Author: sascha-guest Date: 2012-07-09 11:40:22 +0000 (Mon, 09 Jul 2012) New Revision: 11648
Added: trunk/packages/genometools/trunk/debian/patches/libbam-fix Modified: trunk/packages/genometools/trunk/debian/control trunk/packages/genometools/trunk/debian/patches/series trunk/packages/genometools/trunk/debian/rules Log: fix GenomeTools package Modified: trunk/packages/genometools/trunk/debian/control =================================================================== --- trunk/packages/genometools/trunk/debian/control 2012-07-09 11:14:19 UTC (rev 11647) +++ trunk/packages/genometools/trunk/debian/control 2012-07-09 11:40:22 UTC (rev 11648) @@ -2,7 +2,9 @@ Section: science Priority: extra Maintainer: Sascha Steinbiss <[email protected]> -Build-Depends: debhelper (>= 7.0.50~), quilt, liblua5.1-0-dev, liblua5.1-lpeg-dev, liblua5.1-md5-dev, liblua5.1-filesystem-dev, libcairo2-dev, zlib1g-dev, libbz2-dev, libexpat1-dev, libpth-dev, libncurses5-dev +Build-Depends: debhelper (>= 7.0.50~), quilt, + liblua5.1-0-dev, liblua5.1-md5-dev, liblua5.1-filesystem-dev, liblua5.1-lpeg-dev, + libcairo2-dev, zlib1g-dev, libbz2-dev, libexpat1-dev, libncurses5-dev, libsqlite3-dev, libbam-dev Standards-Version: 3.9.3 Homepage: http://genometools.org Vcs-Browser: http://svn.debian.org/viewvc/debian-med/trunk/packages/genometools/trunk/ @@ -21,7 +23,7 @@ Package: genometools-common Architecture: all -Depends: ${misc:Depends}, libbam-dev, liblua5.1-md5-0, liblua5.1-0, liblua5.1-lpeg2, liblua5.1-filesystem0, libcairo2, zlib1g, libbz2-1.0, libexpat1, libpth20, libncurses5 +Depends: ${misc:Depends}, liblua5.1-md5-0|liblua5.1-0, liblua5.1-lpeg2|liblua5.1-0, liblua5.1-filesystem0|liblua5.1-0, liblua5.1-0, libcairo2, zlib1g, libbz2-1.0, libexpat1, libpth20, libncurses5, libsqlite3-0 Description: shared data files for GenomeTools This package contains configuration files such as alphabet transformations, style files, etc. required to use the Added: trunk/packages/genometools/trunk/debian/patches/libbam-fix =================================================================== --- trunk/packages/genometools/trunk/debian/patches/libbam-fix (rev 0) +++ trunk/packages/genometools/trunk/debian/patches/libbam-fix 2012-07-09 11:40:22 UTC (rev 11648) @@ -0,0 +1,111 @@ +--- genometools-1.4.0.orig/Makefile ++++ genometools-1.4.0/Makefile +@@ -235,7 +235,7 @@ + # add necessary shared lib dependencies then not building them ourselves + ifeq ($(useshared),yes) + DEPLIBS:=-lm -lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \ +- -llua5.1-filesystem -llua5.1-des56 -lbam ++ -llua5.1-filesystem -llua5.1-des56 + EXP_LDLIBS += $(DEPLIBS) + GTSHAREDLIB_LIBDEP += $(DEPLIBS) + endif +@@ -555,6 +555,10 @@ + @$(RANLIB) $@ + endif + ++ifeq ($(useshared),yes) ++ ADDITIONAL_STATIC_DEPS:=/usr/lib/libbam.a ++endif ++ + lib/libgenometools.a: obj/gt_config.h $(LIBGENOMETOOLS_OBJ) + @echo "[link $(@F)]" + @test -d $(@D) || mkdir -p $(@D) +@@ -563,19 +567,13 @@ + @$(RANLIB) $@ + endif + +-ifneq ($(useshared),yes) +- ADDITIONAL_SO_DEPS:=lib/libbz2.a \ +- lib/libexpat.a \ +- lib/libz.a +-endif +- + lib/libgenometools$(SHARED_OBJ_NAME_EXT): obj/gt_config.h \ + $(LIBGENOMETOOLS_OBJ) \ +- $(ADDITIONAL_SO_DEPS) ++ $(ADDITIONAL_STATIC_DEPS) + @echo "[link $(@F)]" + @test -d $(@D) || mkdir -p $(@D) + @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $(SHARED) -Wl,-soname,$(notdir $@) $(LIBGENOMETOOLS_OBJ) \ +- -o $@$(SONAME_VERSION) $(GTSHAREDLIB_LIBDEP) ++ -o $@$(SONAME_VERSION) $(GTSHAREDLIB_LIBDEP) $(ADDITIONAL_STATIC_DEPS) + + lib/libtecla.a: $(LIBTECLA_OBJ) + @echo "[link $(@F)]" +@@ -603,48 +601,62 @@ + + $(eval $(call PROGRAM_template, bin/skproto, $(SKPROTO_OBJ) \ + lib/libgenometools.a\ ++ $(ADDITIONAL_STATIC_DEPS) \ + $(OVERRIDELIBS))) + + $(eval $(call PROGRAM_template, bin/gt, $(GTMAIN_OBJ) $(TOOLS_OBJ) \ + lib/libgenometools.a \ ++ $(ADDITIONAL_STATIC_DEPS) \ + $(GTLIBS) \ + $(OVERRIDELIBS))) + + $(eval $(call PROGRAM_template, bin/examples/custom_stream, \ + obj/src/examples/custom_stream.o \ + lib/libgenometools.a \ ++ $(ADDITIONAL_STATIC_DEPS) \ + $(OVERRIDELIBS))) + + $(eval $(call PROGRAM_template, bin/examples/gff3sort, \ + obj/src/examples/gff3sort.o \ + lib/libgenometools.a \ ++ $(ADDITIONAL_STATIC_DEPS) \ + $(OVERRIDELIBS))) + + $(eval $(call PROGRAM_template, bin/examples/gff3validator, \ + obj/src/examples/gff3validator.o \ + lib/libgenometools.a \ ++ $(ADDITIONAL_STATIC_DEPS) \ + $(OVERRIDELIBS))) + + $(eval $(call PROGRAM_template, bin/examples/noop, \ + obj/src/examples/noop.o \ + lib/libgenometools.a \ ++ $(ADDITIONAL_STATIC_DEPS) \ + $(OVERRIDELIBS))) + + $(eval $(call PROGRAM_template, bin/examples/sketch_constructed, \ + obj/src/examples/sketch_constructed.o \ +- lib/libgenometools.a $(OVERRIDELIBS))) ++ lib/libgenometools.a \ ++ $(ADDITIONAL_STATIC_DEPS) \ ++ $(OVERRIDELIBS))) + + $(eval $(call PROGRAM_template, bin/examples/sketch_parsed, \ + obj/src/examples/sketch_parsed.o \ +- lib/libgenometools.a $(OVERRIDELIBS))) ++ lib/libgenometools.a \ ++ $(ADDITIONAL_STATIC_DEPS) \ ++ $(OVERRIDELIBS))) + + $(eval $(call PROGRAM_template, bin/examples/sketch_parsed_with_ctrack, \ + obj/src/examples/sketch_parsed_with_ctrack.o \ +- lib/libgenometools.a $(OVERRIDELIBS))) ++ lib/libgenometools.a \ ++ $(ADDITIONAL_STATIC_DEPS) \ ++ $(OVERRIDELIBS))) + + $(eval $(call PROGRAM_template, bin/examples/sketch_parsed_with_ordering, \ + obj/src/examples/sketch_parsed_with_ordering.o \ +- lib/libgenometools.a $(OVERRIDELIBS))) ++ lib/libgenometools.a \ ++ $(ADDITIONAL_STATIC_DEPS) \ ++ $(OVERRIDELIBS))) + + bin/lua: $(LUAMAIN_OBJ) + @echo "[link $(@F)]" Modified: trunk/packages/genometools/trunk/debian/patches/series =================================================================== --- trunk/packages/genometools/trunk/debian/patches/series 2012-07-09 11:14:19 UTC (rev 11647) +++ trunk/packages/genometools/trunk/debian/patches/series 2012-07-09 11:40:22 UTC (rev 11648) @@ -1 +1,2 @@ adding_soname +libbam-fix Modified: trunk/packages/genometools/trunk/debian/rules =================================================================== --- trunk/packages/genometools/trunk/debian/rules 2012-07-09 11:14:19 UTC (rev 11647) +++ trunk/packages/genometools/trunk/debian/rules 2012-07-09 11:40:22 UTC (rev 11648) @@ -8,11 +8,11 @@ ifeq ($(BITS),64) 64BIT:=yes else - 54BIT:=no + 64BIT:=no endif %: - dh $@ + dh $@ --parallel override_dh_auto_clean: $(MAKE) cleanup _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
