/null 2>&1; cd ..; fi; \
- echo "......[ 66%] Compiling the LAPACK library (using cmake + make)"; \
- if [ ! -f src/lapack-3.8.0/build/lib/liblapack.a ]; then mkdir src/lapack-3.8.0/build 2> /dev/null; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=$(CXX) > /dev/null; make all -j4 > /dev/null 2>&1; cd ../../.. ; fi; \
- echo "......[ 99%] Building **proteinortho_clustering** with LAPACK (dynamic linking)"; \
-- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -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 "" ) ; ) ) ) )
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -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 "" ) ; ) ) ) )
- endif
- @if [ ! -e $(BUILDDIR)/proteinortho_clustering ]; then echo "proteinortho_clustering compilation failed. Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes"; false; fi
- else
-@@ -205,14 +205,14 @@
- @echo "[ 18%] Compiling the LAPACK library (using cmake + make)";
- @if [ ! -f src/lapack-3.8.0/build/lib/liblapack.a ]; then mkdir src/lapack-3.8.0/build; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=$(CXX) > /dev/null 2>&1; make all -j4 > /dev/null 2>&1; cd ../../.. ; fi;
- @echo "[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking)";
-- @$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran;
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran;
- endif
- endif
- ifeq ($(USELAPACK),FALSE)
- @echo "[ 20%] Building **proteinortho_clustering** WITHOUT(!) LAPACK";
-- @$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
- echo "......$(ORANGE)static linking failed of proteinortho_clustering_nolapack, now i switch to dynamic linking.$(NC)"; \
-- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS) && echo "......OK dynamic linking was successful for proteinortho_clustering_nolapack!"; )
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS) && echo "......OK dynamic linking was successful for proteinortho_clustering_nolapack!"; )
- endif
- endif
-
-@@ -220,33 +220,33 @@
- $(dir_guard)
- @echo "[ 50%] Building **cleanupblastgraph**"
- ifeq ($(STATIC),TRUE)
-- @$(CXX) -std=c++11 $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
-+ $(CXX) -std=c++11 $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
- echo "......$(ORANGE)static linking failed of cleanupblastgraph, now i switch to dynamic linking.$(NC)"; \
-- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< && echo "......OK dynamic linking was successful of cleanupblastgraph!"; )
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< && echo "......OK dynamic linking was successful of cleanupblastgraph!"; )
- else
-- @$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS)
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS)
- endif
-
- $(BUILDDIR)/proteinortho_graphMinusRemovegraph: src/graphMinusRemovegraph.cpp
- $(dir_guard)
- @echo "[ 25%] Building **graphMinusRemovegraph**"
- ifeq ($(STATIC),TRUE)
-- @$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
- echo "......$(ORANGE)static linking failed of graphMinusRemovegraph, now i switch to dynamic linking.$(NC)"; \
-- $(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< && echo "......OK dynamic linking was successful of graphMinusRemovegraph!"; )
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< && echo "......OK dynamic linking was successful of graphMinusRemovegraph!"; )
- else
-- @$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS)
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS)
- endif
-
- $(BUILDDIR)/proteinortho_treeBuilderCore: src/po_tree.c
- $(dir_guard)
- @echo "[ 75%] Building **po_tree**"
- ifeq ($(STATIC),TRUE)
-- @$(CC) $(CCFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
-+ $(CC) $(CPPFLAGS) $(CCFLAGS) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
- echo "......$(ORANGE)static linking failed of po_tree, now i switch to dynamic linking.$(NC)"; \
-- $(CC) $(CCFLAGS) -o $@ $< && echo "......OK dynamic linking was successful of po_tree!"; )
-+ $(CC) $(CPPFLAGS) $(CCFLAGS) $(CFLAGS) -o $@ $< && echo "......OK dynamic linking was successful of po_tree!"; )
- else
-- @$(CC) $(CCFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS)
-+ $(CC) $(CPPFLAGS) $(CCFLAGS) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS)
- endif
-
- .PHONY: install
=====================================
debian/patches/series
=====================================
@@ -1,3 +1 @@
-hardening
deb_diamond
-spelling
=====================================
debian/patches/spelling deleted
=====================================
@@ -1,36 +0,0 @@
-From: Michael R. Crusoe <crusoe at debian.org>
-Subject: Fix a typo
-Forwarded: https://gitlab.com/paulklemm_PHD/proteinortho/-/merge_requests/6
-
-Found via Debian's "lintian"
---- proteinortho.orig/src/proteinortho_clustering.cpp
-+++ proteinortho/src/proteinortho_clustering.cpp
-@@ -1851,7 +1851,7 @@
- }else{
- do_normalPartitionAlgorithm:
-
-- if (debug_level > 0) cerr << getTime() << " [DEBUG] perfoming a normal split of " << nodes.size()<< " nodes" << "\n";
-+ if (debug_level > 0) cerr << getTime() << " [DEBUG] performing a normal split of " << nodes.size()<< " nodes" << "\n";
-
- // Store data about two groups (Zero cannot be assigned with certainty)
- map<unsigned int,bool> groupA, groupB, groupZero;
-@@ -1869,7 +1869,7 @@
- }
- if( (groupA.size() == 0 && groupB.size() == 0) ){
-
-- cerr << " [WARNING] All nodes are below the purty threshold. Continue without purity." << "\n";
-+ cerr << " [WARNING] All nodes are below the purity threshold. Continue without purity." << "\n";
-
- for (unsigned int i = 0; i < y.size(); i++) {
- if (y[i] < 0) {
---- proteinortho.orig/src/proteinortho_clustering_nolapack.cpp
-+++ proteinortho/src/proteinortho_clustering_nolapack.cpp
-@@ -1611,7 +1611,7 @@
- }else{
- do_normalPartitionAlgorithm:
-
-- if (debug_level > 0) cerr << getTime() << " [DEBUG] perfoming a normal split of " << nodes.size()<< " nodes" << endl;
-+ if (debug_level > 0) cerr << getTime() << " [DEBUG] performing a normal split of " << nodes.size()<< " nodes" << endl;
-
- // Store data about two groups (Zero cannot be assigned with certainty)
- map<unsigned int,bool> groupA, groupB, groupZero;
=====================================
proteinortho6.pl
=====================================
@@ -464,7 +464,7 @@ use POSIX;
##########################################################################################
# Variables
##########################################################################################
-our $version = "6.0.23";
+our $version = "6.0.24";
our $step = 0; # 0/1/2/3 -> do all / only apply step 1 / only apply step 2 / only apply step 3
our $verbose = 1; # 0/1 -> don't / be verbose
our $debug = 0; # 0/1 -> don't / show debug data
@@ -698,7 +698,6 @@ if ($jobnumber != -1) {
}
-
our $gccversionstr = `gcc --version 2>/dev/null`;
our $gccversion_main = "";
if ($? == 0) {
@@ -842,6 +841,28 @@ if ($step == 0 || $step == 1) {
}
}
+# start the daemon
+if($debug){
+ my $updateIntervalInSeconds=1;
+ system("pstree >/dev/null 2>&1");
+ my $masterpid = getppid;
+ if($? == 0){
+ if ((my $pid = fork) == 0) { # make a fork of the current process
+ # this is now executed in parallel !
+ my $ppid = getppid; # parent pid
+ while (1) {
+ sleep $updateIntervalInSeconds;
+ unless (kill 0, $ppid) { # check if parent is still alive (kill 0 = no kill is send but checked for errors)
+ exit;
+ } else {
+ print STDERR "ps --forest -o pid,tty,stat,time,cmd -g $masterpid\n".`ps --forest -o pid,tty,stat,time,cmd -g $masterpid`."\n";
+ }
+ }
+ }
+ }
+}
+
+
# Step 2, run blast and synteny algorithm
if ($step == 0 || $step == 2) {
@@ -2144,6 +2165,7 @@ sub blast {
#
# note: e.g. diamond can directly pass the output to @data
#
+ # sh -ic '{ cat 1>&3; kill 0; } | { sleep 2; kill 0; }' 3>&1
if ($blastmode eq "blastp_legacy" || $blastmode eq "blastn_legacy" || $blastmode eq "tblastx_legacy") {lock($threads_per_process); $command = $binpath."blastall -a $threads_per_process -d '$a.$blastmode' -i '$b' -p $blastmode -m8 -e $evalue $blastOptions $printSTDERR ".($keep ? " | tee '$bla.tmp'" : "");}
elsif ($blastmode eq "autoblast" && $autoblast_fileis{$a} eq "prot" && $autoblast_fileis{$b} eq "prot") {lock($threads_per_process); $command = $binpath."blastp -num_threads $threads_per_process -db '$a.$blastmode' -query '$b' -evalue $evalue -outfmt 6 $blastOptions $printSTDERR ".($keep ? " | tee '$bla.tmp'" : "");}
@@ -2178,7 +2200,6 @@ sub blast {
if ($debug || $verbose==2) {print STDERR "$command\n";} # 5.16
if ($blastmode eq "diamond") {
-
@data=`$command`; # run diamond
if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
if($debug eq "test_sort"){while (<"$bla.tmp">){if ($_ =~ /[^\t]+([,])[^\t]+[eE]/) {print "found forbidden symbol '$1' at $_ in $bla\n";&reset_locale();die;}}}
=====================================
src/proteinortho_clustering.cpp
=====================================
@@ -276,7 +276,7 @@ size_t getCurrentRSS( )
// Main
///////////////////////////////////////////////////////////
void printHelp() {
- cerr << "proteinortho_clustering - Spectral partitioning algorithm (v6.0.6)" << "\n";
+ cerr << "proteinortho_clustering - Spectral partitioning algorithm (last updated with proteinortho v6.0.6)" << "\n";
cerr << "-----------------------------------------------------" << "\n";
cerr << "This tool is part of Proteinortho" << "\n";
cerr << "" << "\n";
@@ -1851,7 +1851,7 @@ void splitGroups(vector<floattype>& y, vector<unsigned int>& nodes , bool useLap
}else{
do_normalPartitionAlgorithm:
- if (debug_level > 0) cerr << getTime() << " [DEBUG] perfoming a normal split of " << nodes.size()<< " nodes" << "\n";
+ if (debug_level > 0) cerr << getTime() << " [DEBUG] performing a normal split of " << nodes.size()<< " nodes" << "\n";
// Store data about two groups (Zero cannot be assigned with certainty)
map<unsigned int,bool> groupA, groupB, groupZero;
@@ -1869,7 +1869,7 @@ void splitGroups(vector<floattype>& y, vector<unsigned int>& nodes , bool useLap
}
if( (groupA.size() == 0 && groupB.size() == 0) ){
- cerr << " [WARNING] All nodes are below the purty threshold. Continue without purity." << "\n";
+ cerr << " [WARNING] All nodes are below the purity threshold. Continue without purity." << "\n";
for (unsigned int i = 0; i < y.size(); i++) {
if (y[i] < 0) {
=====================================
src/proteinortho_clustering_nolapack.cpp
=====================================
@@ -1611,7 +1611,7 @@ void splitGroups(vector<floattype>& y, vector<unsigned int>& nodes , bool useLap
}else{
do_normalPartitionAlgorithm:
- if (debug_level > 0) cerr << getTime() << " [DEBUG] perfoming a normal split of " << nodes.size()<< " nodes" << endl;
+ if (debug_level > 0) cerr << getTime() << " [DEBUG] performing a normal split of " << nodes.size()<< " nodes" << endl;
// Store data about two groups (Zero cannot be assigned with certainty)
map<unsigned int,bool> groupA, groupB, groupZero;
View it on GitLab: https://salsa.debian.org/med-team/proteinortho/-/compare/b890797e4e372912280698443a33aca648d6641c...af2d491e9b7426efc8a261bc270d27896b821bef
--
View it on GitLab: https://salsa.debian.org/med-team/proteinortho/-/compare/b890797e4e372912280698443a33aca648d6641c...af2d491e9b7426efc8a261bc270d27896b821bef
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