diff options
Diffstat (limited to 'sci-chemistry')
4 files changed, 339 insertions, 1 deletions
diff --git a/sci-chemistry/pdb-extract/ChangeLog b/sci-chemistry/pdb-extract/ChangeLog index 8ab5774be2b3..2fbf3987590e 100644 --- a/sci-chemistry/pdb-extract/ChangeLog +++ b/sci-chemistry/pdb-extract/ChangeLog @@ -1,6 +1,13 @@ # ChangeLog for sci-chemistry/pdb-extract # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-extract/ChangeLog,v 1.20 2012/04/24 06:55:49 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-extract/ChangeLog,v 1.21 2012/06/23 18:57:05 jlec Exp $ + +*pdb-extract-3.11 (23 Jun 2012) + + 23 Jun 2012; Justin Lecher <jlec@gentoo.org> +pdb-extract-3.11.ebuild, + +files/pdb-extract-3.11-cflags-install.patch, + +files/pdb-extract-3.11-gcc-4.7.patch: + Version Bump, #379159 24 Apr 2012; Justin Lecher <jlec@gentoo.org> -files/respect-cflags-and-fix-install.patch: diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch new file mode 100644 index 000000000000..7383811b5bfd --- /dev/null +++ b/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch @@ -0,0 +1,207 @@ + Makefile | 2 +- + etc/make.platform.darwin3 | 4 ++-- + etc/make.platform.darwin4 | 4 ++-- + etc/make.platform.gnu3 | 20 +++++++++++--------- + etc/make.platform.gnu4 | 20 +++++++++++--------- + 5 files changed, 27 insertions(+), 23 deletions(-) + +diff --git a/Makefile b/Makefile +index 627d256..72c7e59 100644 +--- a/Makefile ++++ b/Makefile +@@ -52,7 +52,7 @@ compile: + echo "------------------------------------------------------------"; \ + echo "**** Making $$libdir ****"; \ + echo "------------------------------------------------------------"; \ +- (cd $$libdir && $(MAKE) -f $(MAKEFILE) "OPT=-O" install) || exit 1; \ ++ (cd $$libdir && $(MAKE) -f $(MAKEFILE) C_OPT="${CFLAGS}" CCC_OPT="${CXXFLAGS}" F_OPT="${FFLAGS}" LDFLAGS_OPT="${LDFLAGS}" install) || exit 1; \ + done + + beta: +diff --git a/etc/make.platform.darwin3 b/etc/make.platform.darwin3 +index c5f7b06..4c1c97c 100644 +--- a/etc/make.platform.darwin3 ++++ b/etc/make.platform.darwin3 +@@ -91,7 +91,7 @@ GDEFINES=$(PLATFORM) $(COMPILER) + DEFINES=$(GDEFINES) $(LDEFINES) + + ## Global include directories +-GINCLUDES= ++GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj + + # Collect all include directories from global include directories and + # include directories specified in module makefile +@@ -159,7 +159,7 @@ F77LIBS= + STATIC_LINKING= + + # Linker flags +-LDFLAGS=$(ABI) -w $(STATIC_LINKING) ++LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) + + # Fortran linker + F77_LINKER=f77 +diff --git a/etc/make.platform.darwin4 b/etc/make.platform.darwin4 +index 4619b34..f481fdb 100644 +--- a/etc/make.platform.darwin4 ++++ b/etc/make.platform.darwin4 +@@ -92,7 +92,7 @@ GDEFINES=$(PLATFORM) $(COMPILER) + DEFINES=$(GDEFINES) $(LDEFINES) + + ## Global include directories +-GINCLUDES= ++GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj + + # Collect all include directories from global include directories and + # include directories specified in module makefile +@@ -160,7 +160,7 @@ F77LIBS= + STATIC_LINKING= + + # Linker flags +-LDFLAGS=$(ABI) -w $(STATIC_LINKING) ++LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) + + # Fortran linker + F77_LINKER=f77 +diff --git a/etc/make.platform.gnu3 b/etc/make.platform.gnu3 +index 7fd442e..9bec4dc 100644 +--- a/etc/make.platform.gnu3 ++++ b/etc/make.platform.gnu3 +@@ -6,6 +6,8 @@ + ## + ########################################################################## + ++LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR ++ + #-----Lexer and Parser section-------------------------------------------# + + # Lexer executable +@@ -89,7 +91,7 @@ GDEFINES=$(PLATFORM) $(COMPILER) + DEFINES=$(GDEFINES) $(LDEFINES) + + ## Global include directories +-GINCLUDES= ++GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj + + # Collect all include directories from global include directories and + # include directories specified in module makefile +@@ -107,8 +109,8 @@ NON_ANSI_C_FLAG= + C_WARNINGS=$(WARNINGS) + + # C compiler flags +-CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) +-CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \ ++CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) ++CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \ + $(INCLUDES) + + ## C++ compiler +@@ -128,9 +130,9 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED) + EXT=C + + # C++ compiler flags +-C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ ++C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ + $(INCLUDES) +-C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ ++C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ + $(DEFINES) $(INCLUDES) + # C++FLAGS_RELAXED should be set to avoid warnings reported by third party + # source code that is not maintained by PDB +@@ -144,7 +146,7 @@ C++FLAGS_RELAXED=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \ + F77=f77 + + # Fortran compiler flags +-FFLAGS=-O -u ++FFLAGS=$(F_OPT) + + # Additional Fortran libraries + F77LIBS= +@@ -154,11 +156,11 @@ F77LIBS= + #-----Linkers section----------------------------------------------------# + + # Static linking option. If not defined, dynamic linking is used. +-STATIC_LINKING=-static ++STATIC_LINKING= + + # Linker flags +-LDFLAGS=$(ABI) -w $(STATIC_LINKING) +-LDFLAGS_NO_STATIC=$(ABI) -w ++LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) ++LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w + + # Fortran linker + F77_LINKER=f77 +diff --git a/etc/make.platform.gnu4 b/etc/make.platform.gnu4 +index 78a0007..bc85308 100644 +--- a/etc/make.platform.gnu4 ++++ b/etc/make.platform.gnu4 +@@ -6,6 +6,8 @@ + ## + ########################################################################## + ++LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR ++ + #-----Lexer and Parser section-------------------------------------------# + + # Lexer executable +@@ -34,7 +36,7 @@ ABI= + + # WARNINGS_AS_ERRORS defines flags to instruct all compilers to treat all + # warnings as errors. +-WARNINGS_AS_ERRORS=-Werror ++WARNINGS_AS_ERRORS= + + # ALL_WARNINGS defines flags to instruct all compilers to report all + # warnings. +@@ -90,7 +92,7 @@ GDEFINES=$(PLATFORM) $(COMPILER) + DEFINES=$(GDEFINES) $(LDEFINES) + + ## Global include directories +-GINCLUDES= ++GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj + + # Collect all include directories from global include directories and + # include directories specified in module makefile +@@ -108,8 +110,8 @@ NON_ANSI_C_FLAG= + C_WARNINGS=$(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) $(INCLUDES) ++CFLAGS=$(C_OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) ++CFLAGS_NONANSI=$(C_OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES) + + ## C++ compiler + ## This part defines C++ compiler information +@@ -128,9 +130,9 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED) + EXT=C + + # C++ compiler flags +-C++FLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ ++C++FLAGS=$(CCC_OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ + $(DEFINES) $(INCLUDES) +-C++FLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \ ++C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \ + $(C_PLUS_WARNINGS) $(DEFINES) $(INCLUDES) + + # C++FLAGS_RELAXED should be set to avoid warnings reported by third party +@@ -145,7 +147,7 @@ C++FLAGS_RELAXED=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \ + F77=f77 + + # Fortran compiler flags +-FFLAGS=-O -u ++FFLAGS=$(F_OPT) + + # Additional Fortran libraries + F77LIBS= +@@ -158,8 +160,8 @@ F77LIBS= + STATIC_LINKING= + + # Linker flags +-LDFLAGS=$(ABI) -w $(STATIC_LINKING) +-LDFLAGS_NO_STATIC=$(ABI) -w ++LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) ++LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w + + # Fortran linker + F77_LINKER=f77 diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch new file mode 100644 index 000000000000..5284bd745d53 --- /dev/null +++ b/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch @@ -0,0 +1,64 @@ + common-v4.5/src/mapped_ptr_vector.C | 14 +++++++------- + 1 files changed, 7 insertions(+), 7 deletions(-) + +diff --git a/common-v4.5/src/mapped_ptr_vector.C b/common-v4.5/src/mapped_ptr_vector.C +index d7c61f3..e20a236 100644 +--- a/common-v4.5/src/mapped_ptr_vector.C ++++ b/common-v4.5/src/mapped_ptr_vector.C +@@ -263,12 +263,12 @@ void mapped_ptr_vector<T, StringCompareT>::push_back(T* inP, + _vector.push_back(inP); + + typename tIndex::value_type valuePair(inP->GetName(), +- make_pair(_vector.size() - 1, fileIndex)); ++ std::make_pair(_vector.size() - 1, fileIndex)); + + _index.insert(valuePair); + + _currentName = inP->GetName(); +- _currentIndices = make_pair(_vector.size() - 1, fileIndex); ++ _currentIndices = std::make_pair(_vector.size() - 1, fileIndex); + + } + +@@ -281,12 +281,12 @@ void mapped_ptr_vector<T, StringCompareT>::push_back(const string& name, + _vector.push_back(NULL); + + typename tIndex::value_type valuePair(name, +- make_pair(_vector.size() - 1, fileIndex)); ++ std::make_pair(_vector.size() - 1, fileIndex)); + + _index.insert(valuePair); + + _currentName = name; +- _currentIndices = make_pair(_vector.size() - 1, fileIndex); ++ _currentIndices = std::make_pair(_vector.size() - 1, fileIndex); + } + + +@@ -454,7 +454,7 @@ void mapped_ptr_vector<T, StringCompareT>::erase(const string& name) + if (is_equal(_currentName, name, keyComp)) + { + _currentName.clear(); +- _currentIndices = make_pair(_vector.size(), (unsigned int)0); ++ _currentIndices = std::make_pair(_vector.size(), (unsigned int)0); + } + + } +@@ -539,7 +539,7 @@ pair<unsigned int, unsigned int> mapped_ptr_vector<T, StringCompareT>::get_indic + if (_vector.empty()) + { + // Empty container. Return invalid index. +- return(make_pair(_vector.size(), (unsigned int)0)); ++ return(std::make_pair(_vector.size(), (unsigned int)0)); + } + + typename tIndex::key_compare keyComp = _index.key_comp(); +@@ -563,7 +563,7 @@ pair<unsigned int, unsigned int> mapped_ptr_vector<T, StringCompareT>::get_indic + else + { + // Not found. Return invalid index. +- return(make_pair(_vector.size(), (unsigned int)0)); ++ return(std::make_pair(_vector.size(), (unsigned int)0)); + } + } + diff --git a/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild b/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild new file mode 100644 index 000000000000..48ee2c1ed3f2 --- /dev/null +++ b/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild,v 1.1 2012/06/23 18:57:05 jlec Exp $ + +EAPI=4 + +inherit eutils toolchain-funcs multilib prefix + +MY_P="${PN}-v${PV}-prod-src" + +DESCRIPTION="Tools for extracting mmCIF data from structure determination applications" +HOMEPAGE="http://sw-tools.pdb.org/apps/PDB_EXTRACT/index.html" +SRC_URI="http://sw-tools.pdb.org/apps/PDB_EXTRACT/${MY_P}.tar.gz" + +LICENSE="PDB" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="!<app-text/html-xml-utils-5.3" +DEPEND="${RDEPEND} + >=sci-libs/cifparse-obj-7.025" + +S="${WORKDIR}/${MY_P}" + +MAKEOPTS+=" -j1" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-cflags-install.patch \ + "${FILESDIR}"/${P}-gcc-4.7.patch \ + "${FILESDIR}"/${PN}-3.004-env.patch + + sed -i \ + -e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \ + -e "s:^\(CC=\).*:\1$(tc-getCC):g" \ + -e "s:^\(GINCLUDES=\).*:\1-I${EPREFIX}/usr/include/cifparse-obj:g" \ + -e "s:^\(LIBDIR=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \ + "${S}"/etc/make.* \ + || die "Failed to fix makefiles" + + eprefixify pdb-extract-v3.0/Makefile etc/* +} + +src_install() { + exeinto /usr/libexec/ccp4/bin + doexe bin/pdb_extract{,_sf} bin/extract + insinto /usr/include/rcsb + doins include/* + dodoc README* + insinto /usr/share/rcsb/ + doins -r pdb-extract-data + + cat >> "${T}"/envd <<- EOF + PDB_EXTRACT="${EPREFIX}/usr/share/rcsb/" + PDB_EXTRACT_ROOT="${EPREFIX}/usr/" + EOF + + newenvd "${T}"/envd 20pdb-extract +} |