debian/changelog

+proteinortho (6.0.12+dfsg-2) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * patch: Use #!/usr/bin/python3 (fixes autopkgtests)
+  * patch: Find the packaged version of the Diamond aligner
+  * patch: Improve build hardening via CPPFLAGS & CFLAGS
+  * Expanded autopkgtests, following `make test`
+  * patch: fix a spelling typo
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Mon, 13 Jan 2020 11:45:52 +0100
+
 proteinortho (6.0.12+dfsg-1) unstable; urgency=medium
 
   * Team upload.

debian/control

@@ -6,7 +6,8 @@ Priority: optional
 Build-Depends: debhelper-compat (= 12),
                ncbi-blast+,
                liblapack-dev | libatlas-base-dev | liblapack.so,
-               diamond-aligner
+               diamond-aligner,
+               procps
 Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/proteinortho
 Vcs-Git: https://salsa.debian.org/med-team/proteinortho.git
@@ -16,10 +17,12 @@ Package: proteinortho
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         ${python3:Depends},
+         ${perl:Depends},
+         python3,
          ncbi-blast+,
          diamond-aligner,
-         liblapack3
+         liblapack3,
+         procps
 Description: Detection of (Co-)orthologs in large-scale protein analysis
  Proteinortho is a stand-alone tool that is geared towards large datasets
  and makes use of distributed computing techniques when run on multi-core

debian/patches/deb_diamond

+Author: Michael R. Crusoe <michael.crusoe@gmail.com>
+Description: Find some Debian packaged software under their original names
+--- proteinortho.orig/proteinortho6.pl
++++ proteinortho/proteinortho6.pl
+@@ -535,6 +535,9 @@
+   $NC="";
+ }
+ 
++# Find some Debian packaged software under their original names
++$ENV{PATH} = "$ENV{PATH}:/usr/lib/debian-med/bin";
++
+ ##########################################################################################
+ # Parameters
+ ##########################################################################################
+--- proteinortho.orig/Makefile
++++ proteinortho/Makefile
+@@ -265,7 +265,7 @@
+ 	fi
+ 
+ 	@echo -n " [3/12] -p=diamond test: "
+-	@if [ "$(shell which diamond)" = "" ]; then\
++	@if [ "$(shell which diamond-aligner)" = "" ]; then\
+ 		echo "$(ORANGE)diamond missing, skipping...$(NC)"; \
+ 	else \
+ 		./proteinortho6.pl -silent -force -project=test_diamond -p=diamond test/*.faa; \

debian/patches/hardening

+From: Michael R. Crusoe <michael.crusoe@gmail.com>
+Subject: Add CPPFLAGS & CFLAGS
+
+And make the build more verbose so we can confirm this.
+--- proteinortho.orig/Makefile
++++ proteinortho/Makefile
+@@ -152,13 +152,13 @@
+ ifeq ($(USEPRECOMPILEDLAPACK),TRUE)
+ ifeq ($(STATIC),TRUE)
+ 	@echo "[ 20%] Building **proteinortho_clustering** with LAPACK (static linking)";
+-	@$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -static -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath && ([ $$? -eq 0 ] ) || ( \
++	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -static -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath && ([ $$? -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 && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
++		$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && 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 && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
++			$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -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 && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
++				$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread && ([ $$? -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; \
+@@ -168,18 +168,18 @@
+ 					$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran && echo "......OK dynamic linking was successful for proteinortho_clustering!" || ( echo "" ) ; ) ) ) )
+ else
+ 	@echo "[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking)";
+-	@$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
++	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && 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 && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
++		$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -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 && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
++			$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread && ([ $$? -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 $(BUILDDIR)/proteinortho_clustering ]; then echo "proteinortho_clustering compilation failed. Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes"; false; fi
+ else
+@@ -188,47 +188,47 @@
+ 	@echo "[ 18%] Compiling the LAPACK library (using cmake + make)";
+ 	@if [ ! -f src/lapack-3.8.0/build/lib/liblapack.a ]; then mkdir src/lapack-3.8.0/build; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=$(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
+ 
+ $(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 && ([ $$? -eq 0 ] ) || ( \
++	$(CXX) -std=c++11 $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -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/python3

+From: Michael R. Crusoe <michael.crusoe@gmail.com>
+Description: For Debian, we are only supporting Python version 3
+--- proteinortho.orig/src/proteinortho_ffadj_mcs.py
++++ proteinortho/src/proteinortho_ffadj_mcs.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ from sys import stderr, exit, argv, maxsize
+ from copy import deepcopy

debian/patches/series

+python3
+hardening
+deb_diamond
+spelling

debian/patches/spelling

+From: Michael R. Crusoe <michael.crusoe@gmail.com>
+Subject: Fix a typo
+
+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" << 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;
+--- 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;

debian/source/lintian-overrides

-proteinortho source: python3-depends-but-no-python3-helper proteinortho

debian/tests/run-unit-test

@@ -13,7 +13,57 @@ mkdir test
 cp -a /usr/share/doc/${pkg}/examples/* test
 gunzip -r *
 
-proteinortho -project=test -synteny -singles test/*.faa
-./test/chk_test.pl test.proteinortho.tsv
-./test/chk_test.pl test.poff.tsv
+proteinortho -force -project=test_blastp -p=blastp+ test/*.faa
+./test/chk_test.pl test_blastp.proteinortho.tsv
+
+proteinortho -force -project=test_synteny -synteny -singles -p=blastp+ test/*.faa
+./test/chk_test.pl test_synteny.proteinortho.tsv
+./test/chk_test.pl test_synteny.poff.tsv
+
+proteinortho  -force -project=test_diamond -p=diamond test/*.faa
+./test/chk_test.pl test_diamond.proteinortho.tsv
+
+proteinortho -force -project=test_diamondmoresensitive -p=diamond -subparaBlast="--more-sensitive" test/*.faa
+./test/chk_test.pl test_diamondmoresensitive.proteinortho.tsv
+
+# Not yet packaged?
+#proteinortho -force -project=test_lastp -p=lastp test/*.faa
+#./test/chk_test.pl test_lastp.proteinortho.tsv
+
+# Not yet packaged?
+#proteinortho -force -project=test_topaz -p=topaz test/*.faa
+#./test/chk_test.pl test_topaz.proteinortho.tsv
+
+# Not yet packaged
+#proteinortho -force -project=test_usearch -p=usearch test/*.faa
+#./test/chk_test.pl test_usearch.proteinortho.tsv
+
+# Not yet packaged?
+#proteinortho -force -project=test_ublast -p=ublast test/*.faa
+#./test/chk_test.pl test_ublast.proteinortho.tsv
+
+# Not yet packaged?
+#proteinortho -force -project=test_rapsearch -p=rapsearch test/*.faa
+#./test/chk_test.pl test_rapsearch.proteinortho.tsv
+
+# Not yet packaged?
+#proteinortho -force -project=test_blatp -p=blatp test/*.faa
+#./test/chk_test.pl test_blatp.proteinortho.tsv
+
+# Not yet packaged?
+#proteinortho -force -project=test_mmseqsp -p=mmseqsp test/*.faa
+#./test/chk_test.pl test_blatp.proteinortho.tsv
+
+proteinortho -force -project=test_blastall -p=blastp test/*.faa
+./test/chk_test.pl test_blastall.proteinortho.tsv
+
+/usr/lib/proteinortho/proteinortho_clustering -test
+
+# Compare results of 'with lapack' and 'without lapack'
+/usr/lib/proteinortho/proteinortho_clustering -epsilon 0 test_blastp.blast-graph
+sort remove.graph -o test.A
+/usr/lib/proteinortho/proteinortho_clustering -epsilon 0 -lapack 0 test_blastp.blast-graph
+sort remove.graph -o test.B
+diff test.A test.B
+
 echo "Test okay"