Source: proteinortho Version: 6.3.1+dfsg-1 Tags: patch User: [email protected] Usertags: ftcbfs
When trying to cross build proteinortho using sbuild, the result is a 150 minute build timeout via inactivity. What actually happens is that after linking proteinortho_clustering, the build system runs it and as that fails proceeds to silently rebuilding lapack. Given that lapack is non-trivial to compile and all of its output is hidden, this times out the build. We cannot expect to run this test during cross compilation. I therefore propose to make the build system aware of cross compilation. Then, it trusts that a successful link is ok. Once doing so, proteinortho quickly cross builds successfully saving a lot of QA resources. The failure mode has wasted around 9 CPU days so far. Please consider applying the attached patch. Helmut
diff -Nru proteinortho-6.3.1+dfsg/debian/changelog proteinortho-6.3.1+dfsg/debian/changelog --- proteinortho-6.3.1+dfsg/debian/changelog 2024-01-12 06:50:22.000000000 +0100 +++ proteinortho-6.3.1+dfsg/debian/changelog 2026-10-14 09:17:54.000000000 +0200 @@ -1,3 +1,10 @@ +proteinortho (6.3.1+dfsg-1.1) UNRELEASED; urgency=medium + + * Non-maintainer upload. + * Fix FTCBFS: Avoid running tests during cross builds. (Closes: #-1) + + -- Helmut Grohne <[email protected]> Wed, 14 Oct 2026 09:17:54 +0200 + proteinortho (6.3.1+dfsg-1) unstable; urgency=medium * New upstream version diff -Nru proteinortho-6.3.1+dfsg/debian/patches/cross.patch proteinortho-6.3.1+dfsg/debian/patches/cross.patch --- proteinortho-6.3.1+dfsg/debian/patches/cross.patch 1970-01-01 01:00:00.000000000 +0100 +++ proteinortho-6.3.1+dfsg/debian/patches/cross.patch 2026-10-14 09:17:03.000000000 +0200 @@ -0,0 +1,41 @@ +--- proteinortho-6.3.1+dfsg.orig/Makefile ++++ proteinortho-6.3.1+dfsg/Makefile +@@ -36,6 +36,7 @@ + # compile statically + STATIC=FALSE + DEPLOY=FALSE ++CROSS_COMPILING=FALSE + + ifdef static + STATIC=$(static) +@@ -189,6 +190,9 @@ + ifeq ($(USEPRECOMPILEDLAPACK),TRUE) + ifeq ($(STATIC),TRUE) + @echo "[ 20%] Building **proteinortho_clustering** with LAPACK (static linking)"; ++ifeq ($(CROSS_COMPILING),TRUE) ++ $(CXX) -std=c++11 -O3 -funroll-loops -static $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath ++else + @echo "$(CXX) -std=c++11 -O3 -funroll-loops -static $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath" && $(CXX) -std=c++11 -O3 -funroll-loops -static $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -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) -std=c++11 -O3 -funroll-loops -static $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath" && $(CXX) -std=c++11 -O3 -funroll-loops -static $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -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 ] ) || ( \ +@@ -205,8 +209,12 @@ + 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)"; \ + echo "$(CXX) -std=c++11 -O3 -funroll-loops $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran" && $(CXX) -std=c++11 -O3 -funroll-loops $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran && echo "......OK dynamic linking was successful for proteinortho_clustering!" || ( echo "" ) ; ) ) ) ) ) ++endif + else + @echo "[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking)"; ++ifeq ($(CROSS_COMPILING),TRUE) ++ $(CXX) -std=c++11 -O3 -funroll-loops $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive ++else + @echo "$(CXX) -std=c++11 -O3 -funroll-loops $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive" && $(CXX) -std=c++11 -O3 -funroll-loops $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -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) -std=c++11 -O3 -funroll-loops $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread" && $(CXX) -std=c++11 -O3 -funroll-loops $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \ +@@ -220,6 +228,7 @@ + echo "......[ 99%] Building **proteinortho_clustering** with LAPACK (dynamic linking)"; \ + echo "$(CXX) -std=c++11 -O3 -funroll-loops $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran" && $(CXX) -std=c++11 -O3 -funroll-loops $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -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 ++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"; diff -Nru proteinortho-6.3.1+dfsg/debian/patches/series proteinortho-6.3.1+dfsg/debian/patches/series --- proteinortho-6.3.1+dfsg/debian/patches/series 2024-01-12 06:50:22.000000000 +0100 +++ proteinortho-6.3.1+dfsg/debian/patches/series 2026-10-14 09:10:57.000000000 +0200 @@ -1 +1,2 @@ deb_diamond +cross.patch diff -Nru proteinortho-6.3.1+dfsg/debian/rules proteinortho-6.3.1+dfsg/debian/rules --- proteinortho-6.3.1+dfsg/debian/rules 2024-01-12 06:50:22.000000000 +0100 +++ proteinortho-6.3.1+dfsg/debian/rules 2026-10-14 09:17:47.000000000 +0200 @@ -9,6 +9,11 @@ %: dh $@ +ifneq ($(DEB_BUILD_ARCH),$(DEB_HOST_ARCH)) +override_dh_auto_build: + dh_auto_build -- CROSS_COMPILING=TRUE +endif + override_dh_auto_test: ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) dh_auto_test --no-parallel
