diff options
6 files changed, 0 insertions, 335 deletions
diff --git a/sci-libs/cifparse-obj/Manifest b/sci-libs/cifparse-obj/Manifest index b6b72d039897..b4e1510dc6e6 100644 --- a/sci-libs/cifparse-obj/Manifest +++ b/sci-libs/cifparse-obj/Manifest @@ -1,2 +1 @@ -DIST cifparse-obj-v7.025-prod-src.tar.gz 928484 BLAKE2B 4f510f4826e235ecd87d81d51ceef84b717bb0c174f4a263cae44765bd0ddb35e2bb6edce1c5cadcf18c5e9892630f43cda2ca004f09d84dc44499d457eef5c1 SHA512 bf5d6b55592aca8678396eb9819f5bd7bff4d912410590dfb750c9ad85bdcdbd251425c45b67e2db027a8ce8d028b77c91edcc5333279ed1190f6049c01f5cc9 DIST cifparse-obj-v7.105-prod-src.tar.gz 931151 BLAKE2B c362fc528e0c88b41ef8433c6d0235ae0bd4055c8c1704d2f1be8ba8aa27a7526b3d19172f2a4ffda79c323140a54dcb2b0a2eb78f30780473c9bcfb2ab6c6f9 SHA512 d626aa055bdd6762eda4b5b04121f37fff3bc09460b12cd6cb80566545d23e5c08a8ad54fa184076932d2cff38aa9d91fa659fbe9a70d4a07b8b1677c28549f4 diff --git a/sci-libs/cifparse-obj/cifparse-obj-7.025-r1.ebuild b/sci-libs/cifparse-obj/cifparse-obj-7.025-r1.ebuild deleted file mode 100644 index 44d186a798cc..000000000000 --- a/sci-libs/cifparse-obj/cifparse-obj-7.025-r1.ebuild +++ /dev/null @@ -1,52 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils toolchain-funcs - -MY_P="${PN}-v${PV}-prod-src" - -DESCRIPTION="Provides an object-oriented application interface to information in mmCIF format" -HOMEPAGE="http://sw-tools.pdb.org/apps/CIFPARSE-OBJ/index.html" -SRC_URI="http://sw-tools.pdb.org/apps/CIFPARSE-OBJ/source/${MY_P}.tar.gz" - -LICENSE="PDB" -SLOT="0" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x64-macos" -IUSE="" - -RDEPEND="" -DEPEND=" - sys-devel/bison - sys-devel/flex" - -S="${WORKDIR}/${MY_P}" - -src_prepare() { - epatch \ - "${FILESDIR}"/${P}-makefile.patch \ - "${FILESDIR}"/${P}-gcc4.3.patch \ - "${FILESDIR}"/${P}-gcc4.7.patch \ - "${FILESDIR}"/${P}-gcc5_6.patch \ - "${FILESDIR}"/${PN}-7.025-strncasecmp-declaration.patch - - sed \ - -e "s:^\(CC=\).*:\1$(tc-getCC):g" \ - -e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \ - -e "s:^\(F77=\).*:\1${FORTRANC}:g" \ - -e "s:^\(F77_LINKER=\).*:\1${FORTRANC}:g" \ - -e "s:-static::g" \ - -i "${S}"/etc/make.* || die "Failed to fix makefile" -} - -src_compile() { - # parallel make fails - emake -j1 -} - -src_install() { - dolib.a lib/* - insinto /usr/include/${PN} - doins include/* -} diff --git a/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc4.3.patch b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc4.3.patch deleted file mode 100644 index 1715f493a6e0..000000000000 --- a/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc4.3.patch +++ /dev/null @@ -1,87 +0,0 @@ -diff -Naur cifparse-obj-v7.025-prod-src/cif-file-v1.0/src/CifFile.C cifparse-obj-v7.025-prod-src.new/cif-file-v1.0/src/CifFile.C ---- cifparse-obj-v7.025-prod-src/cif-file-v1.0/src/CifFile.C 2008-02-06 07:17:50.000000000 -0500 -+++ cifparse-obj-v7.025-prod-src.new/cif-file-v1.0/src/CifFile.C 2008-09-03 09:36:41.000000000 -0400 -@@ -153,6 +153,7 @@ - // VLAD - Carefully examine all methods that accept with, for cases where - // with is 0. This may happen if the value is empty !! - -+#include <algorithm> - #include "GenString.h" - #include "CifString.h" - #include "regex.h" -diff -Naur cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/FOtest3.C cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/FOtest3.C ---- cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/FOtest3.C 2008-02-06 07:17:51.000000000 -0500 -+++ cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/FOtest3.C 2008-09-03 09:40:12.000000000 -0400 -@@ -1,4 +1,5 @@ - #include <iostream> -+#include <cstdlib> - #include "GenString.h" - #include "CifFile.h" - -diff -Naur cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/FOtest7.C cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/FOtest7.C ---- cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/FOtest7.C 2008-02-06 07:17:51.000000000 -0500 -+++ cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/FOtest7.C 2008-09-03 09:40:42.000000000 -0400 -@@ -3,6 +3,7 @@ - */ - #include "CifFile.h" - #include <iostream> -+#include <cstdlib> - - void FillTestTable(ISTable *s); - void TwoCifFileObj(); -diff -Naur cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/FOtest8.C cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/FOtest8.C ---- cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/FOtest8.C 2008-02-06 07:17:51.000000000 -0500 -+++ cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/FOtest8.C 2008-09-03 09:41:06.000000000 -0400 -@@ -1,6 +1,7 @@ - /* Test for reading binary files of two different versions*/ - #include "CifFile.h" - #include <iostream> -+#include <cstdlib> - - - #define FALSE 0 -diff -Naur cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/SdbReader.C cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/SdbReader.C ---- cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/SdbReader.C 2008-02-06 07:17:51.000000000 -0500 -+++ cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/SdbReader.C 2008-09-03 09:41:50.000000000 -0400 -@@ -1,4 +1,5 @@ - #include <iostream> -+#include <cstdlib> - #include "CifFile.h" - - -diff -Naur cifparse-obj-v7.025-prod-src/common-v4.5/src/GenString.C cifparse-obj-v7.025-prod-src.new/common-v4.5/src/GenString.C ---- cifparse-obj-v7.025-prod-src/common-v4.5/src/GenString.C 2008-02-06 07:17:49.000000000 -0500 -+++ cifparse-obj-v7.025-prod-src.new/common-v4.5/src/GenString.C 2008-09-03 09:32:17.000000000 -0400 -@@ -138,7 +138,7 @@ - POSSIBILITY THEREOF. - */ - -- -+#include <cstring> - // Needed, since some platforms do not define std:: elsewhere - #include <ctype.h> - -diff -Naur cifparse-obj-v7.025-prod-src/tables-v8.0/src/ISTable.C cifparse-obj-v7.025-prod-src.new/tables-v8.0/src/ISTable.C ---- cifparse-obj-v7.025-prod-src/tables-v8.0/src/ISTable.C 2008-02-06 07:17:50.000000000 -0500 -+++ cifparse-obj-v7.025-prod-src.new/tables-v8.0/src/ISTable.C 2008-09-03 09:35:57.000000000 -0400 -@@ -150,6 +150,8 @@ - #include <sstream> - #include <iostream> - #include <iomanip> -+#include <algorithm> -+#include <climits> - - #include "Exceptions.h" - #include "GenString.h" -diff -Naur cifparse-obj-v7.025-prod-src/tables-v8.0/src/ITTable.C cifparse-obj-v7.025-prod-src.new/tables-v8.0/src/ITTable.C ---- cifparse-obj-v7.025-prod-src/tables-v8.0/src/ITTable.C 2008-02-06 07:17:50.000000000 -0500 -+++ cifparse-obj-v7.025-prod-src.new/tables-v8.0/src/ITTable.C 2008-09-03 09:35:29.000000000 -0400 -@@ -150,6 +150,8 @@ - #include <sstream> - #include <iostream> - #include <iomanip> -+#include <algorithm> -+#include <climits> - - #include "Exceptions.h" - #include "GenString.h" diff --git a/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc4.7.patch b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc4.7.patch deleted file mode 100644 index b828ae618caa..000000000000 --- a/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc4.7.patch +++ /dev/null @@ -1,64 +0,0 @@ - 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 0ffff35..993d0b9 100644 ---- a/common-v4.5/src/mapped_ptr_vector.C -+++ b/common-v4.5/src/mapped_ptr_vector.C -@@ -256,12 +256,12 @@ 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); - - } - -@@ -274,12 +274,12 @@ 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); - } - - -@@ -447,7 +447,7 @@ 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); - } - - } -@@ -532,7 +532,7 @@ 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(); -@@ -556,7 +556,7 @@ 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-libs/cifparse-obj/files/cifparse-obj-7.025-makefile.patch b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-makefile.patch deleted file mode 100644 index 9e9a61788ddf..000000000000 --- a/sci-libs/cifparse-obj/files/cifparse-obj-7.025-makefile.patch +++ /dev/null @@ -1,115 +0,0 @@ -diff -Naur cifparse-obj-v7.025-prod-src/etc/make.platform.gnu3 cifparse-obj-v7.025-prod-src.new/etc/make.platform.gnu3 ---- cifparse-obj-v7.025-prod-src/etc/make.platform.gnu3 2008-02-06 07:17:49.000000000 -0500 -+++ cifparse-obj-v7.025-prod-src.new/etc/make.platform.gnu3 2008-09-03 09:18:55.000000000 -0400 -@@ -107,8 +107,8 @@ - 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) \ - $(INCLUDES) - - ## C++ compiler -@@ -128,13 +128,13 @@ - EXT=C - - # C++ compiler flags --C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ -+C++FLAGS=$(CXX_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ - $(INCLUDES) --C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ -+C++FLAGS_NONANSI=$(CXX_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ - $(DEFINES) $(INCLUDES) - # C++FLAGS_RELAXED should be set to avoid warnings reported by third party - # source code that is not maintained by PDB --C++FLAGS_RELAXED=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \ -+C++FLAGS_RELAXED=$(CXX_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \ - $(INCLUDES) - - ## Fortran compiler -@@ -144,7 +144,7 @@ - F77=f77 - - # Fortran compiler flags --FFLAGS=-O -u -+FFLAGS=$(F_OPT) - - # Additional Fortran libraries - F77LIBS= -@@ -157,7 +157,7 @@ - STATIC_LINKING=-static - - # Linker flags --LDFLAGS=$(ABI) -w $(STATIC_LINKING) -+LDFLAGS=$(ABI) -w $(STATIC_LINKING) $(LD_OPT) - LDFLAGS_NO_STATIC=$(ABI) -w - - # Fortran linker -diff -Naur cifparse-obj-v7.025-prod-src/etc/make.platform.gnu4 cifparse-obj-v7.025-prod-src.new/etc/make.platform.gnu4 ---- cifparse-obj-v7.025-prod-src/etc/make.platform.gnu4 2008-02-06 07:17:49.000000000 -0500 -+++ cifparse-obj-v7.025-prod-src.new/etc/make.platform.gnu4 2008-09-03 09:20:16.000000000 -0400 -@@ -107,12 +107,12 @@ - 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) \ - $(INCLUDES) - - ## C++ compiler --## This part defines C++ compiler information -+ - - # C++ compiler executable - CCC=g++ -@@ -128,13 +128,13 @@ - EXT=C - - # C++ compiler flags --C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ -+C++FLAGS=$(CXX_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ - $(INCLUDES) --C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ -+C++FLAGS_NONANSI=$(CXX_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ - $(DEFINES) $(INCLUDES) - # C++FLAGS_RELAXED should be set to avoid warnings reported by third party - # source code that is not maintained by PDB --C++FLAGS_RELAXED=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \ -+C++FLAGS_RELAXED=$(CXX_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \ - $(INCLUDES) - - ## Fortran compiler -@@ -144,7 +144,7 @@ - F77=f77 - - # Fortran compiler flags --FFLAGS=-O -u -+FFLAGS=$(F_OPT) - - # Additional Fortran libraries - F77LIBS= -@@ -157,7 +157,7 @@ - STATIC_LINKING=-static - - # Linker flags --LDFLAGS=$(ABI) -w $(STATIC_LINKING) -+LDFLAGS=$(ABI) -w $(STATIC_LINKING) $(LD_OPT) - LDFLAGS_NO_STATIC=$(ABI) -w - - # Fortran linker -diff -Naur cifparse-obj-v7.025-prod-src/Makefile cifparse-obj-v7.025-prod-src.new/Makefile ---- cifparse-obj-v7.025-prod-src/Makefile 2008-02-06 07:17:48.000000000 -0500 -+++ cifparse-obj-v7.025-prod-src.new/Makefile 2008-09-03 09:19:12.000000000 -0400 -@@ -62,7 +62,7 @@ - echo "------------------------------------------------------------"; \ - echo "**** Making $$libdir ****"; \ - echo "------------------------------------------------------------"; \ -- (cd $$libdir && $(MAKE) -f $(MAKEFILE) "OPT=-O" install) || exit 1; \ -+ (cd $$libdir && $(MAKE) -f $(MAKEFILE) C_OPT="${CFLAGS}" CXX_OPT="${CXXFLAGS}" F_OPT="${FFLAGS}" LD_OPT="${LDFLAGS}" install) || exit 1; \ - done - - debug: diff --git a/sci-libs/cifparse-obj/files/cifparse-obj-7.025-strncasecmp-declaration.patch b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-strncasecmp-declaration.patch deleted file mode 100644 index 9222ff27699e..000000000000 --- a/sci-libs/cifparse-obj/files/cifparse-obj-7.025-strncasecmp-declaration.patch +++ /dev/null @@ -1,16 +0,0 @@ -Remove incorrect prototypes of the 'strcasecmp' and 'strncasecmp' functions. -See also: https://bugs.gentoo.org/show_bug.cgi?id=594054 - ---- a/misclib-v2.2/include/ndb_misclib.h -+++ b/misclib-v2.2/include/ndb_misclib.h -@@ -167,10 +167,6 @@ - #define NDB_MSG_BUFFER_LEN 200000 - - --#if !defined(HAVE_STRCASECMP) --int strcasecmp (const char *s1, const char *s2); --int strncasecmp (const char *s1, const char *s2, unsigned int n); --#endif - /* - * ndb_misclib.c prototypes - */ |