[med-svn] [Git][med-team/lagan][master] 3 commits: fix insane upstream build system

Andreas Tille gitlab at salsa.debian.org
Tue Jun 11 12:46:28 BST 2019 


Andreas Tille pushed to branch master at Debian Med / lagan


Commits:
811676ac by Andreas Tille at 2019-06-11T11:39:03Z
fix insane upstream build system

- - - - -
bbd5c6b0 by Andreas Tille at 2019-06-11T11:40:05Z
Standards-Version: 4.3.0

- - - - -
9c5675b5 by Andreas Tille at 2019-06-11T11:41:32Z
Upload to unstable

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/cross.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+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 at debian.org>  Tue, 11 Jun 2019 13:40:14 +0200
+
 lagan (2.0-3) unstable; urgency=medium
 
   * Upload to unstable


=====================================
debian/control
=====================================
@@ -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
=====================================
@@ -0,0 +1,105 @@
+From: Helmut Grohne <helmut at 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
=====================================
@@ -4,3 +4,4 @@ ambiuousEnd.patch
 addTest.patch
 adjustPerlPaths.patch
 hardening.patch
+cross.patch



View it on GitLab: https://salsa.debian.org/med-team/lagan/compare/ffe9c3ccde5968ba1a6f2302641bae7af9fa71a8...9c5675b502681e38d975e3f89095b54799fddaa1

-- 
View it on GitLab: https://salsa.debian.org/med-team/lagan/compare/ffe9c3ccde5968ba1a6f2302641bae7af9fa71a8...9c5675b502681e38d975e3f89095b54799fddaa1
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