Skip to content
GitLab
Explore
Sign in
Register
Commits on Source (3)
fix insane upstream build system
· 811676ac
Andreas Tille
authored
Jun 11, 2019
811676ac
Standards-Version: 4.3.0
· bbd5c6b0
Andreas Tille
authored
Jun 11, 2019
bbd5c6b0
Upload to unstable
· 9c5675b5
Andreas Tille
authored
Jun 11, 2019
9c5675b5
Hide whitespace changes
Inline
Side-by-side
debian/changelog
View file @
9c5675b5
lagan (2.0-4) unstable; urgency=medium
[ Helmut Grohne ]
* fix insane upstream build system
Closes: #929590
[ Andreas Tille ]
* Standards-Version: 4.3.0
-- Andreas Tille <tille@debian.org> Tue, 11 Jun 2019 13:40:14 +0200
lagan (2.0-3) unstable; urgency=medium
* Upload to unstable
...
...
debian/control
View file @
9c5675b5
...
...
@@ -6,7 +6,7 @@ Section: science
Priority: optional
Build-Depends: debhelper (>= 11~),
libboost-dev
Standards-Version: 4.
2.1
Standards-Version: 4.
3.0
Vcs-Browser: https://salsa.debian.org/med-team/lagan
Vcs-Git: https://salsa.debian.org/med-team/lagan.git
Homepage: http://lagan.stanford.edu/lagan_web/index.shtml
...
...
debian/patches/cross.patch
0 → 100644
View file @
9c5675b5
From: Helmut Grohne <helmut@subdivi.de>
Date: Sun, 26 May 2019 19:29:13 +0200
Bug-Debian: https://bugs.debian.org/929590
Description: fix insane upstream build system
--- a/src/Makefile
+++ b/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 @@
clean:
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)
--- a/src/glocal/Makefile
+++ b/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 @@
TRGT = glocal
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)
debian/patches/series
View file @
9c5675b5
...
...
@@ -4,3 +4,4 @@ ambiuousEnd.patch
addTest.patch
adjustPerlPaths.patch
hardening.patch
cross.patch
Andreas Tille authored811676ac
Andreas Tille authoredbbd5c6b0
Andreas Tille authored9c5675b5