Fixed as-needed problem

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

4 files changed, 143 insertions, 12 deletions

diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog
index 1a8fdbbd3898..05f5be575736 100644
--- a/sci-biology/ncbi-tools++/ChangeLog
+++ b/sci-biology/ncbi-tools++/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/ncbi-tools++
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ChangeLog,v 1.15 2010/06/26 07:28:40 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ChangeLog,v 1.16 2010/06/26 11:04:59 jlec Exp $
+
+*ncbi-tools++-2009.05.15-r6 (26 Jun 2010)
+
+  26 Jun 2010; Justin Lecher <jlec@gentoo.org>
+  -ncbi-tools++-2009.05.15-r5.ebuild, +ncbi-tools++-2009.05.15-r6.ebuild,
+  +files/ncbi-tools++-2009.05.15-asneeded.patch:
+  Fixed as-needed problem
 
   26 Jun 2010; Justin Lecher <jlec@gentoo.org>
   ncbi-tools++-2009.05.15-r5.ebuild:
diff --git a/sci-biology/ncbi-tools++/Manifest b/sci-biology/ncbi-tools++/Manifest
index 2c215c477a59..87c1f387877b 100644
--- a/sci-biology/ncbi-tools++/Manifest
+++ b/sci-biology/ncbi-tools++/Manifest
@@ -1,15 +1,16 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA1
 
+AUX ncbi-tools++-2009.05.15-asneeded.patch 3620 RMD160 393db694f0824b0d47571e3b64250b8398c33e58 SHA1 541f00f4d2170d9bb4721468f1c350dcc92552bb SHA256 71a4b2040417a9bfaa7254b5c6668d09ec69f5836a372f1b2bbc938f41ff7657
 AUX ncbi-tools++-2009.05.15-gcc44.patch 554 RMD160 57a23cbaad59b6011124f684db55f4ac2e4a43ab SHA1 7ed63addba554bf87a347d25ea2d4ea6b6552a1a SHA256 ddc2379ff636851e1bb4fb601930ee926c396819e06812b1ba76da001255d5c6
 DIST ncbi_cxx--May_15_2009.tar.gz 13986626 RMD160 131a04d43056fd4d4fd1781d38a5c1b9e3089a13 SHA1 0cecad93774ce40b3455149b2c3538dfce032b85 SHA256 ccb86f2e33251580e23c94b8d2a4aa4832c278171ded29513f0c9859b303f1d8
-EBUILD ncbi-tools++-2009.05.15-r5.ebuild 2875 RMD160 a587b5054cfedfdbbb787244198f1107b6538da0 SHA1 09b3b4a2edcd53ffa505db0a616491ce925532db SHA256 aa01f8bdf4da3340a1233cc440edd47529cdc39d2dd4cd3be5738ad347796136
-MISC ChangeLog 2833 RMD160 aecd3a8812eec6ad2c552c005f34aa9da88f6ced SHA1 654c4bcf621a949faaafbfaf69d70bc3c40f7fa6 SHA256 48a1517d3bd9c82a9c3b402a3aae3b566b6bb04e81202e5a542904303b1301a3
+EBUILD ncbi-tools++-2009.05.15-r6.ebuild 2861 RMD160 22529f1cc1deef1557fd4be48e3436a83cd8c48f SHA1 a7b463d309a19393cd9b1d5325f25aeaf20f633b SHA256 78445abf6420b85956289d33e1b1d9ffc1f72c00b7652a942f52c4662e48cf04
+MISC ChangeLog 3073 RMD160 4823e874a6fa53d57ab91b0275d5d5a83064b3bb SHA1 4377e43b6a258f87d73b3e48aa0c33e3334f7379 SHA256 0633c0f2d4f8d4d65673e33c9b94419e797b052607acee2c8e180f3b6b6cfb3b
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
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diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-2009.05.15-asneeded.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-2009.05.15-asneeded.patch
new file mode 100644
index 000000000000..fde794b1a20e
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-2009.05.15-asneeded.patch
@@ -0,0 +1,123 @@
+--- src/build-system/Makefile.mk.in
++++ src/build-system/Makefile.mk.in
+@@ -547,7 +547,7 @@
+ #################################
+ # Useful sets of object libraries
+ # Interdependent sequence libraries + seqcode.  Does not include seqset.
+-COMPRESS_LDEP = $(CMPRS_LIB)
++COMPRESS_LDEP = $(CMPRS_LIB) xutil xncbi
+ COMPRESS_LIBS = xcompress $(COMPRESS_LDEP)
+ 
+ GENBANK_LDEP = \
+--- src/util/compress/Makefile.compress.lib
++++ src/util/compress/Makefile.compress.lib
+@@ -4,7 +4,7 @@
+ 
+ LIB = xcompress
+ 
+-DLL_LIB = 
+-#$(COMPRESS_LDEP)
++DLL_LIB = $(COMPRESS_LDEP)
++LIBS = $(CMPRS_LIBS)
+
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
+--- src/serial/Makefile.serial.lib
++++ src/serial/Makefile.serial.lib
+@@ -17,3 +17,5 @@
+ 	objostrjson serializable serialobject pathhook
+ 
+ LIB    = xser
++
++DLL_LIB = xutil xncbi
+--- src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
++++ src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
+@@ -12,4 +12,4 @@
+ LIB_OR_DLL = both
+ 
+ # Dependencies for shared library
+-DLL_LIB = 
++DLL_LIB = xcompress
+--- src/objtools/readers/Makefile.xobjread.lib
++++ src/objtools/readers/Makefile.xobjread.lib
+@@ -8,4 +8,4 @@
+       wiggle_reader wiggle_data gff3_reader \
+       ucscid idmap idmapper idmapper_builtin idmapper_user idmapper_site \
+       idmapper_database
+-DLL_LIB = creaders
++DLL_LIB = creaders seq seqset
+--- src/objects/seq/Makefile.seq.lib
++++ src/objects/seq/Makefile.seq.lib
+@@ -10,3 +10,5 @@
+ SRC = $(ASN:%=%__) $(ASN:%=%___) seqport_util \
+       seq_id_tree seq_id_handle seq_id_mapper \
+       seq_loc_mapper_base seq_align_mapper_base
++
++DLL_LIB = biblio general pub seqcode sequtil xncbi
+--- src/objects/pub/Makefile.pub.lib
++++ src/objects/pub/Makefile.pub.lib
+@@ -1,2 +1,4 @@
+ LIB = pub
+ SRC = pub__ pub___
++
++DLL_LIB = medline
+--- src/objects/general/Makefile.general.lib
++++ src/objects/general/Makefile.general.lib
+@@ -1,2 +1,4 @@
+ LIB = general
+ SRC = general__ general___ uoconv
++
++DLL_LIB = xsoap xser
+--- src/objects/omssa/Makefile.omssa.lib
++++ src/objects/omssa/Makefile.omssa.lib
+@@ -2,3 +2,5 @@
+ 
+ LIB = omssa
+ SRC = omssa__ omssa___
++
++DLL_LIB = seq
+--- src/algo/blast/api/Makefile.xblast.lib
++++ src/algo/blast/api/Makefile.xblast.lib
+@@ -73,7 +73,8 @@
+ 
+ LIB = xblast
+ 
+-DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS)
++DLL_LIB = xalgodustmask xalgowinmask xobjutil xnetblast xnetblastcli blastdb composition_adjustment \
++   blast tables xalgoblastdbindex_search xalgoblastdbindex $(OBJMGR_LIBS)
+ 
+ CFLAGS   = $(FAST_CFLAGS)
+ # Strict gcc flags
+--- src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
++++ src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
+@@ -12,3 +12,4 @@
+ LDFLAGS  = $(FAST_LDFLAGS)
+ 
+ ASN_DEP = seqset
++DLL_LIB = xobjread
+--- src/objects/biblio/Makefile.biblio.lib
++++ src/objects/biblio/Makefile.biblio.lib
+@@ -1,2 +1,4 @@
+ LIB = biblio
+ SRC = biblio__ biblio___ label_util
++
++DLL_LIB = general
+--- src/objects/medline/Makefile.medline.lib
++++ src/objects/medline/Makefile.medline.lib
+@@ -1,2 +1,4 @@
+ LIB = medline
+ SRC = medline__ medline___
++
++DLL_LIB = biblio
+--- src/objects/Makefile.in
++++ src/objects/Makefile.in
+@@ -5,8 +5,8 @@
+ 
+ USR_PROJ = sources
+ 
+-SUB_PROJ = tinyseq omssa general biblio medline pub pubmed \
+-           featdef seqcode seqset seq genomecoll biotree \
++SUB_PROJ = tinyseq general biblio medline pub pubmed \
++           featdef seqcode seqset seq omssa genomecoll biotree \
+            id1 id2 gbseq insdseq entrez2 submit medlars mla proj mmdb \
+            cdd cn3d scoremat ncbimime access objprt docsum taxon1 mim \
+            entrezgene blast blastdb blastxml pcsubstance pcassay remap \
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-2009.05.15-r5.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-2009.05.15-r6.ebuild
index b29b6fad8f13..576abdf21470 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-2009.05.15-r5.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-2009.05.15-r6.ebuild
@@ -1,10 +1,10 @@
 # Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ncbi-tools++-2009.05.15-r5.ebuild,v 1.2 2010/06/26 07:28:40 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ncbi-tools++-2009.05.15-r6.ebuild,v 1.1 2010/06/26 11:04:59 jlec Exp $
 
 EAPI="3"
 
-inherit eutils multilib
+inherit eutils flag-o-matic multilib toolchain-funcs
 
 MY_TAG="May_15_2009"
 MY_Y="${MY_TAG/*_/}"
@@ -47,7 +47,8 @@ RDEPEND="${DEPEND}"
 S="${WORKDIR}/${MY_P}"
 
 src_prepare() {
-	epatch "${FILESDIR}"/${P}-gcc44.patch
+	epatch "${FILESDIR}"/${P}-gcc44.patch \
+		"${FILESDIR}"/${P}-asneeded.patch
 	sed -i -e 's/-print-file-name=libstdc++.a//' \
 		-e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
 		src/build-system/configure || die
@@ -55,10 +56,9 @@ src_prepare() {
 
 src_configure() {
 	# required with gcc-4.4 and code turned on by --with-mt
-	export CPPFLAGS="${CPPFLAGS} -fpermissive"
+	append-cxxflags -fpermissive
 
-	# I add this until the as-needed fix is in the tree
-	append-ldflags $(no-as-needed)
+	tc-export CXX CC
 
 	# econf fails
 	# --with-bin-release and --without-ftds are workarounds for build system bugs