gentoo resync : 15.12.2019

3 files changed, 0 insertions, 128 deletions

diff --git a/sci-biology/velvet/Manifest b/sci-biology/velvet/Manifest
index 88cc05d2f45e..40f51b903d70 100644
--- a/sci-biology/velvet/Manifest
+++ b/sci-biology/velvet/Manifest
@@ -1,6 +1,3 @@
-AUX velvet-1.0.18-gentoo-r1.diff 7879 BLAKE2B a1aaa683c82d7c69669c815b2b3351ba115fddb600fe0eea46d2cc002b75b752565ed9e289c2f0143550e5ffcea13587bb8f8cb31227d38ed63a769da3b05b88 SHA512 7aa112850c1d83220e1545ef29aa3e445ce55bc4334d062c353a5c5681723a3492c8dec52aeb58cfb5d464d1c748b721dc6400509fa872a48c428a2e0f9cdbf0
-DIST velvet_1.0.18.tgz 7598196 BLAKE2B acaee0fef39afe34d80a6be0bcb0069fd2daab396741034fc9d298a3a828303dcba50f2cd40d94f2b97f5066b281df810716f548cd88a64ae2c661ad3e012c1f SHA512 6823265bae085df85513f29e0ac5f17951de4d39aa62bce205f1b1579e274c08047360f25f1936c89361281f66b8a4b755f611890a6a98c02751c74e69ae03ad
 DIST velvet_1.2.10.tgz 18818559 BLAKE2B 5723c9c040e570cd88b774e5b0044dd04def88778fe2b137ec7c007ab83fc98e5423ad1d9d0499780cf6d3152347ca1a4e4e6b6c1900ce4adfc4930f1f6d3c34 SHA512 a6f3e35cebceb22cc10e83088b8cd9758492da78866237cae63d8826d6f5cfb44d82dd8bfcb1185d37cd434d4c7a0f2ac7135bb80a51db86e754afd6156ea874
-EBUILD velvet-1.0.18-r1.ebuild 1506 BLAKE2B 53b3c71ae3cf401f5626215b418c15ac4dbc96817bbadf127dbc2739d6686a8a227ec61f5112a0aff444d4fee53ed5513042c78c28c3a8086158c249f43040f4 SHA512 13551819ee7eb7a86dd388a31cd48688fabced7cd42cfbdb536615c314ea9da5a94fb1fd4a52695c8a931c62407991592948f53a2d191133a6d394d15c2708c2
 EBUILD velvet-1.2.10.ebuild 2106 BLAKE2B d7ea6a576303cffaf8785fc125b6848d3dde0775756867c952d196f0f1e55959e5d7a3b29c0096108208db043658d5f7e382e3ef701b20c4c6a383cc3f561934 SHA512 6c02607cd77b12cd2a64a92cc2a469994aba906823b3acf5c36537749a6268e8766bbc4e319d057430204af1ae36c9351f68ff579d4065048851fac9e12ccc3b
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/velvet/files/velvet-1.0.18-gentoo-r1.diff b/sci-biology/velvet/files/velvet-1.0.18-gentoo-r1.diff
deleted file mode 100644
index ed53a1229b5b..000000000000
--- a/sci-biology/velvet/files/velvet-1.0.18-gentoo-r1.diff
+++ /dev/null
@@ -1,72 +0,0 @@
-diff -durr Makefile Makefile
---- Makefile	2011-01-27 16:52:58.853408562 +0000
-+++ Makefile	2011-01-27 17:01:45.088065521 +0000
-@@ -1,8 +1,4 @@
--CC = gcc
--CFLAGS = -Wall
--DEBUG = -g
--LDFLAGS = -lm
--OPT = -O3
-+LIBS = -lm -lz
- MAXKMERLENGTH=31
- CATEGORIES=2
- DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)
-@@ -41,29 +37,29 @@
- 	-rm obj/*.o obj/dbg/*.o 
- 
- zlib : 
--	cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o
-+	echo "unbundled zlib"
- 
- velveth : obj 
--	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(Z_LIB_FILES)
-+	$(CC) $(CFLAGS)  $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(LIBS) 
- 
- 
- velvetg : obj
--	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES)
-+	$(CC) $(CFLAGS)  $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(LIBS)
- 
- debug : override DEF := $(DEF) -D DEBUG 
- debug : cleanobj obj/dbg
--	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
--	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
-+	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(LIBS) 
-+	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(LIBS) 
- 
- color : override DEF := $(DEF) -D COLOR
- color : cleanobj obj_de
--	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES)
--	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES)
-+	$(CC) $(CFLAGS)  $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(LIBS) 
-+	$(CC) $(CFLAGS)  $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(LIBS) 
- 
- colordebug : override DEF := $(DEF) -D COLOR -D DEBUG
- colordebug : cleanobj obj/dbg_de
--	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
--	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
-+	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(LIBS) 
-+	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(LIBS) 
- 
- objdir:
- 	mkdir -p obj
-@@ -83,7 +79,7 @@
- obj/dbg_de: zlib cleanobj obj/dbgdir $(OBJDBG)
- 
- obj/%.o: src/%.c
--	$(CC) $(CFLAGS) $(OPT) $(DEF) -c $? -o $@ 
-+	$(CC) $(CFLAGS)  $(DEF) -c $? -o $@ 
- 
- obj/dbg/%.o: src/%.c
- 	$(CC) $(CFLAGS) $(DEBUG) $(DEF) -c $? -o $@ 
-diff -durr src/readSet.c src/readSet.c
---- src/readSet.c	2011-01-27 16:52:58.804084948 +0000
-+++ src/readSet.c	2011-01-27 17:02:55.380324786 +0000
-@@ -24,6 +24,7 @@
- #include <math.h>
- #include <time.h>
- #include <limits.h>
-+#include <zlib.h>
- 
- #include "globals.h"
- #include "tightString.h"
diff --git a/sci-biology/velvet/velvet-1.0.18-r1.ebuild b/sci-biology/velvet/velvet-1.0.18-r1.ebuild
deleted file mode 100644
index a8ec87b6625a..000000000000
--- a/sci-biology/velvet/velvet-1.0.18-r1.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit eutils toolchain-funcs flag-o-matic
-
-MY_P=${PN}_${PV}
-
-DESCRIPTION="A sequence assembler for very short reads"
-HOMEPAGE="https://www.ebi.ac.uk/~zerbino/velvet/"
-SRC_URI="https://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE="-doc"
-KEYWORDS="amd64 x86"
-
-RDEPEND="sys-libs/zlib"
-DEPEND="${RDEPEND}
-	doc? ( virtual/latex-base )"
-
-S="${WORKDIR}"/${MY_P}
-
-src_prepare() {
-	# necessary?
-	# append-flags -O3 # as recommended by upstream
-	epatch "${FILESDIR}"/${P}-gentoo-r1.diff
-	use doc || sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die
-}
-
-src_compile() {
-	tc-export CC
-	MAKE_XOPTS=""
-	if [[ $VELVET_MAXKMERLENGTH != "" ]]; then MAKE_XOPTS="$MAKE_XOPTS MAXKMERLENGTH=$VELVET_MAXKMERLENGTH"; fi
-	if [[ $VELVET_CATEGORIES != "" ]]; then MAKE_XOPTS="$MAKE_XOPTS CATEGORIES=$VELVET_CATEGORIES"; fi
-	emake -j1 $MAKE_XOPTS || die
-	emake -j1 $MAKE_XOPTS color || die
-}
-
-src_install() {
-	dobin velvet{g,h,g_de,h_de} || die
-	insinto /usr/share/${PN}
-	doins -r contrib || die
-	dodoc Manual.pdf CREDITS.txt ChangeLog || die
-}
-
-pkg_postinst() {
-	elog "To adjust the MAXKMERLENGTH or CATEGORIES parameters as described in the manual,"
-	elog "please set the variables VELVET_MAXKMERLENGTH or VELVET_CATEGORIES in your"
-	elog "environment or /etc/portage/make.conf, then re-emerge the package. For example:"
-	elog "	VELVET_MAXKMERLENGTH=NN emerge [options] velvet"
-}