From 0871a4ded56757306f3749a7d0f379f2de2810d1 Mon Sep 17 00:00:00 2001 From: Kacper Kowalik Date: Sun, 20 Jun 2010 18:05:08 +0000 Subject: Fix parallel build, respect FLAGS, fix --as-needed issues wrt bug 277938. Thanks Diego for reporting. Package-Manager: portage-2.1.8.3/cvs/Linux x86_64 --- sci-biology/velvet/ChangeLog | 7 +- sci-biology/velvet/Manifest | 17 ++- sci-biology/velvet/files/velvet-0.7.62-gentoo.diff | 126 +++++++++++++++++++++ sci-biology/velvet/velvet-0.7.62.ebuild | 23 ++-- 4 files changed, 157 insertions(+), 16 deletions(-) create mode 100644 sci-biology/velvet/files/velvet-0.7.62-gentoo.diff (limited to 'sci-biology/velvet') diff --git a/sci-biology/velvet/ChangeLog b/sci-biology/velvet/ChangeLog index 83bfa5aea41b..27b2f0e1d335 100644 --- a/sci-biology/velvet/ChangeLog +++ b/sci-biology/velvet/ChangeLog @@ -1,6 +1,11 @@ # ChangeLog for sci-biology/velvet # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/velvet/ChangeLog,v 1.10 2010/05/05 07:14:47 weaver Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/velvet/ChangeLog,v 1.11 2010/06/20 18:05:05 xarthisius Exp $ + + 20 Jun 2010; Kacper Kowalik velvet-0.7.62.ebuild, + +files/velvet-0.7.62-gentoo.diff: + Fix parallel build, respect FLAGS, fix --as-needed issues wrt bug 277938. + Thanks Diego for reporting. *velvet-0.7.62 (05 May 2010) diff --git a/sci-biology/velvet/Manifest b/sci-biology/velvet/Manifest index bd0c42eb51a9..6f4487682e66 100644 --- a/sci-biology/velvet/Manifest +++ b/sci-biology/velvet/Manifest @@ -1,8 +1,21 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + +AUX velvet-0.7.62-gentoo.diff 8934 RMD160 4fa5e7bf70c1a9adf5ad5086e856c742e72382d7 SHA1 5dccccb0f6049e0203d4008d5a00e500cf13ef74 SHA256 0c18060bc3283800d44de8895b3417782eca8fb2be4e2256c1a57f43ed628139 DIST velvet_0.7.50.tgz 3459899 RMD160 cb516e1580d121bcc4c16a3a57372b008a7a7ad0 SHA1 29e8df5acd47b3cbaed02525b9edba7c205a5816 SHA256 fb12352872cc7ef4b482731dd6c82edc199a2f6ccd53728027735deac802842c DIST velvet_0.7.55.tgz 3475289 RMD160 f27ee2f74342f09ae1da95cd011da493c3c288c1 SHA1 e4b458b70b1cf64fca09f629a95570bd09c37b0e SHA256 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a/sci-biology/velvet/files/velvet-0.7.62-gentoo.diff b/sci-biology/velvet/files/velvet-0.7.62-gentoo.diff new file mode 100644 index 000000000000..883211a557d6 --- /dev/null +++ b/sci-biology/velvet/files/velvet-0.7.62-gentoo.diff @@ -0,0 +1,126 @@ +Debundle zlib, fixes parallel build, respect user FLAGS + +--- src/readSet.c ++++ src/readSet.c +@@ -23,18 +23,13 @@ + #include + #include + #include ++#include + + #include "globals.h" + #include "tightString.h" + #include "readSet.h" + #include "utility.h" + +-#if defined(_WIN32) || defined(__WIN32__) || defined(WIN32) +-#include "../third-party/zlib-1.2.3/Win32/include/zlib.h" +-#else +-#include "../third-party/zlib-1.2.3/zlib.h" +-#endif +- + #if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__) + # include + # include + +--- Makefile ++++ Makefile +@@ -1,77 +1,62 @@ +-CC = gcc +-CFLAGS = -Wall +-DEBUG = -g +-LDFLAGS = -lm +-OPT = -O3 ++LIBS = -lm -lz + MAXKMERLENGTH=31 + CATEGORIES=2 + DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES) + +-Z_LIB_DIR=third-party/zlib-1.2.3 +-Z_LIB_FILES=$(Z_LIB_DIR)/*.o +- +-# Mac OS users: uncomment the following lines +-# Z_LIB_FILES= +-# LDFLAGS = -lm -lz +-# CFLAGS = -Wall -m64 +- +-# Sparc/Solaris users: uncomment the following line +-# CFLAGS = -Wall -m64 +- + OBJ = obj/tightString.o obj/run.o obj/splay.o obj/splayTable.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/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/crc.o obj/utility.o obj/kmer.o obj/scaffold.o + OBJDBG = $(subst obj,obj/dbg,$(OBJ)) ++OBJDE = $(subst obj,objde,$(OBJ)) + +-default : cleanobj zlib obj velveth velvetg doc ++default : cleanobj obj velveth velvetg + + clean : +- -rm obj/*.o obj/dbg/*.o ./velvet* +- cd $(Z_LIB_DIR) && make clean ++ -rm -f obj/*.o obj/dbg/*.o ./velvet* objde/*.o + -rm -f doc/manual_src/Manual.toc doc/manual_src/Manual.aux doc/manual_src/Manual.out doc/manual_src/Manual.log + + cleanobj: +- -rm obj/*.o obj/dbg/*.o +- +-zlib : +- cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o ++ -rm -f obj/*.o obj/dbg/*.o objde/*.o + + 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 $(Z_LIB_FILES) ++ $(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 $(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 $(Z_LIB_FILES) ++ $(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 $(LIBS) + + 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 $(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 $(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 $(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 $(LIBS) + + 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 $(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 $(Z_LIB_FILES) ++ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de objde/tightString.o objde/run.o objde/recycleBin.o objde/splay.o objde/splayTable.o objde/readSet.o objde/crc.o objde/utility.o objde/kmer.o $(LIBS) ++ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de objde/tightString.o objde/graph.o objde/run2.o objde/fibHeap.o objde/fib.o objde/concatenatedGraph.o objde/passageMarker.o objde/graphStats.o objde/correctedGraph.o objde/dfib.o objde/dfibHeap.o objde/recycleBin.o objde/readSet.o objde/shortReadPairs.o objde/scaffold.o objde/locallyCorrectedGraph.o objde/graphReConstruction.o objde/roadMap.o objde/preGraph.o objde/preGraphConstruction.o objde/concatenatedPreGraph.o objde/readCoherentGraph.o objde/utility.o objde/kmer.o $(LIBS) + + 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 $(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 $(Z_LIB_FILES) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de objde/dbg/tightString.o objde/dbg/run.o objde/dbg/recycleBin.o objde/dbg/splay.o objde/dbg/splayTable.o objde/dbg/readSet.o objde/dbg/crc.o objde/dbg/utility.o objde/dbg/kmer.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de objde/dbg/tightString.o objde/dbg/graph.o objde/dbg/run2.o objde/dbg/fibHeap.o objde/dbg/fib.o objde/dbg/concatenatedGraph.o objde/dbg/passageMarker.o objde/dbg/graphStats.o objde/dbg/correctedGraph.o objde/dbg/dfib.o objde/dbg/dfibHeap.o objde/dbg/recycleBin.o objde/dbg/readSet.o objde/dbg/shortReadPairs.o objde/dbg/scaffold.o objde/dbg/locallyCorrectedGraph.o objde/dbg/graphReConstruction.o objde/dbg/roadMap.o objde/dbg/preGraph.o objde/dbg/preGraphConstruction.o objde/dbg/concatenatedPreGraph.o objde/dbg/readCoherentGraph.o objde/dbg/utility.o objde/dbg/kmer.o $(LIBS) + + objdir: + mkdir -p obj ++ mkdir -p objde + +-obj: zlib objdir $(OBJ) ++obj: objdir $(OBJ) + +-obj_de: override DEF := $(DEF) -D COLOR +-obj_de: zlib cleanobj objdir $(OBJ) ++obj_de: cleanobj objdir $(OBJDE) + + obj/dbgdir: + mkdir -p obj/dbg + +-obj/dbg: zlib obj/dbgdir $(OBJDBG) ++obj/dbg: obj/dbgdir $(OBJDBG) + + obj/dbg_de: override DEF := $(DEF) -D COLOR +-obj/dbg_de: zlib cleanobj obj/dbgdir $(OBJDBG) ++obj/dbg_de: cleanobj obj/dbgdir $(OBJDBG) + + obj/%.o: src/%.c + $(CC) $(CFLAGS) $(OPT) $(DEF) -c $? -o $@ + ++objde/%.o: src/%.c ++ $(CC) $(CFLAGS) $(OPT) $(DEF) -D COLOR -c $? -o $@ ++ + obj/dbg/%.o: src/%.c + $(CC) $(CFLAGS) $(DEBUG) $(DEF) -c $? -o $@ + diff --git a/sci-biology/velvet/velvet-0.7.62.ebuild b/sci-biology/velvet/velvet-0.7.62.ebuild index 71f6c0976e4e..e59dadf22291 100644 --- a/sci-biology/velvet/velvet-0.7.62.ebuild +++ b/sci-biology/velvet/velvet-0.7.62.ebuild @@ -1,10 +1,12 @@ # Copyright 1999-2010 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/velvet/velvet-0.7.62.ebuild,v 1.1 2010/05/05 07:14:47 weaver Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/velvet/velvet-0.7.62.ebuild,v 1.2 2010/06/20 18:05:05 xarthisius Exp $ EAPI="2" -MY_P="${PN}_${PV}" +inherit eutils toolchain-funcs + +MY_P=${PN}_${PV} DESCRIPTION="A sequence assembler for very short reads" HOMEPAGE="http://www.ebi.ac.uk/~zerbino/velvet/" @@ -18,32 +20,27 @@ KEYWORDS="~amd64 ~x86" DEPEND="doc? ( virtual/latex-base )" RDEPEND="" -S="${WORKDIR}/${MY_P}" +S=${WORKDIR}/${MY_P} src_prepare() { - rm -rf "${S}"/third-party/zlib* - sed -i -e '/\(CFLAGS\|LDFLAGS\|Z_LIB_DIR\|Z_LIB_FILES\) *= */d' \ - -e '1 a CFLAGS+= -Wall' -e '1 a LDFLAGS+= -lm -lz' \ - -e '/default :/ s/zlib//' -e '/color :/ s/zlib//' \ - -e '/obj:/ s/zlib//' -e '/obj_de:/ s/zlib//' \ - "${S}"/Makefile || die + epatch "${FILESDIR}"/${P}-gentoo.diff use doc || sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die - sed -i -e '/zlib.h/d' -e '1 i #include ' "${S}"/src/readSet.c || 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 + emake $MAKE_XOPTS || die + emake $MAKE_XOPTS color || die } src_install() { dobin velvet{g,h,g_de,h_de} || die insinto /usr/share/${PN} doins -r contrib || die - dodoc Manual.pdf CREDITS.txt + dodoc Manual.pdf CREDITS.txt ChangeLog || die } pkg_postinst() { -- cgit v1.2.3-65-gdbad