[med-svn] r17477 - in trunk/packages/genometools/trunk/debian: . patches
Sascha Steinbiss
sascha-guest at moszumanska.debian.org
Wed Jul 16 20:12:57 UTC 2014
Author: sascha-guest
Date: 2014-07-16 20:12:56 +0000 (Wed, 16 Jul 2014)
New Revision: 17477
Removed:
trunk/packages/genometools/trunk/debian/patches/missing-libs
trunk/packages/genometools/trunk/debian/patches/no-xmllint
trunk/packages/genometools/trunk/debian/patches/spelling
Modified:
trunk/packages/genometools/trunk/debian/changelog
trunk/packages/genometools/trunk/debian/control
trunk/packages/genometools/trunk/debian/patches/adding_soname
trunk/packages/genometools/trunk/debian/patches/libbam-fix
trunk/packages/genometools/trunk/debian/patches/series
Log:
update to new upstream release
Modified: trunk/packages/genometools/trunk/debian/changelog
===================================================================
--- trunk/packages/genometools/trunk/debian/changelog 2014-07-16 15:13:16 UTC (rev 17476)
+++ trunk/packages/genometools/trunk/debian/changelog 2014-07-16 20:12:56 UTC (rev 17477)
@@ -1,3 +1,9 @@
+genometools (1.5.3-1) unstable; urgency=low
+
+ * New upstream release.
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Wed, 16 Jul 2014 20:32:19 +0100
+
genometools (1.5.2-4) unstable; urgency=low
* Incorporate patches addressing type conversion errors (thanks to
Modified: trunk/packages/genometools/trunk/debian/control
===================================================================
--- trunk/packages/genometools/trunk/debian/control 2014-07-16 15:13:16 UTC (rev 17476)
+++ trunk/packages/genometools/trunk/debian/control 2014-07-16 20:12:56 UTC (rev 17477)
@@ -1,6 +1,6 @@
Source: genometools
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>,
+Uploaders: Sascha Steinbiss <sascha at steinbiss.name>,
Andreas Tille <tille at debian.org>
Section: science
Priority: optional
Modified: trunk/packages/genometools/trunk/debian/patches/adding_soname
===================================================================
--- trunk/packages/genometools/trunk/debian/patches/adding_soname 2014-07-16 15:13:16 UTC (rev 17476)
+++ trunk/packages/genometools/trunk/debian/patches/adding_soname 2014-07-16 20:12:56 UTC (rev 17477)
@@ -13,19 +13,19 @@
# compiled executables
GTMAIN_SRC:=src/gt.c src/gtr.c src/gtt.c src/interactive.c
-@@ -540,8 +541,9 @@
- $(ADDITIONAL_ZLIBS)
+@@ -559,8 +560,9 @@
@echo "[link $(@F)]"
@test -d $(@D) || mkdir -p $(@D)
-- @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $(ADDITIONAL_SO_DEPS) $(SHARED) $(LIBGENOMETOOLS_OBJ) \
-- -o $@ $(GTSHAREDLIB_LIBDEP)
-+ @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $(ADDITIONAL_SO_DEPS) $(SHARED) \
-+ -Wl,-soname,$(notdir $@)$(SONAME_VERSION) $(LIBGENOMETOOLS_OBJ) \
-+ -o $@$(SONAME_VERSION) $(GTSHAREDLIB_LIBDEP)
+ @$(CC) $(EXP_LDFLAGS) $(VERSION_SCRIPT_PARAM) \
+- $(GT_LDFLAGS) $(ADDITIONAL_SO_DEPS) $(SHARED) $(LIBGENOMETOOLS_OBJ) \
+- -o $@ $(GTSHAREDLIB_LIBDEP)
++ $(GT_LDFLAGS) $(ADDITIONAL_SO_DEPS) $(SHARED) \
++ -Wl,-soname,$(notdir $@)$(SONAME_VERSION) $(LIBGENOMETOOLS_OBJ) \
++ -o $@$(SONAME_VERSION) $(GTSHAREDLIB_LIBDEP)
define PROGRAM_template
$(1): $(2)
-@@ -880,7 +882,8 @@
+@@ -915,7 +917,8 @@
$(RANLIB) $(prefix)/lib/libgenometools.a
endif
ifneq ($(sharedlib),no)
Modified: trunk/packages/genometools/trunk/debian/patches/libbam-fix
===================================================================
--- trunk/packages/genometools/trunk/debian/patches/libbam-fix 2014-07-16 15:13:16 UTC (rev 17476)
+++ trunk/packages/genometools/trunk/debian/patches/libbam-fix 2014-07-16 20:12:56 UTC (rev 17477)
@@ -9,15 +9,15 @@
# add necessary shared lib dependencies then not building them ourselves
ifeq ($(useshared),yes)
DEPLIBS:=-lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \
-- -llua5.1-filesystem -llua5.1-des56 -lbam -ltre
-+ -llua5.1-filesystem -llua5.1-des56 -ltre
+- -llua5.1-filesystem -llua5.1-des56 -lbam -ltre -lm -lpthread
++ -llua5.1-filesystem -llua5.1-des56 -ltre -lm -lpthread
else
DEPLIBS:=
endif
-@@ -521,6 +521,10 @@
+@@ -538,6 +538,10 @@
@$(RANLIB) $@
endif
-
+
+ifeq ($(useshared),yes)
+ ADDITIONAL_STATIC_DEPS:=/usr/lib/libbam.a
+endif
@@ -25,76 +25,75 @@
lib/libgenometools.a: obj/gt_config.h $(LIBGENOMETOOLS_OBJ)
@echo "[link $(@F)]"
@test -d $(@D) || mkdir -p $(@D)
-@@ -538,12 +542,13 @@
- lib/libgenometools$(SHARED_OBJ_NAME_EXT): obj/gt_config.h \
+@@ -556,13 +560,14 @@
$(LIBGENOMETOOLS_OBJ) \
$(ADDITIONAL_SO_DEPS) \
-- $(ADDITIONAL_ZLIBS)
-+ $(ADDITIONAL_ZLIBS) \
-+ $(ADDITIONAL_STATIC_DEPS)
+ $(ADDITIONAL_ZLIBS) \
++ $(ADDITIONAL_STATIC_DEPS) \
+ $(VERSION_SCRIPT)
@echo "[link $(@F)]"
@test -d $(@D) || mkdir -p $(@D)
- @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $(ADDITIONAL_SO_DEPS) $(SHARED) \
- -Wl,-soname,$(notdir $@)$(SONAME_VERSION) $(LIBGENOMETOOLS_OBJ) \
-- -o $@$(SONAME_VERSION) $(GTSHAREDLIB_LIBDEP)
-+ -o $@$(SONAME_VERSION) $(GTSHAREDLIB_LIBDEP) $(ADDITIONAL_STATIC_DEPS)
-
+ @$(CC) $(EXP_LDFLAGS) $(VERSION_SCRIPT_PARAM) \
+ $(GT_LDFLAGS) $(ADDITIONAL_SO_DEPS) $(SHARED) \
+ -Wl,-soname,$(notdir $@)$(SONAME_VERSION) $(LIBGENOMETOOLS_OBJ) \
+- -o $@$(SONAME_VERSION) $(GTSHAREDLIB_LIBDEP)
++ -o $@$(SONAME_VERSION) $(GTSHAREDLIB_LIBDEP) $(ADDITIONAL_STATIC_DEPS)
+
define PROGRAM_template
$(1): $(2)
-@@ -557,46 +562,55 @@
+@@ -575,46 +580,55 @@
+
$(eval $(call PROGRAM_template, bin/gt, $(GTMAIN_OBJ) $(TOOLS_OBJ) \
lib/libgenometools.a \
- $(GTLIBS) \
+ $(ADDITIONAL_STATIC_DEPS) \
$(ADDITIONAL_ZLIBS)))
-
+
$(eval $(call PROGRAM_template, bin/examples/custom_stream, \
obj/src/examples/custom_stream.o \
-- lib/libgenometools.a\
-+ lib/libgenometools.a \
+ lib/libgenometools.a\
+ $(ADDITIONAL_STATIC_DEPS) \
$(ADDITIONAL_ZLIBS)))
-
+
$(eval $(call PROGRAM_template, bin/examples/gff3sort, \
obj/src/examples/gff3sort.o \
lib/libgenometools.a \
+ $(ADDITIONAL_STATIC_DEPS) \
$(ADDITIONAL_ZLIBS)))
-
+
$(eval $(call PROGRAM_template, bin/examples/gff3validator, \
obj/src/examples/gff3validator.o \
lib/libgenometools.a \
+ $(ADDITIONAL_STATIC_DEPS) \
$(ADDITIONAL_ZLIBS)))
-
+
$(eval $(call PROGRAM_template, bin/examples/noop, \
obj/src/examples/noop.o \
lib/libgenometools.a \
+ $(ADDITIONAL_STATIC_DEPS) \
$(ADDITIONAL_ZLIBS)))
-
+
$(eval $(call PROGRAM_template, bin/examples/sketch_constructed, \
obj/src/examples/sketch_constructed.o \
lib/libgenometools.a \
+ $(ADDITIONAL_STATIC_DEPS) \
$(ADDITIONAL_ZLIBS)))
-
+
$(eval $(call PROGRAM_template, bin/examples/sketch_parsed, \
obj/src/examples/sketch_parsed.o \
lib/libgenometools.a \
+ $(ADDITIONAL_STATIC_DEPS) \
$(ADDITIONAL_ZLIBS)))
-
+
$(eval $(call PROGRAM_template, bin/examples/sketch_parsed_with_ctrack, \
obj/src/examples/sketch_parsed_with_ctrack.o \
lib/libgenometools.a \
+ $(ADDITIONAL_STATIC_DEPS) \
$(ADDITIONAL_ZLIBS)))
-
+
$(eval $(call PROGRAM_template, bin/examples/sketch_parsed_with_ordering, \
obj/src/examples/sketch_parsed_with_ordering.o \
lib/libgenometools.a \
+ $(ADDITIONAL_STATIC_DEPS) \
$(ADDITIONAL_ZLIBS)))
-
+
bin/lua: $(LUAMAIN_OBJ)
Deleted: trunk/packages/genometools/trunk/debian/patches/missing-libs
===================================================================
--- trunk/packages/genometools/trunk/debian/patches/missing-libs 2014-07-16 15:13:16 UTC (rev 17476)
+++ trunk/packages/genometools/trunk/debian/patches/missing-libs 2014-07-16 20:12:56 UTC (rev 17477)
@@ -1,44 +0,0 @@
-Description: Fix linking.
-Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
---- a/Makefile
-+++ b/Makefile
-@@ -192,7 +192,7 @@
- # add necessary shared lib dependencies then not building them ourselves
- ifeq ($(useshared),yes)
- DEPLIBS:=-lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \
-- -llua5.1-filesystem -llua5.1-des56 -ltre
-+ -llua5.1-filesystem -llua5.1-des56 -ltre -lm -lpthread
- else
- DEPLIBS:=
- endif
-@@ -381,19 +381,19 @@
- LIBGENOMETOOLS_DIRS := $(SQLITE3_DIR) $(LIBGENOMETOOLS_DIRS)
- GT_CPPFLAGS += -I$(CURDIR)/$(SQLITE3_DIR)
- OVERRIDELIBS += lib/libsqlite.a
-+ ifeq ($(threads),yes)
-+ EXP_CPPFLAGS += -DSQLITE_THREADSAFE=1
-+ else
-+ EXP_CPPFLAGS += -DSQLITE_THREADSAFE=0
-+ endif
-+ ifneq ($(SYSTEM),Windows)
-+ EXP_LDLIBS += -lpthread
-+ ifneq ($(SYSTEM),FreeBSD)
-+ EXP_LDLIBS += -ldl
-+ endif
-+ endif
- endif
- EXP_CPPFLAGS += -DHAVE_SQLITE
-- ifeq ($(threads),yes)
-- EXP_CPPFLAGS += -DSQLITE_THREADSAFE=1
-- else
-- EXP_CPPFLAGS += -DSQLITE_THREADSAFE=0
-- endif
-- ifneq ($(SYSTEM),Windows)
-- EXP_LDLIBS += -lpthread
-- ifneq ($(SYSTEM),FreeBSD)
-- EXP_LDLIBS += -ldl
-- endif
-- endif
- else
- SQLITE_FILTER_OUT:=src/extended/rdb_sqlite.c
- endif
Deleted: trunk/packages/genometools/trunk/debian/patches/no-xmllint
===================================================================
--- trunk/packages/genometools/trunk/debian/patches/no-xmllint 2014-07-16 15:13:16 UTC (rev 17476)
+++ trunk/packages/genometools/trunk/debian/patches/no-xmllint 2014-07-16 20:12:56 UTC (rev 17477)
@@ -1,12 +0,0 @@
-Description: Skip xmllint on manpage generation.
-Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
---- a/scripts/create_manpages
-+++ b/scripts/create_manpages
-@@ -3,6 +3,6 @@
- for FILE in $1/*.mansrc;
- do
- echo -n '.'
-- a2x --doctype manpage --format manpage -D $2 $FILE
-+ a2x --no-xmllint --doctype manpage --format manpage -D $2 $FILE
- done
- echo ''
Modified: trunk/packages/genometools/trunk/debian/patches/series
===================================================================
--- trunk/packages/genometools/trunk/debian/patches/series 2014-07-16 15:13:16 UTC (rev 17476)
+++ trunk/packages/genometools/trunk/debian/patches/series 2014-07-16 20:12:56 UTC (rev 17477)
@@ -1,13 +1,5 @@
-fix-unsigned-char
-add-libtre
adding_soname
libbam-fix
remove-gitignores
fix-exports
-missing-libs
-mips-64
-no-xmllint
-spelling
split-manuals
-arm64-no-m64
-typecheck-fixes
Deleted: trunk/packages/genometools/trunk/debian/patches/spelling
===================================================================
--- trunk/packages/genometools/trunk/debian/patches/spelling 2014-07-16 15:13:16 UTC (rev 17476)
+++ trunk/packages/genometools/trunk/debian/patches/spelling 2014-07-16 20:12:56 UTC (rev 17477)
@@ -1,25 +0,0 @@
-Description: Fix spelling in hop.
-Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
---- a/src/tools/gt_hop.c
-+++ b/src/tools/gt_hop.c
-@@ -141,7 +141,8 @@
- "the corrected reads are output in the currect working directory "
- "in files which are named as the input files, each prepended "
- "by a prefix (see -outprefix option)\n"
-- "-reads allows one to output the reads in the same order as in the input "
-+ "-reads allows one one to output the reads in the same order as "
-+ "in the input "
- "and is mandatory if the SAM contains more than a single primary "
- "alignment for each read (e.g. output of bwasw)\n"
- "see also -o option as an alternative",
---- a/gtdata/doc/hop.lua
-+++ b/gtdata/doc/hop.lua
-@@ -25,7 +25,7 @@
- mode to minimize the false positives. An even more conservative set
- of corrections can be achieved using the '-ann' option (see '-help+').
-
--The '-expert' mode allows to manually set each parameter; the default
-+The '-expert' mode allows one to manually set each parameter; the default
- values are the same as in the '-conservative' mode.
-
- (Finally, for evaluation purposes only, the '-state-of-truth' mode can be used:
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