[med-svn] [Git][med-team/gcsa2][master] 4 commits: Rebase patches for gcsa2 1.4 source layout

Andreas Tille (@tille) gitlab at salsa.debian.org
Thu Oct 22 09:14:52 BST 2026 


Andreas Tille pushed to branch master at Debian Med / gcsa2


Commits:
aeae7c22 by Andreas Tille at 2026-10-22T09:57:39+02:00
Rebase patches for gcsa2 1.4 source layout

- - - - -
f9c5630a by Andreas Tille at 2026-10-22T09:59:14+02:00
Updates do not really matter to rectify Assisted-By fields, add Last-Updated

- - - - -
ed9a7432 by Andreas Tille at 2026-10-22T10:00:18+02:00
Adjust packaging for the new build directory layout

- - - - -
4f65e223 by Andreas Tille at 2026-10-22T10:02:44+02:00
Add myself to uploaders

- - - - -


7 changed files:

- debian/changelog
- debian/control
- debian/gcsa2.install
- debian/patches/add_ldflags_cppflags
- debian/patches/drop_unneeded_divsufsort
- debian/patches/use_debian_sdsl
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,14 +1,5 @@
 gcsa2 (1.4-1) UNRELEASED; urgency=medium
 
-  [ Michael R. Crusoe ]
   * Initial release. (Closes: #XXXXXX)
 
-  [ Andreas Tille ]
-  * New upstream version
-  * Standards-Version: 4.7.4 (routine-update)
-  * debhelper-compat 13 (routine-update)
-  * Reflow Uploaders field (cme)
-  * Remove Priority field (cme)
-  * lintian-brush: add d/u/metadata (routine-update)
-
  -- Andreas Tille <tille at debian.org>  Wed, 21 Oct 2026 21:19:31 +0200


=====================================
debian/control
=====================================
@@ -3,6 +3,7 @@ Standards-Version: 4.7.4
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders:
  Michael R. Crusoe <michael.crusoe at gmail.com>,
+ Andreas Tille <tille at debian.org>,
 Section: science
 Build-Depends:
  debhelper-compat (= 14),


=====================================
debian/gcsa2.install
=====================================
@@ -1,4 +1,4 @@
-build_gcsa /usr/bin
-convert_graph /usr/bin
-gcsa_format /usr/bin
-try_extend /usr/bin
+bin/build_gcsa /usr/bin
+bin/convert_graph /usr/bin
+bin/gcsa_format /usr/bin
+bin/try_extend /usr/bin


=====================================
debian/patches/add_ldflags_cppflags
=====================================
@@ -1,50 +1,19 @@
---- gcsa2.orig/Makefile
-+++ gcsa2/Makefile
-@@ -6,34 +6,40 @@
+Description: Honour the build flags exported by dpkg-buildpackage
+ The upstream Makefile already uses CPPFLAGS, CXXFLAGS and LDFLAGS, but
+ they are only populated if dpkg's buildflags.mk is included.
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Last-Update: 2026-10-22
+
+--- a/Makefile
++++ b/Makefile
+@@ -3,6 +3,10 @@
+ BUILD_OBJ=obj
+ SOURCE_DIR=src
  
- OTHER_FLAGS=$(VERIFY_FLAGS) $(PARALLEL_FLAGS)
- 
--CXX_FLAGS=$(MY_CXX_FLAGS) $(OTHER_FLAGS) $(MY_CXX_OPT_FLAGS) -I$(INC_DIR) -Iinclude
 +export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 +DPKG_EXPORT_BUILDFLAGS = 1
 +include /usr/share/dpkg/buildflags.mk
 +
-+CXXFLAGS += $(OTHER_FLAGS) $(MY_CXX_OPT_FLAGS)
-+CPPFLAGS += -Iinclude
- LIBOBJS=algorithms.o dbg.o files.o gcsa.o internal.o lcp.o path_graph.o support.o utils.o
- SOURCES=$(wildcard *.cpp)
- HEADERS=$(wildcard include/gcsa/*.h)
- OBJS=$(SOURCES:.cpp=.o)
--LIBS=-L$(LIB_DIR) -lsdsl
-+LDFLAGS += $(PARALLEL_FLAGS)
-+LDLIBS += -lsdsl
- LIBRARY=libgcsa2.a
- PROGRAMS=build_gcsa convert_graph gcsa_format try_extend
- 
- all: $(LIBRARY) $(PROGRAMS)
- 
- %.o:%.cpp $(HEADERS)
--	$(MY_CXX) $(CXX_FLAGS) -c $<
-+	$(MY_CXX) $(CPPFLAGS) $(CXXFLAGS) -c $<
- 
- $(LIBRARY):$(LIBOBJS)
- 	ar rcs $@ $(LIBOBJS)
- 
- build_gcsa:build_gcsa.o $(LIBRARY)
--	$(MY_CXX) $(CXX_FLAGS) -o $@ $< $(LIBRARY) $(LIBS)
-+	$(MY_CXX) $(LDFLAGS) -o $@ $< $(LIBRARY) $(LDLIBS)
- 
- gcsa_format:gcsa_format.o $(LIBRARY)
--	$(MY_CXX) $(CXX_FLAGS) -o $@ $< $(LIBRARY) $(LIBS)
-+	$(MY_CXX) $(LDFLAGS) -o $@ $< $(LIBRARY) $(LDLIBS)
- 
- convert_graph:convert_graph.o $(LIBRARY)
--	$(MY_CXX) $(CXX_FLAGS) -o $@ $< $(LIBRARY) $(LIBS)
-+	$(MY_CXX) $(LDFLAGS) -o $@ $< $(LIBRARY) $(LDLIBS)
- 
- try_extend:try_extend.o $(LIBRARY)
--	$(MY_CXX) $(CXX_FLAGS) -o $@ $< $(LIBRARY) $(LIBS)
-+	$(MY_CXX) $(LDFLAGS) -o $@ $< $(LIBRARY) $(LDLIBS)
+ # This enables various debugging options in build_gcsa.
+ #VERIFY_FLAGS=-DVERIFY_CONSTRUCTION
  
- clean:
- 	rm -f $(PROGRAMS) $(OBJS) $(LIBRARY)


=====================================
debian/patches/drop_unneeded_divsufsort
=====================================
@@ -1,22 +1,28 @@
---- gcsa2.orig/Makefile
-+++ gcsa2/Makefile
-@@ -11,7 +11,7 @@
- SOURCES=$(wildcard *.cpp)
- HEADERS=$(wildcard include/gcsa/*.h)
- OBJS=$(SOURCES:.cpp=.o)
+Description: Drop unneeded divsufsort libraries from the link line
+ The Debian packaged libsdsl-dev does not require linking against
+ divsufsort explicitly.
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Last-Update: 2026-10-22
+
+--- a/Makefile
++++ b/Makefile
+@@ -8,7 +8,7 @@
+ 
+ # Multithreading with OpenMP.
+ PARALLEL_FLAGS=-fopenmp -pthread
 -LIBS=-L$(LIB_DIR) -lsdsl -ldivsufsort -ldivsufsort64
 +LIBS=-L$(LIB_DIR) -lsdsl
- LIBRARY=libgcsa2.a
- PROGRAMS=build_gcsa convert_graph gcsa_format try_extend
  
---- gcsa2.orig/benchmark/Makefile
-+++ gcsa2/benchmark/Makefile
-@@ -9,7 +9,7 @@
- LIBOBJS=algorithms.o dbg.o files.o gcsa.o internal.o lcp.o path_graph.o support.o utils.o
- SOURCES=$(wildcard *.cpp)
- OBJS=$(SOURCES:.cpp=.o)
--LIBS=-L$(LIB_DIR) -L$(GCSA_DIR) -lgcsa2 -lsdsl -ldivsufsort -ldivsufsort64
-+LIBS=-L$(LIB_DIR) -L$(GCSA_DIR) -lgcsa2 -lsdsl
- PROGRAMS=count_kmers query_gcsa csa_builder csa_query
+ # Apple Clang does not support OpenMP directly, so we need special handling.
+ ifeq ($(shell uname -s), Darwin)
+--- a/benchmark/Makefile
++++ b/benchmark/Makefile
+@@ -3,7 +3,7 @@
+ 
+ # Multithreading with OpenMP and libstdc++ Parallel Mode.
+ PARALLEL_FLAGS=-fopenmp -pthread
+-LIBS=-L$(LIB_DIR) -lsdsl -ldivsufsort -ldivsufsort64
++LIBS=-L$(LIB_DIR) -lsdsl
  
- all: $(PROGRAMS)
+ # Apple Clang does not support OpenMP directly, so we need special handling.
+ ifeq ($(shell uname -s), Darwin)


=====================================
debian/patches/use_debian_sdsl
=====================================
@@ -1,18 +1,21 @@
+Description: Use the Debian packaged SDSL instead of a bundled sdsl-lite
 Author: Michael R. Crusoe <michael.crusoe at gmail.com>
-Description: Use sdsl from libsdsl-dev
---- gcsa2.orig/Makefile
-+++ gcsa2/Makefile
-@@ -1,5 +1,3 @@
+Last-Update: 2026-10-22
+
+--- a/Makefile
++++ b/Makefile
+@@ -1,6 +1,3 @@
 -SDSL_DIR=../sdsl-lite
+-include $(SDSL_DIR)/Make.helper
 -
- # This enables various debugging options in build_gcsa.
- #VERIFY_FLAGS=-DVERIFY_CONSTRUCTION
- 
-@@ -8,7 +6,6 @@
- 
- OTHER_FLAGS=$(VERIFY_FLAGS) $(PARALLEL_FLAGS)
- 
+ BUILD_BIN=bin
+ BUILD_LIB=lib
+ BUILD_OBJ=obj
+--- a/benchmark/Makefile
++++ b/benchmark/Makefile
+@@ -1,5 +1,2 @@
+-SDSL_DIR=../../sdsl-lite
 -include $(SDSL_DIR)/Make.helper
- CXX_FLAGS=$(MY_CXX_FLAGS) $(OTHER_FLAGS) $(MY_CXX_OPT_FLAGS) -I$(INC_DIR) -Iinclude
- LIBOBJS=algorithms.o dbg.o files.o gcsa.o internal.o lcp.o path_graph.o support.o utils.o
- SOURCES=$(wildcard *.cpp)
+-
+ GCSA_DIR=..
+ LIBRARY=$(GCSA_DIR)/lib/libgcsa2.a


=====================================
debian/rules
=====================================
@@ -24,7 +24,7 @@ override_dh_auto_build:
 override_dh_auto_install:
 	dh_auto_install
 	mkdir -p debian/libgcsa2-dev/usr/lib/$(shell dpkg-architecture --query DEB_HOST_MULTIARCH)/
-	cp libgcsa2.a debian/libgcsa2-dev/usr/lib/$(shell dpkg-architecture --query DEB_HOST_MULTIARCH)/
+	cp lib/libgcsa2.a debian/libgcsa2-dev/usr/lib/$(shell dpkg-architecture --query DEB_HOST_MULTIARCH)/
 
 ### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
 #override_dh_auto_test:



View it on GitLab: https://salsa.debian.org/med-team/gcsa2/-/compare/08742e53c5301a8363eb9a7e06a1aed538a699a3...4f65e223d319b20a234b32bc0e61371fa5e87688

-- 
View it on GitLab: https://salsa.debian.org/med-team/gcsa2/-/compare/08742e53c5301a8363eb9a7e06a1aed538a699a3...4f65e223d319b20a234b32bc0e61371fa5e87688
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