From 8eccda982236f2cfe9188bdcaffd9168134f39a9 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Fri, 27 Jan 2023 13:58:28 +0000 Subject: gentoo auto-resync : 27:01:2023 - 13:58:28 --- sci-libs/libmems/Manifest | 11 -- .../libmems-1.6_p1-boost-1.62-type-traits.patch | 15 --- sci-libs/libmems/files/libmems-1.6_p1-boost.patch | 120 --------------------- .../files/libmems-1.6_p1-broken-constness.patch | 24 ----- sci-libs/libmems/files/libmems-1.6_p1-build.patch | 29 ----- .../libmems/files/libmems-1.6_p1-fix-c++14.patch | 18 ---- .../files/libmems-1.6_p1-format-security.patch | 16 --- .../libmems/files/libmems-1.6_p1-gcc-4.7.patch | 71 ------------ sci-libs/libmems/libmems-1.6_p1-r3.ebuild | 59 ---------- sci-libs/libmems/libmems-9999.ebuild | 31 ------ sci-libs/libmems/metadata.xml | 8 -- 11 files changed, 402 deletions(-) delete mode 100644 sci-libs/libmems/Manifest delete mode 100644 sci-libs/libmems/files/libmems-1.6_p1-boost-1.62-type-traits.patch delete mode 100644 sci-libs/libmems/files/libmems-1.6_p1-boost.patch delete mode 100644 sci-libs/libmems/files/libmems-1.6_p1-broken-constness.patch delete mode 100644 sci-libs/libmems/files/libmems-1.6_p1-build.patch delete mode 100644 sci-libs/libmems/files/libmems-1.6_p1-fix-c++14.patch delete mode 100644 sci-libs/libmems/files/libmems-1.6_p1-format-security.patch delete mode 100644 sci-libs/libmems/files/libmems-1.6_p1-gcc-4.7.patch delete mode 100644 sci-libs/libmems/libmems-1.6_p1-r3.ebuild delete mode 100644 sci-libs/libmems/libmems-9999.ebuild delete mode 100644 sci-libs/libmems/metadata.xml (limited to 'sci-libs/libmems') diff --git a/sci-libs/libmems/Manifest b/sci-libs/libmems/Manifest deleted file mode 100644 index 000a9af685b1..000000000000 --- a/sci-libs/libmems/Manifest +++ /dev/null @@ -1,11 +0,0 @@ -AUX libmems-1.6_p1-boost-1.62-type-traits.patch 537 BLAKE2B f8c8e5d84c2eadd220a4a065495d9cfd7d66817a564cba6a31ff73e5ae88fe952ad149f37cb69abf2b90355596a202ab71eea8f1592f3a529af191632aafcd88 SHA512 6f3cd95004fb5a8a8f9649593029ed313b9dde368a8f9c72fed8374ca913303442f6e47519a3163b6a05b4306be888dde1201f51ffb1b244bdd7eebbf5fb2f33 -AUX libmems-1.6_p1-boost.patch 4223 BLAKE2B d99dc901ab209fcebd5fd19373177f1e9d81d8c5b6b174f8f31cab7be0e46cbd3aa31e09c04cab40000ca0a5bea6932d193950cc9e6795e68e4e231bb1a5cbbd SHA512 296d0149d83e7fe87973088febe8a47e7e71f40379a8c9acb980264a7966dc43bed331326f86cab11cfd968192075ebcf684feb4998aa8b12ed5eaf2875de709 -AUX libmems-1.6_p1-broken-constness.patch 803 BLAKE2B 8622a4dcec47f4322a97f6122243fc87c4938a991188fa27f58d9bc5a0a57b7794b32eb856458e4c63ede63abfa978cce1b13e243f538adcdeffc088e7498929 SHA512 dc4234972789412af2833ae2f3741a9e4ef309e34bc55e28b08d08f5d9a3fb973d0885ac0e88ff44a9d5ec4cfe474cf5f85656f1fe50fb34d5679e849c32e67b -AUX libmems-1.6_p1-build.patch 844 BLAKE2B e75e882f7bb3be40815dcfeb11a3849b6a5abf45aa92ec10c6d609cb22de1bf41191d833f198b1cf1d1ef4360ccc5b65707a42327122af17087afce89472b9d9 SHA512 cb333dbe99dd03ad563b218c2b553735012ff5ce8d841e4ee56138253ab4cc33a5ab4521df2c51c99620c3b0a1e9ab976f4994c9b707b557c8979c6fb237bbde -AUX libmems-1.6_p1-fix-c++14.patch 715 BLAKE2B 23496cf231ae7bb7ce6eda9d5c465ec02a838293dd846d625ac0e943e461fa0eb1f7293330d74bf7ecc49e55acecb039ba3627fa9f331f8bc4dba8e6926e2781 SHA512 e298d0badcc0b84e291e60a450e90c343ea76ffc201d8bd09c5f70264cac3532507659eb940927586171e2ee753972c1cb09b71d7c1a5bfe2ba8ce4ea0f1e570 -AUX libmems-1.6_p1-format-security.patch 547 BLAKE2B fed9a7684dda9f4f5b6b7e46b3810ec4cdad614d70dea3f7644927749a6abd53f613e6d377717460f74ac838ea9e29255a70a7e966abe153ea0cbda33e723e77 SHA512 5f441833249dd3b0ebed17bd16d5ad5f0bdae777025b3432fb2a9e527ac9edd410239ee2ab02fca2f24125dca2c0c64ebda15fb03d59b65b238f5d1d65ff6629 -AUX libmems-1.6_p1-gcc-4.7.patch 2220 BLAKE2B d0f3db3808318b4ce5c6e6d531b062faee403ade57046fe112471eeda05317853e6dfc0faf61ce88f922d1c4c9a5cdcfb95bb6044048bcb97fc6ad388dd75dac SHA512 685c24779b00c18b08b2d548d03c2412d502dcacc0e14a64ab44c14406293265fb96a33041a7b13d96132cf6372bf8e2a7a0402606055084c1fb37d92dbfa77b -DIST libmems-1.6_p1.tar.xz 226628 BLAKE2B 6410f8e0dc40855ce7a09127f4aa70face9007d5edbe424d595d8607a341137d8892008c5e6d9a37cbed05158d04b7d5a5ff5f02ba441b90cb30cbea2d21c88a SHA512 c6336f69b767bba010617deb2de9bb8fbbbaf516de3b1d293b062c76c6a763166080badd730938c6d849602d64a968edb6d4622b5d3e7ea7a6d8bc38164d3d73 -EBUILD libmems-1.6_p1-r3.ebuild 1082 BLAKE2B f83cd716c866a2ff953e1a85e58c5408c3a01f2e0e8e0c9dce245dfc13ddb543cfe16572d1eee47db3c6291f2aabc9dd1ed9884752fd1097810c366bb6e5be63 SHA512 820172885a2b88725d7745e0efbac43be50ef18968ddf824b8c245b9178f1bde7d72609daf9bfbcbdde467b955cdff3a8e8224da4df93d3a30d5f1737a9442ce -EBUILD libmems-9999.ebuild 553 BLAKE2B f80afb98ed438e587556988fe894850c582039a19e9bcde9f89c8da70bffc1dd074f18642a52f495928653e4c40a8173df002bc742021e268055c0b7bd9ab63d SHA512 dac9d6144d57e4cc04d2ea8f4cd7390dd979b622f4633bf6583c1922d15a5aead4be577697deccd2ab57102d682f3ee37f0c310676c350496450aad9a035de38 -MISC metadata.xml 262 BLAKE2B adaacf2ac22ce09f8b1b68f538773c1e2101156181ff302eca2ce1280ee5d45db4eb302a8eee1bbead5e55942443dd16ef924cfbfdc95a1658dc6a9f460468a2 SHA512 ac924b6b530d96645f173d40f7a2bf0e3abbf49048ebf7fadcea3dd553cd25504f0e68a103395de1fb59a2e5e11497dcead601be01cc6f0295ccbc4155f67e3f diff --git a/sci-libs/libmems/files/libmems-1.6_p1-boost-1.62-type-traits.patch b/sci-libs/libmems/files/libmems-1.6_p1-boost-1.62-type-traits.patch deleted file mode 100644 index 609d0de0c478..000000000000 --- a/sci-libs/libmems/files/libmems-1.6_p1-boost-1.62-type-traits.patch +++ /dev/null @@ -1,15 +0,0 @@ -Shuffle around Boost type_traits, which otherwise causes issues with boost 1.62. -See also: https://bugs.gentoo.org/show_bug.cgi?id=595986 - ---- a/libMems/AbstractMatch.h -+++ b/libMems/AbstractMatch.h -@@ -16,8 +16,7 @@ - #include "libGenome/gnClone.h" - #include - #include --#include --#include -+#include - #include - #include - #include diff --git a/sci-libs/libmems/files/libmems-1.6_p1-boost.patch b/sci-libs/libmems/files/libmems-1.6_p1-boost.patch deleted file mode 100644 index 4f0c775a6d9c..000000000000 --- a/sci-libs/libmems/files/libmems-1.6_p1-boost.patch +++ /dev/null @@ -1,120 +0,0 @@ - libMems/Backbone.cpp | 2 +- - libMems/Files.h | 64 +++++++++++++++++++++--------------------- - libMems/ProgressiveAligner.cpp | 2 +- - 3 files changed, 34 insertions(+), 34 deletions(-) - -diff --git a/libMems/Backbone.cpp b/libMems/Backbone.cpp -index 86698a9..0025cd8 100644 ---- a/libMems/Backbone.cpp -+++ b/libMems/Backbone.cpp -@@ -15,7 +15,7 @@ - #include "libMems/Islands.h" - #include "libMems/CompactGappedAlignment.h" - --#include -+#include - #include - #include - #include -diff --git a/libMems/Files.h b/libMems/Files.h -index 8d6e9be..8191065 100644 ---- a/libMems/Files.h -+++ b/libMems/Files.h -@@ -22,44 +22,44 @@ - - #include "boost/filesystem/operations.hpp" - #include "boost/filesystem/exception.hpp" --#include "boost/algorithm/string.hpp" -+#include "boost/algorithm/string.hpp" - #include - #include - #include - #include - - --/** -- * Register a file name to be deleted before the process exits -- * When passed an empty string, it does not add to the list of files to delete -- * @param fname The name of a file to delete, empty strings are ignored -- * @return A vector of file names registered for deletion -- */ --std::vector< std::string >& registerFileToDelete( std::string fname = "" ); -- --inline --std::vector< std::string >& registerFileToDelete( std::string fname ) { -- // since this vector is needed when atexit() is called we allocate it -- // on the heap so its destructor won't get called -- static std::vector< std::string >* files = new std::vector< std::string >(); --#pragma omp critical --{ -- if( fname != "" ) -- files->push_back( fname ); --} -- return *files; --} -+/** -+ * Register a file name to be deleted before the process exits -+ * When passed an empty string, it does not add to the list of files to delete -+ * @param fname The name of a file to delete, empty strings are ignored -+ * @return A vector of file names registered for deletion -+ */ -+std::vector< std::string >& registerFileToDelete( std::string fname = "" ); - --void deleteRegisteredFiles(); --inline --void deleteRegisteredFiles() { -- // don't be a slob, clean up after yourself: -- // delete any files that are laying around -- std::vector< std::string >& del_files = registerFileToDelete(); -- for( int fileI = 0; fileI < del_files.size(); fileI++ ) -- boost::filesystem::remove( del_files[ fileI ] ); -- del_files.clear(); // clear the deleted files from the list --} -+inline -+std::vector< std::string >& registerFileToDelete( std::string fname ) { -+ // since this vector is needed when atexit() is called we allocate it -+ // on the heap so its destructor won't get called -+ static std::vector< std::string >* files = new std::vector< std::string >(); -+#pragma omp critical -+{ -+ if( fname != "" ) -+ files->push_back( fname ); -+} -+ return *files; -+} -+ -+void deleteRegisteredFiles(); -+inline -+void deleteRegisteredFiles() { -+ // don't be a slob, clean up after yourself: -+ // delete any files that are laying around -+ std::vector< std::string >& del_files = registerFileToDelete(); -+ for( int fileI = 0; fileI < del_files.size(); fileI++ ) -+ boost::filesystem::remove( del_files[ fileI ] ); -+ del_files.clear(); // clear the deleted files from the list -+} - - - /** -@@ -80,7 +80,7 @@ std::string CreateTempFileName(const std::string& prefix) - #endif - boost::filesystem::path path( prefix ); - dir = path.branch_path().string(); -- name = path.leaf(); -+ name = path.filename().string(); - if( name == "/" ) - { - dir += name; -diff --git a/libMems/ProgressiveAligner.cpp b/libMems/ProgressiveAligner.cpp -index 3be5fe0..5667a9e 100644 ---- a/libMems/ProgressiveAligner.cpp -+++ b/libMems/ProgressiveAligner.cpp -@@ -27,7 +27,7 @@ - - #include - #include --#include -+#include - #include - #include - #include diff --git a/sci-libs/libmems/files/libmems-1.6_p1-broken-constness.patch b/sci-libs/libmems/files/libmems-1.6_p1-broken-constness.patch deleted file mode 100644 index 0bd922c9e111..000000000000 --- a/sci-libs/libmems/files/libmems-1.6_p1-broken-constness.patch +++ /dev/null @@ -1,24 +0,0 @@ -Fix bug 529770 caused by non-const copy constructor. - ---- libmems-1.6_p1/libMems/Aligner.cpp -+++ libmems-1.6_p1/libMems/Aligner.cpp -@@ -939,7 +939,7 @@ - MatchLeftEndComparator( unsigned seq = 0 ){ - m_seq = seq; - } -- MatchLeftEndComparator( MatchLeftEndComparator& msc ){ -+ MatchLeftEndComparator( const MatchLeftEndComparator& msc ){ - m_seq = msc.m_seq; - } - // TODO?? make this do a wraparound comparison if all is equal? ---- libmems-1.6_p1/libMems/Aligner.h -+++ libmems-1.6_p1/libMems/Aligner.h -@@ -49,7 +49,7 @@ - LabeledMemComparator( uint seq ){ - m_seq = seq; - } -- LabeledMemComparator( LabeledMemComparator& lmc ){ -+ LabeledMemComparator( const LabeledMemComparator& lmc ){ - m_seq = lmc.m_seq; - } - boolean operator()(const LabeledMem& a, const LabeledMem& b) const{ diff --git a/sci-libs/libmems/files/libmems-1.6_p1-build.patch b/sci-libs/libmems/files/libmems-1.6_p1-build.patch deleted file mode 100644 index 04d5dd9c82ac..000000000000 --- a/sci-libs/libmems/files/libmems-1.6_p1-build.patch +++ /dev/null @@ -1,29 +0,0 @@ - libMems/Makefile.am | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/libMems/Makefile.am b/libMems/Makefile.am -index 6101f71..d66053d 100644 ---- a/libMems/Makefile.am -+++ b/libMems/Makefile.am -@@ -2,10 +2,10 @@ - if DEBUG - D_CXXFLAGS = -Wall -g -D__GNDEBUG__ - endif --OPTIMIZATION = -O2 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize - AM_CFLAGS = $(OPTIMIZATION) @DEPS_CFLAGS@ -DUSE_POSIX_AIO @OPENMP_CFLAGS@ - AM_CXXFLAGS = $(OPTIMIZATION) @DEPS_CFLAGS@ @BOOST_CPPFLAGS@ $(D_CXXFLAGS) @EXTRA_CXX_FLAGS@ @OPENMP_CXXFLAGS@ - AM_LDFLAGS = $(OPTIMIZATION) -+AM_CPPFLAGS=-I$(top_srcdir) - - LIBMEMS_H = \ - RepeatHash.h MatchHashEntry.h \ ---- a/libMems/dmSML/util.c -+++ b/libMems/dmSML/util.c -@@ -2,6 +2,7 @@ - #include "config.h" - #endif - -+#include - #include - #include "libMems/dmSML/util.h" - diff --git a/sci-libs/libmems/files/libmems-1.6_p1-fix-c++14.patch b/sci-libs/libmems/files/libmems-1.6_p1-fix-c++14.patch deleted file mode 100644 index bde8efeb4c9c..000000000000 --- a/sci-libs/libmems/files/libmems-1.6_p1-fix-c++14.patch +++ /dev/null @@ -1,18 +0,0 @@ -Description: Correct compilation with g++-6 -Author: Gert Wollny -Bug-Debian: https://bugs.debian.org/811870 -Forwarded: yes -Bug: https://sourceforge.net/p/mauve/bugs/46/ -Last-Update: 2016-06-30 - ---- a/libMems/ProgressiveAligner.cpp -+++ b/libMems/ProgressiveAligner.cpp -@@ -1599,7 +1599,7 @@ - c.SetLeftEnd(child_1, ancestral_matches[mI]->LeftEnd(1)); - c.SetOrientation(child_1, ancestral_matches[mI]->Orientation(1)); - c.SetLength(ancestral_matches[mI]->Length(1), child_1); -- cga_list.push_back(make_tuple(c.Copy(), &bs[mI], ancestral_matches[mI])); -+ cga_list.push_back(boost::tuples::make_tuple(c.Copy(), &bs[mI], ancestral_matches[mI])); - } - - stack node_stack; diff --git a/sci-libs/libmems/files/libmems-1.6_p1-format-security.patch b/sci-libs/libmems/files/libmems-1.6_p1-format-security.patch deleted file mode 100644 index 3ad3da2a8d80..000000000000 --- a/sci-libs/libmems/files/libmems-1.6_p1-format-security.patch +++ /dev/null @@ -1,16 +0,0 @@ - libMems/dmSML/dmsort.c | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/libMems/dmSML/dmsort.c b/libMems/dmSML/dmsort.c -index 4c99215..2cbfa7e 100644 ---- a/libMems/dmSML/dmsort.c -+++ b/libMems/dmSML/dmsort.c -@@ -825,7 +825,7 @@ int InitdmSML( long working_mb, long buffer_size, const char* input_filename, co - if ( fgets(buf, sizeof(buf), fp) ) - { - sscanf(buf, "MemTotal: %ld kB", &memTotal); -- fprintf( stderr, buf ); -+ fprintf( stderr, "%s", buf ); - } - fclose(fp); - // allocate about 6/10 of physical memory diff --git a/sci-libs/libmems/files/libmems-1.6_p1-gcc-4.7.patch b/sci-libs/libmems/files/libmems-1.6_p1-gcc-4.7.patch deleted file mode 100644 index ec620ebb35aa..000000000000 --- a/sci-libs/libmems/files/libmems-1.6_p1-gcc-4.7.patch +++ /dev/null @@ -1,71 +0,0 @@ - libMems/CompactGappedAlignment.h | 36 ++++++++++++++++++------------------ - 1 file changed, 18 insertions(+), 18 deletions(-) - -diff --git a/libMems/CompactGappedAlignment.h b/libMems/CompactGappedAlignment.h -index bf78477..942d4aa 100644 ---- a/libMems/CompactGappedAlignment.h -+++ b/libMems/CompactGappedAlignment.h -@@ -13,7 +13,7 @@ - #include "config.h" - #endif - --#include "libGenome/gnDebug.h" -+#include "libGenome/gnDebug.h" - #include "libGenome/gnFilter.h" - #include "libGenome/gnSequence.h" - #include "libMems/SparseAbstractMatch.h" -@@ -103,15 +103,15 @@ public: - /** Eliminates any columns that contain only gap characters */ - void CondenseGapColumns(); - -- void swap( CompactGappedAlignment& other ){ swap(&other); } -- --protected: -- // for use by derived classes in order to swap contents -- void swap( CompactGappedAlignment* other ){ -- std::swap( align_matrix, other->align_matrix ); -- std::swap( bcount, other->bcount ); -- BaseType::swap( other ); -- } -+ void swap( CompactGappedAlignment& other ){ swap(&other); } -+ -+protected: -+ // for use by derived classes in order to swap contents -+ void swap( CompactGappedAlignment* other ){ -+ std::swap( align_matrix, other->align_matrix ); -+ std::swap( bcount, other->bcount ); -+ BaseType::swap( other ); -+ } - - std::vector< bitset_t > align_matrix; /**< aligned positions have true values, gaps are false */ - std::vector< std::vector< size_t > > bcount; -@@ -572,7 +572,7 @@ void CompactGappedAlignment::CropEnd(gnSeqI crop_amount){ - this->SetStart(i, 0); - } - } -- SetAlignmentLength( this->AlignmentLength() - crop_amount ); -+ this->SetAlignmentLength( this->AlignmentLength() - crop_amount ); - this->create_bitcount(); - if( !this->validate() ) - std::cerr << "CropEnd error\n"; -@@ -806,13 +806,13 @@ void CompactGappedAlignment::CondenseGapColumns() - - } - --namespace std { --template<> inline --void swap( mems::CompactGappedAlignment<>& a, mems::CompactGappedAlignment<>& b ) --{ -- a.swap(b); --} --} -+namespace std { -+template<> inline -+void swap( mems::CompactGappedAlignment<>& a, mems::CompactGappedAlignment<>& b ) -+{ -+ a.swap(b); -+} -+} - - - #endif // __CompactGappedAlignment_h__ diff --git a/sci-libs/libmems/libmems-1.6_p1-r3.ebuild b/sci-libs/libmems/libmems-1.6_p1-r3.ebuild deleted file mode 100644 index 513fd1f3af61..000000000000 --- a/sci-libs/libmems/libmems-1.6_p1-r3.ebuild +++ /dev/null @@ -1,59 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit autotools - -DESCRIPTION="Library for sci-biology/mauve" -HOMEPAGE="http://gel.ahabs.wisc.edu/mauve/" -SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" - -SLOT="0" -LICENSE="GPL-2" -IUSE="doc static-libs" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-libs/boost:= - sci-libs/libgenome - sci-libs/libmuscle" -DEPEND="${RDEPEND} - doc? ( app-doc/doxygen )" - -PATCHES=( - "${FILESDIR}"/${P}-build.patch - "${FILESDIR}"/${P}-boost.patch - "${FILESDIR}"/${P}-gcc-4.7.patch - "${FILESDIR}"/${P}-broken-constness.patch - "${FILESDIR}"/${P}-format-security.patch - "${FILESDIR}"/${P}-fix-c++14.patch - "${FILESDIR}"/${P}-boost-1.62-type-traits.patch -) - -src_prepare() { - default - eautoreconf -} - -src_configure() { - econf \ - --enable-shared \ - $(use_enable static-libs static) -} - -src_compile() { - default - - if use doc; then - doxygen doxygen.am || die - HTML_DOCS+=( html/. ) - fi -} - -src_install() { - default - - # package provides .pc files - find "${D}" -name '*.la' -delete || die -} diff --git a/sci-libs/libmems/libmems-9999.ebuild b/sci-libs/libmems/libmems-9999.ebuild deleted file mode 100644 index 782686270355..000000000000 --- a/sci-libs/libmems/libmems-9999.ebuild +++ /dev/null @@ -1,31 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit autotools subversion - -DESCRIPTION="Library for sci-biology/mauve" -HOMEPAGE="http://gel.ahabs.wisc.edu/mauve/" -SRC_URI="" -ESVN_REPO_URI="https://svn.code.sf.net/p/mauve/code/libMems/trunk" - -SLOT="0" -LICENSE="GPL-2" -IUSE="doc" -KEYWORDS="" - -CDEPEND=" - dev-libs/boost - sci-libs/libgenome - sci-libs/libmuscle" -DEPEND="${CDEPEND} - doc? ( app-doc/doxygen )" -RDEPEND="${CDEPEND}" - -S="${WORKDIR}" - -src_prepare() { - default - eautoreconf -} diff --git a/sci-libs/libmems/metadata.xml b/sci-libs/libmems/metadata.xml deleted file mode 100644 index bdabd1d83788..000000000000 --- a/sci-libs/libmems/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ - - - - - sci-biology@gentoo.org - Gentoo Biology Project - - -- cgit v1.2.3