Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

29 files changed, 411 insertions, 1109 deletions

diff --git a/profiles/updates/1Q-2011 b/profiles/updates/1Q-2011
index 98a3af9ad..5faa2ed71 100644
--- a/profiles/updates/1Q-2011
+++ b/profiles/updates/1Q-2011
@@ -1 +1,2 @@
 move www-apps/SwishE www-apps/py-swish-e
+move sys-cluster/os-mpi sys-cluster/native-mpi
diff --git a/sci-biology/bambus/Manifest b/sci-biology/bambus/Manifest
index d256fc82c..cb44ac5df 100644
--- a/sci-biology/bambus/Manifest
+++ b/sci-biology/bambus/Manifest
@@ -1,4 +1,5 @@
 AUX TigrFoundation-all-patches.patch 2071 RMD160 ce194684d054613b254fa5f41fd31e520fe1cf5b SHA1 4a3f0d061b8024abb21178feeef3b1256e4117ac SHA256 e13f6136ef336e54ecc24d0e34e65e1ab827cfb7365b2d2686541ceed3cd6ac5
+AUX goBambus.pl 4195 RMD160 d9b028c3f5fbe9035be92a54a485404e62c855c1 SHA1 e1a1f1ca01e3be50300c1d376d07bbb2c8371634 SHA256 28f9e591ff58454910965a4854e85f8f5e72d6aab9318e4dcfddbab0d99379d6
 DIST bambus-2.33.tar.gz 504535 RMD160 a5b7fe0e96fb4969d19b6b2e9519dac800d005b7 SHA1 5657fc5db1a829ffdf1b0e88f54df79bd718e16c SHA256 bc8e3c712719bccb00357001713e56f58aac57ae452fd73148eeccff291eefdc
-EBUILD bambus-2.33.ebuild 4861 RMD160 a2550f13d129e0424cee6613a4acde0d7fa491c1 SHA1 f68b6628b57b3343f94dbd060ebdb08273cf7fb0 SHA256 6acc2a279c4a699ce17637d8d358d5871242a33ba3d324bdc297d00943888947
-MISC metadata.xml 886 RMD160 7506f8556635205b2b963c1c860165db982798e6 SHA1 b2a8dc61ac03d6b16960ae6e9eb416e45c87cecd SHA256 25bc492efe42150ff5d7cd57fb3f7807fc9da3530296726708d32fe3de4041c7
+EBUILD bambus-2.33.ebuild 5003 RMD160 3d97907ac5a945c9974073168079bafbccfa2ae0 SHA1 f1ed0463a6460580e4b0ea5fe5dcdc2a5228760a SHA256 1f6cd9640fcfad622bd8a03e2a42e5685d717c53145a16d084e29d29ca98b6fa
+MISC metadata.xml 894 RMD160 db355baa910d9a8b944a8c13490e0cee78430799 SHA1 6e9a7e6cddd8964be1ca4f411b3204b5f887239c SHA256 29bb4cf93b76b33523a7e823ab01066c39165c05e1701d3407d84c50381996a9
diff --git a/sci-biology/bambus/bambus-2.33.ebuild b/sci-biology/bambus/bambus-2.33.ebuild
index 2a46d9c72..045c267a3 100644
--- a/sci-biology/bambus/bambus-2.33.ebuild
+++ b/sci-biology/bambus/bambus-2.33.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -18,6 +18,8 @@ IUSE=""
 
 DEPEND="sci-biology/tigr-foundation-libs"
 RDEPEND="${DEPEND}
+		dev-lang/perl
+		dev-lang/python
 		dev-perl/XML-Parser
 		dev-perl/Config-IniFiles
 		dev-perl/GraphViz"
@@ -95,6 +97,8 @@ src_install() {
 	mkdir -p "${D}"/usr/share/doc/"${P}" || die
 	mv "${D}"/usr/doc/* "${D}"/usr/share/doc/"${P}" || die
 	rmdir "${D}"/usr/doc || die
+
+	dobin "${FILESDIR}"/goBambus.pl || die "Failed to install the alternative of goBambus.py written in perl"
 }
 
 pkg_postinst(){
diff --git a/sci-biology/bambus/files/goBambus.pl b/sci-biology/bambus/files/goBambus.pl
new file mode 100644
index 000000000..61f9ed3d9
--- /dev/null
+++ b/sci-biology/bambus/files/goBambus.pl
@@ -0,0 +1,244 @@
+#!/usr/bin/perl -w
+
+## Very simple perl script to drive the Bambus 2.0 pipeline (as I
+## currently understand it).
+## http://sourceforge.net/apps/mediawiki/amos/index.php?title=Bambus_2.0/goBambus-perl
+## as of 201103021123
+
+use strict;
+use Getopt::Long;
+
+
+
+## Configure defaults
+
+my $verbose = 1;
+
+my $contig_file = '';
+my $fasta_file  = '';
+my $mates_file  = '';
+
+my $output_prefix = 'out';
+
+## The threshold used to accept or reject a link between contigs
+my $link_redundancy = 1;
+
+## Weather or not to run the (crappy) 'repeat filter' code
+my $filter_repeats  = 0;
+
+## Not running dot saves time on 'big' runs
+my $run_dot = 1;
+
+
+
+## Process command line arguments
+
+GetOptions
+  ("contig_file=s"   => \$contig_file,
+   "fasta_file=s"    => \$fasta_file,
+   "mates_file=s"    => \$mates_file,
+   "output_prefix=s" => \$output_prefix,
+
+   "link_redundancy|r=i" => \$link_redundancy,
+   "repeat_filter|x"     => \$filter_repeats,
+   "dot|d!"              => \$run_dot,
+   "verbose+"            => \$verbose,
+  )
+  or die "failure to communicate\n";
+
+die "-c contig file plz!\n" unless -s $contig_file;
+die "-f fasta  file plz!\n" unless -s $fasta_file;
+die "-m mates  file plz!\n" unless -s $mates_file;
+
+die "are you crazy?\n"
+  if $output_prefix eq '';
+
+warn
+  join("\n",
+       "contig file     : $contig_file",
+       "fasta file      : $fasta_file",
+       "mates file      : $mates_file",
+       "output prefix   : $output_prefix",
+       "link redundancy : $link_redundancy",
+       "repeat filter   : $filter_repeats",
+       "run dot?        : $run_dot",
+       "verbose         : $verbose",
+      ), "\n"
+  if $verbose > 0;
+#exit;
+
+
+
+## Run the pipeline
+
+## Get data into bank format
+
+run(qq/
+ toAmos
+  -s $fasta_file
+  -c $contig_file
+  -m $mates_file
+  -o $output_prefix.afg
+/);
+
+## Debugging mates file
+#exit;
+
+run(qq/
+  bank-transact -cf
+    -m $output_prefix.afg
+    -b $output_prefix.bnk
+/);
+
+
+
+## Run the new Bambus pipeline
+
+run(qq/
+  clk
+    -b $output_prefix.bnk
+/);
+
+run(qq/
+  Bundler
+    -b $output_prefix.bnk
+/);
+
+## Repeat filtering?
+my $filter_repeats_option_string = '';
+if($filter_repeats){
+  run(qq/
+    MarkRepeats
+      -noCoverageRepeats
+      -b $output_prefix.bnk
+      -redundancy $link_redundancy
+       > $output_prefix.repeats
+  /);
+  
+  $filter_repeats_option_string =
+    "-repeats $output_prefix.repeats";
+}
+
+run(qq/
+  OrientContigs
+    -noreduce
+   $filter_repeats_option_string
+    -b $output_prefix.bnk
+    -redundancy $link_redundancy
+    -prefix $output_prefix
+/);
+
+
+
+## Generate some additional TEXT output
+
+## ouput a fasta sequence for the contigs from the bank (passed to
+## printScaff with -f)
+
+#run(qq/
+#  bank2fasta -iid
+#    -b $output_prefix.bnk
+#     > $output_prefix.contig.fasta
+#/);
+
+## Generates the useful .details, .oo, .sum and .stats files
+#    -f $output_prefix.contig.fasta
+run(qq/
+  printScaff -detail -oo -sum
+    -e $output_prefix.evidence.xml
+    -s $output_prefix.out.xml
+    -l $output_prefix.library
+    -o $output_prefix
+/);
+
+run(qq/
+  mv -f
+    printScaff.error
+    $output_prefix.printScaff.error
+/)
+  if -s 'printScaff.error';
+
+
+
+
+
+## UNTANGLE
+
+run(qq/
+  untangle
+    -e $output_prefix.evidence.xml
+    -s $output_prefix.out.xml
+    -o $output_prefix.out.untangle.xml
+/);
+
+run(qq/
+  mv -f
+    untangle.error
+    $output_prefix.untangle.error
+/)
+  if -s 'untangle.error';
+
+
+
+## Generates the useful .details, .oo, .sum and .stats files
+#    -f $output_prefix.contig.fasta
+run(qq/
+  printScaff -detail -oo -sum -dot
+    -e $output_prefix.evidence.xml
+    -s $output_prefix.out.untangle.xml
+    -l $output_prefix.library
+    -o $output_prefix.untangle
+/);
+
+run(qq/
+  mv -f
+    printScaff.error
+    $output_prefix.untangle.printScaff.error
+/)
+  if -s 'printScaff.error';
+
+
+
+
+
+## FINALLY, DOT
+
+if($run_dot){
+  # output before untangle
+  run(qq/
+    dot -Tps
+      $output_prefix.dot
+    > $output_prefix.ps
+  /);
+  
+  # output after untangle
+  run(qq/
+    dot -Tps
+      $output_prefix.untangle.dot
+    > $output_prefix.untangle.ps
+  /);
+}
+
+warn "OK\n";
+
+
+
+
+
+## Yup
+
+sub run{
+  my $cmd = shift;
+  
+  $cmd =~ s/\n/ /g;
+  
+  print "\n\n\nRUN: $cmd\n\n"
+    if $verbose > 0;
+  
+  `$cmd`;
+  
+  die if $? != 0;
+  
+  return 1;
+}
+
diff --git a/sci-biology/smalt-bin/Manifest b/sci-biology/smalt-bin/Manifest
new file mode 100644
index 000000000..25f5fff0b
--- /dev/null
+++ b/sci-biology/smalt-bin/Manifest
@@ -0,0 +1,3 @@
+DIST smalt-0.5.0.tgz 526031 RMD160 575e96bdeaada5acf6cfa8ab8b4a247be50b148f SHA1 70ff52bd66ec72a581abd9c8bbb0315fc4b6704b SHA256 bbd5e3f34c17d7ffcaf405c212a65d53dfd23cd6af99325a8d323cff4c0802f3
+EBUILD smalt-bin-0.5.0.ebuild 729 RMD160 4c922261ea6e0546ea2aa4c52463c6b48de28782 SHA1 fe766d8cbfde7602078e32f402ec951459f365ce SHA256 06dd5eb4a21989c66660906223e01fd31b3e2b502cfc9350082e7e2160623a7f
+MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85
diff --git a/sci-libs/opencascade/metadata.xml b/sci-biology/smalt-bin/metadata.xml
index 5c33b98fa..07b525505 100644
--- a/sci-libs/opencascade/metadata.xml
+++ b/sci-biology/smalt-bin/metadata.xml
@@ -1,8 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci</herd>
-	<use>
-		<flag name="stlport"> Enables support for STL files</flag>
-	</use>
+	<herd>sci-biology</herd>
+	<maintainer>
+		<email>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
 </pkgmetadata>
diff --git a/sci-biology/smalt-bin/smalt-bin-0.5.0.ebuild b/sci-biology/smalt-bin/smalt-bin-0.5.0.ebuild
new file mode 100644
index 000000000..1e13f95e1
--- /dev/null
+++ b/sci-biology/smalt-bin/smalt-bin-0.5.0.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+DESCRIPTION="Pairwise sequence alignment mapping DNA reads onto genomic reference, better over SSAHA2."
+HOMEPAGE="http://www.sanger.ac.uk/resources/software/smalt/"
+SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt/smalt-0.5.0.tgz"
+
+LICENSE="GRL"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/smalt-"${PV}"
+
+src_install(){
+	if use x86; then
+		newbin smalt_i386 smalt || die
+	fi
+	if use amd64; then
+		newbin smalt_x86_64 smalt || die
+	fi
+	if use ia64; then
+		newbin smalt_ia64 || die
+	fi
+	dodoc NEWS smalt_manual.pdf || die
+	doman smalt.1 || die
+}
diff --git a/sci-biology/ssaha2-bin/Manifest b/sci-biology/ssaha2-bin/Manifest
new file mode 100644
index 000000000..148bbd392
--- /dev/null
+++ b/sci-biology/ssaha2-bin/Manifest
@@ -0,0 +1,7 @@
+DIST samflag.c 2424 RMD160 a338182d756bdcd1214861d6273c0149df5e3177 SHA1 631282cc7fe88bac4f43011a0db09d9a1494859a SHA256 945958214ef1adc40029a6b3c323c37338e095e9e2bcbff5e5ec05aadbdb67d0
+DIST ssaha2-manual.pdf 163188 RMD160 903bc1dc7f7bf89966f957c9df3c82128e233a53 SHA1 8e332b01628a3b64ea3dcc86d654a99d59277934 SHA256 1a0529168b71ac55e13b34264a854daa6a5dac9468f81ccb5b63bd5e1baafdbf
+DIST ssaha2_i686.tgz 288481 RMD160 0c493b917f40f5f259b6a6fe564ebc6a9e4409ec SHA1 b042e36c57f5e89098b6c5f07a2d646c02e76110 SHA256 7d173d763d9f685ef3d0075124bf8b763c6d2d3ed1a1f823bc66d6b6b029abed
+DIST ssaha2_ia64.tgz 458507 RMD160 8c3c821d292db94036f8d93342357ff0a8773bbe SHA1 a7ac847a64240f85eca3aff0df21bf9d339eed8f SHA256 3eb2a31559911f3ee87e11f3b977962da31b60c25ea0c9a064edfd1165b6b5dd
+DIST ssaha2_x86_64.tgz 287790 RMD160 93938da9898f30cf77f020329316228fd47ebe41 SHA1 d16d38e3bdab97994b4a70e4c0fc737a09b94d3a SHA256 0135ab2e285a898d450744b7c9d643efbeb6048783169a6647f310ce2e7b8138
+EBUILD ssaha2-bin-2.5.3.ebuild 1262 RMD160 316d8a8bfa9141159ce98215ee2a8ef121dfcb65 SHA1 7e4f63058267190dea68478ef20935bda63b848a SHA256 0929206dc3c0376c038507a234a2f54e5ad581514030e1131867c78cd2ddd07a
+MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85
diff --git a/sci-biology/ssaha2-bin/metadata.xml b/sci-biology/ssaha2-bin/metadata.xml
new file mode 100644
index 000000000..07b525505
--- /dev/null
+++ b/sci-biology/ssaha2-bin/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-biology</herd>
+	<maintainer>
+		<email>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+</pkgmetadata>
diff --git a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild
new file mode 100644
index 000000000..eaf02be74
--- /dev/null
+++ b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit toolchain-funcs
+
+DESCRIPTION="SSAHA2: Sequence Search and Alignment by Hashing Algorithm"
+HOMEPAGE="http://www.sanger.ac.uk/resources/software/ssaha2"
+SRC_URI="x86? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_i686.tgz )
+		amd64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_x86_64.tgz )
+		ia64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_ia64.tgz )
+		ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/samflag.c
+		ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2-manual.pdf"
+
+LICENSE="GRL"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+if use x86; then
+	S="${WORKDIR}"/ssaha2_v"${PV}"_i686
+fi
+if use amd64; then
+	S="${WORKDIR}"/ssaha2_v"${PV}"_x86_64
+fi
+if use ia64; then
+	S="${WORKDIR}"/ssaha2_v"${PV}"_ia64
+fi
+
+src_compile() {
+	$(tc-getCC) ${CFLAGS} -o samflag "${DISTDIR}"/samflag.c || die "Failed to compile samflags"
+}
+
+src_install() {
+	dobin samflag ssaha2 ssaha2Build ssahaSNP || die "dobin failed"
+	dodoc README || die "dodoc failed"
+	dodoc "${DISTDIR}"/ssaha2-manual.pdf || die "Failed to install ssaha2-manual.pdf"
+}
diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 954daf862..d02adf0ee 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  03 Mar 2011; Justin Lecher <jlec@gentoo.org> files/9999-lidia.patch,
+  coot-9999.ebuild:
+  Coot live fixes
+
   20 Jan 2011; Justin Lecher <jlec@gentoo.org> coot-9999.ebuild:
   Fix tests
 
diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest
index d18069644..6ab4d3c00 100644
--- a/sci-chemistry/coot/Manifest
+++ b/sci-chemistry/coot/Manifest
@@ -5,20 +5,20 @@ AUX 9999-clipper.patch 314 RMD160 23780b108f2cabb1ba54de038b2e1716e4e4566e SHA1
 AUX 9999-goocanvas.patch 702 RMD160 9b26975eb658f15dfd806e47be9c11bcb7f850db SHA1 37bb70847ced34b754fe7cf5fea878b93bb6ed12 SHA256 162b21a3afb2d523df315ec021faf7a6497eb3b4fe00f90f601527fe1c22621a
 AUX 9999-gsl.patch 478 RMD160 c3df04b30699b8a534dc69cde67c805bb5ac1fdb SHA1 b32b9404c85df75e8149c8ec8f6dc48d0b4c64fa SHA256 fc6b256c655d7390f5270f266cbf22d34d6e27e1726d09f1747fd3d14ab393a4
 AUX 9999-include.patch 345 RMD160 6e42ce2afa7141f9cdcda0ca3ea5a11ef4f0f15f SHA1 3df3955307115ed8527f55fb49452905991c36cc SHA256 07b61fb298da857c5c37abb492cf192c65f9b538a3fc2d316aca7f4269e25a75
-AUX 9999-lidia.patch 531 RMD160 45c5929020a735121e54b4a1240c8f3fb0d97ec5 SHA1 ca0b119af0e39dfc19b606cb629c26f55ca3bf01 SHA256 c7b49c6a0689c467e9298a230f1a8c8f8c669ef04b51632e581f9a63f43c0a34
+AUX 9999-lidia.patch 634 RMD160 0c2d7f1ae5d8891637322c8e0ca28482214de33d SHA1 262e15e9b8b5c74b1780a3f7252cf9385397756b SHA256 c1e7c244950bce29d733b95dff92003afd20e7c34b33ae54e52dba9bece6f363
 AUX 9999-openmp.patch 850 RMD160 5d128c3451a496f95ca33d7cd5447a0c85d55c13 SHA1 ee8a8823a70cf4c194daf7879c6b3ff011c99e3d SHA256 97da619ba47f16ff14a5b9496cb3e377f65c533dfe861c5cb4c7f19d293cae5c
 AUX 9999-rappermc.patch 477 RMD160 5d67f80be6e4bc303d7999cfa645ea36dbfc834a SHA1 4c2ff98125b6a4664f77e8b5f39f6a9a1ac72622 SHA256 83dd4ddda627baec52a0754117741d97e7b2c61e42813a314b258db93903d7c0
 AUX fix-namespace-error.patch 1081 RMD160 ebecd51b87c39dc2c37e565f18fc88b7aa837d05 SHA1 f732df5f4795e728bdf217aac9c9f53952e2890c SHA256 fd271dd22eec5725fcbd20c68b57008eed0f435d1e0ac212fbfd389a0a970beb
 AUX glib.m4 8444 RMD160 f3f4b2987796f16d17758f2af3459279351d6f2c SHA1 201eb58c2b3f3c5395dacd3913a4fb9d950d3276 SHA256 ada4a0a46bd00eda39afe77f675b721f60cd20c0080170848f4d7e92b4ba4dc8
 AUX gtk.m4 8516 RMD160 3860fe211902d5b9290f0a70e7d75ebec6b0ec67 SHA1 98b93b820423a52ebd80e3f1822a8f2bd4b3f15d SHA256 4eb6e0bb2c6863139d1fb4ca2d1d0f0ef07e3a85fdbb5ba98d03373f610f0c37
 DIST greg-data.tar.gz 8041681 RMD160 dc03bc233bed69fd6288a92a48b9a7e0bbf56129 SHA1 6e27bd0053758cf829a3ff8bd07b94c9e1ffb777 SHA256 46b9bb2dc9f5dfff463a5fe95e8e583e2a44760ae96fc0b8b5b4bd455e35862d
-EBUILD coot-9999.ebuild 4036 RMD160 433191b762140ee2647d29d8c576649b3270b2c2 SHA1 b51284796734511e2a7d77c0e05b1958afdaa064 SHA256 fd4d6387e110f747ffda5fc3dcfb0590d5fa6465ffe5fdeadce4ada87f18ecd4
-MISC ChangeLog 8982 RMD160 72892a4f191adc2805a04ac0eb4e9208856a5189 SHA1 7c717bc535cfa6237e8e23ee80218f0e276b7f6b SHA256 71702dfd2169da210e67f29b4e941120ec6df0963239d86ff65c3314aed23cf0
+EBUILD coot-9999.ebuild 4067 RMD160 3bba472cf11f65794d072cf04b7290da5b7d4c26 SHA1 ad478158a4366dba8ca02e30e0fb016dbcdd4ada SHA256 4c330d919924e61c143ae31f547af8e7479e7c8b6bcd3896376c83675c188447
+MISC ChangeLog 9092 RMD160 a3e68dd7538ccaee80eed1e0eb490ccb5e3c3c6b SHA1 f1f4584555bf381633dcbdee57d658fa696a07f7 SHA256 57be9fefadd4928d8a79cc2658cdda58ad27adc228cdd93dee4d0d26bce771c8
 MISC metadata.xml 306 RMD160 303613d4bb58ea149f418efc0d41f550ecbb94ca SHA1 1caeb2549f7f6a1dd44f2200784be8f2a7f294ab SHA256 f0ead885a2ede3186db2797473c72249fb525de661c279ca2ce7b8b152399bf6
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.16 (GNU/Linux)
+Version: GnuPG v2.0.17 (GNU/Linux)
 
-iEYEARECAAYFAk04hXkACgkQgAnW8HDreRZLEACfVAxVBphmSHyR07ErRS6HlVQt
-ZJQAnjNiqGnMhx8Zwyc1W9Yk1E6jyyOR
-=M8g9
+iEYEARECAAYFAk1vnt4ACgkQgAnW8HDreRYQVQCfY006Xy0RtV9OOy4Oy6jzeF/L
+P1wAnjDQ1xkACKwlFNx/pUlFLc+GZ4Jf
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 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index f95710760..d12f36d94 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -37,10 +37,10 @@ SCIDEPS="
 
 XDEPS="
 	gnome-base/libgnomecanvas
-	gnome-base/librsvg
+	gnome-base/librsvg:2
 	media-libs/libpng
 	media-libs/freeglut
-	>=x11-libs/gtk+-2.2
+	x11-libs/gtk+:2
 	x11-libs/goocanvas
 	x11-libs/gtkglext"
 
@@ -71,6 +71,7 @@ pkg_setup() {
 }
 
 PATCHES=(
+	"${FILESDIR}"/${PV}-lidia.patch
 	"${FILESDIR}"/${PV}-goocanvas.patch
 	"${FILESDIR}"/${PV}-clipper.patch
 	"${FILESDIR}"/${PV}-include.patch
diff --git a/sci-chemistry/coot/files/9999-lidia.patch b/sci-chemistry/coot/files/9999-lidia.patch
index 2ac3fccb9..5b5039c47 100644
--- a/sci-chemistry/coot/files/9999-lidia.patch
+++ b/sci-chemistry/coot/files/9999-lidia.patch
@@ -1,16 +1,17 @@
 Index: lbg/Makefile.am
 ===================================================================
---- lbg/Makefile.am	(revision 3299)
+--- lbg/Makefile.am	(revision 3406)
 +++ lbg/Makefile.am	(working copy)
-@@ -24,6 +24,11 @@
-     lbg-search.cc some-coot-utils.cc residue-circles.cc rdkit-interface.cc \
+@@ -25,6 +25,12 @@
+     lbg-search.cc  residue-circles.cc rdkit-interface.cc \
      flev-annotations.cc
  
 +libcoot_lidia_la_LIBADD = \
 +	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
 +	$(top_builddir)/lidia-core/libcoot-lidia-core.la \
-+	$(GSL_LIBS) $(GTK_LIBS) $(GOOCANVAS_LIBS)
++	$(top_builddir)/geometry/libcoot-geometry.la \
++	$(GTK_LIBS) $(GSL_LIBS) $(GOOCANVAS_LIBS)
 +
- lidia_SOURCES = lidia-main.cc
+ lidia_SOURCES = lidia-main.cc lbg-callbacks-outer.cc
  
- # some-coot-utils.hh needed?
+ include_HEADERS = lbg.hh wmolecule.hh rdkit-interface.hh flev-annotations.hh 
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 90116ff62..1efbc6545 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,23 +1,29 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
+Hash: SHA256
 
 DIST ffamber_v4.0-doc.tar.gz 7915520 RMD160 aeadb18bd88bcd9e6fc45af22af15c51e32c66a3 SHA1 8d4969fa7eec660b41f769874be9698980b49ed0 SHA256 0b3395570dfe9bf808a297fcb120e1f525f38a91791fbafe6e444d542d7754aa
 DIST gmxtest-4.0.4.tgz 14845017 RMD160 c7c583415438bdef4c9996da9064254e9460cf16 SHA1 998179aa2bfbc4f80514f10ed774762f85c854c3 SHA256 6a7f787f4bb7cbecb688115ff0854a5ffd2ef33487d7bce4b031e63848b6f361
 DIST gromacs-manual-4.0.pdf 2135100 RMD160 b963642f8e1433f11328c3d0c4b1645c9de506da SHA1 8ae951ee15b2a7dc626331fce36511bc8766144c SHA256 646f810477eee2d710de6019c52056550413d0ba77baf9680195c835ddafe80a
 DIST gromacs-manual-4.5.3.pdf 2438528 RMD160 07f5ec0db1a773e77806c79554e5bb4fa8533dfd SHA1 7c81fc18e426d1090c485968d81957977ff10fc9 SHA256 6794fca3a2125918a03cd6bae3c031ab9b213c42a5f68a720c955b9107508717
 EBUILD gromacs-4.0.9999.ebuild 9246 RMD160 95001d304942bd265c0e70427fe63ca49e770a7e SHA1 ad25ea57c49b1128e0cfca42b7b32650fffd38b0 SHA256 440f06529eaf1532846f490da3bf403e6f84dec0a1b81b5e35a121d06dd999e6
-EBUILD gromacs-4.5.9999.ebuild 7670 RMD160 d71968c5d4e4b1043b45173c9d68d7210b451f0a SHA1 ff8f12c9494fb0873f509a729196b056a46b95fd SHA256 994a76880fd6ebfbca905d459ac26e695925276f3430564d9f8a107487ea096d
-EBUILD gromacs-9999.ebuild 7143 RMD160 d8076214c09578f0486f93ce19af9e5ffe699c0f SHA1 6bab1cc9548402c89b2ddbf622672d3b9a2a84a4 SHA256 9766c4ef55d310c5144efff3e04fbf8fd12a706040d4d541a934be43c016a213
+EBUILD gromacs-4.5.9999.ebuild 7758 RMD160 34553e74c0befed99276f079c28406f2aef942a0 SHA1 4299fb279ec0db5c4c0ba20107d82ac49ac55383 SHA256 a72fb20c9a41522e8b5bfc0556a4bdeba5c3ae9fcef338cd24ce1271b09e38fd
+EBUILD gromacs-9999.ebuild 7231 RMD160 e002067fc81e7a753af33fe4173add5b41492885 SHA1 3f6a77450939bab4f228db0e19e1f6554562ebb4 SHA256 92c664e87b9fdd136bec0ed38d1be50d3ac8abda610416c72c517f1a7e54c744
 MISC ChangeLog 7790 RMD160 1bae12cc584b31636144baba2c38888b77399bdb SHA1 484033800d98740f6556da1bf4906194c291450b SHA256 5a0796b4b7617b267daa23b641dc1565af13b634dadac5b5ff02aa4522bf7dcb
 MISC metadata.xml 684 RMD160 d2da359b5a70a1ea21b0ed25fb211a6994b93f17 SHA1 f76568a11d5beb77d678b6ad9892df300c31ff97 SHA256 81dc22d39c8fb53718bb0b8d336961125313b461905480f5de0d64ac0dd10031
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.16 (GNU/Linux)
+Version: GnuPG v2.0.17 (GNU/Linux)
 
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-aidSacN3xm8gUdlQcKi1PUDljISnwyKKRtNHLEQDyqg/HzV7goyNWS6LyeBYpMzd
-QlNKZcc51xWFN5MsvCHVTbYY/dO46GuD6Br4qYa/ZdThWSISxkR6ZPNuOV2H/M5o
-w56T4SiLeEVpFNXPSeyhbH7FGAv3FU0okBfW9DU/gaXzU0hL/I8BF4c1yEVOvEOw
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-=dSRw
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+xc4rreiO3CamC1scHBx8frxizsaR/ylzC5Rs10njEkVJg9yk2FL0qW8aXwMr81lR
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 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
index ac987b206..111bb375b 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
@@ -8,7 +8,7 @@ LIBTOOLIZE="true"
 TEST_PV="4.0.4"
 MANUAL_PV="4.5.3"
 
-inherit autotools-utils bash-completion flag-o-matic multilib toolchain-funcs
+inherit autotools-utils bash-completion eutils flag-o-matic multilib toolchain-funcs
 
 SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
 		doc? (
@@ -52,6 +52,9 @@ QA_EXECSTACK="usr/lib/libgmx.so.*
 	usr/lib/libgmx_d.so.*"
 
 src_prepare() {
+	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
+	epatch_user
+
 	if use mpi && use threads; then
 		elog "mdrun uses only threads OR mpi, and gromacs favours the"
 		elog "use of mpi over threads, so a mpi-version of mdrun will"
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index b6f511949..15dbf24ab 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -10,7 +10,7 @@ TEST_PV="4.0.4"
 EGIT_REPO_URI="git://git.gromacs.org/gromacs"
 EGIT_BRANCH="master"
 
-inherit bash-completion cmake-utils git multilib toolchain-funcs
+inherit bash-completion cmake-utils eutils git multilib toolchain-funcs
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
@@ -44,6 +44,9 @@ QA_EXECSTACK="usr/lib/libgmx.so.*
 	usr/lib/libgmx_d.so.*"
 
 src_prepare() {
+	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
+	epatch_user
+
 	if use mpi && use threads; then
 		elog "mdrun uses only threads OR mpi, and gromacs favours the"
 		elog "use of mpi over threads, so a mpi-version of mdrun will"
diff --git a/sci-libs/opencascade/ChangeLog b/sci-libs/opencascade/ChangeLog
deleted file mode 100644
index 3b8bccc26..000000000
--- a/sci-libs/opencascade/ChangeLog
+++ /dev/null
@@ -1,68 +0,0 @@
-# ChangeLog for sci-libs/opencascade
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-  19 Sep 2010; Justin Lecher <jlec@gentoo.org> opencascade-6.3-r1.ebuild,
-  opencascade-6.3-r2.ebuild:
-  virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl
-  Correction
-
-*opencascade-6.3-r2 (18 Mar 2010)
-
-  18 Mar 2010; Oliver Borm (boroli) <oli.borm@web.de>
-  +opencascade-6.3-r2.ebuild:
-  New version with additional USE-flag source; Changed the paths in
-  50opencascade a lttle bit
-
-  16 Mar 2010; Oliver Borm (boroli) <oli.borm@web.de>
-  opencascade-6.3-r1.ebuild:
-  Changed all installation paths to ${INSTALL_DIR}; Added examples USE-flag
-
-  15 Mar 2010; Oliver Borm (boroli) <oli.borm@web.de>
-  -opencascade-6.2-r1.ebuild, -files/opencascade-6.2-gcc4.patch,
-  -files/opencascade-6.2-malloc.patch, opencascade-6.3-r1.ebuild:
-  fixed src_uri and changed to eapi=2 in 6.3; removed old version 6.2
-
-  02 Nov 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  opencascade-6.3-r1.ebuild:
-  fixed java include path to
-  --with-java-include=/opt/sun-jdk-1.6.0.15/include
-
-*opencascade-6.3-r1 (17 Sep 2009)
-
-  17 Sep 2009; Etienne Lorriaux <etienne.lorriaux@gmail.com>
-  -opencascade-6.3.ebuild, +opencascade-6.3-r1.ebuild,
-  +files/opencascade-6.3-fixed-DESTDIR.patch,
-  +files/opencascade-6.3-missing-mode.patch:
-  Replaced the broken opencascade-6.3 by opencascade-6.3-r1
-
-  new file: files/opencascade-6.3-fixed-DESTDIR.patch
-
-  deleted: opencascade-6.3.ebuild
-
-  new file: files/opencascade-6.3-missing-mode.patch
-
-  new file: opencascade-6.3-r1.ebuild
-
-
-  05 January 2009; Daniel Tourde <daniel.tourde@caelae.se>
-  Added EAPI=1 in opencascade-6.2-r1.ebuild
-  +opencascade-6.3.ebuild
-	
-  27 May 2008; Daniel Tourde <daniel.tourde@caelae.se>
-  Corrected bugs in the way the --with-include and --with-library were handled (OpenGL, X). A big thank to Richard Westwell <garlicbread@ntlworld.com> for having discovered and corrected the issue.
-
-  20 May 2008; Daniel Tourde <daniel.tourde@caelae.se>
-  Corrected a bug in the ebuild. Now the tcl related variables should be corrected set and the values available all over the ebuild. A big thank to Dewald Pieterse <dewald.pieterse@gmail.com> for his testing and his good advices.
-
-  12 May 2008; Daniel Tourde <daniel.tourde@caelae.se>
-  +opencascade-6.2-r1.ebuild
-  General improvement of the ebuild, better amd64 support, removal of the wok and draw-harness flags (They had no effects). Many thanks to Dewald Pieterse and Álvaro Castro Castilla.
-  See bug #118656 for anything relating the building process.
-
-  15 Jan 2008; Sébastien Fabbro <bicatali@gentoo.org>
-  +files/opencascade-6.2-gcc4.patch, +files/opencascade-6.2-malloc.patch,
-  +files/env.ksh.template, +metadata.xml, +opencascade-6.2.ebuild:
-  Initial import. See bug #118656 for anything relating the building process.
-  Ebuild from Daniel Tourde <daniel.tourde@caelae.se> and Alvaro Castro
-  <alvcastro@yahoo.es>.
diff --git a/sci-libs/opencascade/Manifest b/sci-libs/opencascade/Manifest
deleted file mode 100644
index dd2ab344b..000000000
--- a/sci-libs/opencascade/Manifest
+++ /dev/null
@@ -1,19 +0,0 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
-AUX env.ksh.template 1412 RMD160 aaf7c74e1aef841d669cf44c279e747cb336fd2b SHA1 e6f3a1157fdededd671c832ebeb8b25a900ec7ab SHA256 ac13e6d2b0dddbbac1350b24ab4fb44d38963fe43dc7732362500f8870dcccb7
-AUX opencascade-6.3-fixed-DESTDIR.patch 16811 RMD160 4cecc900ec5b3835f7d6f9b14e6655e82d496d1a SHA1 298df55796e208aee3e04798d69b5079b1ea8fce SHA256 84743f54bb8b8b9568b5a32b5af0384efe746d20500972c66050c3a1d5ebe814
-AUX opencascade-6.3-missing-mode.patch 625 RMD160 a2c7b729a121c4b25aaa7f1ee3e42020af5b58f8 SHA1 b3b95a8a93a2f14513ce8222f0e3a695e9c513b5 SHA256 4aa7338175c7b2dbbcb12eef72c61eb55ade58ad2c698c94ae16e1bc4b451e0a
-DIST OpenCASCADE_src.tgz 105877329 RMD160 b71f1b9a57d9624d2f079d4f7a8090f700c6126f SHA1 21a177fae5fa73263517aedbe60a4ee4926156f2 SHA256 1f1fc8d8be1d4ff6fe8df1059f856eec156385887880f3f69d147824957c2411
-DIST opencascade-6.3.tgz 105877329 RMD160 b71f1b9a57d9624d2f079d4f7a8090f700c6126f SHA1 21a177fae5fa73263517aedbe60a4ee4926156f2 SHA256 1f1fc8d8be1d4ff6fe8df1059f856eec156385887880f3f69d147824957c2411
-EBUILD opencascade-6.3-r1.ebuild 6895 RMD160 49ae51ba7059c77bfb5db2ef405fdbff18806807 SHA1 fe735e967f3121b9a4ed1c301241faf8b6745851 SHA256 e48b125c01a63f4941d4cb429d9eab964e2f483fecb78e5e6531f2f32f7a681c
-EBUILD opencascade-6.3-r2.ebuild 6953 RMD160 567f45fea5fed3e7da55255839f1ae7801f61b81 SHA1 43d5a77b1f76f7891c1953878dc4eca26701e11b SHA256 135184ae8abccc01cb0db00d4c8e28c928fe977bd9612d7b185e516196b45741
-MISC ChangeLog 2971 RMD160 6289c80ed2b33e73daf2f7030946bc5124adae4e SHA1 f33a962a09126d4c8f2d45b80440e0e4985cc1d5 SHA256 33741536c14f5f4ed19567f961fea543f49dab6ecb84b8a154df0966f565f02b
-MISC metadata.xml 232 RMD160 1feb28c8cb12774e88680282a51435f7b17c9f9d SHA1 bfd350e21f306acd5a0e8878bcf5a768e87d5a4c SHA256 715678a1b891ca00fa94cd82e694532b2a47a06a0debddc15a8be907006235b0
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-=+8UN
------END PGP SIGNATURE-----
diff --git a/sci-libs/opencascade/files/env.ksh.template b/sci-libs/opencascade/files/env.ksh.template
deleted file mode 100644
index 55d772a9f..000000000
--- a/sci-libs/opencascade/files/env.ksh.template
+++ /dev/null
@@ -1,39 +0,0 @@
-#!/bin/ksh -f
-
-export CASROOT=VAR_CASROOT
-
-if [ -z "PATH" ];
-then PATH=VAR_CASROOT/Linux/bin;
-else PATH=VAR_CASROOT/Linux/bin:$PATH;
-fi
-export PATH
-if [ -z "LD_LIBRARY_PATH" ];
-then LD_LIBRARY_PATH=VAR_CASROOT/Linux/lib;
-else LD_LIBRARY_PATH=VAR_CASROOT/Linux/lib:$LD_LIBRARY_PATH;
-fi
-export LD_LIBRARY_PATH
-export CSF_MDTVFontDirectory=VAR_CASROOT/src/FontMFT
-export CSF_LANGUAGE=us
-export MMGT_CLEAR=1
-export CSF_EXCEPTION_PROMPT=1
-export CSF_SHMessage=VAR_CASROOT/src/SHMessage
-export CSF_MDTVTexturesDirectory=VAR_CASROOT/src/Textures
-export CSF_XSMessage=VAR_CASROOT/src/XSMessage
-export CSF_StandardDefaults=VAR_CASROOT/src/StdResource
-export CSF_PluginDefaults=VAR_CASROOT/src/StdResource
-export CSF_XCAFDefaults=VAR_CASROOT/src/StdResource
-export CSF_StandardLiteDefaults=VAR_CASROOT/src/StdResource
-export CSF_GraphicShr=VAR_CASROOT/Linux/lib/libTKOpenGl.so
-export CSF_UnitsLexicon=VAR_CASROOT/src/UnitsAPI/Lexi_Expr.dat
-export CSF_UnitsDefinition=VAR_CASROOT/src/UnitsAPI/Units.dat
-export CSF_IGESDefaults=VAR_CASROOT/src/XSTEPResource
-export CSF_STEPDefaults=VAR_CASROOT/src/XSTEPResource
-export CSF_XmlOcafResource=VAR_CASROOT/src/XmlOcafResource
-
-export TCLHOME=VAR_SYS_BIN
-export TCLLIBPATH=VAR_SYS_LIB
-export ITK_LIBRARY=VAR_SYS_LIB/VAR_ITK
-export ITCL_LIBRARY=VAR_SYS_LIB/VAR_ITCL
-export TIX_LIBRARY=VAR_SYS_LIB/VAR_TIX
-export TK_LIBRARY=VAR_SYS_LIB/VAR_TK
-export TCL_LIBRARY=VAR_SYS_LIB/VAR_TCL
diff --git a/sci-libs/opencascade/files/opencascade-6.3-fixed-DESTDIR.patch b/sci-libs/opencascade/files/opencascade-6.3-fixed-DESTDIR.patch
deleted file mode 100644
index 757f65982..000000000
--- a/sci-libs/opencascade/files/opencascade-6.3-fixed-DESTDIR.patch
+++ /dev/null
@@ -1,358 +0,0 @@
-diff -urN OpenCASCADE6.3.0/ros/Makefile.am OpenCASCADE6.3.0.FixedInstall/ros/Makefile.am
---- OpenCASCADE6.3.0/ros/Makefile.am	2008-09-09 18:49:10.000000000 +0300
-+++ OpenCASCADE6.3.0.FixedInstall/ros/Makefile.am	2009-02-20 15:01:08.000000000 +0200
-@@ -108,126 +108,126 @@
- dir_SunOS=sun
- 
- install-exec-local:
--	$(INSTALL) -d $(prefix)/$(platform)
--	if [ -e $(prefix)/bin -a ! -e $(prefix)/$(platform)/bin ]; then \
--		cd $(prefix)/$(platform) && ln -s ../bin bin; \
-+	$(INSTALL) -d $(DESTDIR)$(prefix)/$(platform)
-+	if [ -e $(DESTDIR)$(prefix)/bin -a ! -e $(DESTDIR)$(prefix)/$(platform)/bin ]; then \
-+		cd $(DESTDIR)$(prefix)/$(platform) && ln -s ../bin bin; \
- 	fi
--	if [ -e $(prefix)/lib -a ! -e $(prefix)/$(platform)/lib ]; then \
--		cd $(prefix)/$(platform) && ln -s ../lib lib; \
-+	if [ -e $(DESTDIR)$(prefix)/lib -a ! -e $(DESTDIR)$(prefix)/$(platform)/lib ]; then \
-+		cd $(DESTDIR)$(prefix)/$(platform) && ln -s ../lib lib; \
- 	fi
--	$(INSTALL) -d $(prefix)/$(dir_$(platform))
--	if [ -e $(prefix)/bin -a ! -e $(prefix)/$(dir_$(platform))/bin ]; then \
--		cd $(prefix)/$(dir_$(platform)) && ln -s ../bin bin; \
-+	$(INSTALL) -d $(DESTDIR)$(prefix)/$(dir_$(platform))
-+	if [ -e $(DESTDIR)$(prefix)/bin -a ! -e $(DESTDIR)$(prefix)/$(dir_$(platform))/bin ]; then \
-+		cd $(DESTDIR)$(prefix)/$(dir_$(platform)) && ln -s ../bin bin; \
- 	fi
--	if [ -e $(prefix)/lib -a ! -e $(prefix)/$(dir_$(platform))/lib ]; then \
--		cd $(prefix)/$(dir_$(platform)) && ln -s ../lib lib; \
-+	if [ -e $(DESTDIR)$(prefix)/lib -a ! -e $(DESTDIR)$(prefix)/$(dir_$(platform))/lib ]; then \
-+		cd $(DESTDIR)$(prefix)/$(dir_$(platform)) && ln -s ../lib lib; \
- 	fi
--	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(prefix); pd=`pwd`; cd $$bd; \
-+	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(DESTDIR)$(prefix); pd=`pwd`; cd $$bd; \
- 	if [ "$$pd" != "$$sd" ]; then \
--		$(INSTALL) -d $(prefix)/inc; \
--		cp -fr$(CP_$(platform)) $(top_srcdir)/inc $(prefix); \
-+		$(INSTALL) -d $(DESTDIR)$(prefix)/inc; \
-+		cp -fr$(CP_$(platform)) $(top_srcdir)/inc $(DESTDIR)$(prefix); \
- 	fi; \
- 	if [ "$$pd" != "$$bd" ]; then \
--		cp -fr$(CP_$(platform)) $$bd/config.h $(prefix); \
-+		cp -fr$(CP_$(platform)) $$bd/config.h $(DESTDIR)$(prefix); \
- 	fi
--	if [ -e $(prefix)/inc/config.h ]; then \
--		unlink $(prefix)/inc/config.h; \
-+	if [ -e $(DESTDIR)$(prefix)/inc/config.h ]; then \
-+		unlink $(DESTDIR)$(prefix)/inc/config.h; \
- 	fi
--	cd $(prefix)/inc && ln -s ../config.h config.h 
--	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(prefix); pd=`pwd`; cd $$bd; \
-+	cd $(DESTDIR)$(prefix)/inc && ln -s ../config.h config.h 
-+	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(DESTDIR)$(prefix); pd=`pwd`; cd $$bd; \
- 	if [ "$$pd" != "$$sd" -a -d $(top_srcdir)/src/UnitsAPI ]; then \
--		$(INSTALL) -d $(prefix)/src; \
--		$(INSTALL) -d $(prefix)/src/UnitsAPI; \
--		cp -fr$(CP_$(platform)) $(top_srcdir)/src/UnitsAPI $(prefix)/src; \
--		cp -f$(CP_$(platform)) $(top_srcdir)/env_DRAW.sh $(prefix); \
-+		$(INSTALL) -d $(DESTDIR)$(prefix)/src; \
-+		$(INSTALL) -d $(DESTDIR)$(prefix)/src/UnitsAPI; \
-+		cp -fr$(CP_$(platform)) $(top_srcdir)/src/UnitsAPI $(DESTDIR)$(prefix)/src; \
-+		cp -f$(CP_$(platform)) $(top_srcdir)/env_DRAW.sh $(DESTDIR)$(prefix); \
- 	fi
--	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(prefix); pd=`pwd`; cd $$bd; \
-+	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(DESTDIR)$(prefix); pd=`pwd`; cd $$bd; \
- 	if [ "$$pd" != "$$sd" ]; then \
- 		inst_dirs="$(FoundationClasses_DIRS)"; \
- 		if test "x$(FoundationClasses_DIRS)" != "x"; then \
- 			for d in $$inst_dirs; do \
--				$(INSTALL) -d $(prefix)/src/$$d; \
--				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(prefix)/src; \
-+				$(INSTALL) -d $(DESTDIR)$(prefix)/src/$$d; \
-+				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(DESTDIR)$(prefix)/src; \
- 			done; \
- 		fi; \
- 	fi
--	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(prefix); pd=`pwd`; cd $$bd; \
-+	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(DESTDIR)$(prefix); pd=`pwd`; cd $$bd; \
- 	if [ "$$pd" != "$$sd" ]; then \
- 		inst_dirs="$(ModelingData_DIRS)"; \
- 		if test "x$(ModelingData_DIRS)" != "x"; then \
- 			for d in $$inst_dirs; do \
--				$(INSTALL) -d $(prefix)/src/$$d; \
--				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(prefix)/src; \
-+				$(INSTALL) -d $(DESTDIR)$(prefix)/src/$$d; \
-+				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(DESTDIR)$(prefix)/src; \
- 			done; \
- 		fi; \
- 	fi
--	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(prefix); pd=`pwd`; cd $$bd; \
-+	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(DESTDIR)$(prefix); pd=`pwd`; cd $$bd; \
- 	if [ "$$pd" != "$$sd" ]; then \
- 		inst_dirs="$(ModelingAlgorithms_DIRS)"; \
- 		if test "x$(ModelingAlgorithms_DIRS)" != "x"; then \
- 			for d in $$inst_dirs; do \
--				$(INSTALL) -d $(prefix)/src/$$d; \
--				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(prefix)/src; \
-+				$(INSTALL) -d $(DESTDIR)$(prefix)/src/$$d; \
-+				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(DESTDIR)$(prefix)/src; \
- 			done; \
- 		fi; \
- 	fi
--	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(prefix); pd=`pwd`; cd $$bd; \
-+	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(DESTDIR)$(prefix); pd=`pwd`; cd $$bd; \
- 	if [ "$$pd" != "$$sd" ]; then \
- 		inst_dirs="$(Visualization_DIRS)"; \
- 		if test "x$(Visualization_DIRS)" != "x"; then \
- 			for d in $$inst_dirs; do \
--				$(INSTALL) -d $(prefix)/src/$$d; \
--				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(prefix)/src; \
-+				$(INSTALL) -d $(DESTDIR)$(prefix)/src/$$d; \
-+				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(DESTDIR)$(prefix)/src; \
- 			done; \
- 		fi; \
- 	fi
--	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(prefix); pd=`pwd`; cd $$bd; \
-+	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(DESTDIR)$(prefix); pd=`pwd`; cd $$bd; \
- 	if [ "$$pd" != "$$sd" ]; then \
- 		inst_dirs="$(ApplicationFramework_DIRS)"; \
- 		if test "x$(ApplicationFramework_DIRS)" != "x"; then \
- 			for d in $$inst_dirs; do \
--				$(INSTALL) -d $(prefix)/src/$$d; \
--				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(prefix)/src; \
-+				$(INSTALL) -d $(DESTDIR)$(prefix)/src/$$d; \
-+				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(DESTDIR)$(prefix)/src; \
- 			done; \
- 		fi; \
- 	fi
--	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(prefix); pd=`pwd`; cd $$bd; \
-+	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(DESTDIR)$(prefix); pd=`pwd`; cd $$bd; \
- 	if [ "$$pd" != "$$sd" ]; then \
- 		inst_dirs="$(DataExchange_DIRS)"; \
- 		if test "x$(DataExchange_DIRS)" != "x"; then \
- 			for d in $$inst_dirs; do \
--				$(INSTALL) -d $(prefix)/src/$$d; \
--				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(prefix)/src; \
-+				$(INSTALL) -d $(DESTDIR)$(prefix)/src/$$d; \
-+				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(DESTDIR)$(prefix)/src; \
- 			done; \
- 		fi; \
- 	fi
--	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(prefix); pd=`pwd`; cd $$bd; \
-+	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(DESTDIR)$(prefix); pd=`pwd`; cd $$bd; \
- 	if [ "$$pd" != "$$sd" ]; then \
- 		inst_dirs="$(Draw_DIRS)"; \
- 		if test "x$(Draw_DIRS)" != "x"; then \
- 			for d in $$inst_dirs; do \
--				$(INSTALL) -d $(prefix)/src/$$d; \
--				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(prefix)/src; \
-+				$(INSTALL) -d $(DESTDIR)$(prefix)/src/$$d; \
-+				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(DESTDIR)$(prefix)/src; \
- 			done; \
- 		fi; \
- 	fi
--	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(prefix); pd=`pwd`; cd $$bd; \
-+	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(DESTDIR)$(prefix); pd=`pwd`; cd $$bd; \
- 	if [ "$$pd" != "$$sd" ]; then \
- 		inst_dirs="$(WOK_DIRS)"; \
- 		if test "x$(WOK_DIRS)" != "x"; then \
- 			for d in $$inst_dirs; do \
--				$(INSTALL) -d $(prefix)/src/$$d; \
--				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(prefix)/src; \
-+				$(INSTALL) -d $(DESTDIR)$(prefix)/src/$$d; \
-+				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(DESTDIR)$(prefix)/src; \
- 			done; \
- 		fi; \
- 	fi
--	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(prefix); pd=`pwd`; cd $$bd; \
-+	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(DESTDIR)$(prefix); pd=`pwd`; cd $$bd; \
- 	if [ "$$pd" != "$$sd" ]; then \
- 		inst_dirs="$(Wrappers_DIRS)"; \
- 		if test "x$(Wrappers_DIRS)" != "x"; then \
- 			for d in $$inst_dirs; do \
--				$(INSTALL) -d $(prefix)/src/$$d; \
--				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(prefix)/src; \
-+				$(INSTALL) -d $(DESTDIR)$(prefix)/src/$$d; \
-+				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(DESTDIR)$(prefix)/src; \
- 			done; \
- 		fi; \
- 	fi
-diff -urN OpenCASCADE6.3.0/ros/Makefile.in OpenCASCADE6.3.0.FixedInstall/ros/Makefile.in
---- OpenCASCADE6.3.0/ros/Makefile.in	2008-09-09 18:52:16.000000000 +0300
-+++ OpenCASCADE6.3.0.FixedInstall/ros/Makefile.in	2009-02-20 15:01:59.000000000 +0200
-@@ -646,126 +646,126 @@
- 	cd $(top_builddir)/adm/make && $(MAKE) $(AM_MAKEFLAGS) Wrappers
- 
- install-exec-local:
--	$(INSTALL) -d $(prefix)/$(platform)
--	if [ -e $(prefix)/bin -a ! -e $(prefix)/$(platform)/bin ]; then \
--		cd $(prefix)/$(platform) && ln -s ../bin bin; \
-+	$(INSTALL) -d $(DESTDIR)$(prefix)/$(platform)
-+	if [ -e $(DESTDIR)$(prefix)/bin -a ! -e $(DESTDIR)$(prefix)/$(platform)/bin ]; then \
-+		cd $(DESTDIR)$(prefix)/$(platform) && ln -s ../bin bin; \
- 	fi
--	if [ -e $(prefix)/lib -a ! -e $(prefix)/$(platform)/lib ]; then \
--		cd $(prefix)/$(platform) && ln -s ../lib lib; \
-+	if [ -e $(DESTDIR)$(prefix)/lib -a ! -e $(DESTDIR)$(prefix)/$(platform)/lib ]; then \
-+		cd $(DESTDIR)$(prefix)/$(platform) && ln -s ../lib lib; \
- 	fi
--	$(INSTALL) -d $(prefix)/$(dir_$(platform))
--	if [ -e $(prefix)/bin -a ! -e $(prefix)/$(dir_$(platform))/bin ]; then \
--		cd $(prefix)/$(dir_$(platform)) && ln -s ../bin bin; \
-+	$(INSTALL) -d $(DESTDIR)$(prefix)/$(dir_$(platform))
-+	if [ -e $(DESTDIR)$(prefix)/bin -a ! -e $(DESTDIR)$(prefix)/$(dir_$(platform))/bin ]; then \
-+		cd $(DESTDIR)$(prefix)/$(dir_$(platform)) && ln -s ../bin bin; \
- 	fi
--	if [ -e $(prefix)/lib -a ! -e $(prefix)/$(dir_$(platform))/lib ]; then \
--		cd $(prefix)/$(dir_$(platform)) && ln -s ../lib lib; \
-+	if [ -e $(DESTDIR)$(prefix)/lib -a ! -e $(DESTDIR)$(prefix)/$(dir_$(platform))/lib ]; then \
-+		cd $(DESTDIR)$(prefix)/$(dir_$(platform)) && ln -s ../lib lib; \
- 	fi
--	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(prefix); pd=`pwd`; cd $$bd; \
-+	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(DESTDIR)$(prefix); pd=`pwd`; cd $$bd; \
- 	if [ "$$pd" != "$$sd" ]; then \
--		$(INSTALL) -d $(prefix)/inc; \
--		cp -fr$(CP_$(platform)) $(top_srcdir)/inc $(prefix); \
-+		$(INSTALL) -d $(DESTDIR)$(prefix)/inc; \
-+		cp -fr$(CP_$(platform)) $(top_srcdir)/inc $(DESTDIR)$(prefix); \
- 	fi; \
- 	if [ "$$pd" != "$$bd" ]; then \
--		cp -fr$(CP_$(platform)) $$bd/config.h $(prefix); \
-+		cp -fr$(CP_$(platform)) $$bd/config.h $(DESTDIR)$(prefix); \
- 	fi
--	if [ -e $(prefix)/inc/config.h ]; then \
--		unlink $(prefix)/inc/config.h; \
-+	if [ -e $(DESTDIR)$(prefix)/inc/config.h ]; then \
-+		unlink $(DESTDIR)$(prefix)/inc/config.h; \
- 	fi
--	cd $(prefix)/inc && ln -s ../config.h config.h 
--	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(prefix); pd=`pwd`; cd $$bd; \
-+	cd $(DESTDIR)$(prefix)/inc && ln -s ../config.h config.h 
-+	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(DESTDIR)$(prefix); pd=`pwd`; cd $$bd; \
- 	if [ "$$pd" != "$$sd" -a -d $(top_srcdir)/src/UnitsAPI ]; then \
--		$(INSTALL) -d $(prefix)/src; \
--		$(INSTALL) -d $(prefix)/src/UnitsAPI; \
--		cp -fr$(CP_$(platform)) $(top_srcdir)/src/UnitsAPI $(prefix)/src; \
--		cp -f$(CP_$(platform)) $(top_srcdir)/env_DRAW.sh $(prefix); \
-+		$(INSTALL) -d $(DESTDIR)$(prefix)/src; \
-+		$(INSTALL) -d $(DESTDIR)$(prefix)/src/UnitsAPI; \
-+		cp -fr$(CP_$(platform)) $(top_srcdir)/src/UnitsAPI $(DESTDIR)$(prefix)/src; \
-+		cp -f$(CP_$(platform)) $(top_srcdir)/env_DRAW.sh $(DESTDIR)$(prefix); \
- 	fi
--	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(prefix); pd=`pwd`; cd $$bd; \
-+	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(DESTDIR)$(prefix); pd=`pwd`; cd $$bd; \
- 	if [ "$$pd" != "$$sd" ]; then \
- 		inst_dirs="$(FoundationClasses_DIRS)"; \
- 		if test "x$(FoundationClasses_DIRS)" != "x"; then \
- 			for d in $$inst_dirs; do \
--				$(INSTALL) -d $(prefix)/src/$$d; \
--				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(prefix)/src; \
-+				$(INSTALL) -d $(DESTDIR)$(prefix)/src/$$d; \
-+				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(DESTDIR)$(prefix)/src; \
- 			done; \
- 		fi; \
- 	fi
--	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(prefix); pd=`pwd`; cd $$bd; \
-+	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(DESTDIR)$(prefix); pd=`pwd`; cd $$bd; \
- 	if [ "$$pd" != "$$sd" ]; then \
- 		inst_dirs="$(ModelingData_DIRS)"; \
- 		if test "x$(ModelingData_DIRS)" != "x"; then \
- 			for d in $$inst_dirs; do \
--				$(INSTALL) -d $(prefix)/src/$$d; \
--				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(prefix)/src; \
-+				$(INSTALL) -d $(DESTDIR)$(prefix)/src/$$d; \
-+				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(DESTDIR)$(prefix)/src; \
- 			done; \
- 		fi; \
- 	fi
--	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(prefix); pd=`pwd`; cd $$bd; \
-+	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(DESTDIR)$(prefix); pd=`pwd`; cd $$bd; \
- 	if [ "$$pd" != "$$sd" ]; then \
- 		inst_dirs="$(ModelingAlgorithms_DIRS)"; \
- 		if test "x$(ModelingAlgorithms_DIRS)" != "x"; then \
- 			for d in $$inst_dirs; do \
--				$(INSTALL) -d $(prefix)/src/$$d; \
--				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(prefix)/src; \
-+				$(INSTALL) -d $(DESTDIR)$(prefix)/src/$$d; \
-+				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(DESTDIR)$(prefix)/src; \
- 			done; \
- 		fi; \
- 	fi
--	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(prefix); pd=`pwd`; cd $$bd; \
-+	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(DESTDIR)$(prefix); pd=`pwd`; cd $$bd; \
- 	if [ "$$pd" != "$$sd" ]; then \
- 		inst_dirs="$(Visualization_DIRS)"; \
- 		if test "x$(Visualization_DIRS)" != "x"; then \
- 			for d in $$inst_dirs; do \
--				$(INSTALL) -d $(prefix)/src/$$d; \
--				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(prefix)/src; \
-+				$(INSTALL) -d $(DESTDIR)$(prefix)/src/$$d; \
-+				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(DESTDIR)$(prefix)/src; \
- 			done; \
- 		fi; \
- 	fi
--	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(prefix); pd=`pwd`; cd $$bd; \
-+	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(DESTDIR)$(prefix); pd=`pwd`; cd $$bd; \
- 	if [ "$$pd" != "$$sd" ]; then \
- 		inst_dirs="$(ApplicationFramework_DIRS)"; \
- 		if test "x$(ApplicationFramework_DIRS)" != "x"; then \
- 			for d in $$inst_dirs; do \
--				$(INSTALL) -d $(prefix)/src/$$d; \
--				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(prefix)/src; \
-+				$(INSTALL) -d $(DESTDIR)$(prefix)/src/$$d; \
-+				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(DESTDIR)$(prefix)/src; \
- 			done; \
- 		fi; \
- 	fi
--	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(prefix); pd=`pwd`; cd $$bd; \
-+	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(DESTDIR)$(prefix); pd=`pwd`; cd $$bd; \
- 	if [ "$$pd" != "$$sd" ]; then \
- 		inst_dirs="$(DataExchange_DIRS)"; \
- 		if test "x$(DataExchange_DIRS)" != "x"; then \
- 			for d in $$inst_dirs; do \
--				$(INSTALL) -d $(prefix)/src/$$d; \
--				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(prefix)/src; \
-+				$(INSTALL) -d $(DESTDIR)$(prefix)/src/$$d; \
-+				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(DESTDIR)$(prefix)/src; \
- 			done; \
- 		fi; \
- 	fi
--	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(prefix); pd=`pwd`; cd $$bd; \
-+	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(DESTDIR)$(prefix); pd=`pwd`; cd $$bd; \
- 	if [ "$$pd" != "$$sd" ]; then \
- 		inst_dirs="$(Draw_DIRS)"; \
- 		if test "x$(Draw_DIRS)" != "x"; then \
- 			for d in $$inst_dirs; do \
--				$(INSTALL) -d $(prefix)/src/$$d; \
--				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(prefix)/src; \
-+				$(INSTALL) -d $(DESTDIR)$(prefix)/src/$$d; \
-+				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(DESTDIR)$(prefix)/src; \
- 			done; \
- 		fi; \
- 	fi
--	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(prefix); pd=`pwd`; cd $$bd; \
-+	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(DESTDIR)$(prefix); pd=`pwd`; cd $$bd; \
- 	if [ "$$pd" != "$$sd" ]; then \
- 		inst_dirs="$(WOK_DIRS)"; \
- 		if test "x$(WOK_DIRS)" != "x"; then \
- 			for d in $$inst_dirs; do \
--				$(INSTALL) -d $(prefix)/src/$$d; \
--				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(prefix)/src; \
-+				$(INSTALL) -d $(DESTDIR)$(prefix)/src/$$d; \
-+				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(DESTDIR)$(prefix)/src; \
- 			done; \
- 		fi; \
- 	fi
--	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(prefix); pd=`pwd`; cd $$bd; \
-+	bd=`pwd`; cd $(top_srcdir); sd=`pwd`; cd $(DESTDIR)$(prefix); pd=`pwd`; cd $$bd; \
- 	if [ "$$pd" != "$$sd" ]; then \
- 		inst_dirs="$(Wrappers_DIRS)"; \
- 		if test "x$(Wrappers_DIRS)" != "x"; then \
- 			for d in $$inst_dirs; do \
--				$(INSTALL) -d $(prefix)/src/$$d; \
--				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(prefix)/src; \
-+				$(INSTALL) -d $(DESTDIR)$(prefix)/src/$$d; \
-+				cp -fr$(CP_$(platform)) $(top_srcdir)/src/$$d $(DESTDIR)$(prefix)/src; \
- 			done; \
- 		fi; \
- 	fi
diff --git a/sci-libs/opencascade/files/opencascade-6.3-missing-mode.patch b/sci-libs/opencascade/files/opencascade-6.3-missing-mode.patch
deleted file mode 100644
index 32b5aae9d..000000000
--- a/sci-libs/opencascade/files/opencascade-6.3-missing-mode.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -aur OpenCASCADE6.3.0.old/ros/src/WOKUnix/WOKUnix_FDescr.cxx OpenCASCADE6.3.0/ros/src/WOKUnix/WOKUnix_FDescr.cxx
---- OpenCASCADE6.3.0.old/ros/src/WOKUnix/WOKUnix_FDescr.cxx	2009-02-15 14:00:22.000000000 +0100
-+++ OpenCASCADE6.3.0/ros/src/WOKUnix/WOKUnix_FDescr.cxx	2009-02-15 14:08:50.000000000 +0100
-@@ -202,7 +202,7 @@
-   if(mknod(apath.ToCString(), 0700 |  S_IFIFO, 0)) 
-     { perror(apath.ToCString());}
- 
--  myFileChannel = open(apath.ToCString(),  O_RDONLY | O_NDELAY | O_CREAT);
-+  myFileChannel = open(apath.ToCString(),  O_RDONLY | O_NDELAY );
-   SetUnBuffered();
- 
-   // write end of pipe is unbuffered also 
diff --git a/sci-libs/opencascade/opencascade-6.3-r1.ebuild b/sci-libs/opencascade/opencascade-6.3-r1.ebuild
deleted file mode 100644
index 64bd4f730..000000000
--- a/sci-libs/opencascade/opencascade-6.3-r1.ebuild
+++ /dev/null
@@ -1,217 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=2
-
-inherit autotools eutils flag-o-matic check-reqs java-pkg-opt-2 multilib toolchain-funcs versionator
-
-DESCRIPTION="Software development platform for CAD/CAE, 3D surface/solid modeling and data exchange."
-HOMEPAGE="http://www.opencascade.org"
-SRC_URI="http://files.opencascade.com/OCC_${PV}_release/OpenCASCADE_src.tgz"
-
-LICENSE="Open-CASCADE-Technology-Public-License"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug doc examples java opengl stlport X"
-DEPEND="java? ( virtual/jdk )
-	opengl? ( virtual/opengl
-		virtual/opengl )
-	X? ( x11-libs/libXmu
-		app-text/dgs )
-	>=dev-lang/tcl-8.4
-	>=dev-lang/tk-8.4
-	>=dev-tcltk/itcl-3.2
-	>=dev-tcltk/itk-3.2
-	x86? ( >=dev-tcltk/tix-8.1 )
-	amd64? ( >=dev-tcltk/tix-8.4.2 )
-	stlport? ( dev-libs/STLport )"
-RDEPEND=${DEPEND}
-
-S=${WORKDIR}/OpenCASCADE${PV}.0/ros
-INSTALL_DIR=/opt/${P}/ros
-
-pkg_setup() {
-	# Determine itk, itcl, tix, tk and tcl versions
-	itk_version=$(grep ITK_VER /usr/include/itk.h | sed 's/^.*"\(.*\)".*/\1/')
-	itcl_version=$(grep ITCL_VER /usr/include/itcl.h | sed 's/^.*"\(.*\)".*/\1/')
-	tix_version=$(grep TIX_VER /usr/include/tix.h | sed 's/^.*"\(.*\)".*/\1/')
-	tk_version=$(grep TK_VER /usr/include/tk.h | sed 's/^.*"\(.*\)".*/\1/')
-	tcl_version=$(grep TCL_VER /usr/include/tcl.h | sed 's/^.*"\(.*\)".*/\1/')
-
-	ewarn
-	ewarn " It is important to note that OpenCascade is a very large package. "
-	ewarn " Please note that building OpenCascade takes a lot of time and "
-	ewarn " hardware ressources: 3.5-4 GB free diskspace and 256 MB RAM are "
-	ewarn " the minimum requirements. "
-	ewarn
-
-	# Check if we have enough RAM and free diskspace to build this beast
-	CHECKREQS_MEMORY="256"
-	CHECKREQS_DISK_BUILD="3584"
-	check_reqs
-}
-
-src_prepare() {
-	# Substitute with our ready-made env.ksh script
-	cp -f "${FILESDIR}"/env.ksh.template "${S}"/env.ksh || die "Cannot copy env.ksh.template"
-
-	# Feed environment variables used by Opencascade compilation
-	sed -i \
-		-e "s:VAR_CASROOT:${S}:g" \
-		-e 's:VAR_SYS_BIN:/usr/bin:g' \
-		-e "s:VAR_SYS_LIB:/usr/$(get_libdir):g" env.ksh \
-	|| die "Environment variables feed in env.ksh failed!"
-
-	# Tweak itk, itcl, tix, tk and tcl versions
-	sed -i \
-		-e "s:VAR_ITK:itk${itk_version}:g" \
-		-e "s:VAR_ITCL:itcl${itcl_version}:g" \
-		-e "s:VAR_TIX:tix${tix_version}:g" \
-		-e "s:VAR_TK:tk${tk_version}:g" \
-		-e "s:VAR_TCL:tcl${tcl_version}:g" env.ksh \
-	|| die "itk, itcl, tix, tk and tcl version tweaking failed!"
-
-	# epatch "${FILESDIR}"/${P}-Makefile.am.patch
-	epatch "${FILESDIR}"/${P}-fixed-DESTDIR.patch
-	epatch "${FILESDIR}"/${P}-missing-mode.patch
-
-	chmod u+x configure
-
-	# Autotools version update
-	source env.ksh
-	eaclocal || die "eaclocal failed"
-	eautoheader || die "eautoheader failed"
-	eautomake -a -c -f
-	_elibtoolize --force --copy || die "elibtoolize failed"
-	eautoconf || die "eautoconf failed"
-}
-
-src_configure() {
-	# Add the configure options
-	local confargs="--prefix=${INSTALL_DIR}/lin --exec-prefix=${INSTALL_DIR}/lin --with-tcl=/usr/$(get_libdir) --with-tk=/usr/$(get_libdir)"
-
-	if use X ; then
-		confargs="${confargs} --with-dps-include=/usr/include --with-dps-library=/usr/$(get_libdir)"
-		confargs="${confargs} --with-xmu-include=/usr/include --with-xmu-library=/usr/$(get_libdir)"
-		if use !opengl; then
-			ewarn "Activate OpenGL if you want to be able to visualize geometry. Set "opengl" USE flag."
-		else
-			confargs="${confargs} --with-gl-include=/usr/include --with-gl-library=/usr/$(get_libdir)"
-		fi
-	else
-		if use opengl; then
-			die "OpenGL imply X support! Add "X" USE flag."
-		else
-			ewarn "Activate X and OpenGL if you want to be able to visualize geometry. Set "X" and "opengl" USE flags."
-		fi
-	fi
-
-	if use java ; then
-		local java_path
-		java_path=`java-config -O`
-		confargs="${confargs} --with-java-include=${java_path}/include"
-	else
-		ewarn "Java wrapping is not going to be compiled. USE flag: "java""
-	fi
-
-	# NOTES: To clearly state --with-stlport-include and --with-stlport-library cause troubles. I don't know why....
-	if use stlport ; then
-		confargs="${confargs} --with-stlport-libname=stlport_gcc"
-		#confargs="${confargs} --with-stlport-include=/usr/include --with-stlport-library=/usr/$(get_libdir)"
-	fi
-
-	# Compiler and linker flags
-	if use amd64 ; then
-		append-flags -m64
-	fi
-	append-ldflags -lpthread
-
-	econf	${confargs} \
-		$(use_with X x ) \
-		$(use_enable debug ) \
-		$(use_enable !debug production ) \
-	|| die "Configuration failed"
-}
-
-src_install() {
-	rm *~
-	emake DESTDIR="${D}" install || die "Installation failed"
-
-	# Symlinks for keeping original OpenCascade folder structure and
-	# add a link lib to lib64 in ros/Linux if we are on amd64
-	dosym lin ${INSTALL_DIR}/Linux
-
-	if use amd64 ; then
-		mv "${D}""${INSTALL_DIR}"/lin/lib "${D}""${INSTALL_DIR}"/lin/lib64
-		dosym lib64 ${INSTALL_DIR}/lin/lib
-	fi
-
-	#symlink for config.h
-	dosym ${INSTALL_DIR}/config.h ${INSTALL_DIR}/inc/config.h
-
-	# Tweak the environment variables script
-	cp "${FILESDIR}"/env.ksh.template env.ksh
-	sed -i "s:VAR_CASROOT:${INSTALL_DIR}:g" env.ksh
-
-	# Build the env.d environment variables
-	cp "${FILESDIR}"/env.ksh.template 50${PN}
-	sed -i \
-		-e 's:export ::g' \
-		-e "s:VAR_CASROOT:${INSTALL_DIR}:g" \
-		-e '1,2d' \
-		-e '4,14d' \
-		-e "s:ros/Linux/lib/:ros/Linux/$(get_libdir)/:g" ./50${PN} \
-	|| die "Creation of the /etc/env.d/50opencascade failed!"
-	sed -i "2i\PATH=${INSTALL_DIR}/Linux/bin/\nLDPATH=${INSTALL_DIR}/Linux/$(get_libdir)" ./50${PN} \
-	|| die "Creation of the /etc/env.d/50opencascade failed!"
-
-	# Update both env.d and script with the libraries variables
-	sed -i \
-		-e 's:VAR_SYS_BIN:/usr/bin:g' \
-		-e "s:VAR_SYS_LIB:/usr/$(get_libdir):g" \
-		-e "s:VAR_ITK:itk${itk_version}:g" \
-		-e "s:VAR_ITCL:itcl${itcl_version}:g" \
-		-e "s:VAR_TIX:tix${tix_version}:g" \
-		-e "s:VAR_TK:tk${tk_version}:g" \
-		-e "s:VAR_TCL:tcl${tcl_version}:g" env.ksh 50${PN} \
-	|| die "Tweaking of the Tcl/Tk libraries location in env.ksh and 50opencascade failed!"
-
-	# Install the env.d variables file
-	doenvd 50${PN}
-	rm 50${PN} env.csh
-
-	# Clean before copying everything
-	emake clean || die "emake clean failed"
-
-	# Install folders
-	cd "${S}"/../
-
-	## why is this needed?
-	insinto ${INSTALL_DIR}/../
-	doins -r ros
-
-	if use examples; then
-		insinto /usr/share/doc/${PF}/examples
-		doins -r data
-
-		insinto /usr/share/doc/${PF}/examples/samples
-		doins -r samples/tutorial
-
-		if use java ; then
-			insinto /usr/share/doc/${PF}/examples/samples/standard
-			doins -r samples/standard/java
-		fi
-	fi
-
-	# Install the documentation
-	if use doc; then
-		cd "${S}"/../doc
-		insinto /usr/share/doc/${PF}
-		doins -r {Overview,ReferenceDocumentation} || die "dodoc failed"
-	fi
-}
-
-pkg_postinst() {
-	einfo "Open CASCADE ebuild needs further development. Please inform any problems or improvements in http://bugs.gentoo.org/show_bug.cgi?id=118656"
-}
diff --git a/sci-libs/opencascade/opencascade-6.3-r2.ebuild b/sci-libs/opencascade/opencascade-6.3-r2.ebuild
deleted file mode 100644
index 732791d2e..000000000
--- a/sci-libs/opencascade/opencascade-6.3-r2.ebuild
+++ /dev/null
@@ -1,219 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=2
-
-inherit autotools eutils flag-o-matic check-reqs java-pkg-opt-2 multilib toolchain-funcs versionator
-
-DESCRIPTION="Software development platform for CAD/CAE, 3D surface/solid modeling and data exchange."
-HOMEPAGE="http://www.opencascade.org"
-SRC_URI="http://files.opencascade.com/OCC_${PV}_release/OpenCASCADE_src.tgz -> ${P}.tgz"
-
-LICENSE="Open-CASCADE-Technology-Public-License"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug doc examples java opengl source stlport X"
-DEPEND="java? ( virtual/jdk )
-	opengl? ( virtual/opengl
-		virtual/opengl )
-	X? ( x11-libs/libXmu
-		app-text/dgs )
-	>=dev-lang/tcl-8.4
-	>=dev-lang/tk-8.4
-	>=dev-tcltk/itcl-3.2
-	>=dev-tcltk/itk-3.2
-	x86? ( >=dev-tcltk/tix-8.1 )
-	amd64? ( >=dev-tcltk/tix-8.4.2 )
-	stlport? ( dev-libs/STLport )"
-RDEPEND=${DEPEND}
-
-S=${WORKDIR}/OpenCASCADE${PV}.0/ros
-INSTALL_DIR=/opt/${P}/ros
-
-pkg_setup() {
-	# Determine itk, itcl, tix, tk and tcl versions
-	itk_version=$(grep ITK_VER /usr/include/itk.h | sed 's/^.*"\(.*\)".*/\1/')
-	itcl_version=$(grep ITCL_VER /usr/include/itcl.h | sed 's/^.*"\(.*\)".*/\1/')
-	tix_version=$(grep TIX_VER /usr/include/tix.h | sed 's/^.*"\(.*\)".*/\1/')
-	tk_version=$(grep TK_VER /usr/include/tk.h | sed 's/^.*"\(.*\)".*/\1/')
-	tcl_version=$(grep TCL_VER /usr/include/tcl.h | sed 's/^.*"\(.*\)".*/\1/')
-
-	ewarn
-	ewarn " It is important to note that OpenCascade is a very large package. "
-	ewarn " Please note that building OpenCascade takes a lot of time and "
-	ewarn " hardware ressources: 3.5-4 GB free diskspace and 256 MB RAM are "
-	ewarn " the minimum requirements. "
-	ewarn
-
-	# Check if we have enough RAM and free diskspace to build this beast
-	CHECKREQS_MEMORY="256"
-	CHECKREQS_DISK_BUILD="3584"
-	check_reqs
-}
-
-src_prepare() {
-	# Substitute with our ready-made env.ksh script
-	cp -f "${FILESDIR}"/env.ksh.template "${S}"/env.ksh || die "Cannot copy env.ksh.template"
-
-	# Feed environment variables used by Opencascade compilation
-	sed -i \
-		-e "s:VAR_CASROOT:${S}:g" \
-		-e 's:VAR_SYS_BIN:/usr/bin:g' \
-		-e "s:VAR_SYS_LIB:/usr/$(get_libdir):g" env.ksh \
-	|| die "Environment variables feed in env.ksh failed!"
-
-	# Tweak itk, itcl, tix, tk and tcl versions
-	sed -i \
-		-e "s:VAR_ITK:itk${itk_version}:g" \
-		-e "s:VAR_ITCL:itcl${itcl_version}:g" \
-		-e "s:VAR_TIX:tix${tix_version}:g" \
-		-e "s:VAR_TK:tk${tk_version}:g" \
-		-e "s:VAR_TCL:tcl${tcl_version}:g" env.ksh \
-	|| die "itk, itcl, tix, tk and tcl version tweaking failed!"
-
-	# epatch "${FILESDIR}"/${P}-Makefile.am.patch
-	epatch "${FILESDIR}"/${P}-fixed-DESTDIR.patch
-	epatch "${FILESDIR}"/${P}-missing-mode.patch
-
-	chmod u+x configure
-
-	# Autotools version update
-	source env.ksh
-	eaclocal || die "eaclocal failed"
-	eautoheader || die "eautoheader failed"
-	eautomake -a -c -f
-	_elibtoolize --force --copy || die "elibtoolize failed"
-	eautoconf || die "eautoconf failed"
-}
-
-src_configure() {
-	# Add the configure options
-	local confargs="--prefix=${INSTALL_DIR}/lin --exec-prefix=${INSTALL_DIR}/lin --with-tcl=/usr/$(get_libdir) --with-tk=/usr/$(get_libdir)"
-
-	if use X ; then
-		confargs="${confargs} --with-dps-include=/usr/include --with-dps-library=/usr/$(get_libdir)"
-		confargs="${confargs} --with-xmu-include=/usr/include --with-xmu-library=/usr/$(get_libdir)"
-		if use !opengl; then
-			ewarn "Activate OpenGL if you want to be able to visualize geometry. Set "opengl" USE flag."
-		else
-			confargs="${confargs} --with-gl-include=/usr/include --with-gl-library=/usr/$(get_libdir)"
-		fi
-	else
-		if use opengl; then
-			die "OpenGL imply X support! Add "X" USE flag."
-		else
-			ewarn "Activate X and OpenGL if you want to be able to visualize geometry. Set "X" and "opengl" USE flags."
-		fi
-	fi
-
-	if use java ; then
-		local java_path
-		java_path=`java-config -O`
-		confargs="${confargs} --with-java-include=${java_path}/include"
-	else
-		ewarn "Java wrapping is not going to be compiled. USE flag: "java""
-	fi
-
-	# NOTES: To clearly state --with-stlport-include and --with-stlport-library cause troubles. I don't know why....
-	if use stlport ; then
-		confargs="${confargs} --with-stlport-libname=stlport_gcc"
-		#confargs="${confargs} --with-stlport-include=/usr/include --with-stlport-library=/usr/$(get_libdir)"
-	fi
-
-	# Compiler and linker flags
-	if use amd64 ; then
-		append-flags -m64
-	fi
-	append-ldflags -lpthread
-
-	econf	${confargs} \
-		$(use_with X x ) \
-		$(use_enable debug ) \
-		$(use_enable !debug production ) \
-	|| die "Configuration failed"
-}
-
-src_install() {
-	rm *~
-	emake DESTDIR="${D}" install || die "Installation failed"
-
-	# Symlinks for keeping original OpenCascade folder structure and
-	# add a link lib to lib64 in ros/Linux if we are on amd64
-	# dosym lin ${INSTALL_DIR}/Linux
-
-	if use amd64 ; then
-		mv "${D}""${INSTALL_DIR}"/lin/lib "${D}""${INSTALL_DIR}"/lin/lib64
-		dosym lib64 ${INSTALL_DIR}/lin/lib
-	fi
-
-	# Tweak the environment variables script
-	cp "${FILESDIR}"/env.ksh.template env.ksh
-	sed -i "s:VAR_CASROOT:${INSTALL_DIR}/lin:g" env.ksh
-
-	# Build the env.d environment variables
-	cp "${FILESDIR}"/env.ksh.template 50${PN}
-	sed -i \
-		-e 's:export ::g' \
-		-e "s:VAR_CASROOT:${INSTALL_DIR}/lin:g" \
-		-e '1,2d' \
-		-e '4,14d' \
-		-e "s:/Linux/lib/:/$(get_libdir)/:g" ./50${PN} \
-	|| die "Creation of the /etc/env.d/50opencascade failed!"
-	sed -i "2i\PATH=${INSTALL_DIR}/lin/bin\nLDPATH=${INSTALL_DIR}/lin/$(get_libdir)" ./50${PN} \
-	|| die "Creation of the /etc/env.d/50opencascade failed!"
-
-	# Update both env.d and script with the libraries variables
-	sed -i \
-		-e 's:VAR_SYS_BIN:/usr/bin:g' \
-		-e "s:VAR_SYS_LIB:/usr/$(get_libdir):g" \
-		-e "s:VAR_ITK:itk${itk_version}:g" \
-		-e "s:VAR_ITCL:itcl${itcl_version}:g" \
-		-e "s:VAR_TIX:tix${tix_version}:g" \
-		-e "s:VAR_TK:tk${tk_version}:g" \
-		-e "s:VAR_TCL:tcl${tcl_version}:g" env.ksh 50${PN} \
-	|| die "Tweaking of the Tcl/Tk libraries location in env.ksh and 50opencascade failed!"
-
-	# Install the env.d variables file
-	doenvd 50${PN}
-	rm 50${PN} env.csh
-
-	# Clean before copying everything
-	emake clean || die "emake clean failed"
-
-	# Install folders
-	cd "${S}"/../
-
-	## Do we really need this USE-flag?
-	if use source; then
-		#symlink for config.h
-		dosym ${INSTALL_DIR}/lin/config.h ${INSTALL_DIR}/inc/config.h
-
-		insinto ${INSTALL_DIR}/../
-		doins -r ros
-	fi
-
-	if use examples; then
-		insinto /usr/share/doc/${PF}/examples
-		doins -r data
-
-		insinto /usr/share/doc/${PF}/examples/samples
-		doins -r samples/tutorial
-
-		if use java ; then
-			insinto /usr/share/doc/${PF}/examples/samples/standard
-			doins -r samples/standard/java
-		fi
-	fi
-
-	# Install the documentation
-	if use doc; then
-		cd "${S}"/../doc
-		insinto /usr/share/doc/${PF}
-		doins -r {Overview,ReferenceDocumentation} || die "dodoc failed"
-	fi
-}
-
-pkg_postinst() {
-	einfo "Open CASCADE ebuild needs further development. Please inform any problems or improvements in http://bugs.gentoo.org/show_bug.cgi?id=118656"
-}
diff --git a/sci-mathematics/frama-c/Manifest b/sci-mathematics/frama-c/Manifest
index 9b9983b43..13a646009 100644
--- a/sci-mathematics/frama-c/Manifest
+++ b/sci-mathematics/frama-c/Manifest
@@ -1,8 +1,7 @@
 AUX frama-c-20100401-plugin_install.patch 1442 RMD160 41ee9fc7b2e057497baf3af63a5d3325c8dc9826 SHA1 519a30d1988309606596411c38c40885dea26ee6 SHA256 2c496724bf528fa3e60cc660fcf9767a44bba070bf4538aa6407186ba718225a
-AUX frama-c-20101202_beta2-local_tmps.patch 5793 RMD160 81ae05faa40470c801796a4ad4275590f4c3f658 SHA1 dbfe3e000a44b480554ddc770140e29a11263245 SHA256 123663c3b4c077ba529f425386b7e2749372e6efa236c7a52d13d49d03961f0c
 DIST frama-c-Boron-20100401.tar.gz 24143452 RMD160 ff2a7571cbc80cf2cb6896ab7b5d9250e3b8098c SHA1 77063ba16e2371310a70b950b5c28301db6b58a0 SHA256 78070b9899ba806740f583fb63e22f89bf5dd6508498a79567dec6bab16d5ac6
 DIST frama-c-Carbon-20101202-beta2.tar.gz 34025440 RMD160 3654fbb90d4a3e3405c988c6697cd24e24d16896 SHA1 0a1d907f3a23b06806497b85b09c82e4bdf342cf SHA256 d95f73b675f9f3defd939e81e4d1c4dd58a06d8a0ba411d8781ac6d9c2a248e1
 EBUILD frama-c-20100401.ebuild 1519 RMD160 0a4a610862fc4081cc45d851d2f773f7f57f488e SHA1 7a749f903c9f5dc1626111845788630ed2cd46b0 SHA256 81a91a4b6ef0726fafce961b3cb3f81d11df19263ce55cfd12dbafc5bcdb6fac
-EBUILD frama-c-20101202_beta2.ebuild 1560 RMD160 9ed52d85f678634b3b18401015f78c47a889df4e SHA1 9947e0213e8a4bbe435c13df209cd7c821da51b1 SHA256 a03551b6001277773def4de16860923ee7d5c89878ed6b133033490ae8375345
+EBUILD frama-c-20101202_beta2.ebuild 1660 RMD160 b739c2c17473bba6f53c05786b436cec4127e366 SHA1 4b02e04d7e2876b63204f4276def889a0aa2721c SHA256 438027f089439da2afad6657c2c20b4288accea25a20c0221f0a68a064c2043e
 MISC ChangeLog 654 RMD160 3947b413ec8d0339aa60d2c2e91068c2a27d40a3 SHA1 18cc6ae253523cad9e35d531f4cd0da41305cdba SHA256 a3b70b0cb3f8470d2c4c2acc5e15075e3d1e51ac1d11cc677bbc5d4f1bf94a2b
 MISC metadata.xml 815 RMD160 464879bb226169c1b7e06f13c90f70639b25487e SHA1 abeb18a64d38099e51e2b6c0c1027cb9671f30e4 SHA256 e03ee0bab13f2fb45987440ec7498bf629aa5a8f7217ae7dbeab461c23e89ea8
diff --git a/sci-mathematics/frama-c/files/frama-c-20101202_beta2-local_tmps.patch b/sci-mathematics/frama-c/files/frama-c-20101202_beta2-local_tmps.patch
deleted file mode 100644
index bd131a09e..000000000
--- a/sci-mathematics/frama-c/files/frama-c-20101202_beta2-local_tmps.patch
+++ /dev/null
@@ -1,125 +0,0 @@
-diff -Naurp frama-c-Carbon-20101202-beta2-orig/cil/src/frontc/cabs2cil.ml frama-c-Carbon-20101202-beta2/cil/src/frontc/cabs2cil.ml
---- frama-c-Carbon-20101202-beta2-orig/cil/src/frontc/cabs2cil.ml	2010-12-17 13:17:07.000000000 +0000
-+++ frama-c-Carbon-20101202-beta2/cil/src/frontc/cabs2cil.ml	2011-02-23 15:20:36.000000000 +0000
-@@ -671,13 +671,11 @@ let newTempVar descr (descrpure:bool) ty
-   vi.vdescrpure <- descrpure;
-   (* Rename if clash, but do not add to the environment *)
-   let vi = alphaConvertVarAndAddToEnv false vi in
--  (*
-   (* the temporary is local to the function: the normalization can use it
-      wherever it wants.
-    *)
-   !currentFunctionFDEC.sbody.blocals <-
-     vi :: !currentFunctionFDEC.sbody.blocals;
--   *)
-   vi
- 
- let mkAddrOfAndMark loc ((b, off) as lval) : exp =
-@@ -4715,7 +4713,7 @@ and doExp local_env
-                     (if uop = A.POSINCR then "++" else "--") in
-                 let tmp = newTempVar (Some descr) true t in
-                 ([var tmp],
--                 local_var_chunk se' tmp +++
-+                 se' +++
-                    (mkStmtOneInstr ~ghost:local_env.is_ghost
-                       (Set(var tmp, e', CurrentLoc.get ())),[],[],[]),
-                 (* the tmp variable should not be investigated for
-@@ -4811,13 +4809,11 @@ and doExp local_env
-               if needsTemp then
-                 let descr = Some (Pretty_utils.sfprintf "%a" dd_lval lv) in
-                 let tmp = newTempVar descr true lvt in
--                let chunk =
--                  i2c
--                    (mkStmtOneInstr ~ghost:local_env.is_ghost
--                       (Set(lv, new_exp (Lval(var tmp)), loc)),
--                    [lv],[lv],var tmp :: r1')
--                in
--                ([],var tmp, local_var_chunk chunk tmp)
-+                ([],var tmp,
-+                 i2c
-+                   (mkStmtOneInstr ~ghost:local_env.is_ghost
-+                      (Set(lv, new_exp (Lval(var tmp)), loc)),
-+                    [lv],[lv],var tmp :: r1'))
-               else r1',lv, empty
-             in
-             let (r2,se2, _, _) =
-@@ -4939,17 +4935,14 @@ and doExp local_env
-             let tmp =
-               newTempVar (Some "<boolean expression>") true intType
-             in
--            let condChunk =
--              compileCondExp false ce
-+            finishExp []
-+              (compileCondExp false ce
-                 (empty +++
-                    (mkStmtOneInstr ~ghost:local_env.is_ghost
-                       (Set(var tmp, integer 1,loc)),[],[],[]))
-                 (empty +++
-                    (mkStmtOneInstr ~ghost:local_env.is_ghost
--                      (Set(var tmp, integer 0,loc)),[],[],[]))
--            in
--            finishExp []
--              (local_var_chunk condChunk tmp)
-+                      (Set(var tmp, integer 0,loc)),[],[],[])))
-               (new_exp ~loc (Lval (var tmp)))
-               intType
-       end
-@@ -5046,7 +5039,6 @@ and doExp local_env
-               newTempVar
-                 (Some (Pretty_utils.sfprintf "%a" dd_exp e)) true t
-             in
--            let c = local_var_chunk c tmp in
- 	    (* create an instruction to give the e to the temporary *)
- 	    let i = mkStmtOneInstr ~ghost:local_env.is_ghost
-               (Set(var tmp, e, loc)) in
-@@ -5145,7 +5137,6 @@ and doExp local_env
-                        ASet (is_real,lv, r, lvt) -> is_real, lv, r, lvt
-                      | _ ->
-                          let v = newTempVar None true resTyp in
--                         prechunk:= local_var_chunk !prechunk v;
-                          false, var v, [], resTyp
-                    in
-                    pwhat := (ASet (is_real, destlv, r, destlvtyp));
-@@ -5275,7 +5266,6 @@ and doExp local_env
-                   (Pretty_utils.pp_list ~sep:", " dd_exp) !pargs
-               in
-               let tmp = newTempVar (Some descr) false restype'' in
--              prechunk:=local_var_chunk !prechunk tmp;
-               (* Remember that this variable has been created for this
-                * specific call. We will use this in collapseCallCast. *)
-               IH.add callTempVars tmp.vid ();
-@@ -5371,7 +5361,6 @@ and doExp local_env
-                 let (r1,se1, _, _) =
-                   doExp local_env asconst e1 (ASet(false, tmp_var, [], tresult))
-                 in
--                let se1 = local_var_chunk se1 tmp in
-                 let r3,se3,_,_ =
-                   finishExp
-                     ~newWhat:(ASet(false,tmp_var, [], tresult)) r3 se3 e3' t3
-@@ -5388,7 +5377,7 @@ and doExp local_env
-                   | ASet (is_real, lv, r, lvt) -> is_real, lv, r, lvt, empty
-                   | _ ->
-                       let tmp = newTempVar None true tresult in
--                      false, var tmp, [], tresult, local_var_chunk empty tmp
-+                      false, var tmp, [], tresult, empty
-                 in
-                 (* Now do e2 and e3 for real *)
-                 let (r2,se2, _, _) =
-@@ -5461,7 +5450,7 @@ and doExp local_env
-                     b.bstmts @
-                     [Cil.mkStmtOneInstr ~ghost:local_env.is_ghost
-                        (Set (Cil.var vi, e,loc))];
--                  (local_var_chunk se vi,Cil.new_exp ~loc (Lval (Cil.var vi)))
-+                  (se,Cil.new_exp ~loc (Lval (Cil.var vi)))
-               | _ -> se,e
-             in
-             finishExp [] se e t
-@@ -6583,7 +6572,7 @@ and createLocal ghost ((_, sto, _, _) as
-                 (Some (Pretty_utils.sfprintf "alloca(%a)" d_exp sizeof))
-                 false rt
-             in
--            (local_var_chunk setlen tmp)
-+            setlen
-             +++ (mkStmtOneInstr ~ghost
-                    (Call(Some(var tmp), new_exp ~loc (Lval(var alloca)),
- 			 [ sizeof  ], CurrentLoc.get ())),[],[],[])
diff --git a/sci-mathematics/frama-c/frama-c-20101202_beta2.ebuild b/sci-mathematics/frama-c/frama-c-20101202_beta2.ebuild
index 1bf19771a..170ddf23c 100644
--- a/sci-mathematics/frama-c/frama-c-20101202_beta2.ebuild
+++ b/sci-mathematics/frama-c/frama-c-20101202_beta2.ebuild
@@ -33,8 +33,11 @@ src_prepare(){
 	rm share/libc/test.c
 	rm -Rf src/wp
 
-	epatch "${FILESDIR}/${P}-local_tmps.patch"
-	
+	mkdir cil/pdf
+	mv cil/doc/*.pdf cil/doc/*.tex cil/pdf
+	mv cil/doc cil/html
+	mv doc/manuals doc/pdf
+
 	touch config_file
 	sed -i configure.in \
 		-e "s:1.7):1.6):g"
@@ -63,6 +66,8 @@ src_install(){
 	dodoc Changelog doc/README
 
 	if use doc; then
-		dodoc doc/manuals/*
+		dodoc doc/pdf/*.pdf
+		dodoc cil/pdf/*.pdf
+		dohtml -r cil/html/*
 	fi
 }
diff --git a/virtual/mpi/Manifest b/virtual/mpi/Manifest
index 8a1c52b7c..e3533beca 100644
--- a/virtual/mpi/Manifest
+++ b/virtual/mpi/Manifest
@@ -1,13 +1,3 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
-EBUILD mpi-2.0-r2.ebuild 565 RMD160 6289bd2ad0c2b03d3a9d2d71e78d114a02ac9418 SHA1 559d24a026a6ddd69162e471507fef9c29b6234c SHA256 db9d8939419d73b04ac952d1aea675c82774b7393e018f739b0c956c5f260c45
+EBUILD mpi-2.0-r2.ebuild 613 RMD160 521622e962d7f2b95ce86ab11bfb6d3b6bea9068 SHA1 572b7e9d0a0531caf0f560ac4b3b4bbe4b024068 SHA256 02d377ae917bbf85525682ff63d1836caeddf5adf0b335741963ccbd0ef2f7ec
 MISC ChangeLog 284 RMD160 457cc4119b79de2d3e6a508a9b3421614439f3c4 SHA1 d2611bd4c92b04a1686707d0e1be884d692bb58c SHA256 8e60473b7d8bf4ccac6cc49101a5e9e9caf8c074e63d95e988c5601349bdb172
 MISC metadata.xml 253 RMD160 c53a7fc23706a45d10368f8915628a448139d0ad SHA1 48ab46fc25df70151b204e9d942aedfed4f4fdca SHA256 1021d10eb7dc0f85a2a7993ad2a8301bf804fe93141b133e77d63625a3619e62
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.16 (GNU/Linux)
-
-iEYEARECAAYFAk08UhQACgkQy0OE/ans1/nnZQCeKDjDQRZ4/8wZohsA4PG1tXbk
-SHYAn0tYh9ChMGIDu3nCQntfZHTGe50A
-=+4AS
------END PGP SIGNATURE-----
diff --git a/virtual/mpi/mpi-2.0-r2.ebuild b/virtual/mpi/mpi-2.0-r2.ebuild
index 1c31ab6d3..9907d484a 100644
--- a/virtual/mpi/mpi-2.0-r2.ebuild
+++ b/virtual/mpi/mpi-2.0-r2.ebuild
@@ -9,13 +9,14 @@ HOMEPAGE=""
 SRC_URI=""
 LICENSE=""
 SLOT="0"
-KEYWORDS="~alpha ~amd64 ~hppa ~ia64 ~ppc ~ppc64 ~sparc ~x86"
+KEYWORDS="~alpha ~amd64 ~hppa ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
 IUSE="cxx fortran romio"
 
 RDEPEND="|| (
 	sys-cluster/openmpi[cxx?,fortran?,romio?]
 	sys-cluster/mpich2[cxx?,fortran?,romio?]
 	sys-cluster/nullmpi
+	sys-cluster/native-mpi
 )"
 
 DEPEND=""