gentoo auto-resync : 27:01:2023 - 13:58:28

22 files changed, 0 insertions, 768 deletions

diff --git a/sci-libs/Manifest.gz b/sci-libs/Manifest.gz
index 7139e2593dd7..56fd1a32f2b8 100644
--- a/sci-libs/Manifest.gz
+++ b/sci-libs/Manifest.gz
diff --git a/sci-libs/libgenome/Manifest b/sci-libs/libgenome/Manifest
deleted file mode 100644
index 4b091a7a0ea6..000000000000
--- a/sci-libs/libgenome/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-AUX libgenome-1.3-fix-c++14.patch 979 BLAKE2B 84f2affdaabd36923b92dd9cb91d90b6626845a44acfd1d79fa39f0f46803386b645b608d67515a02603de7771e5ad7bcca7c89e278235758e368de70e34f130 SHA512 9b527401e9d3708adbf5c97727a6c337d776c2a8b097644dc732192e114cfa679413975007aa1c9e2814c27a3617e1e6bb1fc23e6bae30ac146fde1fac6ec6bd
-DIST libgenome-1.3-r1.tar.bz2 128503 BLAKE2B d64784f8b220fa5bf32a4e22b8884755e38ce03fa9d17fc11cd79dfe662051f5518852631bd5a081ab52f0139434d5571d0dde49ae873297cb52a9153949e478 SHA512 0fd1895d9ea1ac75e4efaeae9abd5241193dba17f91426a5be7b244331ac7939c37d51bb08f8378d64a96573ad38b39e2583a928aadf9421e8b5c17fe217dfd4
-EBUILD libgenome-1.3-r1.ebuild 692 BLAKE2B 60760d10a46118af2bfdf2ee4e7d75483948368bd34c89abeae9710206e0f3b9fde1b0970e1f10318b9c37b3a6560855cbb593360d16a618a02299a4fbf6ad2f SHA512 e8a0eda85242af55698bb84d442926293886424af20640b78807aa7ac3aef58358aba4ff83351b456b7fa7262a68618a053eb52649fcd4f57681a4e59d8e6912
-MISC metadata.xml 262 BLAKE2B adaacf2ac22ce09f8b1b68f538773c1e2101156181ff302eca2ce1280ee5d45db4eb302a8eee1bbead5e55942443dd16ef924cfbfdc95a1658dc6a9f460468a2 SHA512 ac924b6b530d96645f173d40f7a2bf0e3abbf49048ebf7fadcea3dd553cd25504f0e68a103395de1fb59a2e5e11497dcead601be01cc6f0295ccbc4155f67e3f
diff --git a/sci-libs/libgenome/files/libgenome-1.3-fix-c++14.patch b/sci-libs/libgenome/files/libgenome-1.3-fix-c++14.patch
deleted file mode 100644
index ffe30ef91fa2..000000000000
--- a/sci-libs/libgenome/files/libgenome-1.3-fix-c++14.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-Fix building with C++14, which errors out due to collisions with internal abs() function.
-See also: https://bugs.gentoo.org/show_bug.cgi?id=594372
- 
---- a/libGenome/gnDefs.h
-+++ b/libGenome/gnDefs.h
-@@ -175,13 +175,6 @@
- 

- #define CONTIG_SECTION_SIZE 3

- 

--// some compilers don't have abs() for 64 bit ints

--#if (defined(__GNUG__) && ( __GNUC__ <= 2 )) || defined(__INTEL_COMPILER) || (defined _MSC_VER && defined __cplusplus)

--

--int64 abs( int64 a );

--

--#endif

--

- #ifdef __cplusplus

- namespace genome {

- #endif

---- a/libGenome/Makefile.am
-+++ b/libGenome/Makefile.am
-@@ -29,7 +29,7 @@
- gnGenomeSpec.cpp  gnLocation.cpp  \
- gnRAWSource.cpp gnBaseFeature.cpp gnSEQSource.cpp gnSequence.cpp \
- gnContigSpec.cpp gnSourceHeader.cpp gnException.cpp \
--gnFastTranslator.cpp gnPosSpecificTranslator.cpp gnDefs.cpp
-+gnFastTranslator.cpp gnPosSpecificTranslator.cpp
- 
- library_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)-$(GENERIC_API_VERSION)/$(GENERIC_LIBRARY_NAME)
- 
diff --git a/sci-libs/libgenome/libgenome-1.3-r1.ebuild b/sci-libs/libgenome/libgenome-1.3-r1.ebuild
deleted file mode 100644
index 03f05c029ad0..000000000000
--- a/sci-libs/libgenome/libgenome-1.3-r1.ebuild
+++ /dev/null
@@ -1,39 +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="mirror://gentoo/${PF}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE="doc static-libs"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="doc? ( app-doc/doxygen )"
-RDEPEND=""
-
-PATCHES=( "${FILESDIR}/${PN}-1.3-fix-c++14.patch" )
-
-src_prepare() {
-	default
-	rm libGenome/gnDefs.cpp || die
-	eautoreconf
-}
-
-src_configure() {
-	econf \
-		--enable-shared \
-		$(use_enable static-libs static)
-}
-
-src_install() {
-	default
-
-	# package provides .pc files
-	find "${D}" -name '*.la' -delete || die
-}
diff --git a/sci-libs/libgenome/metadata.xml b/sci-libs/libgenome/metadata.xml
deleted file mode 100644
index bdabd1d83788..000000000000
--- a/sci-libs/libgenome/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
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 <vector>

- #include <algorithm>

--#include <boost/type_traits/remove_pointer.hpp>

--#include <boost/type_traits/add_pointer.hpp>

-+#include <boost/type_traits.hpp>

- #include <boost/dynamic_bitset.hpp>

- #include <libMems/SlotAllocator.h>

- #include <libMems/configuration.h>

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 <boost/property_map.hpp>

-+#include <boost/property_map/property_map.hpp>

- #include <boost/graph/graph_traits.hpp>

- #include <boost/graph/adjacency_list.hpp>

- #include <boost/graph/topological_sort.hpp>

-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 <string>
- #include <sstream>
- #include <iostream>
- #include <iomanip>
- 
- 
--/**

-- * 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 <boost/dynamic_bitset.hpp>

- #include <boost/tuple/tuple.hpp>

--#include <boost/property_map.hpp>

-+#include <boost/property_map/property_map.hpp>

- #include <boost/graph/graph_traits.hpp>

- #include <boost/graph/adjacency_list.hpp>

- #include <boost/graph/johnson_all_pairs_shortest.hpp>

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 <stdlib.h>
- #include <stdio.h>
- #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 <gw.fossdev@gmail.com>
-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_id_t> 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<BaseType>::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<BaseType>::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 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-libs/opencascade/Manifest b/sci-libs/opencascade/Manifest
index 36af4a808631..172e17cf2ce5 100644
--- a/sci-libs/opencascade/Manifest
+++ b/sci-libs/opencascade/Manifest
@@ -12,11 +12,9 @@ AUX opencascade-7.7.0-avoid-pre-stripping-binaries.patch 1357 BLAKE2B 2f26c4a4e4
 AUX opencascade-7.7.0-build-against-vtk-9.2.patch 1360 BLAKE2B 39bcae904286687ff2aca6662f18d67e72a341e98281b0b04b7b302ad9d0adfa576ad82ce3cfa646e1b9f4107580231bf8613d0cdb72791fda478485c8072827 SHA512 3afb471767b78b4096e00a8eab4c71a90944c70945a16f45ac372ab824c4c6a140c165882e7cb15c95c95d70ae4c9298cc03fc7cd4ebe920bb7ed4eb38aba0a5
 AUX opencascade-7.7.0-fix-installation-of-cmake-config-files.patch 1823 BLAKE2B e84bb8627ba5cee166c483631511d150ef9af2c1aa966d7154926600da0674214b3fce8363dcff7d94204c36a92f236ede0f7849039a3bd4509d04d91444204f SHA512 242604d59b3596644b1efa95ce9d7b3d30dbb1bd49f79e28a4ea66ac9b6d4728a32cf31ceb9078875a39bb7b8775ba3ce685560045684b803037a61e2f37d2a4
 AUX opencascade.env.in 4571 BLAKE2B 81780f83a476ba5a2691c003c7fde48fec14be4e355480080749800602307d64b88f779cde09aa94a7bb815849d669b054d5ca00908199d1a9857b07518b4f0d SHA512 98e6861469725f6880e38a2d7389f7bc748bcbdf54930aa3fe05ab6a5e1fab5249c4ffed4f45b6ef982325acece0d5acb7ffd8d92adac9be2db9a41ee5356019
-DIST opencascade-7.5.2.tar.gz 47812603 BLAKE2B 86995ea60e24329f91a2cbede26112a70794fb091b34d33614bef412b05b8cc9f1e770aecf78272b54a241c2524422c86f8ff722b3f27b54bf10fa5eda626288 SHA512 f951a941043a56f381cfd25e4d78bb9ae08e5cc29a894e6c0c35daf30aeabf1e44ee09af65bb6b7d62d9325be67741ddcf52266b7186b4c336c70ed8bcfa1676
 DIST opencascade-7.5.3.tar.gz 47817862 BLAKE2B be438a08997c18c3cb2c08c520fff2f439cc8a406cc3f471be3b24f874ac3bd892c4afe6fa37f742ffb5da21b5a29f9c8f737e3160dcbda35a217286218eb5e1 SHA512 2d7cf284a1b3ce8d05151085b41579cc2f4e29489b7920769cd04f86a6d76e49f533b570226d3cf041c75582894ed8a6aff889312c7c507fffae47d3e57c5c47
 DIST opencascade-7.6.3.tar.gz 48216090 BLAKE2B ff0b63250e77b0240bd99bba38cd0e6b0a8c88bf39e495f5d51d7913f097e2cad83a5ad121e9d56de11c74008249c99a41f4615269a085b7cf97c3d7f0477d6d SHA512 c708f76edb707ba18bdfe7442ed8fa500894ee6c1cd8d0313eb906b3aa7dfa40a575f04dbccd70e84395d670f2b93fb8529f3d59726449234e627b9f35b9dded
 DIST opencascade-7.7.0.tar.gz 48393806 BLAKE2B b41da7bdd07aa6ef52f7833bef3e8a9fc2ca16cbf754773cb7adcc059c11c2a7937d279a2b6cf3096e7af6fbb42c6fdc2a5c98340d6b084d2ba100ba2c538f2a SHA512 6c90e2761f752241417ae6f18d819f51e66b32f3a50a97384f29ed73fa07f4cded84c71a6f6ba302d5e35c57e2fc13001619521eaf45757e4e5ff670d94bbf5c
-EBUILD opencascade-7.5.2-r6.ebuild 4944 BLAKE2B 7478866b004cdb0e8a29b0341646e367dda0637b06ef844e159c5e10449d45a62a79f37cf4386a709a082c4b002db7623de7f75f72a8b0c50a031d1e248c7bed SHA512 dd8bf6a0c7d60e9e1cd20b88805e7106f552f773c736df619885479319d81ee54de6a793e56d6189836421e0ba454d1e780294961760ca9914c25a032959830c
 EBUILD opencascade-7.5.3-r8.ebuild 4977 BLAKE2B 09303b0bd2784d3db5eb2ed08f6cfa961a3a520a415612fd85e17d378bdf8783e57d8aa5400f8667fd73f21e272818e1e30def087dee9f88c5fd961e9b372a46 SHA512 1a3b1c38a9c7a3a04360261e995994c762389512aac0cd82687c08f7beb6491350d768d5343b54b83460538e663788bf5e00b503936f5364b3296a20039da935
 EBUILD opencascade-7.6.3-r1.ebuild 4685 BLAKE2B 5351fbd25c858e42f36e1fed3cbb39d22b2e06d0ffe41b69c97239dc27924b2bcb976deac5e33921fe2db8ef0a455d07077181429c4aa81ba800e95050180d7f SHA512 796036d3a0c6d24e5ecd3a3d81df64565f22aed96feaac0ceafad8cf8eb2e8914d64a3cd81c9856d042cd281ab166114e448580fd023f09e76b4f06a56d7a23b
 EBUILD opencascade-7.7.0-r1.ebuild 4808 BLAKE2B 233a0b6b837b0099935ec1cc87c33f9d54eb622a926a29066ff166c8ea064eb86a316f2cc10d148661f5944d988e6222afc4d5bd1d72fff105727f194624e733 SHA512 ac5969f42da17f2fc2965785b420c41831fd46060b42f761f11f67a1c5fe81c0496da994d2dc222dc39168cf3bd38bae887b7c1a3f6cbe6fdb146c1ea94a25da
diff --git a/sci-libs/opencascade/opencascade-7.5.2-r6.ebuild b/sci-libs/opencascade/opencascade-7.5.2-r6.ebuild
deleted file mode 100644
index f2acaba15e74..000000000000
--- a/sci-libs/opencascade/opencascade-7.5.2-r6.ebuild
+++ /dev/null
@@ -1,175 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake flag-o-matic
-
-MY_PV="$(ver_rs 1- '_')"
-PV_MAJ="$(ver_cut 1-2)"
-
-DESCRIPTION="Development platform for CAD/CAE, 3D surface/solid modeling and data exchange"
-HOMEPAGE="https://www.opencascade.com"
-SRC_URI="https://git.dev.opencascade.org/gitweb/?p=occt.git;a=snapshot;h=refs/tags/V${MY_PV};sf=tgz -> ${P}.tar.gz"
-S="${WORKDIR}/occt-V${MY_PV}"
-
-LICENSE="|| ( Open-CASCADE-LGPL-2.1-Exception-1.0 LGPL-2.1 )"
-SLOT="0/${PV_MAJ}"
-KEYWORDS="~amd64 ~arm64 ~x86"
-IUSE="debug doc examples ffmpeg freeimage gles2-only json optimize tbb vtk"
-
-REQUIRED_USE="?? ( optimize tbb )"
-
-# There's no easy way to test. Testing needs a rather big environment
-# properly set up.
-RESTRICT="test"
-
-# ffmpeg: https://dev.opencascade.org/content/build-error-when-compiling-against-ffmpeg-5
-RDEPEND="
-	!app-eselect/eselect-opencascade
-	dev-lang/tcl:=
-	dev-lang/tk:=
-	dev-tcltk/itcl
-	dev-tcltk/itk
-	dev-tcltk/tix
-	media-libs/fontconfig
-	media-libs/freetype:2
-	media-libs/ftgl
-	virtual/glu
-	virtual/opengl
-	x11-libs/libXmu
-	examples? (
-		dev-qt/qtcore:5
-		dev-qt/qtgui:5
-		dev-qt/qtquickcontrols2:5
-		dev-qt/qtwidgets:5
-		dev-qt/qtxml:5
-	)
-	ffmpeg? ( media-video/ffmpeg:= )
-	freeimage? ( media-libs/freeimage )
-	tbb? ( <dev-cpp/tbb-2021.4.0 )
-	vtk? ( <sci-libs/vtk-9.2.0:=[rendering] )
-"
-DEPEND="${RDEPEND}"
-
-BDEPEND="
-	dev-cpp/eigen
-	dev-libs/rapidjson
-	doc? ( app-doc/doxygen )
-	examples? ( dev-qt/linguist-tools:5 )
-"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-7.5.1-0001-allow-default-search-path-for-Qt5.patch
-	"${FILESDIR}"/${PN}-7.5.1-0002-remove-unnecessary-Qt5-check.patch
-	"${FILESDIR}"/${PN}-7.5.1-0003-add-Gentoo-configuration-type.patch
-	"${FILESDIR}"/${PN}-7.5.1-0004-fix-installation-of-cmake-config-files.patch
-	"${FILESDIR}"/${PN}-7.5.1-0005-fix-write-permissions-on-scripts.patch
-	"${FILESDIR}"/${PN}-7.5.1-0006-fix-creation-of-custom.sh-script.patch
-	"${FILESDIR}"/${PN}-7.5.1-fix-AllValues-name-collision-with-vtk-9.0.patch
-	"${FILESDIR}"/${PN}-7.6.2-avoid-pre-stripping-binaries.patch
-)
-
-src_prepare() {
-	cmake_src_prepare
-
-	use debug && append-cppflags -DDEBUG
-
-	sed -e 's|/lib\$|/'$(get_libdir)'\$|' \
-		-i adm/templates/OpenCASCADEConfig.cmake.in || die
-
-	# There is an OCCT_UPDATE_TARGET_FILE cmake macro that fails due to some
-	# assumptions it makes about installation paths. Rather than fixing it, just
-	# get rid of the mechanism altogether - its purpose is to allow a
-	# side-by-side installation of release and debug libraries.
-	sed -e 's|\\${OCCT_INSTALL_BIN_LETTER}||' \
-		-i adm/cmake/occt_toolkit.cmake || die
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DBUILD_DOC_Overview=$(usex doc)
-		-DBUILD_Inspector=$(usex examples)
-		-DBUILD_RELEASE_DISABLE_EXCEPTIONS=OFF # bug #847916
-
-		-DINSTALL_DIR_BIN="$(get_libdir)/${PN}/bin"
-		-DINSTALL_DIR_CMAKE="$(get_libdir)/cmake/${PN}"
-		-DINSTALL_DIR_DATA="share/${PN}/data"
-		-DINSTALL_DIR_DOC="share/doc/${PF}"
-		-DINSTALL_DIR_INCLUDE="include/${PN}"
-		-DINSTALL_DIR_LIB="$(get_libdir)/${PN}"
-		-DINSTALL_DIR_RESOURCE="share/${PN}/resources"
-		-DINSTALL_DIR_SAMPLES="share/${PN}/samples"
-		-DINSTALL_DIR_SCRIPT="$(get_libdir)/${PN}/bin"
-		-DINSTALL_DIR_WITH_VERSION=OFF
-		-DINSTALL_SAMPLES=$(usex examples)
-		-DINSTALL_TEST_CASES=NO
-
-		-DUSE_D3D=NO
-		-DUSE_FFMPEG=$(usex ffmpeg)
-		-DUSE_FREEIMAGE=$(usex freeimage)
-		-DUSE_FREETYPE=ON
-		-DUSE_GLES2=$(usex gles2-only)
-		-DUSE_RAPIDJSON=$(usex json)
-		-DUSE_TBB=$(usex tbb)
-		-DUSE_VTK=$(usex vtk)
-	)
-
-	use doc && mycmakeargs+=( -DINSTALL_DOC_Overview=ON )
-
-	if use examples; then
-		mycmakeargs+=(
-			-D3RDPARTY_QT_DIR="${ESYSROOT}"/usr
-			-DBUILD_SAMPLES_QT=ON
-		)
-	fi
-
-	if use vtk; then
-		if has_version ">=sci-libs/vtk-9.1.0"; then
-			mycmakeargs+=(
-				-D3RDPARTY_VTK_DIR="${ESYSROOT}"/usr
-				-D3RDPARTY_VTK_INCLUDE_DIR="${ESYSROOT}"/usr/include/vtk-9.1
-				-D3RDPARTY_VTK_LIBRARY_DIR="${ESYSROOT}"/usr/$(get_libdir)
-			)
-		elif has_version ">=sci-libs/vtk-9.0.0"; then
-			mycmakeargs+=(
-				-D3RDPARTY_VTK_DIR="${ESYSROOT}"/usr
-				-D3RDPARTY_VTK_INCLUDE_DIR="${ESYSROOT}"/usr/include/vtk-9.0
-				-D3RDPARTY_VTK_LIBRARY_DIR="${ESYSROOT}"/usr/$(get_libdir)
-			)
-		fi
-	fi
-
-	cmake_src_configure
-
-	# prepare /etc/env.d file
-	sed -e "s|lib/|$(get_libdir)/|" \
-		-e "s|VAR_CASROOT|${EPREFIX}/usr|" \
-		< "${FILESDIR}"/${PN}.env.in > "${T}"/99${PN} || die
-
-	# use TBB for memory allocation optimizations
-	if use tbb; then
-		sed -e 's|^#MMGT_OPT=0$|MMGT_OPT=2|' -i "${T}"/99${PN} || die
-	fi
-
-	# use internal optimized memory manager and don't clear memory with this
-	# memory manager.
-	if use optimize ; then
-		sed -e 's|^#MMGT_OPT=0$|MMGT_OPT=1|' \
-			-e 's|^#MMGT_CLEAR=1$|MMGT_CLEAR=0|' \
-			-i "${T}"/99${PN} || die
-	fi
-}
-
-src_install() {
-	cmake_src_install
-
-	doenvd "${T}/99${PN}"
-
-	# remove examples
-	if use !examples; then
-		rm -r "${ED}/usr/share/${PN}/samples" || die
-	fi
-
-	docompress -x /usr/share/doc/${PF}/overview/html
-}
diff --git a/sci-libs/votca-tools/Manifest b/sci-libs/votca-tools/Manifest
deleted file mode 100644
index 23d5b001cdac..000000000000
--- a/sci-libs/votca-tools/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-DIST votca-tools-1.6.4.tar.gz 109929 BLAKE2B 8bc55fcd0a021002f11d412440a369a169c3c62ae5978781010de0a05502e43ed1ccbe5066e3d46ac8ef6fd0c1471baca70d35f6468ccbfd480dc0fa6f2b5047 SHA512 7a334071086e755960a3bd938c1baa1979c4cc9cd8f865af00540fa45365bf1c3153ffb8a5a5948618c47ebafcda9ecc62850d44ea06b7f35ac4587bd423439a
-DIST votca-tools-2021.2.tar.gz 115115 BLAKE2B 9ce16d96b6da7ee9cf9be60a69536555d21eebdad2260100bf35a0c4fe0a5b8cb76c2a3b54476fd843f5428ec5fb3fd33ae79b9fd6b27a90530637c550f06712 SHA512 84e756df4c6e355e149fd105835cfb0fd03935c824e2f7e4149ad92ed6fa81d5a43a7dd6aa532b5ee6e4a79794a94db08f8533e9f0cf99afa604c5ad9f7cb133
-EBUILD votca-tools-1.6.4.ebuild 749 BLAKE2B d5cd0bec7f6d8e375e1786d1c44c006276a9be8912498ae5b5f169bf9d44b097725915d44c1a2d55bd7f287182e597ad1eb4d35796544a971c47871c2109f106 SHA512 1f372e97bcd60d296aa9cc464ba23690ab9d8bed56ac6831f126bee24f3be33d1bf3cc1a5dcd2a90695dd38bc032022de1663e4f014a18068fb7bdf75c822d68
-EBUILD votca-tools-2021.2.ebuild 855 BLAKE2B f635ba0f513812a88ca1945ba50da22213102c6c79a92a7b4cfd0069f70d72058c1ad51586c9e3385013369e3f6c71b7c78a8d97ac3e5c9c3a37d76428db0ee2 SHA512 068dc366b9b2a6858a5ce27cfcc7d949a361992f834b7621fc71d80a30ece2c5e05b9e127a506b88fb295befafb25c38661e3cdc936cfc9b5c9f881177aac4e4
-MISC metadata.xml 456 BLAKE2B 872b69b5cc95376bf9a28d0c1a16ae7fa52b3b0c356ffef0f70f69ed95da623a335edf4e7917da06880747c469dce762ba5534e3c5854264d8b6895f530b33a5 SHA512 741e6734a956099207e96de6d1fce8db9601d0d3582130a2c45b6a7cb7b140ef56a300483b392d556d303aafbd39833e4f4dff7fd4d6605d39eb8d9a88c8b6aa
diff --git a/sci-libs/votca-tools/metadata.xml b/sci-libs/votca-tools/metadata.xml
deleted file mode 100644
index 0368cd91250f..000000000000
--- a/sci-libs/votca-tools/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>junghans@gentoo.org</email>
-		<name>Christoph Junghans</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">votca/tools</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/votca-tools/votca-tools-1.6.4.ebuild b/sci-libs/votca-tools/votca-tools-1.6.4.ebuild
deleted file mode 100644
index 37b977cdd6b1..000000000000
--- a/sci-libs/votca-tools/votca-tools-1.6.4.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-if [[ ${PV} == *9999 ]]; then
-	EGIT_REPO_URI="https://github.com/${PN/-//}.git"
-	inherit git-r3
-else
-	SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-	KEYWORDS="amd64 x86 ~amd64-linux"
-	S="${WORKDIR}/${P#votca-}"
-fi
-
-DESCRIPTION="Votca tools library"
-HOMEPAGE="https://www.votca.org/"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-IUSE=""
-
-RDEPEND="
-	>=dev-cpp/eigen-3.3
-	dev-libs/boost:=
-	dev-libs/expat
-	sci-libs/fftw:3.0=
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
-	>=app-text/txt2tags-2.5
-	virtual/pkgconfig
-"
-
-DOCS=( NOTICE )
-
-src_configure() {
-	local mycmakeargs=(
-		-DWITH_RC_FILES=OFF
-	)
-	cmake_src_configure
-}
diff --git a/sci-libs/votca-tools/votca-tools-2021.2.ebuild b/sci-libs/votca-tools/votca-tools-2021.2.ebuild
deleted file mode 100644
index 184243331d2d..000000000000
--- a/sci-libs/votca-tools/votca-tools-2021.2.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-if [[ ${PV} == *9999 ]]; then
-	EGIT_REPO_URI="https://github.com/${PN/-//}.git"
-	inherit git-r3
-else
-	SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-	KEYWORDS="~amd64 ~x86 ~amd64-linux"
-	S="${WORKDIR}/${P#votca-}"
-fi
-
-DESCRIPTION="Votca tools library"
-HOMEPAGE="https://www.votca.org/"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
-	>=dev-cpp/eigen-3.3
-	dev-libs/boost:=
-	dev-libs/expat
-	sci-libs/fftw:3.0=
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
-	virtual/pkgconfig
-"
-
-DOCS=( NOTICE README.rst CHANGELOG.rst )
-
-src_configure() {
-	local mycmakeargs=(
-		-DINSTALL_RC_FILES=OFF
-		-DENABLE_TESTING=$(usex test)
-		-DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON
-	)
-	cmake_src_configure
-}