[med-svn] r11648 - in trunk/packages/genometools/trunk/debian: . patches
Sascha Steinbiss
sascha-guest at alioth.debian.org
Mon Jul 9 11:40:22 UTC 2012
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 <steinbiss at zbh.uni-hamburg.de>
-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
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