[med-svn] r12070 - in trunk/packages/rcsb-core-wrapper/trunk/debian: . patches
Laszlo Kajan
lkajan-guest at alioth.debian.org
Thu Aug 16 16:54:15 UTC 2012
Author: lkajan-guest
Date: 2012-08-16 16:54:15 +0000 (Thu, 16 Aug 2012)
New Revision: 12070
Added:
trunk/packages/rcsb-core-wrapper/trunk/debian/patches/exit-in-shlib
trunk/packages/rcsb-core-wrapper/trunk/debian/patches/hardening
trunk/packages/rcsb-core-wrapper/trunk/debian/patches/spelling
Modified:
trunk/packages/rcsb-core-wrapper/trunk/debian/patches/docs
trunk/packages/rcsb-core-wrapper/trunk/debian/patches/series
trunk/packages/rcsb-core-wrapper/trunk/debian/rules
Log:
fixed stuff lintian complained about - what I could (in reasonable time)
Modified: trunk/packages/rcsb-core-wrapper/trunk/debian/patches/docs
===================================================================
--- trunk/packages/rcsb-core-wrapper/trunk/debian/patches/docs 2012-08-16 14:01:19 UTC (rev 12069)
+++ trunk/packages/rcsb-core-wrapper/trunk/debian/patches/docs 2012-08-16 16:54:15 UTC (rev 12070)
@@ -18,6 +18,37 @@
# If the EXTRACT_STATIC tag is set to YES all static members of a file
# will be included in the documentation.
+@@ -423,26 +423,26 @@
+ # The QUIET tag can be used to turn on/off the messages that are generated
+ # by doxygen. Possible values are YES and NO. If left blank NO is used.
+
+-QUIET = NO
++QUIET = YES
+
+ # The WARNINGS tag can be used to turn on/off the warning messages that are
+ # generated by doxygen. Possible values are YES and NO. If left blank
+ # NO is used.
+
+-WARNINGS = YES
++WARNINGS = NO
+
+ # If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
+ # for undocumented members. If EXTRACT_ALL is set to YES then this flag will
+ # automatically be disabled.
+
+-WARN_IF_UNDOCUMENTED = YES
++WARN_IF_UNDOCUMENTED = NO
+
+ # If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
+ # potential errors in the documentation, such as not documenting some
+ # parameters in a documented function, or documenting parameters that
+ # don't exist or using markup commands wrongly.
+
+-WARN_IF_DOC_ERROR = YES
++WARN_IF_DOC_ERROR = NO
+
+ # This WARN_NO_PARAMDOC option can be abled to get warnings for
+ # functions that are documented, but have no documentation for their parameters
@@ -798,7 +798,7 @@
# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
# generate Latex output.
Added: trunk/packages/rcsb-core-wrapper/trunk/debian/patches/exit-in-shlib
===================================================================
--- trunk/packages/rcsb-core-wrapper/trunk/debian/patches/exit-in-shlib (rev 0)
+++ trunk/packages/rcsb-core-wrapper/trunk/debian/patches/exit-in-shlib 2012-08-16 16:54:15 UTC (rev 12070)
@@ -0,0 +1,11 @@
+--- a/cif-file/src/ParentChild.C
++++ b/cif-file/src/ParentChild.C
+@@ -287,7 +287,7 @@
+ #ifdef VLAD_FIX
+ if (parKeys.empty())
+ {
+- cout << "EMPTY PARENT KEYS !!!" << endl;
++ cerr << "EMPTY PARENT KEYS !!!" << endl;
+ exit(1);
+ }
+ #endif
Added: trunk/packages/rcsb-core-wrapper/trunk/debian/patches/hardening
===================================================================
--- trunk/packages/rcsb-core-wrapper/trunk/debian/patches/hardening (rev 0)
+++ trunk/packages/rcsb-core-wrapper/trunk/debian/patches/hardening 2012-08-16 16:54:15 UTC (rev 12070)
@@ -0,0 +1,189 @@
+--- a/cif-file/Makefile
++++ b/cif-file/Makefile
+@@ -141,5 +141,5 @@
+
+ # Rule for making object files
+ %.o: $(SRC_DIR)/%.C
+- libtool --mode=compile $(CCC) $(C++FLAGS) -c $< -o $(OBJ_DIR)/$@
++ libtool --mode=compile $(CCC) $(CPPFLAGS) $(C++FLAGS) -c $< -o $(OBJ_DIR)/$@
+
+--- a/cif-file-util/Makefile
++++ b/cif-file-util/Makefile
+@@ -141,5 +141,5 @@
+
+ # Rule for making object files
+ %.o: $(SRC_DIR)/%.C
+- libtool --mode=compile $(CCC) $(C++FLAGS) -c $< -o $(OBJ_DIR)/$@
++ libtool --mode=compile $(CCC) $(CPPFLAGS) $(C++FLAGS) -c $< -o $(OBJ_DIR)/$@
+
+--- a/cif-parser/Makefile
++++ b/cif-parser/Makefile
+@@ -181,14 +181,14 @@
+ @sh -c 'cd $(SRC_DIR); $(YACC) $(${^F:.y=_YACC_FLAGS}) ../$<'
+ mv $(^:.y=.tab.c) $(^:.y=.c)
+ mv $(^:.y=.tab.h) $(^:.y=.h)
+- libtool --mode=compile $(CC) $(CFLAGS_NONANSI) -c $(^:.y=.c) -o $@
++ libtool --mode=compile $(CC) $(CPPFLAGS) $(CFLAGS_NONANSI) -c $(^:.y=.c) -o $@
+
+ obj/%Scanner.o: $(SRC_DIR)/%Scanner.l $(OBJ_DIR)/%Parser.o
+ $(LEX) $($(@F:.o=_LEX_FLAGS)) -t $(SRC_DIR)/$(@F:.o=.l) > $(SRC_DIR)/$(@F:.o=.c)
+- libtool --mode=compile $(CC) $(CFLAGS_NONANSI) -c $(SRC_DIR)/$(@F:.o=.c) -o $(OBJ_DIR)/$(@F)
++ libtool --mode=compile $(CC) $(CPPFLAGS) $(CFLAGS_NONANSI) -c $(SRC_DIR)/$(@F:.o=.c) -o $(OBJ_DIR)/$(@F)
+
+
+ # Rule for making other object files
+ obj/%.o: $(SRC_DIR)/%.C
+- libtool --mode=compile $(CCC) $(C++FLAGS) -c $< -o $(OBJ_DIR)/$(@F)
++ libtool --mode=compile $(CCC) $(CPPFLAGS) $(C++FLAGS) -c $< -o $(OBJ_DIR)/$(@F)
+
+--- a/common/Makefile
++++ b/common/Makefile
+@@ -153,5 +153,5 @@
+
+ # Rule for making object files
+ %.o: $(SRC_DIR)/%.C
+- libtool --mode=compile $(CCC) $(C++FLAGS) -c $< -o $(OBJ_DIR)/$@
++ libtool --mode=compile $(CCC) $(CPPFLAGS) $(C++FLAGS) -c $< -o $(OBJ_DIR)/$@
+
+--- a/dict-obj-file/Makefile
++++ b/dict-obj-file/Makefile
+@@ -142,7 +142,7 @@
+
+ # Rule for making executables
+ %: $(OBJ_DIR)/%.o $(M_MOD_LIB) $(ALL_DEP_LIBS)
+- $(CCC) $(LDFLAGS) $< $(M_MOD_LIB) $(ALL_DEP_LIBS) $(MALLOCLIB) -lm -o $(L_BIN_DIR)/$@
++ $(CCC) $(CPPFLAGS) $(LDFLAGS) $< $(M_MOD_LIB) $(ALL_DEP_LIBS) $(MALLOCLIB) -lm -o $(L_BIN_DIR)/$@
+ @cp -f $(L_BIN_DIR)/$@ $(M_BIN_DIR)/$@
+
+
+@@ -203,10 +203,10 @@
+
+ # Rule for making object files
+ $(OBJ_DIR)/%.o: $(SRC_DIR)/%.C
+- $(CCC) $(C++FLAGS) -c $< -o $@
++ $(CCC) $(CPPFLAGS) $(C++FLAGS) -c $< -o $@
+
+
+ # Phony rule for making object files
+ %.o: $(SRC_DIR)/%.C
+- libtool --mode=compile $(CCC) $(C++FLAGS) -c $< -o $(OBJ_DIR)/$@
++ libtool --mode=compile $(CCC) $(CPPFLAGS) $(C++FLAGS) -c $< -o $(OBJ_DIR)/$@
+
+--- a/etc/make.platform.gnu4
++++ b/etc/make.platform.gnu4
+@@ -108,8 +108,8 @@
+ C_WARNINGS=$(WARNINGS)
+
+ # C compiler flags
+-CFLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
+-CFLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES)
++CFLAGS += $(OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
++CFLAGS_NONANSI += $(OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES)
+
+ ## C++ compiler
+ ## This part defines C++ compiler information
+@@ -128,9 +128,9 @@
+ EXT=C
+
+ # C++ compiler flags
+-C++FLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
++C++FLAGS= $(CXXFLAGS) $(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
+ $(DEFINES) $(INCLUDES)
+-C++FLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \
++C++FLAGS_NONANSI= $(CXXFLAGS) $(OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \
+ $(C_PLUS_WARNINGS) $(DEFINES) $(INCLUDES)
+
+ # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
+@@ -158,8 +158,8 @@
+ STATIC_LINKING=-static
+
+ # Linker flags
+-LDFLAGS=$(ABI) -w $(STATIC_LINKING)
+-LDFLAGS_NO_STATIC=$(ABI) -w
++LDFLAGS += $(ABI) -w $(STATIC_LINKING)
++LDFLAGS_NO_STATIC += $(ABI) -w
+
+ # Fortran linker
+ F77_LINKER=f77
+--- a/pdbml-parser/Makefile
++++ b/pdbml-parser/Makefile
+@@ -157,7 +157,7 @@
+
+ # General rule for making executables
+ %: $(OBJ_DIR)/%.o $(M_MOD_LIB) $(ALL_DEP_LIBS)
+- $(CCC) $(LDFLAGS_NO_STATIC) $(EXT_LIBS_DIRS) $< $(M_MOD_LIB) $(ALL_DEP_LIBS) $(EXT_LIBS) $(MALLOCLIB) -lm -o $(L_BIN_DIR)/$@
++ $(CCC) $(CPPFLAGS) $(LDFLAGS_NO_STATIC) $(EXT_LIBS_DIRS) $< $(M_MOD_LIB) $(ALL_DEP_LIBS) $(EXT_LIBS) $(MALLOCLIB) -lm -o $(L_BIN_DIR)/$@
+ @cp -f $(L_BIN_DIR)/$@ $(M_BIN_DIR)/$@
+
+
+@@ -222,10 +222,10 @@
+
+ # General rule for making object files
+ $(OBJ_DIR)/%.o: $(SRC_DIR)/%.C
+- $(CCC) $(C++FLAGS) -c $< -o $@
++ $(CCC) $(CPPFLAGS) $(C++FLAGS) -c $< -o $@
+
+
+ # Phony rule for making object files
+ %.o: $(SRC_DIR)/%.C
+- libtool --mode=compile $(CCC) $(C++FLAGS) -c $< -o $(OBJ_DIR)/$@
++ libtool --mode=compile $(CCC) $(CPPFLAGS) $(C++FLAGS) -c $< -o $(OBJ_DIR)/$@
+
+--- a/tables/Makefile
++++ b/tables/Makefile
+@@ -138,5 +138,5 @@
+
+ # Rule for making object files
+ %.o: $(SRC_DIR)/%.C
+- libtool --mode=compile $(CCC) $(C++FLAGS) -c $< -o $(OBJ_DIR)/$@
++ libtool --mode=compile $(CCC) $(CPPFLAGS) $(C++FLAGS) -c $< -o $(OBJ_DIR)/$@
+
+--- a/wrapper/Makefile
++++ b/wrapper/Makefile
+@@ -146,10 +146,10 @@
+ $(L_MOD_LIB): $(OBJ_FILES) $(ALL_DEP_LIBS)
+ # Create module library
+
+- cd $(OBJ_DIR); $(CCC) $(LINK_METHOD) $(EXT_LIBS_DIRS) $(OBJ_FILES) -L../../lib/.libs -lrcsb-core-wrapper $(EXT_LIBS) $(SYS_LIBS) -o ../$@
++ cd $(OBJ_DIR); $(CCC) $(CPPFLAGS) $(LINK_METHOD) $(EXT_LIBS_DIRS) $(OBJ_FILES) -L../../lib/.libs -lrcsb-core-wrapper $(EXT_LIBS) $(SYS_LIBS) -o ../$@
+
+
+ # Rule for making object files
+ %.o: $(SRC_DIR)/%.C
+- $(CCC) $(C++FLAGS) $(EXT_COMP_OPT) -c $< -o $(OBJ_DIR)/$@
++ $(CCC) $(CPPFLAGS) $(C++FLAGS) $(EXT_COMP_OPT) -c $< -o $(OBJ_DIR)/$@
+
+--- a/regex/Makefile
++++ b/regex/Makefile
+@@ -152,7 +152,7 @@
+
+ # Rule for making object files
+ %.o: $(SRC_DIR)/%.c
+- libtool --mode=compile $(CC) $(CFLAGS_NONANSI) -DPOSIX_MISTAKE -c $< -o $(OBJ_DIR)/$@
++ libtool --mode=compile $(CC) $(CPPFLAGS) $(CFLAGS_NONANSI) -DPOSIX_MISTAKE -c $< -o $(OBJ_DIR)/$@
+
+
+ # Extra, non-used in PDB build
+@@ -180,18 +180,18 @@
+
+
+ $(OBJ_DIR)/main.o: $(H) $(HEADER_FILES) $(SRC_DIR)/main.c $(L_INCL_DIR)/main.ih
+- $(CC) $(CFLAGS_NONANSI) -DPOSIX_MISTAKE -c $(SRC_DIR)/main.c -o $@
++ $(CC) $(CPPFLAGS) $(CFLAGS_NONANSI) -DPOSIX_MISTAKE -c $(SRC_DIR)/main.c -o $@
+
+ $(OBJ_DIR)/split.o: $(H) $(HEADER_FILES) $(SRC_DIR)/split.c
+- libtool --mode=compile $(CC) $(CFLAGS_NONANSI) -DPOSIX_MISTAKE -c $(SRC_DIR)/split.c -o $@
++ libtool --mode=compile $(CC) $(CPPFLAGS) $(CFLAGS_NONANSI) -DPOSIX_MISTAKE -c $(SRC_DIR)/split.c -o $@
+
+ debug.o: $(H) $(HEADER_FILES) $(SRC_DIR)/debug.c $(L_INCL_DIR)/debug.ih
+- $(CC) $(CFLAGS_NONANSI) -DPOSIX_MISTAKE -c $(SRC_DIR)/debug.c -o $(OBJ_DIR)/$@
++ $(CC) $(CPPFLAGS) $(CFLAGS_NONANSI) -DPOSIX_MISTAKE -c $(SRC_DIR)/debug.c -o $(OBJ_DIR)/$@
+
+
+ # tester
+ $(TARGET): $(ALLOBJS)
+- $(CC) $(CFLAGS) -DPOSIX_MISTAKE $(LDFLAGS) $(ALLOBJS) $(LIBS) -o $@
++ $(CC) $(CPPFLAGS) $(CFLAGS) -DPOSIX_MISTAKE $(LDFLAGS) $(ALLOBJS) $(LIBS) -o $@
+
+
+ # regression test
Modified: trunk/packages/rcsb-core-wrapper/trunk/debian/patches/series
===================================================================
--- trunk/packages/rcsb-core-wrapper/trunk/debian/patches/series 2012-08-16 14:01:19 UTC (rev 12069)
+++ trunk/packages/rcsb-core-wrapper/trunk/debian/patches/series 2012-08-16 16:54:15 UTC (rev 12070)
@@ -9,3 +9,6 @@
objectfiles
wrapper
setup.py.in
+hardening
+spelling
+exit-in-shlib
Added: trunk/packages/rcsb-core-wrapper/trunk/debian/patches/spelling
===================================================================
--- trunk/packages/rcsb-core-wrapper/trunk/debian/patches/spelling (rev 0)
+++ trunk/packages/rcsb-core-wrapper/trunk/debian/patches/spelling 2012-08-16 16:54:15 UTC (rev 12070)
@@ -0,0 +1,31 @@
+--- a/wrapper/src/DataInfoPyWrap.C
++++ b/wrapper/src/DataInfoPyWrap.C
+@@ -31,23 +31,23 @@
+ }
+
+ virtual ::std::vector< std::string > const & GetCatAttribute( ::std::string const & catName, ::std::string const & refCatName, ::std::string const & refAttribName ){
+- throw std::logic_error("warning W1049: This method could not be overriden in Python - method returns reference to local variable!");
++ throw std::logic_error("warning W1049: This method could not be overridden in Python - method returns reference to local variable!");
+ }
+
+ virtual ::std::vector< std::string > const & GetCatKeys( ::std::string const & catName ){
+- throw std::logic_error("warning W1049: This method could not be overriden in Python - method returns reference to local variable!");
++ throw std::logic_error("warning W1049: This method could not be overridden in Python - method returns reference to local variable!");
+ }
+
+ virtual ::std::vector< std::string > const & GetCatNames( ){
+- throw std::logic_error("warning W1049: This method could not be overriden in Python - method returns reference to local variable!");
++ throw std::logic_error("warning W1049: This method could not be overridden in Python - method returns reference to local variable!");
+ }
+
+ virtual ::std::vector< std::string > const & GetItemAttribute( ::std::string const & itemName, ::std::string const & refCatName, ::std::string const & refAttribName ){
+- throw std::logic_error("warning W1049: This method could not be overriden in Python - method returns reference to local variable!");
++ throw std::logic_error("warning W1049: This method could not be overridden in Python - method returns reference to local variable!");
+ }
+
+ virtual ::std::vector< std::string > const & GetItemsNames( ){
+- throw std::logic_error("warning W1049: This method could not be overriden in Python - method returns reference to local variable!");
++ throw std::logic_error("warning W1049: This method could not be overridden in Python - method returns reference to local variable!");
+ }
+
+ virtual void GetItemsTypes( ::std::vector< eTypeCode > & attribsTypes, ::std::string const & catName, ::std::vector< std::string > const & attribsNames ) {
Modified: trunk/packages/rcsb-core-wrapper/trunk/debian/rules
===================================================================
--- trunk/packages/rcsb-core-wrapper/trunk/debian/rules 2012-08-16 14:01:19 UTC (rev 12069)
+++ trunk/packages/rcsb-core-wrapper/trunk/debian/rules 2012-08-16 16:54:15 UTC (rev 12070)
@@ -1,10 +1,11 @@
#!/usr/bin/make -f
+export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
+
export CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
export CFLAGS:=$(shell dpkg-buildflags --get CFLAGS)
export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS)
export LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
-export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
# lkajan: we borrow from libtorrent-rasterbar and pythonmagick here (thank you)
PYVERSIONS=$(shell pyversions -vr)
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