commit: a2bab97dd79b9cef877b3564447074fccc1ee8bc Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Sat Mar 20 10:29:45 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Sat Mar 20 10:29:45 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a2bab97d
sci-biology/grass: remove masked package Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> profiles/package.mask | 5 - .../grass/files/fix_Makefile_variablenames.patch | 267 --------------------- sci-biology/grass/grass-9999.ebuild | 41 ---- sci-biology/grass/metadata.xml | 15 -- 4 files changed, 328 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 639f77fa7..0b7ff0512 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -30,11 +30,6 @@ #--- END OF EXAMPLES --- -# Andrew Ammerlaan <[email protected]> (06 March 2021) -# missing dependency cplex (nonfree IBM thingy) -# Masked for removal in 14 days, if you need this please complain -sci-biology/grass - # Andrew Ammerlaan <[email protected]> (06 March 2021) # Newer versions use gradle build system which is currently not # support by portage, old versions do not build, ebuilds don't 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>[email protected]</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">AlexeyG/GRASS</remote-id> - </upstream> -</pkgmetadata>
