Fix building with --as-needed wrt #363479 by Diego Elio Pettenò <flameeyes@gentoo.org>

Package-Manager: portage-2.2.0_alpha29/cvs/Linux x86_64

4 files changed, 35 insertions, 16 deletions

diff --git a/sci-biology/velvet/ChangeLog b/sci-biology/velvet/ChangeLog
index 61b61ccedd4c..6f36faa95253 100644
--- a/sci-biology/velvet/ChangeLog
+++ b/sci-biology/velvet/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-biology/velvet
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/velvet/ChangeLog,v 1.13 2011/02/03 02:40:47 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/velvet/ChangeLog,v 1.14 2011/04/13 12:32:36 xarthisius Exp $
+
+*velvet-1.0.18-r1 (13 Apr 2011)
+
+  13 Apr 2011; Kacper Kowalik <xarthisius@gentoo.org> -velvet-1.0.18.ebuild,
+  +velvet-1.0.18-r1.ebuild, -files/velvet-1.0.18-gentoo.diff,
+  +files/velvet-1.0.18-gentoo-r1.diff:
+  Fix building with --as-needed wrt #363479 by Diego Elio Pettenò
+  <flameeyes@gentoo.org>
 
 *velvet-1.0.18 (03 Feb 2011)
 
diff --git a/sci-biology/velvet/Manifest b/sci-biology/velvet/Manifest
index 5c9de3ecba4b..b6dbfd2c1c31 100644
--- a/sci-biology/velvet/Manifest
+++ b/sci-biology/velvet/Manifest
@@ -1,10 +1,22 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX velvet-0.7.62-gentoo.diff 8934 RMD160 4fa5e7bf70c1a9adf5ad5086e856c742e72382d7 SHA1 5dccccb0f6049e0203d4008d5a00e500cf13ef74 SHA256 0c18060bc3283800d44de8895b3417782eca8fb2be4e2256c1a57f43ed628139
-AUX velvet-1.0.18-gentoo.diff 7880 RMD160 1c14bc9fa407b0cedad98e8fd4ab2b53f7906f33 SHA1 3ec1f6c2f7e16e075ab73458b16e1d5e059af983 SHA256 e67090f09c2c77bca30175c8db18dc6428556c02c4f89991ac50f7f028d9e1f0
+AUX velvet-1.0.18-gentoo-r1.diff 7879 RMD160 03178853bdcccd2c91cd2978bb31d75d67e784ad SHA1 b936840ea0c4e4562c276c8d10edab63267d0ba8 SHA256 5a177e3d0b027069aa44ce97d964ab7f8ab97561f00aa9c4485f110dafb6fa89
 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
 DIST velvet_1.0.18.tgz 7598196 RMD160 970e5c4222dc6a7b13a38db4c00ad300e126a516 SHA1 ce6b19d09924342c2685f8b49dcde205bb0f62a0 SHA256 e6e108ef16f6c5974617b195ce79c7d2860d335a5122418a883217b8cc48473e
 EBUILD velvet-0.7.55.ebuild 1720 RMD160 3fd31e44ffc0d03fbcaa4bcc347cadfb7c27f8ab SHA1 5f15b11e3954ddee5e3aff284cfd33ef84a5620a SHA256 df6d6959b07c3dab7b42756753effa4b85ca789bd6c8fd5d8a07b30700fb342b
 EBUILD velvet-0.7.62.ebuild 1504 RMD160 848be9f30b0ff82dc7b859656d54a0859e6f0690 SHA1 ddce982d92c6053bc97589dd00e0e95620e49613 SHA256 ffb3ae3c0fbd5267cf30d90b0122a1155c78e9b76543cc75d508d4d679c1f1d1
-EBUILD velvet-1.0.18.ebuild 1654 RMD160 e3bdb72d0e054936e96bc09719e01660be7235f4 SHA1 c70867f1d3a432a665a50c2d66576ed9e43554d4 SHA256 3715e3478023bf8260fc0aaa8942ded96125a360e497daed212368e5c4131b72
-MISC ChangeLog 1982 RMD160 24decea3393149e0859fbec5d6cadeeef2273bba SHA1 63f1ce1ceb483beeecbd2051ef6e312d41e8e93f SHA256 5991e03e0d1160f6f8a4e37a4cf8439ce91ad8c832bb91cc1d6bacb16b891aa1
+EBUILD velvet-1.0.18-r1.ebuild 1578 RMD160 4be773452812b3c8e0883c37faec626595b2cb17 SHA1 872c391815747e752694ddbf7d9def65ec8ea739 SHA256 433320ab41e2d847b9960b2a9fe8d61c52ab62baf0f69188b436b3b7b9f51cf7
+MISC ChangeLog 2290 RMD160 59eac719b968a573ce85a2aff9358e9346bfe404 SHA1 96f9d10ba3ead9343208db8232fc65d7b9d5e735 SHA256 353c017ea3768a8516e11739391b12b0f8890c792262f5400d92f7ab8e52c099
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.17 (GNU/Linux)
+
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+hZ6KsiZOgxVwMDYLrg8=
+=I/ts
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/velvet/files/velvet-1.0.18-gentoo.diff b/sci-biology/velvet/files/velvet-1.0.18-gentoo-r1.diff
index b08bb3537b09..ed53a1229b5b 100644
--- a/sci-biology/velvet/files/velvet-1.0.18-gentoo.diff
+++ b/sci-biology/velvet/files/velvet-1.0.18-gentoo-r1.diff
@@ -20,33 +20,33 @@ diff -durr Makefile Makefile
  
  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) $(LIBS) -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 
++	$(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) $(LIBS) -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 
++	$(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) $(LIBS) $(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 
-+	$(CC) $(CFLAGS) $(LDFLAGS) $(LIBS) $(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 
++	$(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) $(LIBS) -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 
-+	$(CC) $(CFLAGS)  $(LDFLAGS) $(LIBS) -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 
++	$(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) $(LIBS) $(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 
-+	$(CC) $(CFLAGS) $(LDFLAGS) $(LIBS) $(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 
++	$(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
diff --git a/sci-biology/velvet/velvet-1.0.18.ebuild b/sci-biology/velvet/velvet-1.0.18-r1.ebuild
index affea2dd68ce..3ba98c3d6fdc 100644
--- a/sci-biology/velvet/velvet-1.0.18.ebuild
+++ b/sci-biology/velvet/velvet-1.0.18-r1.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/velvet/velvet-1.0.18.ebuild,v 1.1 2011/02/03 02:40:47 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/velvet/velvet-1.0.18-r1.ebuild,v 1.1 2011/04/13 12:32:36 xarthisius Exp $
 
 EAPI="3"
 
@@ -20,12 +20,11 @@ KEYWORDS="~amd64 ~x86"
 DEPEND="doc? ( virtual/latex-base )"
 RDEPEND=""
 
-S="${WORKDIR}/${MY_P}"
+S=${WORKDIR}/${MY_P}
 
 src_prepare() {
 	append-flags -O3 # as recommended by upstream
-	filter-ldflags -Wl,--as-needed # sorry, no time to deal with this. patches welcome
-	epatch "${FILESDIR}"/${P}-gentoo.diff
+	epatch "${FILESDIR}"/${P}-gentoo-r1.diff
 	use doc || sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die
 }