Author: sascha-guest
Date: 2012-10-05 14:07:42 +0000 (Fri, 05 Oct 2012)
New Revision: 12318
Modified:
trunk/packages/genometools/trunk/debian/changelog
trunk/packages/genometools/trunk/debian/patches/adding_soname
trunk/packages/genometools/trunk/debian/patches/libbam-fix
trunk/packages/genometools/trunk/debian/patches/remove-gitignores
Log:
new upstream release 1.4.2
Modified: trunk/packages/genometools/trunk/debian/changelog
===================================================================
--- trunk/packages/genometools/trunk/debian/changelog 2012-10-05 13:36:54 UTC
(rev 12317)
+++ trunk/packages/genometools/trunk/debian/changelog 2012-10-05 14:07:42 UTC
(rev 12318)
@@ -1,3 +1,9 @@
+genometools (1.4.2-1) unstable; urgency=low
+
+ * New upstream release
+
+ -- Sascha Steinbiss <steinb...@zbh.uni-hamburg.de> Fri, 05 Oct 2012 15:47:56
+0200
+
genometools (1.4.1-1) unstable; urgency=low
* Initial release (Closes: #657923)
Modified: trunk/packages/genometools/trunk/debian/patches/adding_soname
===================================================================
--- trunk/packages/genometools/trunk/debian/patches/adding_soname
2012-10-05 13:36:54 UTC (rev 12317)
+++ trunk/packages/genometools/trunk/debian/patches/adding_soname
2012-10-05 14:07:42 UTC (rev 12318)
@@ -1,34 +1,44 @@
---- genometools-1.4.1.orig/Makefile
-+++ genometools-1.4.1/Makefile
-@@ -77,6 +77,7 @@
+--- a/Makefile
++++ b/Makefile
+@@ -86,6 +86,7 @@
SHARED_OBJ_NAME_EXT:=.so
SHARED:=-shared
endif
+SONAME_VERSION:=.0
- # libraries for which we build replacements (that also appear in dependencies)
- EXP_LDLIBS+=-lz -lbz2
-@@ -235,7 +236,7 @@
+ # compiled executables
+ GTMAIN_SRC:=src/gt.c src/gtr.c src/gtt.c src/interactive.c
+@@ -238,7 +239,7 @@
# add necessary shared lib dependencies then not building them ourselves
ifeq ($(useshared),yes)
-- DEPLIBS:=-lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \
-+ DEPLIBS:=-lm -lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \
+- DEPLIBS:=-lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \
++ DEPLIBS:=-lm -lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \
-llua5.1-filesystem -llua5.1-des56 -lbam
- EXP_LDLIBS += $(DEPLIBS)
- GTSHAREDLIB_LIBDEP += $(DEPLIBS)
-@@ -538,8 +539,8 @@
- $(ADDITIONAL_SO_DEPS)
+ else
+ DEPLIBS:=
+@@ -517,7 +518,7 @@
+
+ ifdef DESTDIR
+ prefix:=$(DESTDIR)$(prefix)
+-endif
++ endif
+
+ # allow to set patch program
+ patch ?= patch
+@@ -595,8 +596,9 @@
+ $(ADDITIONAL_ZLIBS)
@echo "[link $(@F)]"
@test -d $(@D) || mkdir -p $(@D)
-- @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $(SHARED) $(LIBGENOMETOOLS_OBJ) \
+- @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $(ADDITIONAL_SO_DEPS) $(SHARED)
$(LIBGENOMETOOLS_OBJ) \
- -o $@ $(GTSHAREDLIB_LIBDEP)
-+ @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $(SHARED) -Wl,-soname,$(notdir
$@)$(SONAME_VERSION) $(LIBGENOMETOOLS_OBJ) \
++ @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $(ADDITIONAL_SO_DEPS) $(SHARED) \
++ -Wl,-soname,$(notdir $@)$(SONAME_VERSION) $(LIBGENOMETOOLS_OBJ) \
+ -o $@$(SONAME_VERSION) $(GTSHAREDLIB_LIBDEP)
lib/libtecla.a: $(LIBTECLA_OBJ)
@echo "[link $(@F)]"
-@@ -872,7 +873,8 @@
+@@ -934,7 +936,8 @@
ifdef RANLIB
$(RANLIB) $(prefix)/lib/libgenometools.a
endif
Modified: trunk/packages/genometools/trunk/debian/patches/libbam-fix
===================================================================
--- trunk/packages/genometools/trunk/debian/patches/libbam-fix 2012-10-05
13:36:54 UTC (rev 12317)
+++ trunk/packages/genometools/trunk/debian/patches/libbam-fix 2012-10-05
14:07:42 UTC (rev 12318)
@@ -1,15 +1,15 @@
---- genometools-1.4.1.orig/Makefile
-+++ genometools-1.4.1/Makefile
-@@ -237,7 +237,7 @@
+--- a/Makefile
++++ b/Makefile
+@@ -240,7 +240,7 @@
# add necessary shared lib dependencies then not building them ourselves
ifeq ($(useshared),yes)
- DEPLIBS:=-lm -lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \
+ 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 += $(DEPLIBS)
+ else
+ DEPLIBS:=
endif
-@@ -520,6 +520,10 @@
+@@ -576,6 +576,10 @@
@$(RANLIB) $@
endif
@@ -20,103 +20,81 @@
lib/libgenometools.a: obj/gt_config.h $(LIBGENOMETOOLS_OBJ)
@echo "[link $(@F)]"
@test -d $(@D) || mkdir -p $(@D)
-@@ -528,19 +532,14 @@
- @$(RANLIB) $@
- endif
-
--ifneq ($(useshared),yes)
-- ADDITIONAL_SO_DEPS:=lib/libbz2.a \
-- lib/libexpat.a \
-- lib/libz.a
--endif
--
+@@ -593,12 +597,13 @@
lib/libgenometools$(SHARED_OBJ_NAME_EXT): obj/gt_config.h \
$(LIBGENOMETOOLS_OBJ) \
-- $(ADDITIONAL_SO_DEPS)
+ $(ADDITIONAL_SO_DEPS) \
+- $(ADDITIONAL_ZLIBS)
++ $(ADDITIONAL_ZLIBS) \
+ $(ADDITIONAL_STATIC_DEPS)
@echo "[link $(@F)]"
@test -d $(@D) || mkdir -p $(@D)
-- @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $(SHARED) -Wl,-soname,$(notdir
$@)$(SONAME_VERSION) $(LIBGENOMETOOLS_OBJ) \
+ @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $(ADDITIONAL_SO_DEPS) $(SHARED) \
+ -Wl,-soname,$(notdir $@)$(SONAME_VERSION) $(LIBGENOMETOOLS_OBJ) \
- -o $@$(SONAME_VERSION) $(GTSHAREDLIB_LIBDEP)
-+ @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $(SHARED) \
-+ -Wl,-soname,$(notdir $@)$(SONAME_VERSION) $(LIBGENOMETOOLS_OBJ) \
-+ -o $@$(SONAME_VERSION) $(GTSHAREDLIB_LIBDEP) $(ADDITIONAL_STATIC_DEPS)
++ -o $@$(SONAME_VERSION) $(GTSHAREDLIB_LIBDEP) $(ADDITIONAL_STATIC_DEPS)
lib/libtecla.a: $(LIBTECLA_OBJ)
@echo "[link $(@F)]"
-@@ -568,48 +567,62 @@
+@@ -619,51 +624,61 @@
$(eval $(call PROGRAM_template, bin/skproto, $(SKPROTO_OBJ) \
- lib/libgenometools.a\
+ lib/libgenometools.a \
+ $(ADDITIONAL_STATIC_DEPS) \
- $(OVERRIDELIBS)))
+ $(ADDITIONAL_ZLIBS)))
$(eval $(call PROGRAM_template, bin/gt, $(GTMAIN_OBJ) $(TOOLS_OBJ) \
lib/libgenometools.a \
+ $(ADDITIONAL_STATIC_DEPS) \
$(GTLIBS) \
- $(OVERRIDELIBS)))
+ $(ADDITIONAL_ZLIBS)))
$(eval $(call PROGRAM_template, bin/examples/custom_stream, \
obj/src/examples/custom_stream.o \
- lib/libgenometools.a \
+ lib/libgenometools.a\
+ $(ADDITIONAL_STATIC_DEPS) \
- $(OVERRIDELIBS)))
+ $(ADDITIONAL_ZLIBS)))
$(eval $(call PROGRAM_template, bin/examples/gff3sort, \
obj/src/examples/gff3sort.o \
lib/libgenometools.a \
+ $(ADDITIONAL_STATIC_DEPS) \
- $(OVERRIDELIBS)))
+ $(ADDITIONAL_ZLIBS)))
$(eval $(call PROGRAM_template, bin/examples/gff3validator, \
obj/src/examples/gff3validator.o \
lib/libgenometools.a \
+ $(ADDITIONAL_STATIC_DEPS) \
- $(OVERRIDELIBS)))
+ $(ADDITIONAL_ZLIBS)))
$(eval $(call PROGRAM_template, bin/examples/noop, \
obj/src/examples/noop.o \
lib/libgenometools.a \
+ $(ADDITIONAL_STATIC_DEPS) \
- $(OVERRIDELIBS)))
+ $(ADDITIONAL_ZLIBS)))
$(eval $(call PROGRAM_template, bin/examples/sketch_constructed, \
obj/src/examples/sketch_constructed.o \
-- lib/libgenometools.a $(OVERRIDELIBS)))
-+ lib/libgenometools.a \
+ lib/libgenometools.a \
+ $(ADDITIONAL_STATIC_DEPS) \
-+ $(OVERRIDELIBS)))
+ $(ADDITIONAL_ZLIBS)))
$(eval $(call PROGRAM_template, bin/examples/sketch_parsed, \
obj/src/examples/sketch_parsed.o \
-- lib/libgenometools.a $(OVERRIDELIBS)))
-+ lib/libgenometools.a \
+ lib/libgenometools.a \
+ $(ADDITIONAL_STATIC_DEPS) \
-+ $(OVERRIDELIBS)))
+ $(ADDITIONAL_ZLIBS)))
$(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 \
+ lib/libgenometools.a \
+ $(ADDITIONAL_STATIC_DEPS) \
-+ $(OVERRIDELIBS)))
+ $(ADDITIONAL_ZLIBS)))
$(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 \
+ lib/libgenometools.a \
+ $(ADDITIONAL_STATIC_DEPS) \
-+ $(OVERRIDELIBS)))
+ $(ADDITIONAL_ZLIBS)))
bin/lua: $(LUAMAIN_OBJ)
- @echo "[link $(@F)]"
-@@ -709,7 +722,7 @@
- @echo "[compile $$(@F)]"
- @test -d $$(@D) || mkdir -p $$(@D)
- @$$(CC) -c $$< -o $$@ $$(EXP_CPPFLAGS) $$(GT_CPPFLAGS) $$(EXP_CFLAGS) \
-- $$(GT_CFLAGS) $(3)
-+ $$(GT_CFLAGS) $(3)
- @$$(CC) -c $$< -o $$(@:.o=.d) $$(EXP_CPPFLAGS) $$(GT_CPPFLAGS) \
- $(3) -MM -MP -MT $$@
- endef
Modified: trunk/packages/genometools/trunk/debian/patches/remove-gitignores
===================================================================
--- trunk/packages/genometools/trunk/debian/patches/remove-gitignores
2012-10-05 13:36:54 UTC (rev 12317)
+++ trunk/packages/genometools/trunk/debian/patches/remove-gitignores
2012-10-05 14:07:42 UTC (rev 12318)
@@ -1,10 +1,10 @@
---- genometools-1.4.1.orig/doc/devguide/.gitignore
+--- a/doc/devguide/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-devguide.pdf
---- genometools-1.4.1.orig/doc/manuals/.gitignore
-+++ /dev/null
-@@ -1,8 +0,0 @@
+--- a/doc/manuals/.gitignore
++++ b/doc/manuals/.gitignore
+@@ -1,10 +1,2 @@
-comment.cut
-*.pdf
-api_reference.tex
@@ -13,3 +13,5 @@
-read1.fna
-read2.fna
-tallymer-tmp.tex
+ Q1.gz
+ tagerator-tmp.tex
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