Source: lagan Version: 2.0-3 Tags: patch upstream User: helm...@debian.org Usertags: rebootstrap
lagan fails to cross build from source. The upstream build system is quite strange. It stuffs CFLAGS into variables such as CC and CXX, which dh_auto_build overrides. Thus CFLAGS go missing. It also stores a C++ compiler in CC. The attached patch makes these variables behave as one would expect. Please consider applying the attached patch. Helmut
--- lagan-2.0.orig/src/Makefile +++ lagan-2.0/src/Makefile @@ -1,5 +1,5 @@ -CC = gcc $(CFLAGS) -CPP = g++ $(CFLAGS) +CC = gcc +CXX = g++ CFLAGS += -O3 # -Wall -W TRGT_DIR = .. @@ -9,46 +9,46 @@ rm -f *.o *~ utils/*~ mlagan.purify core (cd glocal; $(MAKE) clean) ../anchors: anchors.c skiplist.c - $(CC) -o $(TRGT_DIR)/anchors anchors.c skiplist.c $(LDFLAGS) + $(CC) $(CFLAGS) -o $(TRGT_DIR)/anchors anchors.c skiplist.c $(LDFLAGS) ../chaos: fchaos.c thrtrie.c skiplist.c global.c translate.c mempage.c filebuffer.c - $(CC) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG $(LDFLAGS) + $(CC) $(CFLAGS) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG $(LDFLAGS) ../order: order.c diagmatrix.c filebuffer.c - $(CC) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c $(LDFLAGS) + $(CC) $(CFLAGS) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c $(LDFLAGS) ../mlagan: mlagan.c diagmatrix.c multial.c skiplist.c filebuffer.c - $(CC) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG $(LDFLAGS) + $(CC) $(CFLAGS) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG $(LDFLAGS) ../prolagan: prolagan.c diagmatrix.c multial.c skiplist.c filebuffer.c - $(CC) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG $(LDFLAGS) + $(CC) $(CFLAGS) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG $(LDFLAGS) ../utils/bin2mf: utils/bin2mf.c - $(CC) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c $(LDFLAGS) + $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c $(LDFLAGS) ../utils/bin2bl: utils/bin2bl.c - $(CC) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c $(LDFLAGS) + $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c $(LDFLAGS) ../utils/cextract: utils/cextract.c - $(CC) -o $(TRGT_DIR)/utils/cextract utils/cextract.c $(LDFLAGS) + $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/cextract utils/cextract.c $(LDFLAGS) ../utils/cstat: utils/cstat.c - $(CC) -o $(TRGT_DIR)/utils/cstat utils/cstat.c $(LDFLAGS) + $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/cstat utils/cstat.c $(LDFLAGS) ../utils/contigorder: utils/contigorder.c - $(CC) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c $(LDFLAGS) + $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c $(LDFLAGS) ../utils/getbounds: utils/getbounds.c - $(CC) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c $(LDFLAGS) + $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c $(LDFLAGS) ../utils/getcontigpos: utils/getcontigpos.c - $(CC) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c $(LDFLAGS) + $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c $(LDFLAGS) ../utils/getlength: utils/getlength.c - $(CC) -o $(TRGT_DIR)/utils/getlength utils/getlength.c $(LDFLAGS) + $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/getlength utils/getlength.c $(LDFLAGS) ../utils/getoverlap: utils/getoverlap.c - $(CC) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c $(LDFLAGS) + $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c $(LDFLAGS) ../utils/rc: utils/rc.c - $(CC) -o $(TRGT_DIR)/utils/rc utils/rc.c $(LDFLAGS) + $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/rc utils/rc.c $(LDFLAGS) ../utils/seqmerge: utils/seqmerge.c - $(CC) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c $(LDFLAGS) + $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c $(LDFLAGS) ../utils/scorealign: utils/scorealign.c - $(CC) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm $(LDFLAGS) + $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm $(LDFLAGS) ../utils/scorecontigs: utils/scorecontigs.c - $(CC) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm $(LDFLAGS) + $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm $(LDFLAGS) ../utils/fa2xfa: utils/fa2xfa.c - $(CC) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c $(LDFLAGS) + $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c $(LDFLAGS) ../utils/overlay: utils/overlay.c - $(CC) -o $(TRGT_DIR)/utils/overlay utils/overlay.c $(LDFLAGS) + $(CC) $(CFLAGS) -o $(TRGT_DIR)/utils/overlay utils/overlay.c $(LDFLAGS) ../utils/Glue: utils/Glue.cpp - $(CPP) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp $(LDFLAGS) + $(CXX) $(CFLAGS) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp $(LDFLAGS) ../utils/dotplot: utils/dotplot.cpp - $(CPP) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp $(LDFLAGS) + $(CXX) $(CFLAGS) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp $(LDFLAGS) --- lagan-2.0.orig/src/glocal/Makefile +++ lagan-2.0/src/glocal/Makefile @@ -1,7 +1,7 @@ -CC = g++ +CXX = g++ OPTFLAGS = CFLAGS += $(OPTFLAGS) -O3 -CLINKER = g++ +CLINKER = $(CXX) # LIBDIR = -L/usr/local/lib MLIB = -lm INCDIR = -I./ @@ -10,7 +10,7 @@ OBJECTS = glocal.o io.o rightinfluence.o leftinfluence.o score.o .cpp.o: - $(CC) -Wno-deprecated $(CFLAGS) $(INCDIR) -c $*.cpp $(LDFLAGS) + $(CXX) -Wno-deprecated $(CFLAGS) $(INCDIR) -c $*.cpp $(LDFLAGS) $(TRGT): $(OBJECTS) $(CLINKER) $(OPTFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
