sci-libs/cbflib: Version BUmp, fixes compilation problems, #444236

(Portage version: 2.2.0_alpha166/cvs/Linux x86_64, signed Manifest commit with key 70EB7916)

4 files changed, 340 insertions, 4 deletions

diff --git a/sci-libs/cbflib/ChangeLog b/sci-libs/cbflib/ChangeLog
index 68e035ce37a5..000cf7e69a00 100644
--- a/sci-libs/cbflib/ChangeLog
+++ b/sci-libs/cbflib/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-libs/cbflib
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/cbflib/ChangeLog,v 1.33 2012/12/06 08:27:07 jlec Exp $
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/cbflib/ChangeLog,v 1.34 2013/03/12 13:00:51 jlec Exp $
+
+*cbflib-0.9.2.10 (12 Mar 2013)
+
+  12 Mar 2013; Justin Lecher <jlec@gentoo.org> +files/0.9.2.10-Makefile.patch,
+  +cbflib-0.9.2.10.ebuild, metadata.xml:
+  Version BUmp, fixes compilation problems, #444236
 
   06 Dec 2012; Justin Lecher <jlec@gentoo.org> +cbflib-0.9.2.2.ebuild:
   Resurrect old version
diff --git a/sci-libs/cbflib/cbflib-0.9.2.10.ebuild b/sci-libs/cbflib/cbflib-0.9.2.10.ebuild
new file mode 100644
index 000000000000..d0e0073c2436
--- /dev/null
+++ b/sci-libs/cbflib/cbflib-0.9.2.10.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/cbflib/cbflib-0.9.2.10.ebuild,v 1.1 2013/03/12 13:00:51 jlec Exp $
+
+EAPI=5
+
+inherit eutils flag-o-matic fortran-2 toolchain-funcs
+
+MY_P1="CBFlib-${PV}"
+#MY_P2="CBFlib_${PV}"
+MY_P2="CBFlib_0.9.3"
+
+DESCRIPTION="Library providing a simple mechanism for accessing CBF files and imgCIF files"
+HOMEPAGE="http://www.bernstein-plus-sons.com/software/CBF/"
+BASE_TEST_URI="http://arcib.dowling.edu/software/CBFlib/downloads/version_${PV}/"
+SRC_URI="mirror://sourceforge/${PN}/${MY_P1}.tar.gz"
+#	test? (
+#		mirror://sourceforge/${PN}/${MY_P2}_Data_Files_Input.tar.gz
+#		mirror://sourceforge/${PN}/${MY_P2}_Data_Files_Output.tar.gz
+#	)"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc test"
+
+S=${WORKDIR}/${MY_P1}
+
+RESTRICT="test"
+
+src_prepare(){
+	rm -rf Py* drel* dRel* ply*
+	epatch "${FILESDIR}"/${PV}-Makefile.patch
+	cp Makefile_LINUX_gcc42 Makefile
+
+	append-fflags -fno-range-check
+	append-cflags -D_USE_XOPEN_EXTENDED -DCBF_DONT_USE_LONG_LONG
+
+	sed \
+		-e "s|^SOLDFLAGS.*$|SOLDFLAGS = -shared ${LDFLAGS}|g" \
+		-i Makefile || die
+	tc-export CC CXX AR RANLIB
+}
+
+src_compile() {
+	emake -j1 shared
+}
+
+src_test(){
+	emake -j1 basic
+}
+
+src_install() {
+	insinto /usr/include/${PN}
+	doins include/*.h
+
+	dolib.so solib/lib*
+
+	dodoc README
+	use doc && dohtml -r README.html html_graphics doc
+}
diff --git a/sci-libs/cbflib/files/0.9.2.10-Makefile.patch b/sci-libs/cbflib/files/0.9.2.10-Makefile.patch
new file mode 100644
index 000000000000..9c72300873fc
--- /dev/null
+++ b/sci-libs/cbflib/files/0.9.2.10-Makefile.patch
@@ -0,0 +1,269 @@
+ Makefile_LINUX_gcc42 | 93 ++++++++++++++++++++++++++++------------------------
+ 1 file changed, 50 insertions(+), 43 deletions(-)
+
+diff --git a/Makefile_LINUX_gcc42 b/Makefile_LINUX_gcc42
+index 0aa639a..071863d 100644
+--- a/Makefile_LINUX_gcc42
++++ b/Makefile_LINUX_gcc42
+@@ -250,7 +250,11 @@
+ 
+ 
+ # Version string
+-VERSION = 0.9.2
++MAJOR = 0
++MINOR = 9
++MICRO = 3
++VERSION = ${MAJOR}.${MINOR}.${MICRO}
++
+ 
+ 
+ #
+@@ -297,12 +301,12 @@ SHAR	= /usr/bin/shar
+ #
+ # Program to use to create archives
+ #
+-AR	= /usr/bin/ar
++AR	?= ar
+ 
+ #
+ # Program to use to add an index to an archive
+ #
+-RANLIB  = /usr/bin/ranlib
++RANLIB  ?= ranlib
+ 
+ #
+ # Program to use to decompress a data file
+@@ -313,7 +317,7 @@ DECOMPRESS = bunzip2
+ #
+ # Program to use to compress a data file
+ #
+-COMPRESS = /usr/bin/bzip2
++COMPRESS = bzip2
+ 
+ #
+ # Program to use to generate a signature
+@@ -410,12 +414,12 @@ SETUP_PY = setup.py
+ #  with gcc version 4.2
+ #
+ #########################################################
+-CC	= gcc
+-C++	= g++
+-CFLAGS  = -g -O2 -Wall -D_USE_XOPEN_EXTENDED -fno-strict-aliasing
+-F90C = gfortran
+-F90FLAGS = -g -fno-range-check
+-F90LDFLAGS = 
++CC	?= gcc
++CXX	?= g++
++CFLAGS  += -Wall -D_USE_XOPEN_EXTENDED -fno-strict-aliasing
++FC ?= gfortran
++FCFLAGS += -g -fno-range-check
++LDFLAGS += 
+ SOCFLAGS = -fPIC
+ SOLDFLAGS = -shared -Wl,-rpath,$(INSTALLDIR)/lib
+ JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux
+@@ -425,7 +429,7 @@ M4FLAGS = -Dfcb_bytes_in_rec=131072
+ TIME = time
+ 
+ ifneq ($(NOFORTRAN),)
+-F90C =
++FC =
+ endif
+ 
+ #
+@@ -491,9 +495,9 @@ RTLPEXPORTS = export LD_LIBRARY_PATH=$(PWD)/solib:$(PWD)/lib;\
+ .m4.f90:
+ 		m4 -P $(M4FLAGS) $< > $@
+ 
+-ifneq ($(F90C),)
++ifneq ($(FC),)
+ .f90.o:
+-		$(F90C) $(F90FLAGS) -c $< -o $@
++		$(FC) $(FCFLAGS) -c $< -o $@
+ endif
+ 
+ 
+@@ -701,7 +705,7 @@ default:
+ #
+ # Compile the library and examples
+ #
+-all::	$(BIN) $(SOURCE) $(F90SOURCE) $(HEADERS) $(HDF5)\
++all::	$(BIN) $(SOURCE) $(F90SOURCE) $(HEADERS) \
+ 		symlinksdone             \
+ 		$(REGEXDEP)              \
+ 		$(LIB)/libcbf.a          \
+@@ -725,12 +729,12 @@ all::	$(BIN) $(SOURCE) $(F90SOURCE) $(HEADERS) $(HDF5)\
+ 		$(BIN)/tiff2cbf
+ 
+ 
+-ifneq ($(F90C),)
++ifneq ($(FC),)
+ all::	$(BIN)/test_xds_binary   \
+ 		$(BIN)/test_fcb_read_image
+ endif
+ 
+-shared:	$(SOLIB)/libcbf.so $(SOLIB)/libfcb.so $(SOLIB)/libimg.so
++shared:	$(SOLIB)/libcbf.so.${VERSION} $(SOLIB)/libfcb.so.${VERSION} $(SOLIB)/libimg.so.${VERSION}
+ 
+ javawrapper: shared $(JCBF) $(JCBF)/cbflib-$(VERSION).jar $(SOLIB)/libcbf_wrap.so
+ 
+@@ -969,7 +973,7 @@ $(SRC)/cbf_stx.c: $(SRC)/cbf.stx.y
+ #
+ # CBF library
+ #
+-$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) $(LIB) $(HDF5)
++$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) $(LIB)
+ 	$(CC) $(CFLAGS) $(NOLLFLAG) $(NOREGEXFLAG) $(PYCIFRWFLAG) $(INCLUDES) $(WARNINGS) -c $(SOURCE)
+ 	$(AR) cr $@ *.o
+ 	mv *.o $(LIB)
+@@ -977,10 +981,11 @@ ifneq ($(RANLIB),)
+ 	$(RANLIB) $@
+ endif
+ 
+-$(SOLIB)/libcbf.so: $(SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB) $(HDF5)
+-	$(CC) $(CFLAGS) $(NOLLFLAG) $(NOREGEXFLAG) $(PYCIFRWFLAG) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE)
+-	$(CC) -o $@ *.o $(SOLDFLAGS) $(EXTRALIBS) $(HDF5SOLIBS)
+-	rm *.o
++$(SOLIB)/libcbf.so.${VERSION}: $(SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
++	$(CC) $(CFLAGS) $(NOREGEXFLAG) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE)
++	mv *.o $(SOLIB)
++	$(CC) $(LDFLAGS) -Wl,-soname,libcbf.so.$(VERSION) $(SOCFLAGS) $(SOLDFLAGS) -o $@ $(SOLIB)/*.o $(EXTRALIBS) $(HDF5SOLIBS)
++	ln -sf libcbf.so.$(VERSION) $(SOLIB)/libcbf.so
+ 
+ #
+ # IMG library
+@@ -993,9 +998,10 @@ ifneq ($(RANLIB),)
+ endif
+ 	rm img.o
+ 	
+-$(SOLIB)/libimg.so: $(SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
+-	$(CC) $(CFLAGS) $(NOLLFLAG) $(NOREGEXFLAG) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(EXAMPLES)/img.c
+-	$(CC) -o $@ img.o $(SOLDFLAGS)
++$(SOLIB)/libimg.so.${VERSION}: $(SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
++	$(CC) $(CFLAGS) $(NOREGEXFLAG) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(EXAMPLES)/img.c
++	$(CC) $(LDFLAGS) -Wl,-soname,libimg.so.$(VERSION) $(SOCFLAGS) $(SOLDFLAGS) -o $@ img.o -lm
++	ln -sf libimg.so.$(VERSION) $(SOLIB)/libimg.so
+ 	rm img.o
+ 
+ #
+@@ -1007,25 +1013,26 @@ CBF_IMG_LIBS:  $(LIB)/libcbf.a $(LIB)/libimg.a
+ #
+ # FCB library
+ #
+-$(LIB)/libfcb.a: $(F90SOURCE) $(COMMONDEP) $(LIB) $(HDF5)
+-ifneq ($(F90C),)
+-	$(F90C) $(F90FLAGS) -c $(F90SOURCE)
++$(LIB)/libfcb.a: $(F90SOURCE) $(COMMONDEP) $(LIB)
++ifneq ($(FC),)
++	$(FC) $(FCFLAGS) -c $(F90SOURCE)
+ 	$(AR) cr $@ *.o
+ ifneq ($(RANLIB),)
+ 	$(RANLIB) $@
+ endif
+ 	rm *.o
+ else
+-	echo "Define F90C to build $(LIB)/libfcb.a"
++	echo "Define FC to build $(LIB)/libfcb.a"
+ endif
+ 
+-$(SOLIB)/libfcb.so: $(F90SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
+-ifneq ($(F90C),)
+-	$(F90C) $(F90FLAGS) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(F90SOURCE)
+-	$(F90C) $(F90FLAGS) -o $@ *.o $(SOLDFLAGS)
++$(SOLIB)/libfcb.so.${VERSION}: $(F90SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
++ifneq ($(FC),)
++	$(FC) $(FCFLAGS) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(F90SOURCE)
++	$(FC) $(LDFLAGS) -Wl,-soname,libfcb.so.$(VERSION) $(SOCFLAGS) $(SOLDFLAGS) $(FCFLAGS) -o $@ *.o
++	ln -sf libfcb.so.$(VERSION) $(SOLIB)/libfcb.so
+ 	rm *.o
+ else
+-	echo "Define F90C to build $(SOLIB)/libfcb.so"
++	echo "Define FC to build $(SOLIB)/libfcb.so"
+ endif
+ 
+ 
+@@ -1183,7 +1190,7 @@ $(BIN)/cbf_template_t: $(DECTRIS_EXAMPLES)/cbf_template_t.c \
+ # testcell example program
+ #
+ $(BIN)/testcell: $(LIB)/libcbf.a $(EXAMPLES)/testcell.C
+-	$(C++) $(CFLAGS) $(NOLLFLAG) $(NOREGEXFLAG) $(INCLUDES) $(WARNINGS) \
++	$(CXX) $(CFLAGS) $(NOLLFLAG) $(NOREGEXFLAG) $(INCLUDES) $(WARNINGS) \
+ 			  $(EXAMPLES)/testcell.C -L$(LIB) \
+ 		  -lcbf $(EXTRALIBS) $(HDF5LIBS) -o $@
+ 
+@@ -1191,7 +1198,7 @@ $(BIN)/testcell: $(LIB)/libcbf.a $(EXAMPLES)/testcell.C
+ # cif2c example program
+ #
+ $(BIN)/cif2c: $(LIB)/libcbf.a $(EXAMPLES)/cif2c.c
+-	$(C++) $(CFLAGS) $(NOLLFLAG) $(NOREGEXFLAG) $(INCLUDES) $(WARNINGS) \
++	$(CXX) $(CFLAGS) $(NOLLFLAG) $(NOREGEXFLAG) $(INCLUDES) $(WARNINGS) \
+ 			  $(EXAMPLES)/cif2c.c -L$(LIB) \
+ 		  -lcbf $(EXTRALIBS) $(HDF5LIBS) -o $@
+ 
+@@ -1199,7 +1206,7 @@ $(BIN)/cif2c: $(LIB)/libcbf.a $(EXAMPLES)/cif2c.c
+ # sauter_test example program
+ #
+ $(BIN)/sauter_test: $(LIB)/libcbf.a $(EXAMPLES)/sauter_test.C
+-	$(C++) $(CFLAGS) $(NOLLFLAG) $(NOREGEXFLAG) $(INCLUDES) $(WARNINGS) \
++	$(CXX) $(CFLAGS) $(NOLLFLAG) $(NOREGEXFLAG) $(INCLUDES) $(WARNINGS) \
+ 			  $(EXAMPLES)/sauter_test.C -L$(LIB) \
+ 		  -lcbf $(EXTRALIBS) $(HDF5LIBS) -o $@
+ 
+@@ -1253,19 +1260,19 @@ $(BIN)/testflatpacked: $(LIB)/libcbf.a $(EXAMPLES)/testflatpacked.c
+ 			  $(EXAMPLES)/testflatpacked.c -L$(LIB) \
+ 		  -lcbf $(EXTRALIBS) $(HDF5LIBS) -o $@
+ 
+-ifneq ($(F90C),)
++ifneq ($(FC),)
+ #
+ # test_xds_binary example program
+ #
+ $(BIN)/test_xds_binary: $(LIB)/libfcb.a $(EXAMPLES)/test_xds_binary.f90
+-	$(F90C) $(F90FLAGS) $(F90LDFLAGS) $(EXAMPLES)/test_xds_binary.f90 \
++	$(FC) $(FCFLAGS) $(LDFLAGS) $(EXAMPLES)/test_xds_binary.f90 \
+ 		-L$(LIB) -lfcb -o $@
+ 
+ #
+ # test_fcb_read_image example program
+ #
+ $(BIN)/test_fcb_read_image: $(LIB)/libfcb.a $(EXAMPLES)/test_fcb_read_image.f90
+-	$(F90C) $(F90FLAGS) $(F90LDFLAGS) $(EXAMPLES)/test_fcb_read_image.f90 \
++	$(FC) $(FCFLAGS) $(LDFLAGS) $(EXAMPLES)/test_fcb_read_image.f90 \
+ 		-L$(LIB) -lfcb -o $@
+ endif
+ 
+@@ -1520,7 +1527,7 @@ basic:	$(BIN)/makecbf $(BIN)/img2cif $(BIN)/cif2cbf $(TESTINPUT_BASIC)
+ #
+ # Extra Tests
+ #
+-ifneq ($(F90C),)
++ifneq ($(FC),)
+ extra:	$(BIN)/convert_image $(BIN)/convert_minicbf $(BIN)/cif2cbf $(BIN)/testcell \
+ 	$(BIN)/testreals $(BIN)/testflat $(BIN)/testflatpacked \
+ 	$(BIN)/test_xds_binary $(BIN)/test_fcb_read_image $(BIN)/convert_minicbf \
+@@ -1582,7 +1589,7 @@ endif
+ 	-cmp testflatin.cbf testflatout.cbf
+ 	$(TIME) $(BIN)/testflatpacked
+ 	-cmp testflatpackedin.cbf testflatpackedout.cbf
+-ifneq ($(F90C),)
++ifneq ($(FC),)
+ 	echo testflatout.cbf | $(TIME) $(BIN)/test_xds_binary > test_xds_bin_testflatout.out
+ 	-$(DIFF) test_xds_bin_testflatout.out test_xds_bin_testflatout_orig.out
+ 	echo testflatpackedout.cbf | $(TIME) $(BIN)/test_xds_binary > test_xds_bin_testflatpackedout.out
+@@ -1599,7 +1606,7 @@ endif
+ 	$(TIME) $(BIN)/cif2cbf -I 4 -C 100. -L 0. -e n -c b -i XRD1621.cbf -o XRD1621_I4encbC100.cbf
+ 	-$(DIFF) XRD1621_I4encbC100.cbf XRD1621_I4encbC100_orig.cbf
+ 
+-ifneq ($(F90C),)
++ifneq ($(FC),)
+ extra_sigs_only:	$(BIN)/convert_image $(BIN)/convert_minicbf $(BIN)/cif2cbf $(BIN)/testcell \
+ 	$(BIN)/testreals $(BIN)/testflat $(BIN)/testflatpacked \
+ 	$(BIN)/test_xds_binary $(BIN)/test_fcb_read_image $(BIN)/convert_minicbf \
+@@ -1650,7 +1657,7 @@ endif
+ 	-cmp testflatin.cbf testflatout.cbf
+ 	$(TIME) $(BIN)/testflatpacked
+ 	-cmp testflatpackedin.cbf testflatpackedout.cbf
+-ifneq ($(F90C),)
++ifneq ($(FC),)
+ 	echo testflatout.cbf | $(TIME) $(BIN)/test_xds_binary | \
+ 	$(SIGNATURE) | $(DIFF) - test_xds_bin_testflatout_orig.out$(SEXT)
+ 	echo testflatpackedout.cbf | $(TIME) $(BIN)/test_xds_binary | \
diff --git a/sci-libs/cbflib/metadata.xml b/sci-libs/cbflib/metadata.xml
index ee6374a284a9..6c162bd85484 100644
--- a/sci-libs/cbflib/metadata.xml
+++ b/sci-libs/cbflib/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci</herd>
-	<longdescription>
+  <herd>sci</herd>
+  <longdescription>
 CBFLIB is a library of ANSI-C functions providing a simple mechanism
 for accessing Crystallographic Binary Files (CBF files) and Image-supporting
 CIF (imgCIF) files. The CBFLIB API is loosely based on the CIFPARSE API for