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commit 793e425871dd01fc3a0c4ea0e0023a459120acaf Author: Sascha Steinbiss <[email protected]> Date: Mon Mar 7 22:44:08 2016 +0000 use pkg-config for shared lib detection --- debian/changelog | 7 ++ debian/patches/adding_soname | 6 +- debian/patches/libbam-fix | 8 +- debian/patches/series | 1 + debian/patches/use-mx32 | 2 +- debian/patches/use-pkgconfig | 244 +++++++++++++++++++++++++++++++++++++++++++ debian/rules | 2 + 7 files changed, 262 insertions(+), 8 deletions(-) diff --git a/debian/changelog b/debian/changelog index 9ea08c1..3262281 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,10 @@ +genometools (1.5.8-3) UNRELEASED; urgency=medium + + * Make sure external headers are used for compilation. + Thanks to Justus Winter for the patch. + + -- Sascha Steinbiss <[email protected]> Wed, 02 Mar 2016 15:43:46 +0000 + genometools (1.5.8-2) unstable; urgency=medium * Document migration to Git in d/control diff --git a/debian/patches/adding_soname b/debian/patches/adding_soname index 5a30100..091e3e5 100644 --- a/debian/patches/adding_soname +++ b/debian/patches/adding_soname @@ -5,7 +5,7 @@ Description: add soname to linker call in Makefile Author: Sascha Steinbiss <[email protected]> --- a/Makefile +++ b/Makefile -@@ -105,6 +105,7 @@ +@@ -137,6 +137,7 @@ SHARED_OBJ_NAME_EXT:=.so SHARED:=-shared endif @@ -13,7 +13,7 @@ Author: Sascha Steinbiss <[email protected]> # compiled executables GTMAIN_SRC:=src/gt.c src/gtr.c src/gtt.c src/interactive.c -@@ -585,8 +586,9 @@ +@@ -618,8 +619,9 @@ @echo "[link $(@F)]" @test -d $(@D) || mkdir -p $(@D) @$(CC) $(EXP_LDFLAGS) $(VERSION_SCRIPT_PARAM) \ @@ -25,7 +25,7 @@ Author: Sascha Steinbiss <[email protected]> define PROGRAM_template $(1): $(2) -@@ -944,7 +946,8 @@ +@@ -986,7 +988,8 @@ $(RANLIB) $(prefix)/lib/libgenometools.a endif ifneq ($(sharedlib),no) diff --git a/debian/patches/libbam-fix b/debian/patches/libbam-fix index 6d09fdf..fb2b2b9 100644 --- a/debian/patches/libbam-fix +++ b/debian/patches/libbam-fix @@ -5,7 +5,7 @@ Author: Sascha Steinbiss <[email protected]> --- a/Makefile +++ b/Makefile -@@ -195,7 +195,7 @@ +@@ -228,7 +228,7 @@ # add necessary shared lib dependencies then not building them ourselves ifeq ($(useshared),yes) DEPLIBS:=-lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \ @@ -14,7 +14,7 @@ Author: Sascha Steinbiss <[email protected]> else DEPLIBS:= endif -@@ -564,6 +564,10 @@ +@@ -597,6 +597,10 @@ @$(RANLIB) $@ endif @@ -25,7 +25,7 @@ Author: Sascha Steinbiss <[email protected]> lib/libgenometools.a: obj/gt_config.h $(LIBGENOMETOOLS_OBJ) @echo "[link $(@F)]" @test -d $(@D) || mkdir -p $(@D) -@@ -582,13 +586,14 @@ +@@ -615,13 +619,14 @@ $(LIBGENOMETOOLS_OBJ) \ $(ADDITIONAL_SO_DEPS) \ $(ADDITIONAL_ZLIBS) \ @@ -41,7 +41,7 @@ Author: Sascha Steinbiss <[email protected]> define PROGRAM_template $(1): $(2) -@@ -601,46 +606,55 @@ +@@ -634,46 +639,55 @@ $(eval $(call PROGRAM_template, bin/gt, $(GTMAIN_OBJ) $(TOOLS_OBJ) \ lib/libgenometools.a \ diff --git a/debian/patches/series b/debian/patches/series index 692e2de..47c4757 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,5 +1,6 @@ spelling remove_png_timestamps +use-pkgconfig adding_soname libbam-fix remove-gitignores diff --git a/debian/patches/use-mx32 b/debian/patches/use-mx32 index dc922a2..005b988 100644 --- a/debian/patches/use-mx32 +++ b/debian/patches/use-mx32 @@ -1,7 +1,7 @@ Description: Use mx32 --- a/Makefile +++ b/Makefile -@@ -327,17 +327,19 @@ +@@ -360,17 +360,19 @@ endif endif diff --git a/debian/patches/use-pkgconfig b/debian/patches/use-pkgconfig new file mode 100644 index 0000000..5a55300 --- /dev/null +++ b/debian/patches/use-pkgconfig @@ -0,0 +1,244 @@ +From afaed82084071e9d11663b7ce593fa83e6eabbe5 Mon Sep 17 00:00:00 2001 +From: Justus Winter <[email protected]> +Date: Fri, 19 Feb 2016 14:06:41 +0100 +Subject: [PATCH 1/6] Makefile: Drop spurious '$(3)' + +* Makefile: Drop spurious '$(3)', likely a left-over from copying +'COMPILE_template'. +--- + Makefile | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +--- a/Makefile ++++ b/Makefile +@@ -16,17 +16,7 @@ + # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. + # + +-INCLUDEOPT:=-I$(CURDIR)/src -I$(CURDIR)/obj \ +- -I$(CURDIR)/src/external/zlib-1.2.8 \ +- -I$(CURDIR)/src/external/md5-1.1.2/src \ +- -I$(CURDIR)/src/external/lua-5.1.5/src \ +- -I$(CURDIR)/src/external/luafilesystem-1.5.0/src \ +- -I$(CURDIR)/src/external/lpeg-0.10.2 \ +- -I$(CURDIR)/src/external/expat-2.0.1/lib \ +- -I$(CURDIR)/src/external/bzip2-1.0.6 \ +- -I$(CURDIR)/src/external/samtools-0.1.18 \ +- -I$(CURDIR)/src/external/sqlite-3.8.7.1 \ +- -I$(CURDIR)/src/external/tre/include/tre ++INCLUDEOPT:=-I$(CURDIR)/src -I$(CURDIR)/obj + + ifeq ($(shell pkg-config --version > /dev/null 2> /dev/null; echo $$?),0) + HAS_PKGCONFIG:=yes +@@ -37,6 +27,48 @@ + HAS_PKGCONFIG:=no + endif + ++# add necessary shared lib dependencies instead of building them ourselves ++ifeq ($(useshared),yes) ++ ifeq ($(HAS_PKGCONFIG),yes) ++ DEPLIBS:=-lbz2 \ ++ $(shell $(OVERRIDE_PC_PATH) pkg-config --libs zlib) \ ++ $(shell $(OVERRIDE_PC_PATH) pkg-config --libs expat) \ ++ $(shell $(OVERRIDE_PC_PATH) pkg-config --libs lua-5.1) \ ++ $(shell $(OVERRIDE_PC_PATH) pkg-config --libs lua5.1-lpeg) \ ++ $(shell $(OVERRIDE_PC_PATH) pkg-config --libs lua5.1-md5) \ ++ $(shell $(OVERRIDE_PC_PATH) pkg-config --libs lua5.1-filesystem) \ ++ $(shell $(OVERRIDE_PC_PATH) pkg-config --libs lua5.1-des56) \ ++ -lbam \ ++ $(shell $(OVERRIDE_PC_PATH) pkg-config --libs tre) \ ++ -lm -lpthread ++ INCLUDEOPT+=$(shell $(OVERRIDE_PC_PATH) pkg-config --cflags zlib) \ ++ $(shell $(OVERRIDE_PC_PATH) pkg-config --cflags expat) \ ++ $(shell $(OVERRIDE_PC_PATH) pkg-config --cflags lua-5.1) \ ++ $(shell $(OVERRIDE_PC_PATH) pkg-config --cflags lua5.1-lpeg) \ ++ $(shell $(OVERRIDE_PC_PATH) pkg-config --cflags lua5.1-md5) \ ++ $(shell $(OVERRIDE_PC_PATH) pkg-config --cflags lua5.1-filesystem) \ ++ $(shell $(OVERRIDE_PC_PATH) pkg-config --cflags lua5.1-des56) \ ++ $(shell $(OVERRIDE_PC_PATH) pkg-config --cflags tre) ++ else ++ # Requested the use of shared libraries without having pkg-config. ++ # You are on your own. Good luck. ++ DEPLIBS:=-lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \ ++ -llua5.1-filesystem -llua5.1-des56 -lbam -ltre -lm -lpthread ++ endif ++else ++ DEPLIBS:= ++ INCLUDEOPT+=-I$(CURDIR)/src/external/zlib-1.2.8 \ ++ -I$(CURDIR)/src/external/md5-1.1.2/src \ ++ -I$(CURDIR)/src/external/lua-5.1.5/src \ ++ -I$(CURDIR)/src/external/luafilesystem-1.5.0/src \ ++ -I$(CURDIR)/src/external/lpeg-0.10.2 \ ++ -I$(CURDIR)/src/external/expat-2.0.1/lib \ ++ -I$(CURDIR)/src/external/bzip2-1.0.6 \ ++ -I$(CURDIR)/src/external/samtools-0.1.18 \ ++ -I$(CURDIR)/src/external/sqlite-3.8.7.1 \ ++ -I$(CURDIR)/src/external/tre/include ++endif ++ + ifneq ($(cairo),no) + # XXX: check for existence of packages, and emit warning and disable cairo + # if packages are not available +@@ -125,6 +157,7 @@ + LIBEXPAT_DEP:=$(LIBEXPAT_SRC:%.c=obj/%.d) + + TRE_DIR:=src/external/tre/lib ++TRE_CPPFLAGS=-I$(CURDIR)/src/external/tre/include/tre + LIBTRE_SRC:=$(TRE_DIR)/regcomp.c $(TRE_DIR)/regerror.c $(TRE_DIR)/regexec.c \ + $(TRE_DIR)/tre-ast.c $(TRE_DIR)/tre-compile.c \ + $(TRE_DIR)/tre-filter.c $(TRE_DIR)/tre-match-backtrack.c \ +@@ -743,6 +776,15 @@ + @$(CC) -c $< -o $(@:.o=.d) -DHAVE_MALLOC_USABLE_SIZE $(EXP_CPPFLAGS) \ + $(GT_CPPFLAGS) $(3) -MM -MP -MT $@ $(FPIC) + ++# TRE needs special attention ++obj/$(TRE_DIR)/%.o: $(TRE_DIR)/%.c ++ $(V_ECHO) "[compile $(@F)]" ++ $(V_DO)test -d $(@D) || mkdir -p $(@D) ++ $(V_DO)$(CC) -c $< -o $@ $(EXP_CPPFLAGS) \ ++ $(GT_CPPFLAGS) $(EXP_CFLAGS) $(TRE_CPPFLAGS) $(FPIC) ++ $(V_DO)$(CC) -c $< -o $(@:.o=.d) $(EXP_CPPFLAGS) \ ++ $(GT_CPPFLAGS) $(TRE_CPPFLAGS) -MM -MP -MT $@ $(FPIC) ++ + define COMPILE_template + $(1): $(2) + @echo "[compile $$(@F)]" +@@ -1001,10 +1043,10 @@ + src_check src/ltr/* + + splintclean: +- find obj -name '*.splint' | xargs rm -f ++ find obj -name '*.splint' -delete + + sbclean: +- find obj -name '*.sb' | xargs rm -f ++ find obj -name '*.sb' -delete + + obj/%.sb: src/match/%.c + @echo "scan-build $<" +@@ -1070,7 +1112,7 @@ + headercheck:${ALLHEADER} + + headerclean: +- find obj -name '*.check' | xargs rm -f ++ find obj -name '*.check' -delete + + obj/%.check: ${CURDIR}/src/match/%.h + @echo "check include $<" +@@ -1139,7 +1181,7 @@ + + clean: + rm -rf lib +- find obj -name '*.o' |xargs rm -f ++ find obj -name '*.o' -delete + rm -f obj/amalgamation.c + rm -rf testsuite/stest_testsuite testsuite/stest_stest_tests + $(MAKE) -s -C $(CURDIR)/doc/devguide clean +--- a/src/core/grep.c ++++ b/src/core/grep.c +@@ -23,7 +23,7 @@ + #include "core/ma.h" + #include "core/str.h" + #include "core/unused_api.h" +-#include "tre.h" ++#include <tre/tre.h> + + static void grep_error(int errcode, regex_t *matcher, GtError *err) + { +--- a/src/extended/rcr.c ++++ b/src/extended/rcr.c +@@ -48,7 +48,7 @@ + #include "extended/sam_alignment.h" + #include "extended/sam_query_name_iterator.h" + #include "extended/samfile_iterator.h" +-#include "sam.h" ++#include <samtools/sam.h> + + #define BAMBASEA 1 + #define BAMBASEC 2 +--- a/src/extended/sam_alignment.c ++++ b/src/extended/sam_alignment.c +@@ -16,7 +16,7 @@ + OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. + */ + +-#include <sam.h> ++#include <samtools/sam.h> + #include "core/alphabet_api.h" + #include "core/ensure.h" + #include "core/ma_api.h" +--- a/src/extended/sam_alignment_rep.h ++++ b/src/extended/sam_alignment_rep.h +@@ -23,7 +23,7 @@ + /* The contents of this file is to be considered private implementation detail. + */ + +-#include <sam.h> ++#include <samtools/sam.h> + #include "core/alphabet_api.h" + + struct GtSamAlignment{ +--- a/src/extended/samfile_iterator.c ++++ b/src/extended/samfile_iterator.c +@@ -15,7 +15,7 @@ + OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. + */ + +-#include <sam.h> ++#include <samtools/sam.h> + #include "core/cstr_api.h" + #include "core/ensure.h" + #include "core/error_api.h" +--- /dev/null ++++ b/src/external/lpeg-0.10.2/lua-lpeg.h +@@ -0,0 +1,39 @@ ++/* ++** $Id: lpeg.h,v 1.1 2009/12/23 16:15:36 roberto Exp $ ++** LPeg - PEG pattern matching for Lua ++** Copyright 2009, Lua.org & PUC-Rio (see 'lpeg.html' for license) ++** written by Roberto Ierusalimschy ++*/ ++ ++#ifndef lpeg_h ++#define lpeg_h ++ ++#include "lua.h" ++ ++int luaopen_lpeg (lua_State *L); ++ ++#define KEYNEWPATT "lpeg.newpf" ++ ++ ++/* ++** type of extension functions that define new "patterns" for LPEG ++** It should return the new current position or NULL if match fails ++*/ ++typedef const char *(*PattFunc) (const char *s, /* current position */ ++ const char *e, /* string end */ ++ const char *o, /* string start */ ++ const void *ud); /* user data */ ++ ++/* ++** function to create new patterns based on 'PattFunc' functions. ++** This function is available at *registry[KEYNEWPATT]. (Notice ++** the extra indirection; the userdata at the registry points to ++** a variable that points to the function. In ANSI C a void* cannot ++** point to a function.) ++*/ ++typedef void (*Newpf) (lua_State *L, ++ PattFunc f, /* pattern */ ++ const void *ud, /* (user) data to be passed to 'f' */ ++ size_t l); /* size of data to be passed to 'f' */ ++ ++#endif +--- a/src/gtr.c ++++ b/src/gtr.c +@@ -24,7 +24,7 @@ + #include "lauxlib.h" + #include "lualib.h" + #include "lfs.h" +-#include "lpeg.h" ++#include "lua-lpeg.h" + #include "md5.h" + #include "ldes56.h" + #include "core/compat.h" diff --git a/debian/rules b/debian/rules index 6234ade..8a4f38e 100755 --- a/debian/rules +++ b/debian/rules @@ -31,6 +31,7 @@ endif dh $@ --with python2 override_dh_auto_clean: + mkdir obj $(MAKE) cleanup cd doc/manuals; $(MAKE) cleanup # should be deleted inside doc/manuals/Makefile @@ -50,6 +51,7 @@ override_dh_auto_clean: www/genometools.org/htdocs/libgenometools.html \ www/genometools.org/htdocs/tools/gt.html rm -rf gtpython/build + rm -rf obj override_dh_auto_build: $(FAKETIME) dh_auto_build -- useshared=yes x32=$(X32) 64bit=$(64BIT) errorcheck=no all docs manuals -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/genometools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
