sci-biology/grass: remove masked package

Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>

3 files changed, 0 insertions, 323 deletions

diff --git a/sci-biology/grass/files/fix_Makefile_variablenames.patch b/sci-biology/grass/files/fix_Makefile_variablenames.patch
deleted file mode 100644
index 5eaf5da0f..000000000
--- a/sci-biology/grass/files/fix_Makefile_variablenames.patch
+++ /dev/null
@@ -1,267 +0,0 @@
-diff --git a/Common/Makefile b/Common/Makefile
-index bc63a66..f83906a 100644
---- a/Common/Makefile
-+++ b/Common/Makefile
-@@ -14,7 +14,7 @@ $(ODIR) :
- 	$(MD) -p $(ODIR)
- 
- $(ODIR)/%.o : %.cpp %.h | $(ODIR) 
--	$(CCC) -c $(CCCFLAGS) $(CCCINC) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) $(CXXINC) -o $@ $<
- 
- clean :
- 	$(RM) -rf $(ODIR)
-diff --git a/Makefile.config b/Makefile.config
-index c589af5..73b88d2 100644
---- a/Makefile.config
-+++ b/Makefile.config
-@@ -1,16 +1,23 @@
- # C++ compiler
--CCC = g++
-+CXX ?= g++
- # Compiler flags (you probably don't need to change anything here)
--CCCFLAGS = -O2 -m64 -std=gnu++0x -Wall
-+CXXFLAGS += -std=gnu++0x -Wall
-+#
-+BAMTOOLS_INC ?= -I/usr/include/bamtools
-+BAMTOOLS_LIB ?= -lbamtools
-+NCBI_TOOLS_PLUSPLUS_INC ?= -I/usr/include/ncbi-tools++
-+NCBI_TOOLS_PLUSPLUS_LIBS ?= -lxalgoalignnw -lxobjmgr -lgenome_collection -lseqset -lseqedit -lseq -lseqcode -lsequtil -lpub -lmedline -lbiblio -lgeneral -lxser -lxutil -lxncbi -ltables
-+CPLEX_INC ?= -I/data/bio/alexeygritsenk/apps/ILOG/cplex/include
-+CPLEX_LIB ?= -L/data/bio/alexeygritsenk/apps/ILOG/cplex/lib/x86-64_sles10_4.1/static_pic -lilocplex -lcplex -L/data/bio/alexeygritsenk/apps/ILOG/concert/lib/x86-64_sles10_4.1/static_pic -lconcert
- # include directory
--CCCINC = -I../Common/ -I/usr/include/bamtools
-+CXXINC = -I../Common/ $(BAMTOOLS_INC)
- # library directory and libraries
--CCCLIB = -lbamtools
-+CXXLIB = $(BAMTOOLS_LIB)
- 
- # Extra flags. Used for compiling scaffoldOptimizer (it uses the NCBI C++ Toolkit and CPLEX API)
- CCEFLAGS = -fPIC -fexceptions -fopenmp -DNDEBUG -DIL_STD
--CCEINC = -I/data/bio/alexeygritsenk/apps/ILOG/cplex/include -I/data/bio/alexeygritsenk/apps/ILOG/concert/include -I/usr/include/ncbi-tools++
--CCELIB = -lxalgoalignnw -lxobjmgr -lgenome_collection -lseqset -lseqedit -lseq -lseqcode -lsequtil -lpub -lmedline -lbiblio -lgeneral -lxser -lxutil -lxncbi -ltables -L/data/bio/alexeygritsenk/apps/ILOG/cplex/lib/x86-64_sles10_4.1/static_pic -lilocplex -lcplex -L/data/bio/alexeygritsenk/apps/ILOG/concert/lib/x86-64_sles10_4.1/static_pic -lconcert -lm -pthread
-+CCEINC = $(CPLEX_INC) -I/data/bio/alexeygritsenk/apps/ILOG/concert/include $(NCBI_TOOLS_PLUSPLUS_INC)
-+CCELIB = $(NCBI_TOOLS_PLUSPLUS_LIBS) $(CPLEX_LIB) -lm -pthread
- 
- # Do not change anything below unless (you think) you know what you're doing.
- MAKE = make
-diff --git a/breakpointCounter/Makefile b/breakpointCounter/Makefile
-index f042f5d..879528f 100644
---- a/breakpointCounter/Makefile
-+++ b/breakpointCounter/Makefile
-@@ -13,7 +13,7 @@ _COBJ = $(patsubst %,$(CDIR)/$(ODIR)/%,$(COBJ))
- main : Common $(BDIR)/$(BNAME)
- 
- $(BDIR)/$(BNAME) : $(_OBJ) | $(BDIR)
--	$(CCC) $(CCCFLAGS) $(CCCINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CCCLIB)
-+	$(CXX) $(CXXFLAGS) $(CXXINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CXXLIB)
- 
- dirs : | $(ODIR) $(BDIR)
- 
-@@ -27,7 +27,7 @@ Common :
- 	$(MAKE) -C $(CDIR) $(_COBJ)
- 
- $(ODIR)/%.o : %.cpp | $(ODIR)
--	$(CCC) -c $(CCCFLAGS) $(CCCINC) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) $(CXXINC) -o $@ $<
- 
- clean :
- 	rm -f $(BDIR)/$(BNAME)
-diff --git a/coverageUtil/Makefile b/coverageUtil/Makefile
-index c9768ce..b81b1f9 100644
---- a/coverageUtil/Makefile
-+++ b/coverageUtil/Makefile
-@@ -13,7 +13,7 @@ _COBJ = $(patsubst %,$(CDIR)/$(ODIR)/%,$(COBJ))
- main : Common $(BDIR)/$(BNAME)
- 
- $(BDIR)/$(BNAME) : $(_OBJ) | $(BDIR)
--	$(CCC) $(CCCFLAGS) $(CCCINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CCCLIB)
-+	$(CXX) $(CXXFLAGS) $(CXXINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CXXLIB)
- 
- dirs : | $(ODIR) $(BDIR)
- 
-@@ -27,7 +27,7 @@ Common :
- 	$(MAKE) -C $(CDIR) $(_COBJ)
- 
- $(ODIR)/%.o : %.cpp | $(ODIR)
--	$(CCC) -c $(CCCFLAGS) $(CCCINC) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) $(CXXINC) -o $@ $<
- 
- clean :
- 	rm -f $(BDIR)/$(BNAME)
-diff --git a/dataFilter/Makefile b/dataFilter/Makefile
-index 86885a0..aac1281 100644
---- a/dataFilter/Makefile
-+++ b/dataFilter/Makefile
-@@ -13,7 +13,7 @@ _COBJ = $(patsubst %,$(CDIR)/$(ODIR)/%,$(COBJ))
- main : Common $(BDIR)/$(BNAME)
- 
- $(BDIR)/$(BNAME) : $(_OBJ) | $(BDIR)
--	$(CCC) $(CCCFLAGS) $(CCCINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CCCLIB)
-+	$(CXX) $(CXXFLAGS) $(CXXINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CXXLIB)
- 
- dirs : | $(ODIR) $(BDIR)
- 
-@@ -27,7 +27,7 @@ Common :
- 	$(MAKE) -C $(CDIR) $(_COBJ)
- 
- $(ODIR)/%.o : %.cpp | $(ODIR)
--	$(CCC) -c $(CCCFLAGS) $(CCCINC) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) $(CXXINC) -o $@ $<
- 
- clean :
- 	rm -f $(BDIR)/$(BNAME)
-diff --git a/dataLinker/Makefile b/dataLinker/Makefile
-index bb22310..8846d09 100644
---- a/dataLinker/Makefile
-+++ b/dataLinker/Makefile
-@@ -13,7 +13,7 @@ _COBJ = $(patsubst %,$(CDIR)/$(ODIR)/%,$(COBJ))
- main : Common $(BDIR)/$(BNAME)
- 
- $(BDIR)/$(BNAME) : $(_OBJ) | $(BDIR)
--	$(CCC) $(CCCFLAGS) $(CCCINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CCCLIB)
-+	$(CXX) $(CXXFLAGS) $(CXXINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CXXLIB)
- 
- dirs : | $(ODIR) $(BDIR)
- 
-@@ -27,7 +27,7 @@ Common :
- 	$(MAKE) -C $(CDIR) $(_COBJ)
- 
- $(ODIR)/%.o : %.cpp | $(ODIR)
--	$(CCC) -c $(CCCFLAGS) $(CCCINC) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) $(CXXINC) -o $@ $<
- 
- clean :
- 	rm -f $(BDIR)/$(BNAME)
-diff --git a/dataSelector/Makefile b/dataSelector/Makefile
-index 79be6fc..54e45c6 100644
---- a/dataSelector/Makefile
-+++ b/dataSelector/Makefile
-@@ -13,7 +13,7 @@ _COBJ = $(patsubst %,$(CDIR)/$(ODIR)/%,$(COBJ))
- main : Common $(BDIR)/$(BNAME)
- 
- $(BDIR)/$(BNAME) : $(_OBJ) | $(BDIR)
--	$(CCC) $(CCCFLAGS) $(CCCINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CCCLIB)
-+	$(CXX) $(CXXFLAGS) $(CXXINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CXXLIB)
- 
- dirs : | $(ODIR) $(BDIR)
- 
-@@ -27,7 +27,7 @@ Common :
- 	$(MAKE) -C $(CDIR) $(_COBJ)
- 
- $(ODIR)/%.o : %.cpp | $(ODIR)
--	$(CCC) -c $(CCCFLAGS) $(CCCINC) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) $(CXXINC) -o $@ $<
- 
- clean :
- 	rm -f $(BDIR)/$(BNAME)
-diff --git a/dataSimulator/Makefile b/dataSimulator/Makefile
-index 4151efc..a8d4cb6 100644
---- a/dataSimulator/Makefile
-+++ b/dataSimulator/Makefile
-@@ -13,7 +13,7 @@ _COBJ = $(patsubst %,$(CDIR)/$(ODIR)/%,$(COBJ))
- main : Common $(BDIR)/$(BNAME)
- 
- $(BDIR)/$(BNAME) : $(_OBJ) | $(BDIR)
--	$(CCC) $(CCCFLAGS) $(CCCINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CCCLIB)
-+	$(CXX) $(CXXFLAGS) $(CXXINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CXXLIB)
- 
- dirs : | $(ODIR) $(BDIR)
- 
-@@ -27,7 +27,7 @@ Common :
- 	$(MAKE) -C $(CDIR) $(_COBJ)
- 
- $(ODIR)/%.o : %.cpp | $(ODIR)
--	$(CCC) -c $(CCCFLAGS) $(CCCINC) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) $(CXXINC) -o $@ $<
- 
- clean :
- 	rm -f $(BDIR)/$(BNAME)
-diff --git a/kmer/Makefile b/kmer/Makefile
-index 733a007..04bf766 100644
---- a/kmer/Makefile
-+++ b/kmer/Makefile
-@@ -13,7 +13,7 @@ _COBJ = $(patsubst %,$(CDIR)/$(ODIR)/%,$(COBJ))
- main : Common $(BDIR)/$(BNAME)
- 
- $(BDIR)/$(BNAME) : $(_OBJ) | $(BDIR)
--	$(CCC) $(CCCFLAGS) $(CCCINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CCCLIB)
-+	$(CXX) $(CXXFLAGS) $(CXXINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CXXLIB)
- 
- dirs : | $(ODIR) $(BDIR)
- 
-@@ -27,7 +27,7 @@ Common :
- 	$(MAKE) -C $(CDIR) $(_COBJ)
- 
- $(ODIR)/%.o : %.cpp | $(ODIR)
--	$(CCC) -c $(CCCFLAGS) $(CCCINC) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) $(CXXINC) -o $@ $<
- 
- clean :
- 	rm -f $(BDIR)/$(BNAME)
-diff --git a/readCleaner/Makefile b/readCleaner/Makefile
-index d011432..b17c334 100644
---- a/readCleaner/Makefile
-+++ b/readCleaner/Makefile
-@@ -13,7 +13,7 @@ _COBJ = $(patsubst %,$(CDIR)/$(ODIR)/%,$(COBJ))
- main : Common $(BDIR)/$(BNAME)
- 
- $(BDIR)/$(BNAME) : $(_OBJ) | $(BDIR)
--	$(CCC) $(CCCFLAGS) $(CCCINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CCCLIB)
-+	$(CXX) $(CXXFLAGS) $(CXXINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CXXLIB)
- 
- dirs : | $(ODIR) $(BDIR)
- 
-@@ -27,7 +27,7 @@ Common :
- 	$(MAKE) -C $(CDIR) $(_COBJ)
- 
- $(ODIR)/%.o : %.cpp | $(ODIR)
--	$(CCC) -c $(CCCFLAGS) $(CCCINC) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) $(CXXINC) -o $@ $<
- 
- clean :
- 	rm -f $(BDIR)/$(BNAME)
-diff --git a/readDiff/Makefile b/readDiff/Makefile
-index 2d703c0..f1b184e 100644
---- a/readDiff/Makefile
-+++ b/readDiff/Makefile
-@@ -13,7 +13,7 @@ _COBJ = $(patsubst %,$(CDIR)/$(ODIR)/%,$(COBJ))
- main : Common $(BDIR)/$(BNAME)
- 
- $(BDIR)/$(BNAME) : $(_OBJ) | $(BDIR)
--	$(CCC) $(CCCFLAGS) $(CCCINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CCCLIB)
-+	$(CXX) $(CXXFLAGS) $(CXXINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CXXLIB)
- 
- dirs : | $(ODIR) $(BDIR)
- 
-@@ -27,7 +27,7 @@ Common :
- 	$(MAKE) -C $(CDIR) $(_COBJ)
- 
- $(ODIR)/%.o : %.cpp | $(ODIR)
--	$(CCC) -c $(CCCFLAGS) $(CCCINC) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) $(CXXINC) -o $@ $<
- 
- clean :
- 	rm -f $(BDIR)/$(BNAME)
-diff --git a/scaffoldOptimizer/Makefile b/scaffoldOptimizer/Makefile
-index 635cdd4..244c5ff 100644
---- a/scaffoldOptimizer/Makefile
-+++ b/scaffoldOptimizer/Makefile
-@@ -13,7 +13,7 @@ _COBJ = $(patsubst %,$(CDIR)/$(ODIR)/%,$(COBJ))
- main : Common $(BDIR)/$(BNAME)
- 
- $(BDIR)/$(BNAME) : $(_OBJ) | $(BDIR)
--	$(CCC) $(CCCFLAGS) $(CCEFLAGS) $(CCCINC) $(CCEINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CCCLIB) $(CCELIB)
-+	$(CXX) $(CXXFLAGS) $(CCEFLAGS) $(CXXINC) $(CCEINC) -o $(BDIR)/$(BNAME) $(_OBJ) $(_COBJ) $(CXXLIB) $(CCELIB)
- 
- dirs : | $(ODIR) $(BDIR)
- 
-@@ -27,7 +27,7 @@ Common :
- 	$(MAKE) -C $(CDIR) $(_COBJ)
- 
- $(ODIR)/%.o : %.cpp | $(ODIR)
--	$(CCC) -c $(CCCFLAGS) $(CCEFLAGS) $(CCCINC) $(CCEINC) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) $(CCEFLAGS) $(CXXINC) $(CCEINC) -o $@ $<
- 
- clean :
- 	rm -f $(BDIR)/$(BNAME)
diff --git a/sci-biology/grass/grass-9999.ebuild b/sci-biology/grass/grass-9999.ebuild
deleted file mode 100644
index 6d60c4427..000000000
--- a/sci-biology/grass/grass-9999.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit git-r3 eutils
-
-DESCRIPTION="Scaffold next-generation sequencing assemblies"
-HOMEPAGE="https://github.com/AlexeyG/GRASS"
-#SRC_URI="https://github.com/AlexeyG/GRASS/archive/master.zip -> grass-20130628.zip
-#	https://tud-scaffolding.googlecode.com/files/GRASS%20manual.pdf -> grass_manual.pdf"
-EGIT_REPO_URI="https://github.com/AlexeyG/GRASS.git"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-# some IBM development CPLEX library?
-# ilcplex/ilocplex.h: No such file or directory
-# https://github.com/AlexeyG/GRASS/issues/6
-DEPEND="sci-biology/bamtools
-	sci-biology/ncbi-tools++
-	sys-cluster/openmpi"
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	epatch "${FILESDIR}"/fix_Makefile_variablenames.patch
-#	sed -e 's#/data/bio/alexeygritsenk/apps/include/ncbi-tools++#/usr/include/ncbi-tools++#' -i Makefile.config || die
-#	sed -e 's#/data/bio/alexeygritsenk/apps/include/#/usr/include/bamtools#' -i Makefile.config || die
-#	sed -e 's#/data/bio/alexeygritsenk/apps/lib#/usr/lib64#' -i Makefile.config || die
-}
-
-src_compile(){
-	emake all
-}
-
-src_install(){
-	newdoc manual/manual.pdf grass_manual.pdf
-	dobin bin/*
-}
diff --git a/sci-biology/grass/metadata.xml b/sci-biology/grass/metadata.xml
deleted file mode 100644
index b4153fae5..000000000
--- a/sci-biology/grass/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">AlexeyG/GRASS</remote-id>
-	</upstream>
-</pkgmetadata>