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

4 files changed, 157 insertions, 16 deletions

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 <xarthisius@gentoo.org> 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 315331f418c2de89c6c871cea3759d947320c0adbc763fea290ec78ece69b614
 DIST velvet_0.7.62.tgz 3506366 RMD160 1e17ebc03dc135532a3eaeb6e68883116970a128 SHA1 9e5df8b4bca97d0989e06001ae93d9d5bda552b0 SHA256 fb5604dd69300fb833ad9227dce9cf38737b8d2f0a3125361eb5edebc6a4f740
 EBUILD velvet-0.7.50.ebuild 1145 RMD160 df35af8f2ea52700b7951daa24de167e45a50442 SHA1 ffbb71058f5858705caecb887004e43e5c4deacb SHA256 61e9f5315f8616203cc263a99acc1ab64e479af02cd6ab637bf34f7588a149cb
 EBUILD velvet-0.7.55.ebuild 1720 RMD160 3fd31e44ffc0d03fbcaa4bcc347cadfb7c27f8ab SHA1 5f15b11e3954ddee5e3aff284cfd33ef84a5620a SHA256 df6d6959b07c3dab7b42756753effa4b85ca789bd6c8fd5d8a07b30700fb342b
-EBUILD velvet-0.7.62.ebuild 1771 RMD160 abbba8f52114f2db423ea344bfaa04c0e9f91027 SHA1 e1ffca9dea8ff5fbaabac819fa25a78bb7a2ecd1 SHA256 cf08ac594c3d6b1faf333ce9954cea18afc82fc92e6a03b416a696ca0355019a
-MISC ChangeLog 1517 RMD160 6c228acf0f9495d688a54e4936fcd34f643c7f9f SHA1 797103e3ba8f58238ffc22af7b9bd948903f56da SHA256 cbb635b2b117cda6b38f685f0e4df6e0859ba6ec20513b36e93ca7b3c692b449
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 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.15 (GNU/Linux)
+
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+6WOTthATtDkPjyCPfn0=
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+-----END PGP SIGNATURE-----
diff --git 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 <string.h>
+ #include <math.h>
+ #include <time.h>
++#include <zlib.h>
+ 
+ #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 <fcntl.h>
+ #  include <io.h>
+
+--- 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 <zlib.h>' "${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() {