diff options
Diffstat (limited to 'sci-libs/cifparse-obj')
10 files changed, 535 insertions, 0 deletions
diff --git a/sci-libs/cifparse-obj/Manifest b/sci-libs/cifparse-obj/Manifest new file mode 100644 index 000000000000..2f8a991763a5 --- /dev/null +++ b/sci-libs/cifparse-obj/Manifest @@ -0,0 +1,13 @@ +AUX cifparse-obj-7.025-gcc4.3.patch 3926 SHA256 784a0f0a08fae029152c4f995740f94ec13cbc37d193d89d137f539dd4d6e789 SHA512 4ae441c3b576817e0302f69cceb1dd04f17bfff5226c888557732c49f4dac336d12014dc699e2703a248597eb04a118c2037a3defc18e0e3aed1fa73dd5ba892 WHIRLPOOL 5bc3f60946914863f3c6316cd58434e3ca7210e051c6b7c96fda3e0a38cf8506a4f686425c5b3b417b3c58e1c4a675132898b2f856cf6fb85624b54e36de2f5a +AUX cifparse-obj-7.025-gcc4.7.patch 2339 SHA256 41f442585c48e85fd08a41a13817f4223ec24044cbb32386e9f6db83e9676c6a SHA512 f4ca881116a0bfb5688d441f0a29abd81fc173bb496b6640128054fc2307b88a5a02d4ebcc6c9203af091302a104474b0767f9373c334955a691a865853efd03 WHIRLPOOL bc78efcf3287e5e919fce68230dc17c7cc5d79ebea3363476b882db4e0baed950c9eda35058fc39d4c6a68941f8e0eec54b56a1d11f240faa3d2394d9df939fa +AUX cifparse-obj-7.025-gcc5_6.patch 524 SHA256 3ec0853db06d6bb9dd6c3a246a220b6805109874a88f1fb79130d00c5ac11fa3 SHA512 f2469b15eb74192b61b78c165249e8b953c58d0f7478d38f1bebf8c2c884e95ad42ba18af23b1ea7e4915979b5d4f70c2637e083a14a2c40e20f83a09acf616e WHIRLPOOL 6e89983c303f10aaed998845f3f0ba56df75eadd104e57444bb945f8a2c9c50ad1e18e7f496cf97aa3b48f8bd436c51e4001bfff995dfc2e930be5dbc8eea14a +AUX cifparse-obj-7.025-makefile.patch 4405 SHA256 1b70620f492e027f01273f316e6bf543b22c1586555d9df5a589edaa7cdc3a79 SHA512 8e74758f8ff8993a6e304a0cf80e59f60d0d162aee8f3a798552534f51055406d35c2bc1c6b91b6d9e41ff2d2666ea1d5580c71a66f1c3485c7e86deee169c69 WHIRLPOOL 446589a8914e507f0dd98c3a3470d072755a13deb96d1a83fdbaec5034478c92414a5e634bc16473ef7ea38fb8d1df3741b32f63d612aaa079a236b08fdf4384 +AUX cifparse-obj-7.025-strncasecmp-declaration.patch 477 SHA256 f2b5bfcf74b651d3820cd6855b1a3d8d237015f70599b7f0a301a05fe07c1d7f SHA512 536e1f22c82cc88a0f3e24e5785b393ac7b602eb60f05da581afe7f79a7921e3f9e60463f9fec0190d3b85bc222ccc9782380f3c12dbd85172da7d2ccef5e5d0 WHIRLPOOL 98b681497b6d4f6c1818a3caca3d76bcbcff66dec55345c620bbff2d877b6787a245c99ca9e1c6aac8438cef0d7a2f50a1e2cf62b0cbb1afcf2ed3d2ad8b0066 +AUX cifparse-obj-7.105-makefile.patch 3790 SHA256 5e975bfb55d6cd265a02590b7464ba6ca772e708571c5334c909d92daf499406 SHA512 310f13e88f7dfb19ac2bdc003a2ab2f095583a90694d27232c1ab15a298bc88313e89590e062274da10d5eaba53f6bfcb3341d1d4f7d1c388520c75643364d61 WHIRLPOOL bd65c4efc9401bd0c784e2c684c5ac10518f25860fea40ea42f7318de0fd1b4cc812715e5cb035085951772374d3abf1542270bbfe6b4d6092fd4aefb7e7e45d +DIST cifparse-obj-v7.025-prod-src.tar.gz 928484 SHA256 f2fd71fc2af0995839d9ee7825403e383209bb45a1bad68c270e5756476a8ef8 SHA512 bf5d6b55592aca8678396eb9819f5bd7bff4d912410590dfb750c9ad85bdcdbd251425c45b67e2db027a8ce8d028b77c91edcc5333279ed1190f6049c01f5cc9 WHIRLPOOL 0bd0376f3ea1d562c9650186dd1b48eef454f8acd0f4c0e074a1fccbbccf6edbef2d3e2dcd92799c1e15f0e0a4f1d32a50aaee0120c06ef846f6c971cede4924 +DIST cifparse-obj-v7.105-prod-src.tar.gz 931151 SHA256 3a0d48d6101fbe5fca4b65c53e5669726979db1a57bccf11ee769a3e40f2a856 SHA512 d626aa055bdd6762eda4b5b04121f37fff3bc09460b12cd6cb80566545d23e5c08a8ad54fa184076932d2cff38aa9d91fa659fbe9a70d4a07b8b1677c28549f4 WHIRLPOOL e1cb2e89916b40ad3094b2c53050869dfee0dbb4f8a4219153bef51a5c90729bda0922103a1d423bba1c6768c1b65c975f43c9f542ba1c333a85207f6fa09e9a +EBUILD cifparse-obj-7.025-r1.ebuild 1206 SHA256 a32b5453c1536de261bead14f88fba628459eeff94508f0f305782b8d390b4fa SHA512 bd4faf64ea58641708ad9d05c9d2cda01ddbf93759ab1579d6afadbbfc52ffab4daab6699ecc7e163b359d848c599f49dacf75de2e1d2cfaa952b4658a5bee18 WHIRLPOOL b8ac0435fc3989540304396513b5c3b2aa7dea6ba63fbd8d294982d0c211cca79d238f332c890add428c73762ac4af0217e39d199d2acaa5230a8d4676801732 +EBUILD cifparse-obj-7.105.ebuild 1140 SHA256 9efa3db3a98f33506c2d3c68586dd400690f0a1bde3bc2797573354e826dee10 SHA512 72fc0b191f9603e8cd7e42ca2e475d0bdb0120d1841784f7bad9b6a455da655b04129632dbb174b871d9ac5c31449bcefb9d328d723dea5a28629d6cf798b169 WHIRLPOOL d287b8b921f4583264a918e693d0b13d0a374dda9a42ffb4a9688c137ea4ba8b3aa20f0f62890d50ef8438d0615a8498549e2c747932aaeb7a0c341deaed5681 +MISC ChangeLog 3210 SHA256 6003731766f75d153b3aa3bb860b549e29e805d5b48219ecd5f913ff9b2eed63 SHA512 fa3b365b0fe07c0830f1e5b66529e8cbc8b4c98c1e45c974875a268adfecf0b031945a788067437fa45b6d856a5cfa53220d9ff8c5176d57d0376d685efe5e9f WHIRLPOOL d8e965ef898c1f0470fce0408102b9bf6d074155c1742a03ddce60cd7489dd280c2f6f804c620162083d108f43955b8f03bc836ed235172948cf498c616b913f +MISC ChangeLog-2015 3020 SHA256 79f9372c4d2d8e8c5787908a38f5a48db4471fc29af585d121bb9615a82dea45 SHA512 986ba5398f70051a8a3e50c15e01f7589adf8237d629c53dbcbd97985cf45b199ce7579107d0d6109a2f0645877cd58c0d562c9556b0265c1ceb8fd22a1e917c WHIRLPOOL 18c507a690fe2cdd326f78c714703604256e968fb99a6c278c073d32ca0661b3a9afa551dbee9db1de306b66ffcdbde2cdfb24feaab09aa1c7d25a56a3b9a517 +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-libs/cifparse-obj/cifparse-obj-7.025-r1.ebuild b/sci-libs/cifparse-obj/cifparse-obj-7.025-r1.ebuild new file mode 100644 index 000000000000..647673dcd240 --- /dev/null +++ b/sci-libs/cifparse-obj/cifparse-obj-7.025-r1.ebuild @@ -0,0 +1,52 @@ +# Copyright 1999-2017 Gentoo Foundation +# 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/${MY_P}.tar.gz" + +LICENSE="PDB" +SLOT="0" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="" + +RDEPEND="" +DEPEND=" + sys-devel/bison + sys-devel/flex" + +S="${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/${PN} + doins include/* +} diff --git a/sci-libs/cifparse-obj/cifparse-obj-7.105.ebuild b/sci-libs/cifparse-obj/cifparse-obj-7.105.ebuild new file mode 100644 index 000000000000..622af4794346 --- /dev/null +++ b/sci-libs/cifparse-obj/cifparse-obj-7.105.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils toolchain-funcs + +MY_P="${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 ~x86-macos" +IUSE="" + +RDEPEND="" +DEPEND=" + sys-devel/bison + sys-devel/flex" + +S="${WORKDIR}/${MY_P}" + +PATCHES=( + "${FILESDIR}"/${P}-makefile.patch + "${FILESDIR}"/${PN}-7.025-gcc5_6.patch +) + +src_prepare() { + default + + 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 \ + C_OPT="${CFLAGS}" \ + CXX_OPT="${CXXFLAGS}" +} + +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 new file mode 100644 index 000000000000..1715f493a6e0 --- /dev/null +++ b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc4.3.patch @@ -0,0 +1,87 @@ +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 new file mode 100644 index 000000000000..b828ae618caa --- /dev/null +++ b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc4.7.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 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-gcc5_6.patch b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc5_6.patch new file mode 100644 index 000000000000..2ac0ec220d9e --- /dev/null +++ b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc5_6.patch @@ -0,0 +1,16 @@ + etc/platform.sh | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/etc/platform.sh b/etc/platform.sh +index ff0ab51..1b56ab1 100755 +--- a/etc/platform.sh ++++ b/etc/platform.sh +@@ -60,7 +60,7 @@ case `uname -s` in + # Check if it is a Linux platform + Linux) + # Check if it is GCC version 4.x +- gcc_ver=`gcc --version | grep -e " 4\."` ++ gcc_ver=`gcc --version | grep -e " [456]\."` + if [[ -z $gcc_ver ]] + then + # It is not GCC version 4.x. Check if it is GCC version 3.x diff --git a/sci-libs/cifparse-obj/files/cifparse-obj-7.025-makefile.patch b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-makefile.patch new file mode 100644 index 000000000000..9e9a61788ddf --- /dev/null +++ b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-makefile.patch @@ -0,0 +1,115 @@ +diff -Naur cifparse-obj-v7.025-prod-src/etc/make.platform.gnu3 cifparse-obj-v7.025-prod-src.new/etc/make.platform.gnu3 +--- cifparse-obj-v7.025-prod-src/etc/make.platform.gnu3 2008-02-06 07:17:49.000000000 -0500 ++++ cifparse-obj-v7.025-prod-src.new/etc/make.platform.gnu3 2008-09-03 09:18:55.000000000 -0400 +@@ -107,8 +107,8 @@ + C_WARNINGS=$(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="${LDFLAGS}" install) || exit 1; \ + done + + debug: diff --git a/sci-libs/cifparse-obj/files/cifparse-obj-7.025-strncasecmp-declaration.patch b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-strncasecmp-declaration.patch new file mode 100644 index 000000000000..9222ff27699e --- /dev/null +++ b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-strncasecmp-declaration.patch @@ -0,0 +1,16 @@ +Remove incorrect prototypes of the 'strcasecmp' and 'strncasecmp' functions. +See also: https://bugs.gentoo.org/show_bug.cgi?id=594054 + +--- a/misclib-v2.2/include/ndb_misclib.h ++++ b/misclib-v2.2/include/ndb_misclib.h +@@ -167,10 +167,6 @@ + #define NDB_MSG_BUFFER_LEN 200000 + + +-#if !defined(HAVE_STRCASECMP) +-int strcasecmp (const char *s1, const char *s2); +-int strncasecmp (const char *s1, const char *s2, unsigned int n); +-#endif + /* + * ndb_misclib.c prototypes + */ diff --git a/sci-libs/cifparse-obj/files/cifparse-obj-7.105-makefile.patch b/sci-libs/cifparse-obj/files/cifparse-obj-7.105-makefile.patch new file mode 100644 index 000000000000..1716cd6390a4 --- /dev/null +++ b/sci-libs/cifparse-obj/files/cifparse-obj-7.105-makefile.patch @@ -0,0 +1,110 @@ + etc/make.platform.gnu3 | 14 +++++++------- + etc/make.platform.gnu4 | 16 ++++++++-------- + 2 files changed, 15 insertions(+), 15 deletions(-) + +diff --git a/etc/make.platform.gnu3 b/etc/make.platform.gnu3 +index 54b0297..138fa47 100644 +--- a/etc/make.platform.gnu3 ++++ b/etc/make.platform.gnu3 +@@ -107,8 +107,8 @@ NON_ANSI_C_FLAG= + C_WARNINGS=$(WARNINGS) + + # C compiler flags +-CFLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) +-CFLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(C_WARNINGS) \ ++CFLAGS=$(C_OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) ++CFLAGS_NONANSI=$(C_OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(C_WARNINGS) \ + $(DEFINES) $(INCLUDES) + + ## C++ compiler +@@ -128,14 +128,14 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED) + EXT=C + + # C++ compiler flags +-C++FLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ ++C++FLAGS=$(CXX_OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ + $(DEFINES) $(INCLUDES) +-C++FLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \ ++C++FLAGS_NONANSI=$(CXX_OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \ + $(C_PLUS_WARNINGS) $(DEFINES) $(INCLUDES) + + # C++FLAGS_RELAXED should be set to avoid warnings reported by third party + # source code that is not maintained by PDB +-C++FLAGS_RELAXED=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \ ++C++FLAGS_RELAXED=$(CXX_OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \ + $(DEFINES) $(INCLUDES) + + ## Fortran compiler +@@ -145,7 +145,7 @@ C++FLAGS_RELAXED=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \ + F77=f77 + + # Fortran compiler flags +-FFLAGS=-O -u ++FFLAGS=$(F_OPT) + + # Additional Fortran libraries + F77LIBS= +@@ -158,7 +158,7 @@ F77LIBS= + 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 --git a/etc/make.platform.gnu4 b/etc/make.platform.gnu4 +index 6676f35..51681fa 100644 +--- a/etc/make.platform.gnu4 ++++ b/etc/make.platform.gnu4 +@@ -107,11 +107,11 @@ 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) $(INCLUDES) + + ## C++ compiler +-## This part defines C++ compiler information ++ + + # C++ compiler executable + CCC=g++ +@@ -127,14 +127,14 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED) + EXT=C + + # C++ compiler flags +-C++FLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ ++C++FLAGS=$(CXX_OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ + $(DEFINES) $(INCLUDES) +-C++FLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \ ++C++FLAGS_NONANSI=$(CXX_OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \ + $(C_PLUS_WARNINGS) $(DEFINES) $(INCLUDES) + + # C++FLAGS_RELAXED should be set to avoid warnings reported by third party + # source code that is not maintained by PDB +-C++FLAGS_RELAXED=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \ ++C++FLAGS_RELAXED=$(CXX_OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \ + $(DEFINES) $(INCLUDES) + + ## Fortran compiler +@@ -144,7 +144,7 @@ C++FLAGS_RELAXED=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \ + F77=f77 + + # Fortran compiler flags +-FFLAGS=-O -u ++FFLAGS=$(F_OPT) + + # Additional Fortran libraries + F77LIBS= +@@ -157,7 +157,7 @@ F77LIBS= + 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 --git a/sci-libs/cifparse-obj/metadata.xml b/sci-libs/cifparse-obj/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-libs/cifparse-obj/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> |