commit: a3ffd565b7bbfa3491aa1c554fa15c10ad23265d Author: Matt Turner <mattst88 <AT> gentoo <DOT> org> AuthorDate: Sat Aug 10 04:03:21 2019 +0000 Commit: Matt Turner <mattst88 <AT> gentoo <DOT> org> CommitDate: Sat Aug 10 04:05:35 2019 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a3ffd565
sci-chemistry/reduce: Remove Closes: https://bugs.gentoo.org/639760 Signed-off-by: Matt Turner <mattst88 <AT> gentoo.org> sci-chemistry/reduce/Manifest | 1 - .../reduce/files/3.13.080428-LDFLAGS.patch | 11 ----- .../reduce/files/3.14.080821-CFLAGS.patch | 22 ---------- .../files/reduce-3.16.111118-fix-c++14.patch | 14 ------- sci-chemistry/reduce/metadata.xml | 8 ---- sci-chemistry/reduce/reduce-3.16.111118.ebuild | 49 ---------------------- 6 files changed, 105 deletions(-) diff --git a/sci-chemistry/reduce/Manifest b/sci-chemistry/reduce/Manifest deleted file mode 100644 index 6f59e8193a4..00000000000 --- a/sci-chemistry/reduce/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST reduce.3.16.111118.src.zip 20342632 BLAKE2B 8c00e4ca881680404777cb788a0f6b4a5a0683ee33492c0050e503ce765d68117159bafded0f04c76f35ebd2f69fafbe471ff9798bea722be6d1585d128dae61 SHA512 f7b4d8d91f1f57e9e96c91139fa919c570aebd07f3a440faf3df54bf5deb3a05ad998996a24b5fe9aff6280e00329c9914e338cbfe802c047c055f52ce8312a9 diff --git a/sci-chemistry/reduce/files/3.13.080428-LDFLAGS.patch b/sci-chemistry/reduce/files/3.13.080428-LDFLAGS.patch deleted file mode 100644 index a615be088b2..00000000000 --- a/sci-chemistry/reduce/files/3.13.080428-LDFLAGS.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/reduce_src/Makefile -+++ b/reduce_src/Makefile -@@ -34,7 +34,7 @@ - all: reduce - - reduce: $(OBJLIST) -- $(CXX) -o $@ $(OBJLIST) $(LFLAGS) -+ $(CXX) $(LDFLAGS) -o $@ $(OBJLIST) $(LFLAGS) - - clean: - @rm -rf *.o *.ckp ii_files diff --git a/sci-chemistry/reduce/files/3.14.080821-CFLAGS.patch b/sci-chemistry/reduce/files/3.14.080821-CFLAGS.patch deleted file mode 100644 index 8294c8ca385..00000000000 --- a/sci-chemistry/reduce/files/3.14.080821-CFLAGS.patch +++ /dev/null @@ -1,22 +0,0 @@ -diff --git a/reduce_src/Makefile b/reduce_src/Makefile -index 598e367..067ace4 100644 ---- a/reduce_src/Makefile -+++ b/reduce_src/Makefile -@@ -12,7 +12,7 @@ PROG_FLGS = -DAROMATICS_ACCEPT_HBONDS \ - # -DDEBUGMOVABLENODE -DDEBUGDOTCOUNTS - # -DMINPREDEFINED -DMAXPREDEFINED\ - --CFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS) $(DICT_LOC) $(DICT_LOCOLD)\ -+CXXFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS) $(DICT_LOC) $(DICT_LOCOLD)\ - -I$(PDBHOME) -I$(TOOLHOME) - # -Wall - -@@ -26,7 +26,7 @@ OBJLIST = GraphToHoldScores.o reduce.o CTab.o ElementInfo.o StdResH.o ResBlk.o A - CXX = g++ - - .cpp.o: -- $(CXX) -c $*.cpp $(CFLAGS) -+ $(CXX) -c $*.cpp $(CXXFLAGS) - - OPT = -O3 - DEBUG = $(CXXDEBUGFLAGS) diff --git a/sci-chemistry/reduce/files/reduce-3.16.111118-fix-c++14.patch b/sci-chemistry/reduce/files/reduce-3.16.111118-fix-c++14.patch deleted file mode 100644 index 5a45b7cef49..00000000000 --- a/sci-chemistry/reduce/files/reduce-3.16.111118-fix-c++14.patch +++ /dev/null @@ -1,14 +0,0 @@ -Fix building with C++14, which errors out due to an erroneous std::cerr. -See also: https://bugs.gentoo.org/show_bug.cgi?id=594202 - ---- a/reduce_src/GraphToHoldScores.cpp -+++ b/reduce_src/GraphToHoldScores.cpp -@@ -1150,7 +1150,7 @@ - } - } - std::cerr << "CRITICAL ERROR IN whichVertex(" << vertex_index << ") called on edge [" << -- std::cerr << vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]" << std::endl; -+ vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]" << std::endl; - assert(false); - exit(1); - return 0; // to avoid warnings diff --git a/sci-chemistry/reduce/metadata.xml b/sci-chemistry/reduce/metadata.xml deleted file mode 100644 index da36ecbfcd6..00000000000 --- a/sci-chemistry/reduce/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemis...@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/reduce/reduce-3.16.111118.ebuild b/sci-chemistry/reduce/reduce-3.16.111118.ebuild deleted file mode 100644 index ef1349e6ade..00000000000 --- a/sci-chemistry/reduce/reduce-3.16.111118.ebuild +++ /dev/null @@ -1,49 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -MY_P="${PN}.${PV}.src" - -DESCRIPTION="Adds hydrogens to a Protein Data Bank (PDB) molecule structure file" -HOMEPAGE="http://kinemage.biochem.duke.edu/software/reduce.php"; -SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/reduce31/${MY_P}.zip"; - -LICENSE="richardson" -SLOT="0" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND="" -DEPEND="${RDEPEND} - app-arch/unzip" - -S="${WORKDIR}/" -PATCHES=( - "${FILESDIR}"/3.13.080428-LDFLAGS.patch - "${FILESDIR}"/3.14.080821-CFLAGS.patch - "${FILESDIR}"/${PN}-3.16.111118-fix-c++14.patch -) - -src_compile() { - DICT_DIR="/usr/share/reduce" - DICT_FOLD="reduce_het_dict.txt" - DICT_FNEW="reduce_wwPDB_het_dict.txt" - - emake clean - emake \ - CC="$(tc-getCC)" \ - CXX="$(tc-getCXX)" \ - OPT="${CXXFLAGS}" \ - DICT_HOME="${EPREFIX}/${DICT_DIR}/${DICT_FNEW}" \ - DICT_OLD="${EPREFIX}/${DICT_DIR}/${DICT_FOLD}" -} - -src_install() { - dobin "${S}"/reduce_src/reduce - insinto ${DICT_DIR} - doins "${S}"/${DICT_FOLD} "${S}"/${DICT_FNEW} - dodoc README.usingReduce.txt -}
