Merge https://github.com/gentoo-science/sci

author: Andreas Schäfer <gentryx@gmx.de> 2014-07-21 17:06:10 +0200
committer: Andreas Schäfer <gentryx@gmx.de> 2014-07-21 17:06:10 +0200
commit: a2a4f4884319c4ce9b539716ed17951c4abcd3d4 (patch)
tree: 2e4d90db21fa8aff4ca74c75057a5695eb7a92bc
parent: HPX live ebuild now reflects changes in trunk (diff)
parent: fixed dependency issue (diff)
download: sci-a2a4f4884319c4ce9b539716ed17951c4abcd3d4.tar.gz
sci-a2a4f4884319c4ce9b539716ed17951c4abcd3d4.tar.bz2
sci-a2a4f4884319c4ce9b539716ed17951c4abcd3d4.zip
122 files changed, 3410 insertions, 297 deletions
diff --git a/app-doc/root-docs/ChangeLog b/app-doc/root-docs/ChangeLog
index 0589d994c..ca2ea86c5 100644
--- a/app-doc/root-docs/ChangeLog
+++ b/app-doc/root-docs/ChangeLog
@@ -2,6 +2,31 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/app-doc/root-docs/ChangeLog,v 1.42 2014/03/28 18:48:01 bicatali Exp $
 
+*root-docs-5.34.18-r2 (06 Jul 2014)
+
+  06 Jul 2014; Andrew Savchenko <bircoph@gmail.com>
+  +root-docs-5.34.18-r2.ebuild, +files/root-docs-5.34.01-makehtml.patch:
+  Backport PDFs generation and html fixes from ROOT-6 branch.
+
+*root-docs-6.00.02 (05 Jul 2014)
+
+  05 Jul 2014; Andrew Savchenko <bircoph@gmail.com>
+  root-docs-6.00.01-r1.ebuild, +root-docs-6.00.02.ebuild,
+  +files/root-docs-6.00.01-fillpatterns.patch:
+  Version bump. Fix bug with TAttFill generation.
+
+*root-docs-6.00.01-r1 (02 Jul 2014)
+
+  02 Jul 2014; Andrew Savchenko <bircoph@gmail.com> -root-docs-6.00.01.ebuild,
+  +root-docs-6.00.01-r1.ebuild, root-docs-9999.ebuild,
+  -files/root-docs-6.00.01-cernbuild.patch,
+  files/root-docs-6.00.01-makehtml.patch:
+  Remove unneeded cernbuild patch since
+  https://sft.its.cern.ch/jira/browse/ROOT-6421
+  is fixed in sci-physics/root now.
+  Also remove unneeded #include for library load from makehtml.sh
+  patch. Now docs seems to be equivalent to those on root.cern.ch
+
 *root-docs-6.00.01 (29 Jun 2014)
 
   29 Jun 2014; Andrew Savchenko <bircoph@gmail.com> +root-docs-6.00.01.ebuild,
diff --git a/app-doc/root-docs/Manifest b/app-doc/root-docs/Manifest
index 54f204f12..f5533c265 100644
--- a/app-doc/root-docs/Manifest
+++ b/app-doc/root-docs/Manifest
@@ -3,4 +3,6 @@ DIST TMVAUsersGuide-v4.2.0.pdf 4099493 SHA256 b61614d14289a20f5fa429f79e474e596c
 DIST info.png 2060 SHA256 51de6661250f3fb71c6c8250cbc4bdc4dc4283cc90240b4dc1ee6168e8d40279 SHA512 81a730eefbe7a7e15d5840491402c7644bf7ed5d5f8f3830ed9457b343cc7882480e993ea84aef93500742cd0fe8469859cd2c925e5582b91ef56406804ae276 WHIRLPOOL 02ea6daf9e3d21947ebf5dd01c455a13f2fcbf9981be34a150056a3510122ca49e3d137d4f242c7218d4d06ace09566d513a04f09071723ac244f5a38e982bac
 DIST roofit_quickstart_3.00.pdf 501576 SHA256 65aaf9e0c88352e265fd55b97a2503a9ee4a51d3219daff69c6f7f6427fe22cf SHA512 e8e1bd3bb3ead0ae3883512d7ff297651b99937fd5df0b61cf559ea5dd6cfbda35dfd8ebc953ed11a12f471849f6e95e05869b58a1e433ea6e5d1d1aa08bbb93 WHIRLPOOL a58b221272e3b2775639bf934f63cd06919105871ad736a84e18e6f3949a579301d1c6d69df39576dcc11867aa27274f5c78f36146a929698437b1a0c310aebe
 DIST root6-banner.jpg 32319 SHA256 9d6d226bbe61db257a1796a3ad04dfe97b3bb500a29349ff76bf6a929ed1e104 SHA512 f01dd253f24d59c374042efd239ce023e5ca82d3d617ca6763daf9720b169c4fb27a0f4573ea95d807f0e12095924606372df4940f65ce7d859164314d22b9af WHIRLPOOL 69976abe240235a4f4eb25d61a0ceb183dc5ad5f9e57e9130ae10615329dd23125848f45608e1ad2d65a286d1f191f95336316f7c8f1cc052d396c31433cbe4c
+DIST root_v5.34.18.source.tar.gz 74218396 SHA256 9196dce7d76b31e5bcabd985bd31bc4d9b7c8c4d0c7ce84f730efa4ef82a3567 SHA512 7c659d1a92e6ad1b901956cf0a04aacc391c936eb2881528d105f61373128e5fd4caad6e76988050a8a8bc69a8ba0b53055974b4c618800345127ae2e6dd7a14 WHIRLPOOL 15221bbdabd5abd50dc87e3cc8fa3de24c5888e3ac0a75535983c8ec0718433c84c2400da59d27f3b83b687c7c5f5d60bf769c8a1eefce45dd7d39cbc002a6b7
 DIST root_v6.00.01.source.tar.gz 97783289 SHA256 245c75fd6b53b84cae6251f950e259311439da678b2cdebb9578d51561a6b61f SHA512 e5f56750a0637aa884ea2d9d2ebf7b677cd1fac1819042948ba3530a25366cb7d853dba6fa7127764e3ae7cec23f89ed60d8913c0ff10ce2664bcc87df1620cf WHIRLPOOL 92f34c13ee0161d556b54b1bdd971774b2637c5cd57916ee75f0572a30713df820df3bb07f276d16ca31d11fda7e762de673c943b8bffda9db501d2ee8848654
+DIST root_v6.00.02.source.tar.gz 97811067 SHA256 db92818781f842c33b8b583f1f9be02b51cedbf5f2943df986cbbd0c0006a06f SHA512 bd72eb43d2a4ace27738ba2dc509f6d81ec3555e59454426d28c2c5522b4b19d2678ed515b84efaf953146c1f50c65e304532456d76076d03598bda67c69e8a5 WHIRLPOOL 12b87e9b1612ea3625f7ea0970b733887051b5173b728b5f13a032eb103eeda22de8a4c18417e02a92fe02f29b9acd9114fa1420fac42bea31bde07c7a0ce697
diff --git a/app-doc/root-docs/files/root-docs-5.34.01-makehtml.patch b/app-doc/root-docs/files/root-docs-5.34.01-makehtml.patch
new file mode 100644
index 000000000..b339226c8
--- /dev/null
+++ b/app-doc/root-docs/files/root-docs-5.34.01-makehtml.patch
@@ -0,0 +1,51 @@
+--- root/Makefile.orig	2012-07-13 13:42:46.000000000 +0400
++++ root/Makefile	2012-07-22 00:15:03.282994389 +0400
+@@ -1087,16 +1087,7 @@
+ 
+ ifeq ($(BUILDX11),yes)
+ ifeq ($(BUILDASIMAGE),yes)
+-html: rootexecs postbin changelog releasenotes
+-ifneq ($(USECONFIG),FALSE)
+-	@if [ "x`which root.exe`" != "x$(DESTDIR)$(BINDIR)/root.exe" ] \
+-	  || [ "`which root.exe`" -ot "bin/root.exe" ]; then \
+-	  echo 'ERROR: root.exe has not been installed by this build.'; \
+-	  echo '       Run "make install" before running "make html".'; \
+-	  exit 1; \
+-	fi
+-endif
+-	@$(MAKELOGHTML)
++html: compiledata releasenotes
+ 	@$(MAKEHTML)
+ else
+ html:
+--- root/build/unix/makehtml.sh.orig	2012-06-28 11:33:36.000000000 +0400
++++ root/build/unix/makehtml.sh	2012-07-22 00:18:58.705804436 +0400
+@@ -1,16 +1,16 @@
+ #! /bin/sh
+ 
+ dir=`pwd`
+-ROOT=$dir/bin/root
++ROOT=root
+ cd tutorials
+ # we need tutorials/hsimple.root
+ if [ ! -f hsimple.root ]; then
+-   $ROOT -l -b -q hsimple.C
++   $ROOT -l -b -q hsimple.C && exit 1
+ fi
+ cd tree
+ # we need tutorials/tree/cernstaff.root
+ if [ ! -f cernstaff.root ]; then
+-   $ROOT -l -b -q cernbuild.C
++   $ROOT -l -b -q cernbuild.C || exit 1
+ fi
+ cd $dir
+ 
+@@ -20,7 +20,7 @@
+ 
+ # To generate the full documentation, we do need to
+ # use the graphics engine, so do not use '-b'.
+-$ROOT -l <<makedoc
++$ROOT -l <<makedoc || exit 1
+     THtml h;
+     h.LoadAllLibs();
+     h.MakeAll();
diff --git a/app-doc/root-docs/files/root-docs-6.00.01-cernbuild.patch b/app-doc/root-docs/files/root-docs-6.00.01-cernbuild.patch
deleted file mode 100644
index b155795c9..000000000
--- a/app-doc/root-docs/files/root-docs-6.00.01-cernbuild.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-diff --git a/tutorials/tree/cernbuild.C b/tutorials/tree/cernbuild.C
-index ba516b6..793ecb5 100644
---- a/tutorials/tree/cernbuild.C
-+++ b/tutorials/tree/cernbuild.C
-@@ -2,6 +2,11 @@
- // see also a variant in staff.C
- // Author: Rene Brun
-    
-+#include "TFile.h"
-+#include "TSystem.h"
-+#include "TString.h"
-+#include "TTree.h"
-+
- TFile *cernbuild(Int_t get=0, Int_t print=1) {
- 
-    Int_t           Category;
diff --git a/app-doc/root-docs/files/root-docs-6.00.01-fillpatterns.patch b/app-doc/root-docs/files/root-docs-6.00.01-fillpatterns.patch
new file mode 100644
index 000000000..e48a4f775
--- /dev/null
+++ b/app-doc/root-docs/files/root-docs-6.00.01-fillpatterns.patch
@@ -0,0 +1,30 @@
+diff --git a/core/base/doc/macros/fillpatterns.C b/core/base/doc/macros/fillpatterns.C
+index b0a5132..fca81c8 100644
+--- a/core/base/doc/macros/fillpatterns.C
++++ b/core/base/doc/macros/fillpatterns.C
+@@ -20,11 +20,11 @@ TCanvas * fillpatterns()
+ 
+    // Fixed patterns.
+    for (i=1; i<=5; i++) {
+-      box(j++, 0.01, y-bh, 0.19, y);
+-      box(j++, 0.21, y-bh, 0.39, y);
+-      box(j++, 0.41, y-bh, 0.59, y);
+-      box(j++, 0.61, y-bh, 0.79, y);
+-      box(j++, 0.81, y-bh, 0.99, y);
++      box(j, 0.01, y-bh, 0.19, y); j++;
++      box(j, 0.21, y-bh, 0.39, y); j++;
++      box(j, 0.41, y-bh, 0.59, y); j++;
++      box(j, 0.61, y-bh, 0.79, y); j++;
++      box(j, 0.81, y-bh, 0.99, y); j++;
+       y = y-bh-db;
+    }
+ 
+@@ -55,7 +55,7 @@ TCanvas * fillpatterns()
+    return Pat;
+ }
+ 
+-box(Int_t pat, Double_t x1, Double_t y1, Double_t x2, Double_t  y2)
++void box(Int_t pat, Double_t x1, Double_t y1, Double_t x2, Double_t  y2)
+ {
+    // Draw an box using the fill pattern "pat" with the "pat" value
+    // written on top.
diff --git a/app-doc/root-docs/files/root-docs-6.00.01-makehtml.patch b/app-doc/root-docs/files/root-docs-6.00.01-makehtml.patch
index 8ad9b888f..613468629 100644
--- a/app-doc/root-docs/files/root-docs-6.00.01-makehtml.patch
+++ b/app-doc/root-docs/files/root-docs-6.00.01-makehtml.patch
@@ -44,14 +44,12 @@ index a94e790..8b4589d 100755
  fi
  cd $dir
  
-@@ -20,7 +20,9 @@ echo ""
+@@ -20,7 +20,7 @@ echo ""
  
  # To generate the full documentation, we do need to
  # use the graphics engine, so do not use '-b'.
 -$ROOT -n -l <<makedoc
 +$ROOT -n -l <<makedoc || exit 1
-+    #include "THtml.h"
-+    gSystem->Load("libHtml");
      THtml h;
      h.LoadAllLibs();
      h.MakeAll();
diff --git a/app-doc/root-docs/root-docs-5.34.18-r2.ebuild b/app-doc/root-docs/root-docs-5.34.18-r2.ebuild
new file mode 100644
index 000000000..ac00ef207
--- /dev/null
+++ b/app-doc/root-docs/root-docs-5.34.18-r2.ebuild
@@ -0,0 +1,132 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/app-doc/root-docs/root-docs-5.34.18-r1.ebuild,v 1.2 2014/03/28 18:48:01 bicatali Exp $
+
+EAPI=5
+
+ROOT_PN="root"
+ROOFIT_DOC_PV=2.91-33
+ROOFIT_QS_DOC_PV=3.00
+TMVA_DOC_PV=4.2.0
+
+if [[ ${PV} == "9999" ]] ; then
+	inherit git-r3
+	EVCS_OFFLINE=yes # we need exactly the same checkout as root itself
+	EGIT_REPO_URI="http://root.cern.ch/git/root.git"
+	KEYWORDS=""
+else
+	SRC_URI="ftp://root.cern.ch/${ROOT_PN}/${ROOT_PN}_v${PV}.source.tar.gz"
+	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+	S="${WORKDIR}/${ROOT_PN}"
+fi
+
+inherit eutils multilib virtualx
+
+DESCRIPTION="Documentation for ROOT Data Analysis Framework"
+HOMEPAGE="http://root.cern.ch/drupal"
+SRC_URI="${SRC_URI}
+	math? (
+		http://tmva.sourceforge.net/docu/TMVAUsersGuide.pdf -> TMVAUsersGuide-v${TMVA_DOC_PV}.pdf
+		http://root.cern.ch/download/doc/RooFit_Users_Manual_${ROOFIT_DOC_PV}.pdf
+		http://root.cern.ch/drupal/sites/default/files/roofit_quickstart_${ROOFIT_QS_DOC_PV}.pdf )
+	api? (
+		${HOMEPAGE}/sites/default/files/images/root6-banner.jpg
+		${HOMEPAGE}/sites/all/themes/newsflash/images/info.png )"
+
+SLOT="0"
+LICENSE="LGPL-2.1"
+IUSE="api +math +metric"
+
+VIRTUALX_REQUIRED="api"
+
+DEPEND="
+	~sci-physics/root-${PV}[X,graphviz,opengl]
+	app-text/pandoc
+	app-text/texlive
+	dev-haskell/pandoc-citeproc[bibutils]
+	media-fonts/dejavu
+	virtual/pkgconfig"
+RDEPEND=""
+
+DOC_DIR="/usr/share/doc/${ROOT_PN}-${PV}"
+
+src_unpack() {
+	if [[ ${PV} == "9999" ]] ; then
+		# we need to force sci-physics/root checkout here
+		git-r3_checkout "${EGIT_REPO_URI}" "${WORKDIR}/${P}" "sci-physics/root/0"
+	else
+		default
+	fi
+}
+
+src_prepare() {
+	use api && epatch \
+		"${FILESDIR}/${PN}-5.34.01-makehtml.patch" \
+		"${FILESDIR}/${PN}-6.00.01-fillpatterns.patch"
+	# prefixify the configure script
+	sed -i \
+		-e "s:/usr:${EPREFIX}/usr:g" \
+		configure || die "prefixify configure failed"
+}
+
+src_configure() {
+	# we need only to setup paths here, html docs doesn't depend on USE flags
+	if use api; then
+		./configure \
+			--prefix="${EPREFIX}/usr" \
+			--etcdir="${EPREFIX}/etc/root" \
+			--libdir="${EPREFIX}/usr/$(get_libdir)/${PN}" \
+			--docdir="${EPREFIX}/usr/share/doc/${PF}" \
+			--tutdir="${EPREFIX}/usr/share/doc/${PF}/examples/tutorials" \
+			--testdir="${EPREFIX}/usr/share/doc/${PF}/examples/tests" \
+			--with-llvm-config="${EPREFIX}/usr/bin/llvm-config" \
+			--with-sys-iconpath="${EPREFIX}/usr/share/pixmaps" \
+			--nohowto
+	fi
+}
+
+src_compile() {
+	pdf_target=( primer users-guide )
+	local pdf_size=pdfa4
+	use metric || pdf_size=pdfletter
+	use math && pdf_target+=( minuit2 spectrum )
+
+	for (( i=0; i<${#pdf_target[@]}; i++ )); do
+		emake -C documentation/"${pdf_target[i]}" "${pdf_size}"
+	done
+
+	if use api; then
+		# video drivers may want to access hardware devices
+		cards=$(echo -n /dev/dri/card* /dev/ati/card* /dev/nvidiactl* | sed 's/ /:/g')
+		[[ -n "${cards}" ]] && addpredict "${cards}"
+
+		ROOTSYS="${S}" Xemake html
+		# if root.exe crashes, return code will be 0 due to gdb attach,
+		# so we need to check if last html file was generated;
+		# this check is volatile and can't catch crash on the last file.
+		[[ -f htmldoc/tableDescriptor_st.html ]] || die "html doc generation crashed"
+	fi
+}
+
+src_install() {
+	insinto "${DOC_DIR}"
+
+	for (( i=0; i<${#pdf_target[@]}; i++ )); do
+		doins documentation/"${pdf_target[i]}"/*.pdf
+	done
+	unset pdf_target
+
+	use math && doins \
+		"${DISTDIR}/RooFit_Users_Manual_${ROOFIT_DOC_PV}.pdf" \
+		"${DISTDIR}/roofit_quickstart_${ROOFIT_QS_DOC_PV}.pdf" \
+		"${DISTDIR}/TMVAUsersGuide-v${TMVA_DOC_PV}.pdf"
+
+	if use api; then
+		# Install offline replacements for online messages
+		cp "${DISTDIR}"/{root6-banner.jpg,info.png} htmldoc/ || die "cp failed"
+		# too large data to copy
+		dodir "${DOC_DIR}/html"
+		mv htmldoc/* "${ED}${DOC_DIR}/html/" || die
+		docompress -x ${DOC_DIR}/html
+	fi
+}
diff --git a/app-doc/root-docs/root-docs-6.00.01.ebuild b/app-doc/root-docs/root-docs-6.00.01-r1.ebuild
index bb17e86a4..096e0fe96 100644
--- a/app-doc/root-docs/root-docs-6.00.01.ebuild
+++ b/app-doc/root-docs/root-docs-6.00.01-r1.ebuild
@@ -62,7 +62,7 @@ src_unpack() {
 src_prepare() {
 	use api && epatch \
 		"${FILESDIR}/${PN}-6.00.01-makehtml.patch" \
-		"${FILESDIR}/${PN}-6.00.01-cernbuild.patch"
+		"${FILESDIR}/${PN}-6.00.01-fillpatterns.patch"
 	# prefixify the configure script
 	sed -i \
 		-e "s:/usr:${EPREFIX}/usr:g" \
diff --git a/app-doc/root-docs/root-docs-6.00.02.ebuild b/app-doc/root-docs/root-docs-6.00.02.ebuild
new file mode 120000
index 000000000..0ee27bf30
--- /dev/null
+++ b/app-doc/root-docs/root-docs-6.00.02.ebuild
@@ -0,0 +1 @@
+root-docs-6.00.01-r1.ebuild
+\ No newline at end of file
diff --git a/app-doc/root-docs/root-docs-9999.ebuild b/app-doc/root-docs/root-docs-9999.ebuild
index 32ba358c8..0ee27bf30 120000
--- a/app-doc/root-docs/root-docs-9999.ebuild
+++ b/app-doc/root-docs/root-docs-9999.ebuild
@@ -1 +1 @@
-root-docs-6.00.01.ebuild
-\ No newline at end of file
+root-docs-6.00.01-r1.ebuild
+\ No newline at end of file
diff --git a/dev-lang/julia/ChangeLog b/dev-lang/julia/ChangeLog
index b725a6254..3816f2c4d 100644
--- a/dev-lang/julia/ChangeLog
+++ b/dev-lang/julia/ChangeLog
@@ -21,7 +21,7 @@
 
   14 Jul 2013; James Cloos <cloos@jhcloos.com> julia-9999.ebuild:
   Julia uses submodules, so set EGIT_HAS_SUBMODULES=yes
-  
+
   14 Jun 2013; Justin Lecher <jlec@gentoo.org> julia-9999.ebuild, metadata.xml:
   Drop KEYWORDS of live ebuilds
 
diff --git a/dev-lang/julia/julia-9999.ebuild b/dev-lang/julia/julia-9999.ebuild
index 32d93f37e..ae77b7076 100644
--- a/dev-lang/julia/julia-9999.ebuild
+++ b/dev-lang/julia/julia-9999.ebuild
@@ -24,13 +24,14 @@ RDEPEND="
 	dev-libs/mpfr:0=
 	dev-libs/utf8proc:0=
 	sci-libs/arpack:0=
+	sci-libs/camd:0=
 	sci-libs/cholmod:0=
 	sci-libs/fftw:3.0=
 	sci-libs/openlibm:0=
 	sci-libs/spqr:0=
 	sci-libs/umfpack:0=
 	sci-mathematics/glpk:0=
-	>=sys-devel/llvm-3.3
+	=sys-devel/llvm-3.3*
 	>=sys-libs/libunwind-1.1:7=
 	sys-libs/readline:0=
 	sys-libs/zlib:0=
@@ -62,6 +63,7 @@ src_prepare() {
 		-e "s|/usr/include|${EPREFIX}/usr/include|" \
 		-e "s|\$(BUILD)/lib|\$(BUILD)/$(get_libdir)|" \
 		-e "s|^JULIA_COMMIT = .*|JULIA_COMMIT = v${PV}|" \
+		-e '/MARCH = /d' \
 		Make.inc || die
 
 	sed -i \
@@ -103,17 +105,17 @@ src_configure() {
 		USE_SYSTEM_ZLIB=1
 		VERBOSE=1
 	EOF
-}
-
-src_compile() {
-	emake cleanall
+	emake -j1 cleanall
 	if [[ $(get_libdir) != lib ]]; then
 		mkdir -p usr/$(get_libdir) || die
 		ln -s $(get_libdir) usr/lib || die
 	fi
-	emake julia-release
+}
+
+src_compile() {
+	emake -j1 julia-release
 	pax-mark m $(file usr/bin/julia-* | awk -F : '/ELF/ {print $1}')
-	emake
+	emake -j1
 	use doc && emake -C doc html
 	use emacs && elisp-compile contrib/julia-mode.el
 }
@@ -123,7 +125,7 @@ src_test() {
 }
 
 src_install() {
-	emake install PREFIX="${D}/usr"
+	emake install PREFIX="${ED}/usr"
 	cat > 99julia <<-EOF
 		LDPATH=${EROOT%/}/usr/$(get_libdir)/julia
 	EOF
diff --git a/dev-python/ffc/ChangeLog b/dev-python/ffc/ChangeLog
index dfc0baf0b..37662b34f 100644
--- a/dev-python/ffc/ChangeLog
+++ b/dev-python/ffc/ChangeLog
@@ -1,7 +1,21 @@
 # ChangeLog for dev-python/ffc
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jul 2014; Andrew Reisner <andrew@reisner.co> ffc-1.3.0.ebuild:
+  fixed dependency issue
+
+*ffc-1.4.0 (16 Jul 2014)
+
+  16 Jul 2014; Andrew Reisner <andrew@reisner.co> +ffc-1.4.0.ebuild,
+  ffc-1.3.0.ebuild:
+  version bump
+
+*ffc-1.3.0 (11 Jul 2014)
+
+  11 Jul 2014; Andrew Reisner <andrew@reisner.co> +ffc-1.3.0.ebuild:
+  version bump
+
 *ffc-1.2.0 (13 Jun 2013)
 
   13 Jun 2013; Justin Lecher <jlec@gentoo.org> -ffc-0.9.4.ebuild,
@@ -13,4 +27,3 @@
   14 Dec 2010; Nico Schlömer <nico.schloemer@gmail.com> +ffc-0.9.4.ebuild,
   +metadata.xml:
   Initial import.
-
diff --git a/dev-python/ffc/Manifest b/dev-python/ffc/Manifest
index 86ef4948b..7f89f4c76 100644
--- a/dev-python/ffc/Manifest
+++ b/dev-python/ffc/Manifest
@@ -1 +1,3 @@
 DIST ffc-1.2.0.tar.gz 4457544 SHA256 ac7cca537dac4610821c9ecb0338700970d713d03a9bc176567f1979c89ed869 SHA512 fd2a54764716c03894d779c6574deaea732df8e925e9c77474b969168fa2add8c189e0e9e7e163aa67008650fd1918dd2257cc990b5ab19e65a86b95f5eaed1b WHIRLPOOL 2feeadded0a6f2b259e99632bc5999a2bc3a27fa31fac44603badaa375557a2e0224964896eaf388a0e0c921a973562bf9548d0e8fbfd6833b17561f3613c34c
+DIST ffc-1.3.0.tar.gz 261707 SHA256 f4215a210de45cbbeedd56260299c28cf9bd9502f1965e76ec2d7174cf2f3915 SHA512 72151fb37a14afcd5f9e64db4e45a5a523660497c09e37b183150194fdf62496ba804d82518f8a378f0e225be5f47db57783ab8f2917d16ef996e3a84ef09054 WHIRLPOOL 6e7876cca037737cb10e6fab966fc56c2b8efd4ae2373d006e791ee4f12efb26e71c37cf8176e2e6c8b84539c09694ebed3aa32bb41e5e2eff5a444f9725e624
+DIST ffc-1.4.0.tar.gz 366090 SHA256 3e5df8294bd2ca0243e91cbcd9f94ba584b950dccf8028f10bf4d918b80ff71c SHA512 94399bb71768b1a1628206f8d4eadcc31e1631682feb68aa42e364c1bb35d2d6d7753bc574b71b3e3ce20b68e13b8c6266dca3e38e48e68ff1c11cf84acdc101 WHIRLPOOL 29af97b03c5ceb41ed1b268904ae5194be43aeeca5a9d319f2c382b2b3d6c044c41392dd6aa703e8df792b7457763af003e1f606f1ad8bb44e58c2c6f654af4f
diff --git a/dev-python/ffc/ffc-1.3.0.ebuild b/dev-python/ffc/ffc-1.3.0.ebuild
new file mode 100644
index 000000000..d2a291810
--- /dev/null
+++ b/dev-python/ffc/ffc-1.3.0.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit distutils-r1
+
+DESCRIPTION="Compiler for multilinear forms by generating C or C++ code for the evaluation of a multilinear form"
+HOMEPAGE="https://bitbucket.org/fenics-project/ffc/"
+SRC_URI="https://bitbucket.org/fenics-project/ffc/downloads/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="
+	>=sci-mathematics/ufc-2.3.0
+	=dev-python/ufl-${PV}[${PYTHON_USEDEP}]
+	=dev-python/instant-${PV}[${PYTHON_USEDEP}]
+	=dev-python/fiat-${PV}[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	"
diff --git a/dev-python/ffc/ffc-1.4.0.ebuild b/dev-python/ffc/ffc-1.4.0.ebuild
new file mode 100644
index 000000000..9ec9a2057
--- /dev/null
+++ b/dev-python/ffc/ffc-1.4.0.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit distutils-r1
+
+DESCRIPTION="Compiler for multilinear forms by generating C or C++ code for the evaluation of a multilinear form"
+HOMEPAGE="https://bitbucket.org/fenics-project/ffc/"
+SRC_URI="https://bitbucket.org/fenics-project/ffc/downloads/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="
+	!sci-mathematics/ufc
+	=dev-python/ufl-${PV}[${PYTHON_USEDEP}]
+	=dev-python/instant-${PV}[${PYTHON_USEDEP}]
+	=dev-python/fiat-${PV}[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	"
diff --git a/dev-python/fiat/ChangeLog b/dev-python/fiat/ChangeLog
index 563d72b92..26d00d366 100644
--- a/dev-python/fiat/ChangeLog
+++ b/dev-python/fiat/ChangeLog
@@ -1,7 +1,18 @@
 # ChangeLog for dev-python/fiat
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jul 2014; Andrew Reisner <andrew@reisner.co> fiat-1.3.0.ebuild,
+  fiat-1.4.0.ebuild:
+  Added keyword
+
+*fiat-1.3.0 (15 Jul 2014)
+*fiat-1.4.0 (15 Jul 2014)
+
+  15 Jul 2014; Andrew Reisner <andrew@reisner.co> +fiat-1.3.0.ebuild,
+  +fiat-1.4.0.ebuild:
+  version bump
+
 *fiat-1.1 (13 Jun 2013)
 
   13 Jun 2013; Justin Lecher <jlec@gentoo.org> -fiat-0.9.2.ebuild,
@@ -13,4 +24,3 @@
   14 Dec 2010; Nico Schlömer <nico.schloemer@gmail.com> +fiat-0.9.2.ebuild,
   +metadata.xml:
   Initial import.
-
diff --git a/dev-python/fiat/Manifest b/dev-python/fiat/Manifest
index c25fa5a4f..4250e0328 100644
--- a/dev-python/fiat/Manifest
+++ b/dev-python/fiat/Manifest
@@ -1 +1,3 @@
 DIST fiat-1.1.tar.gz 3870562 SHA256 94a9926f478ce9d12e3f0cf4dee0937dfbc7518a37ad4ac701fda3b6cb62a475 SHA512 9f65e1be1d19102fb099ec1ece587f70c04c0567c316e4fb1bcf24c93c104499b6e1baa118527b2e4c942765ea2164f7243dabac2bc0267991a23edc959d14e0 WHIRLPOOL 8e3fecb6a1fdc0441105964e7e9d78ef8c0f0375a7c02eb87e0da9e7abc509e42ca468036655eb157929d20c23e9dc08695240e21267331b53d7fc3675b7036f
+DIST fiat-1.3.0.tar.gz 56774 SHA256 748e5d35821d51e90cdc75dd65d5df3629b7acffec18f65c813064f320e35ba0 SHA512 6b702af7fde06c1442a233e643b4883dab42c4994e76cf4834408b62a2313f971d9650cf377f9074a704fd4e32f66d03a7bf487f656f8cce3a95ca75bd461b55 WHIRLPOOL 2c59ecf16f38be156bb1306626a6a83334d44898963e9816b0792e49ef1831b7ff39a84cc130c5b88a3203d76209d353b7ff64263e1d1df7702c5561ffebe203
+DIST fiat-1.4.0.tar.gz 57087 SHA256 ddd66bfa1a0b30ab1abb12c77f8af66f506fd99bdbf966675281a6b7143bb631 SHA512 4566d2b5b74fbf6fb5ea640a0c86b33009f29e818cbf6d6f19e96b413220bb3ad29ade1ed3739cf2eb4d97caa603ceaafcc77fccff06c5cef7070e87eac37467 WHIRLPOOL d736a1ec25ea2b90198660dfc154c84ec6c0133cedf8e303e56ee57674d20216a5fb2731102a9a030db1aeb03ac2375db304439c6526358ed44712677d511766
diff --git a/dev-python/fiat/fiat-1.3.0.ebuild b/dev-python/fiat/fiat-1.3.0.ebuild
new file mode 100644
index 000000000..3db5363e6
--- /dev/null
+++ b/dev-python/fiat/fiat-1.3.0.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit distutils-r1
+
+DESCRIPTION="Generation of arbitrary order instances of the Lagrange elements on lines, triangles, and tetrahedra"
+HOMEPAGE="https://bitbucket.org/fenics-project/fiat"
+SRC_URI="https://bitbucket.org/fenics-project/fiat/downloads/${P}.tar.gz"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="
+	dev-python/scientificpython[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	"
diff --git a/dev-python/fiat/fiat-1.4.0.ebuild b/dev-python/fiat/fiat-1.4.0.ebuild
new file mode 100644
index 000000000..3db5363e6
--- /dev/null
+++ b/dev-python/fiat/fiat-1.4.0.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit distutils-r1
+
+DESCRIPTION="Generation of arbitrary order instances of the Lagrange elements on lines, triangles, and tetrahedra"
+HOMEPAGE="https://bitbucket.org/fenics-project/fiat"
+SRC_URI="https://bitbucket.org/fenics-project/fiat/downloads/${P}.tar.gz"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="
+	dev-python/scientificpython[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	"
diff --git a/dev-python/instant/ChangeLog b/dev-python/instant/ChangeLog
index 99e1f9e88..af28b7f08 100644
--- a/dev-python/instant/ChangeLog
+++ b/dev-python/instant/ChangeLog
@@ -1,7 +1,14 @@
 # ChangeLog for dev-python/instant
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*instant-1.3.0 (16 Jul 2014)
+*instant-1.4.0 (16 Jul 2014)
+
+  16 Jul 2014; Andrew Reisner <andrew@reisner.co> +instant-1.3.0.ebuild,
+  +instant-1.4.0.ebuild:
+  version bump
+
 *instant-1.2.0 (14 Jun 2013)
 
   14 Jun 2013; Justin Lecher <jlec@gentoo.org> -instant-0.9.8.ebuild,
@@ -13,4 +20,3 @@
   14 Dec 2010; Nico Schlömer <nico.schloemer@gmail.com>
   +instant-0.9.8.ebuild, +metadata.xml:
   Initial import.
-
diff --git a/dev-python/instant/Manifest b/dev-python/instant/Manifest
index 45b695258..1e1f1d06b 100644
--- a/dev-python/instant/Manifest
+++ b/dev-python/instant/Manifest
@@ -1 +1,3 @@
 DIST instant-1.2.0.tar.gz 125833 SHA256 12507f90b75f7ac4e222b2b5048212fa849e650b8dae94534a88ef2fe8378618 SHA512 574f2e56ea14e19928d53f46b781d2e77fd11dd1bb3c84e38466977999b03028a9780f1f3888084484feef2fe42e40b7a500eeb35af360034247fcfe019b86eb WHIRLPOOL 361a72e97c5c9fc7bf1dae49abe6cea1cabc53a97dada83a499ec042452b2ca550528af359071b5ffa39778c1abecd1b25e70d8d69c171301289ac610695c292
+DIST instant-1.3.0.tar.gz 133954 SHA256 4a71d86f15dccf08c05edac7fb0e41daafdcb2e0e330134264284a788b5eecd6 SHA512 2d51f1ccf18902e25d6ee71cc219c2fd44c47202c2c7a1d5a39b220beec4d497a5cd7d8e5f09a3b7db8e72965c369bffa99ab8a22d8675efa5805b0d3b80b96a WHIRLPOOL f4e30709ca086e9742a6cccf8e8575b64238895de33a30bb3ffa10cc177cc4235c9f7864e8f8ed9aef028960855cf663dca432e90c9132c425459a358eaa684a
+DIST instant-1.4.0.tar.gz 147300 SHA256 722f1d91b92ea768f91cd7e4b9ab322e72afc57a7d440564d8b8ae0d1bc27b4e SHA512 80144935f6810d1b20b0b2539f2931ff0e5f6fbdd38b2356eb2d1012bcf28291616564766e9066b748de132e2c100db0788c6f1866a59964d6380fa8380595b8 WHIRLPOOL 09152d19e7aa2fb989f5393fbf1ef4ddcfb77f3e646efe84d4c5701b45a9729c348eb1769104658b2b811f609bee521d4cbb8dfce8ce3ec58da058d37df7c260
diff --git a/dev-python/instant/instant-1.3.0.ebuild b/dev-python/instant/instant-1.3.0.ebuild
new file mode 100644
index 000000000..ffa211a96
--- /dev/null
+++ b/dev-python/instant/instant-1.3.0.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit distutils-r1
+
+DESCRIPTION="Instant inlining of C and C++ code in Python"
+HOMEPAGE="https://bitbucket.org/fenics-project/instant/"
+SRC_URI="https://bitbucket.org/fenics-project/instant/downloads/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="dev-lang/swig"
+RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
diff --git a/dev-python/instant/instant-1.4.0.ebuild b/dev-python/instant/instant-1.4.0.ebuild
new file mode 100644
index 000000000..ffa211a96
--- /dev/null
+++ b/dev-python/instant/instant-1.4.0.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit distutils-r1
+
+DESCRIPTION="Instant inlining of C and C++ code in Python"
+HOMEPAGE="https://bitbucket.org/fenics-project/instant/"
+SRC_URI="https://bitbucket.org/fenics-project/instant/downloads/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="dev-lang/swig"
+RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
diff --git a/dev-python/ufl/ChangeLog b/dev-python/ufl/ChangeLog
index c3982410c..135766527 100644
--- a/dev-python/ufl/ChangeLog
+++ b/dev-python/ufl/ChangeLog
@@ -1,7 +1,14 @@
 # ChangeLog for dev-python/ufl
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*ufl-1.3.0 (16 Jul 2014)
+*ufl-1.4.0 (16 Jul 2014)
+
+  16 Jul 2014; Andrew Reisner <andrew@reisner.co> +ufl-1.3.0.ebuild,
+  +ufl-1.4.0.ebuild, metadata.xml:
+  version bump
+
   14 Jun 2013; Justin Lecher <jlec@gentoo.org> ufl-0.5.4.ebuild, metadata.xml:
   Bump to EAPI=5 and distutils-r1.eclass
 
@@ -10,4 +17,3 @@
   14 Dec 2010; Nico Schlömer <nico.schloemer@gmail.com> +ufl-0.5.4.ebuild,
   +metadata.xml:
   Initial import.
-
diff --git a/dev-python/ufl/Manifest b/dev-python/ufl/Manifest
index d75038156..2f93484dd 100644
--- a/dev-python/ufl/Manifest
+++ b/dev-python/ufl/Manifest
@@ -1 +1,3 @@
-DIST ufl-0.5.4.tar.gz 204883 SHA256 fc032d7a011406764ca3c466d194cfcf7ba165292e1a9da471cde7519ce1a960
+DIST ufl-0.5.4.tar.gz 204883 SHA256 fc032d7a011406764ca3c466d194cfcf7ba165292e1a9da471cde7519ce1a960 SHA512 0ff901fb1c72b0df85d96bb7dbdecbf135939be735ea76c8fa15f33f639db5e0ab17561caecd4bde05d408b85e7747353775f1d602a47198eecba6c5cd99859c WHIRLPOOL 2fa9f536a561453e71d204eeea261066426ed4322d2d0c740cd48a33c7d4362aedc973cc1230e41f2553511e2a26dea621316aa4ac729fadf0406f4eae574350
+DIST ufl-1.3.0.tar.gz 266056 SHA256 8d860585932ac5f0eab5d8c187418dcfe9d9539da9399657bada1453df9c10df SHA512 e6af72736d7142549e72c1fb6cbaa802adafc10134c550ecec02cd20c717f58f5399ae8ccc8cd573e66d4c2e2af2e3a52ac42a93ef449d175d3556625a7f3859 WHIRLPOOL b9cf1074f860534fb9c39fb3ae76ddb8c4579a45e033753b2c7a4a1fb10fd46f894c489603ddd691876a78334f308aac893789870f97bf7a152988787ce21596
+DIST ufl-1.4.0.tar.gz 294109 SHA256 6b26b220cd72f62b582260dcf3d08feffeb9db0664cd4f5345dc2a0727e8dbc9 SHA512 b2d41f58d3ad3493f7714a9944a3a9bdee7f6530e20cdde2d3f4610e81667f4181da172c01afcd46eca8afbc43c84fc214b76e4895253cd2572594a6e7398d2b WHIRLPOOL 61a27a90e6fc29e690c8afdb2628a849db377a673964b07397e341363008feebeae5a033919261767590d369341fccb17b362a7e5bdb53189ee94440894ff404
diff --git a/dev-python/ufl/metadata.xml b/dev-python/ufl/metadata.xml
index f430bd641..c1c80201a 100644
--- a/dev-python/ufl/metadata.xml
+++ b/dev-python/ufl/metadata.xml
@@ -9,4 +9,7 @@
 		spaces and defining expressions for weak forms in a notation close to
 		mathematical notation.
 	</longdescription>
+	<use>
+		<flag name="scipy">Adds support for evaluating Bessel functions using <pkg>dev-python/scipy</pkg></flag>
+	</use>
 </pkgmetadata>
diff --git a/dev-python/ufl/ufl-1.3.0.ebuild b/dev-python/ufl/ufl-1.3.0.ebuild
new file mode 100644
index 000000000..622187c56
--- /dev/null
+++ b/dev-python/ufl/ufl-1.3.0.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit distutils-r1
+
+DESCRIPTION="Domain specific language for declaration of FE discretizations of variational forms"
+HOMEPAGE="https://bitbucket.org/fenics-project/ufl/"
+SRC_URI="https://bitbucket.org/fenics-project/ufl/downloads/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="scipy"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	scipy? ( sci-libs/scipy[${PYTHON_USEDEP}] )
+	"
diff --git a/dev-python/ufl/ufl-1.4.0.ebuild b/dev-python/ufl/ufl-1.4.0.ebuild
new file mode 100644
index 000000000..622187c56
--- /dev/null
+++ b/dev-python/ufl/ufl-1.4.0.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit distutils-r1
+
+DESCRIPTION="Domain specific language for declaration of FE discretizations of variational forms"
+HOMEPAGE="https://bitbucket.org/fenics-project/ufl/"
+SRC_URI="https://bitbucket.org/fenics-project/ufl/downloads/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="scipy"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	scipy? ( sci-libs/scipy[${PYTHON_USEDEP}] )
+	"
diff --git a/dev-util/nvidia-cuda-sdk/ChangeLog b/dev-util/nvidia-cuda-sdk/ChangeLog
new file mode 100644
index 000000000..e5fbe110c
--- /dev/null
+++ b/dev-util/nvidia-cuda-sdk/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for dev-util/nvidia-cuda-sdk
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*nvidia-cuda-sdk-6.5.11 (10 Jul 2014)
+
+  10 Jul 2014; Marius Brehler <marbre@linux.sungazer.de> +metadata.xml,
+  +nvidia-cuda-sdk-6.5.11.ebuild:
+  dev-util/nvidia-cuda-sdk: add version 6.5.11
diff --git a/dev-util/nvidia-cuda-sdk/Manifest b/dev-util/nvidia-cuda-sdk/Manifest
new file mode 100644
index 000000000..cbb8327ea
--- /dev/null
+++ b/dev-util/nvidia-cuda-sdk/Manifest
@@ -0,0 +1 @@
+DIST cuda_6.5.11_rc_linux_64.run 965707668 SHA256 1e8bd68a8eceff880ff631cbf6fdba06696a76933663f77b4a6f71522d732ac7 SHA512 7c5b344c5e8a808f052592753415c2fedb9b45b2bc83fa400b9a6f14eeb1e4308712c3fb1d25e3df72d014b645aa803670e528fd6fd758b2c48d94adc9963fc0 WHIRLPOOL 57085612e0cca66a3436352f8ff4af9fb584e37bf357ba23fc821048fb86dce51bf00a513e28dec06a9a0005bc3ef620f2fa366b895cc096142463fddba05dcf
diff --git a/dev-util/nvidia-cuda-sdk/metadata.xml b/dev-util/nvidia-cuda-sdk/metadata.xml
new file mode 100644
index 000000000..8bd8dab6f
--- /dev/null
+++ b/dev-util/nvidia-cuda-sdk/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci</herd>
+  <use>
+    <flag name="opencl">
+			Build OpenCL binaries.
+		</flag>
+    <flag name="cuda">
+			Build CUDA binaries.
+		</flag>
+  </use>
+</pkgmetadata>
diff --git a/dev-util/nvidia-cuda-sdk/nvidia-cuda-sdk-6.5.11.ebuild b/dev-util/nvidia-cuda-sdk/nvidia-cuda-sdk-6.5.11.ebuild
new file mode 100644
index 000000000..4e76354b9
--- /dev/null
+++ b/dev-util/nvidia-cuda-sdk/nvidia-cuda-sdk-6.5.11.ebuild
@@ -0,0 +1,151 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit cuda eutils flag-o-matic portability toolchain-funcs unpacker versionator
+
+MYD=$(get_version_component_range 1)_$(get_version_component_range 2)
+
+DESCRIPTION="NVIDIA CUDA Software Development Kit"
+HOMEPAGE="http://developer.nvidia.com/cuda"
+CURI="https://developer.nvidia.com/rdp/cuda-65-rc-toolkit-download"
+SRC_URI="amd64? ( cuda_${PV}_rc_linux_64.run )"
+
+LICENSE="CUDPP"
+SLOT="0"
+KEYWORDS="~amd64 ~amd64-linux"
+#IUSE="debug +doc +examples opencl +cuda"
+IUSE="debug +examples opencl +cuda"
+
+RDEPEND="
+	~dev-util/nvidia-cuda-toolkit-${PV}
+	media-libs/freeglut
+	examples? (
+		media-libs/freeimage
+		media-libs/glew
+		virtual/mpi
+		>=x11-drivers/nvidia-drivers-340.21[uvm]
+		)"
+DEPEND="${RDEPEND}"
+
+RESTRICT="test fetch"
+
+pkg_nofetch() {
+	einfo "Please download"
+	einfo "  - cuda_${P}_rc_linux64.run"
+	einfo "from ${CURI} and place it in ${DISTDIR}"
+}
+
+S=${WORKDIR}/cuda-samples
+
+QA_EXECSTACK=(
+	opt/cuda/sdk/0_Simple/cdpSimplePrint/cdpSimplePrint
+	opt/cuda/sdk/0_Simple/cdpSimpleQuicksort/cdpSimpleQuicksort
+	opt/cuda/sdk/bin/x86_64/linux/release/cdpSimplePrint
+	opt/cuda/sdk/bin/x86_64/linux/release/cdpSimpleQuicksort
+	)
+
+src_unpack() {
+	unpacker
+	unpacker run_files/cuda-samples*run
+}
+
+pkg_setup() {
+	if use cuda || use opencl; then
+		cuda_pkg_setup
+	fi
+}
+
+src_prepare() {
+	export RAWLDFLAGS="$(raw-ldflags)"
+
+	sed \
+		-e 's:-O2::g' \
+		-e 's:-O3::g' \
+		-e "/LINK/s:gcc:$(tc-getCC) ${LDFLAGS}:g" \
+		-e "/LINK/s:g++:$(tc-getCXX) ${LDFLAGS}:g" \
+		-e "/CC/s:gcc:$(tc-getCC):g" \
+		-e "/GCC/s:g++:$(tc-getCXX):g" \
+		-e "/ CFLAGS/s|\(:=\)|\1 ${CFLAGS}|g" \
+		-e "/ CXXFLAGS/s|\(:=\)|\1 ${CXXFLAGS}|g" \
+		-e "/NVCCFLAGS/s|\(:=\)|\1 ${NVCCFLAGS} |g" \
+		-e 's:-Wimplicit::g' \
+		-e "s|../../common/lib/linux/\$(OS_ARCH)/libGLEW.a|$(pkg-config --libs glew)|g" \
+		-e "s|../../common/lib/\$(OSLOWER)/libGLEW.a|$(pkg-config --libs glew)|g" \
+		-e "s|../../common/lib/\$(OSLOWER)/\$(OS_ARCH)/libGLEW.a|$(pkg-config --libs glew)|g" \
+		-i $(find . -type f -name "Makefile") || die
+
+#		-e "/ALL_LDFLAGS/s|:=|:= ${RAWLDFLAGS} |g" \
+	find common/inc/GL -delete || die
+	find . -type f -name "*\.a" -delete || die
+}
+
+src_compile() {
+	use examples || return
+	local myopts verbose="verbose=1"
+	use debug && myopts+=" dbg=1"
+	export FAKEROOTKEY=1 # Workaround sandbox issue in #462602
+	emake \
+		cuda-install="${EPREFIX}/opt/cuda" \
+		CUDA_PATH="${EPREFIX}/opt/cuda/" \
+		MPI_GCC=10 \
+		${myopts} ${verbose}
+}
+
+src_test() {
+	local _dir _subdir
+
+	addwrite /dev/nvidiactl
+	addwrite /dev/nvidia0
+
+	for _dir in {0..9}*; do
+		pushd ${_dir} > /dev/null
+		for _subdir in *; do
+			emake -C ${_subdir} run
+		done
+		popd > /dev/null
+	done
+}
+
+src_install() {
+	local i j f t crap=""
+	#if use doc; then
+	#	ebegin "Installing docs ..."
+	#		dodoc -r doc
+	#		dodoc *.txt */*.pdf
+	#		treecopy $(find -type f -name readme.txt) "${ED}"/usr/share/doc/${PF}/
+	#	eend
+	#fi
+
+	crap+=" *.txt doc Samples.htm* */*.pdf"
+
+	ebegin "Cleaning before installation..."
+		for i in ${crap}; do
+			if [[ -e ${i} ]]; then
+				find ${i} -delete || die
+			fi
+		done
+		find -type f -name "*.o" -delete
+		find -type f -name "readme.txt" -delete
+	eend
+
+	ebegin "Moving files..."
+		for f in $(find .); do
+			local t="$(dirname ${f})"
+			if [[ ${t/obj\/} != ${t} || ${t##*.} == a ]]; then
+				continue
+			fi
+			if [[ ! -d ${f} ]]; then
+				if [[ -x ${f} ]]; then
+					exeinto /opt/cuda/sdk/${t}
+					doexe ${f}
+				else
+					insinto /opt/cuda/sdk/${t}
+					doins ${f}
+				fi
+			fi
+	done
+	eend
+}
diff --git a/dev-util/nvidia-cuda-toolkit/ChangeLog b/dev-util/nvidia-cuda-toolkit/ChangeLog
new file mode 100644
index 000000000..d8307ea3a
--- /dev/null
+++ b/dev-util/nvidia-cuda-toolkit/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for dev-util/nvidia-cuda-toolkit
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*nvidia-cuda-toolkit-6.5.11 (10 Jul 2014)
+
+  10 Jul 2014; Marius Brehler <marbre@linux.sungazer.de> +files/cuda-config.in,
+  +metadata.xml, +nvidia-cuda-toolkit-6.5.11.ebuild:
+  dev-util/nvidia-cuda-toolkit: dev-util/nvidia-cuda-toolkit: add version 6.5.11
diff --git a/dev-util/nvidia-cuda-toolkit/Manifest b/dev-util/nvidia-cuda-toolkit/Manifest
new file mode 100644
index 000000000..a3c502527
--- /dev/null
+++ b/dev-util/nvidia-cuda-toolkit/Manifest
@@ -0,0 +1,2 @@
+DIST cuda_6.5.11_rc_linux_32.run 76815336 SHA256 18b4d786cf78258ea0177cd77a33058f81a5f334a99cf342400575247559ed72 SHA512 7e7ab02d9baae10b9115720a58829a267719ba27785d04ec2eb0b5711d158bc174d5c5d300e2e8a5f7cfe9b19f5d0ba798e89f61bf6e48c5ec0c4c12ac02ad97 WHIRLPOOL 151c5bb6f5ccf57a30097af4912fa6e53732bf63eb7a409d850f0133bc7a3ee291347514edcc9fc8221dd712343031c4226e79327e3f42f0442b707d2163dd4f
+DIST cuda_6.5.11_rc_linux_64.run 965707668 SHA256 1e8bd68a8eceff880ff631cbf6fdba06696a76933663f77b4a6f71522d732ac7 SHA512 7c5b344c5e8a808f052592753415c2fedb9b45b2bc83fa400b9a6f14eeb1e4308712c3fb1d25e3df72d014b645aa803670e528fd6fd758b2c48d94adc9963fc0 WHIRLPOOL 57085612e0cca66a3436352f8ff4af9fb584e37bf357ba23fc821048fb86dce51bf00a513e28dec06a9a0005bc3ef620f2fa366b895cc096142463fddba05dcf
diff --git a/dev-util/nvidia-cuda-toolkit/files/cuda-config.in b/dev-util/nvidia-cuda-toolkit/files/cuda-config.in
new file mode 100644
index 000000000..ca0d1d77e
--- /dev/null
+++ b/dev-util/nvidia-cuda-toolkit/files/cuda-config.in
@@ -0,0 +1,28 @@
+#!/bin/bash
+
+SUPPORT_GCC_VERSIONS_BY_CUDA="CUDA_SUPPORTED_GCC"
+
+_print_help() {
+	cat <<- EOF
+	Usage:
+		$(basename $0) [options]
+	
+		-s | --supported   Returns by current CUDA supported gcc versions
+		-h | --help        Shows this help
+	EOF
+}
+
+case ${1} in
+	-s|--supported)
+		echo "${SUPPORT_GCC_VERSIONS_BY_CUDA}"
+		exit 0
+		;;
+	-h|--help)
+		_print_help
+		exit -1
+		;;
+	*)
+		_print_help
+		exit 1
+		;;
+esac
diff --git a/dev-util/nvidia-cuda-toolkit/metadata.xml b/dev-util/nvidia-cuda-toolkit/metadata.xml
new file mode 100644
index 000000000..e099ba557
--- /dev/null
+++ b/dev-util/nvidia-cuda-toolkit/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci</herd>
+  <use>
+    <flag name="profiler">
+			Installs the NVIDIA CUDA visual profiler.
+		</flag>
+    <flag name="debugger">
+			Installs the CUDA debugger.
+		</flag>
+    <flag name="eclipse">Install the <pkg>dev-util/eclipse-sdk</pkg> plugins</flag>
+  </use>
+</pkgmetadata>
diff --git a/dev-util/nvidia-cuda-toolkit/nvidia-cuda-toolkit-6.5.11.ebuild b/dev-util/nvidia-cuda-toolkit/nvidia-cuda-toolkit-6.5.11.ebuild
new file mode 100644
index 000000000..494ee097d
--- /dev/null
+++ b/dev-util/nvidia-cuda-toolkit/nvidia-cuda-toolkit-6.5.11.ebuild
@@ -0,0 +1,152 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit check-reqs cuda unpacker versionator
+
+MYD=$(get_version_component_range 1)_$(get_version_component_range 2)
+
+DESCRIPTION="NVIDIA CUDA Toolkit (compiler and friends)"
+HOMEPAGE="http://developer.nvidia.com/cuda"
+CURI="https://developer.nvidia.com/rdp/cuda-65-rc-toolkit-download"
+SRC_URI="
+	amd64? ( cuda_${PV}_rc_linux_64.run )
+	x86? ( cuda_${PV}_rc_linux_32.run )"
+
+SLOT="0/${PV}"
+LICENSE="NVIDIA-CUDA"
+KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="debugger doc eclipse profiler"
+
+DEPEND=""
+RDEPEND="${DEPEND}
+	<sys-devel/gcc-4.9[cxx]
+	>=x11-drivers/nvidia-drivers-340.24[uvm]
+	debugger? (
+		sys-libs/libtermcap-compat
+		sys-libs/ncurses[tinfo]
+		)
+	eclipse? ( >=virtual/jre-1.6 )
+	profiler? ( >=virtual/jre-1.6 )"
+
+RESTRICT="fetch"
+
+pkg_nofetch() {
+	einfo "Please download"
+	einfo "  - cuda_${P}_rc_linux64.run  or"
+	einfo "  - cuda_${P}_rc_linux32.run"
+	einfo "from ${CURI} and place it in ${DISTDIR}"
+}
+
+S="${WORKDIR}"
+
+QA_PREBUILT="opt/cuda/*"
+
+CHECKREQS_DISK_BUILD="1500M"
+
+pkg_setup() {
+	# We don't like to run cuda_pkg_setup as it depends on us
+	check-reqs_pkg_setup
+}
+
+src_unpack() {
+	unpacker
+	unpacker run_files/cuda-linux*.run
+}
+
+src_prepare() {
+	local cuda_supported_gcc
+
+	cuda_supported_gcc="4.8"
+
+	sed \
+		-e "s:CUDA_SUPPORTED_GCC:${cuda_supported_gcc}:g" \
+		"${FILESDIR}"/cuda-config.in > "${T}"/cuda-config || die
+}
+
+src_install() {
+	local i j
+	local remove="doc jre run_files install-linux.pl "
+	local cudadir=/opt/cuda
+	local ecudadir="${EPREFIX}"${cudadir}
+
+	# dodoc doc/*txt
+	if use doc; then
+		dodoc doc/pdf/*
+		dohtml -r doc/html/*
+	fi
+
+	mv doc/man/man3/{,cuda-}deprecated.3 || die
+	doman doc/man/man*/*
+
+	use debugger || remove+=" bin/cuda-gdb extras/Debugger"
+	( use profiler || use eclipse ) || remove+=" libnsight"
+	use amd64 || remove+=" cuda-installer.pl"
+
+	if use profiler; then
+		# hack found in install-linux.pl
+		for j in nvvp nsight; do
+			cat > bin/${j} <<- EOF
+				#!${EPREFIX}/bin/sh
+				LD_LIBRARY_PATH=\${LD_LIBRARY_PATH}:${ecudadir}/lib:${ecudadir}/lib64 \
+					UBUNTU_MENUPROXY=0 LIBOVERLAY_SCROLLBAR=0 \
+					${ecudadir}/lib${j}/${j} -vm ${EPREFIX}/usr/bin/java
+			EOF
+			chmod a+x bin/${j}
+		done
+	else
+		use eclipse || remove+=" libnvvp"
+		remove+=" extras/CUPTI"
+	fi
+
+	for i in ${remove}; do
+	ebegin "Cleaning ${i}..."
+		if [[ -e ${i} ]]; then
+			find ${i} -delete || die
+			eend
+		else
+			eend $1
+		fi
+	done
+
+	dodir ${cudadir}
+	mv * "${ED}"${cudadir}
+
+	cat > "${T}"/99cuda <<- EOF
+		PATH=${ecudadir}/bin:${ecudadir}/libnvvp
+		ROOTPATH=${ecudadir}/bin
+		LDPATH=${ecudadir}/lib$(use amd64 && echo "64:${ecudadir}/lib")
+	EOF
+	doenvd "${T}"/99cuda
+
+	make_wrapper nvprof "${EPREFIX}"${cudadir}/bin/nvprof "." ${ecudadir}/lib$(use amd64 && echo "64:${ecudadir}/lib")
+
+	dobin "${T}"/cuda-config
+}
+
+pkg_postinst_check() {
+	local a b
+	a="$(version_sort $(cuda-config -s))"; a=( $a )
+	# greatest supported version
+	b=${a[${#a[@]}-1]}
+
+	# if gcc and if not gcc-version is at least greatesst supported
+	if [[ $(tc-getCC) == *gcc* ]] && \
+		! version_is_at_least $(gcc-version) ${b}; then
+			echo
+			ewarn "gcc >= ${b} will not work with CUDA"
+			ewarn "Make sure you set an earlier version of gcc with gcc-config"
+			ewarn "or append --compiler-bindir= pointing to a gcc bindir like"
+			ewarn "--compiler-bindir=${EPREFIX}/usr/*pc-linux-gnu/gcc-bin/gcc${b}"
+			ewarn "to the nvcc compiler flags"
+			echo
+	fi
+}
+
+pkg_postinst() {
+	if [[ ${MERGE_TYPE} != binary ]]; then
+		pkg_postinst_check
+	fi
+}
diff --git a/sci-biology/Atlas-Link/Atlas-Link-0.01.ebuild b/sci-biology/Atlas-Link/Atlas-Link-0.01.ebuild
new file mode 100644
index 000000000..bb15e64d1
--- /dev/null
+++ b/sci-biology/Atlas-Link/Atlas-Link-0.01.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit perl-module
+
+DESCRIPTION="Links and orients genome sequence contigs using mate-pair information or superscaffolds .agp files"
+HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas-link"
+SRC_URI="https://www.hgsc.bcm.edu/sites/default/files/software/Atlas_Link/Atlas-link.tar.gz"
+
+LICENSE="HGSC-BCM"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+# https://github.com/gitpan/Algorithm-ClusterPoints
+DEPEND="dev-lang/perl
+	dev-perl/Graph
+	dev-perl/Algorithm-ClusterPoints
+	dev-perl/XML-DOM
+	dev-perl/Statistics-Descriptive"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/Atlas-link
diff --git a/sci-biology/Atlas-Link/ChangeLog b/sci-biology/Atlas-Link/ChangeLog
new file mode 100644
index 000000000..cb92c11d8
--- /dev/null
+++ b/sci-biology/Atlas-Link/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/Atlas-Link
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*Atlas-Link-0.01 (04 Jul 2014)
+
+  04 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +Atlas-Link-0.01.ebuild, +metadata.xml:
+  sci-biology/Atlas-Link: noted dependence, see bug #516366
+
diff --git a/sci-biology/Atlas-Link/Manifest b/sci-biology/Atlas-Link/Manifest
new file mode 100644
index 000000000..205302da8
--- /dev/null
+++ b/sci-biology/Atlas-Link/Manifest
@@ -0,0 +1 @@
+DIST Atlas-link.tar.gz 4212464 SHA256 5857beb6c8560c85b1271e12d28b00e4b93684357dfd2b49f61bfb78437046eb SHA512 ac3595ca81034de2eb2b4dc206e6e29c59fbb4fededfd2dee3b597ce47bc436907587fc59ac753d81c4ca0fc627e0a9961ebebd7bfcc002df634466c17fd2bce WHIRLPOOL 6788603eb7fd240c09de3f78a7b45a1d1494748ce006252905d469a36f27cc36f9fdc9c466a11ad6f02b92e208273ec95c12030eb1955d236c4685768392f0cc
diff --git a/sci-biology/Atlas-Link/metadata.xml b/sci-biology/Atlas-Link/metadata.xml
new file mode 100644
index 000000000..2bc893037
--- /dev/null
+++ b/sci-biology/Atlas-Link/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/MaSuRCA/MaSuRCA-2.1.0.ebuild b/sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild
index 28934c3b1..5b8f9fbcc 100644
--- a/sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild
+++ b/sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild
@@ -16,7 +16,8 @@ IUSE=""
 
 DEPEND="dev-lang/perl
 		app-arch/bzip2"
-RDEPEND="${DEPEND}"
+RDEPEND="${DEPEND}
+	sci-biology/quorum"
 
 # the ebuild mimics "${S}"/install.sh
 src_configure(){
diff --git a/sci-biology/caftools/ChangeLog b/sci-biology/caftools/ChangeLog
index af2ad47b4..12f9e49f7 100644
--- a/sci-biology/caftools/ChangeLog
+++ b/sci-biology/caftools/ChangeLog
@@ -1,8 +1,11 @@
 # ChangeLog for sci-biology/caftools
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  04 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  caftools-2.0.2.ebuild:
+  sci-biology/caftools: clarified package description
+
   16 Jun 2013; Justin Lecher <jlec@gentoo.org> -caftools-2.0.ebuild,
   caftools-2.0.2.ebuild, metadata.xml:
   Drop old; Bump to EAPI=5 and fix license
-
diff --git a/sci-biology/caftools/caftools-2.0.2.ebuild b/sci-biology/caftools/caftools-2.0.2.ebuild
index 4750f157e..07c11852a 100644
--- a/sci-biology/caftools/caftools-2.0.2.ebuild
+++ b/sci-biology/caftools/caftools-2.0.2.ebuild
@@ -6,7 +6,7 @@ EAPI=5
 
 inherit eutils
 
-DESCRIPTION="CAF is a text format for describing sequence assemblies"
+DESCRIPTION="Manipulate CAF files and convert to GAP4 format (not GAP5), ACE, PHRAP"
 HOMEPAGE="http://www.sanger.ac.uk/resources/software/caf/"
 SRC_URI="
 	ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${P}.tar.gz
diff --git a/sci-biology/clview/ChangeLog b/sci-biology/clview/ChangeLog
new file mode 100644
index 000000000..4df0dcfae
--- /dev/null
+++ b/sci-biology/clview/ChangeLog
@@ -0,0 +1,6 @@
+# ChangeLog for sci-biology/clview
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  04 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> clview-0.1.ebuild:
+  sci-biology/clview: add dependency on =x11-libs/fox-1.6*
diff --git a/sci-biology/clview/Manifest b/sci-biology/clview/Manifest
index cbc77e542..fcf090f45 100644
--- a/sci-biology/clview/Manifest
+++ b/sci-biology/clview/Manifest
@@ -1,2 +1,2 @@
-DIST clview_linux_i386.tar.gz 1050318 SHA256 0ee2f0688afcf649b448662e792e5d44378e9d84d2141ecd3ad8c8d5c6a400e4
-DIST clview_src.tar.gz 62178 SHA256 52936fddb0284b1cf2515b4e57e01ee9ec2a58dab329e49204d70528c75d5bf2
+DIST clview_linux_i386.tar.gz 1050318 SHA256 0ee2f0688afcf649b448662e792e5d44378e9d84d2141ecd3ad8c8d5c6a400e4 SHA512 2fbd5ed5ef7bb96a715537a1b1d8f0957e5733d2603aacc5a0dba5a5002a27483ca57dd53780204a98d5ce05ac1090e3d04a3b2784cec021f0afc545e98b35b1 WHIRLPOOL a0927f8a54e019f9ea8c1104629bfed624811cc2423b277d22c56b2047a7a579d7a0413d0a6d203bd4c2fe626e47777853564c907f735418365da6cd7252e2a4
+DIST clview_src.tar.gz 62178 SHA256 52936fddb0284b1cf2515b4e57e01ee9ec2a58dab329e49204d70528c75d5bf2 SHA512 24c115b76041981d6dba731180485108d92cccc4719fe6982a135d73c3d18deed2e89ebb6d7daeb8d79941084ec912be2c3333369ec0bf403f96a156932909b9 WHIRLPOOL e59c56be971e90d7598cbb178693906b4303140e9bbe5192199aa1cb20b8030bc971dbb3b3c45f5660b2bba1b0327f012cd8d7db1c817be6dfa001bed081b556
diff --git a/sci-biology/clview/clview-0.1.ebuild b/sci-biology/clview/clview-0.1.ebuild
index 906d2d10b..dd43fdf65 100644
--- a/sci-biology/clview/clview-0.1.ebuild
+++ b/sci-biology/clview/clview-0.1.ebuild
@@ -64,7 +64,7 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-DEPEND="x11-libs/fox"
+DEPEND="=x11-libs/fox-1.6*"
 RDEPEND="${DEPEND}"
 
 S=${WORKDIR}
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index 9dd52d92e..b047e8c05 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.61 2011/03/09 16:29:05 jlec Exp $
 
+  04 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +files/emboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch,
+  emboss-6.3.1_p4-r2.ebuild:
+  sci-biology/emboss-6.3.1_p4-r2: added a patch for 'undefined reference to
+  c_plwid' bug #493724
+
   24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   emboss-6.3.1_p4-r2.ebuild:
   sci-biology/emboss-6.3.1_p4-r2: add plplot dependency, trying to get rid of a
diff --git a/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild b/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild
index 59a7d4955..962d4722e 100644
--- a/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild
+++ b/sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild
@@ -42,6 +42,7 @@ src_prepare() {
 	epatch "${WORKDIR}"/${PF}.patch
 	epatch "${FILESDIR}/${PF}"_plcol.patch
 	epatch "${FILESDIR}/${PF}"_compilations-paths.patch
+	epatch "${FILESDIR}/${PF}"_rename_plwid_to_plwidth.patch
 	# cp "${FILESDIR}"/ax_lib_mysql.m4 "${S}"/m4/mysql.m4
 	emboss_src_prepare
 	autoreconf -vfi
diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch
new file mode 100644
index 000000000..e66a696d6
--- /dev/null
+++ b/sci-biology/emboss/files/emboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch
@@ -0,0 +1,13 @@
+--- EMBOSS-6.3.1/ajax/graphics/ajgraph.c.ori	2014-07-04 18:25:18.000000000 +0200
++++ EMBOSS-6.3.1/ajax/graphics/ajgraph.c	2014-07-04 18:25:32.000000000 +0200
+@@ -1329,8 +1329,8 @@
+ 
+ void ajGraphicsSetPenwidth(float penwidth)
+ {
+-    ajDebug("=g= plwid(%.2f) [width]\n", penwidth);
+-    plwid((PLINT)penwidth);
++    ajDebug("=g= plwidth(%.2f) [width]\n", penwidth);
++    plwidth((PLINT)penwidth);
+ 
+     return;
+ }
diff --git a/sci-biology/gap2caf/ChangeLog b/sci-biology/gap2caf/ChangeLog
index 8e35f8604..f2a9c638e 100644
--- a/sci-biology/gap2caf/ChangeLog
+++ b/sci-biology/gap2caf/ChangeLog
@@ -1,8 +1,11 @@
 # ChangeLog for sci-biology/gap2caf
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  04 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  gap2caf-2.1.0.ebuild:
+  sci-biology/gap2caf: remove -rpath-link from src/Makefile
+
   16 Jun 2013; Justin Lecher <jlec@gentoo.org> gap2caf-2.1.0.ebuild,
   metadata.xml:
   Bump to EAPI=5 and fix license; make it build with eautoreconf
-
diff --git a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
index 338c3a3b5..726ca2de7 100644
--- a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
+++ b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
@@ -57,6 +57,7 @@ src_configure(){
 	sed -i 's:-ltk_utils:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden -ltk_utils -rpath-link:' src/Makefile || die
 	sed -i 's:-lgap:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden -lgap:' src/Makefile || die
 	sed -i 's:-lseq_utils:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden -lseq_utils:' src/Makefile || die
+	sed -i 's:-rpath-link::' src/Makefile || die
 }
 
 # TODO: the 2.0.2 archive lacks manpages compared to 2.0, FIXME
diff --git a/sci-biology/jellyfish/ChangeLog b/sci-biology/jellyfish/ChangeLog
new file mode 100644
index 000000000..a5df6d9b6
--- /dev/null
+++ b/sci-biology/jellyfish/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/jellyfish
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*jellyfish-2.1.3 (02 Jul 2014)
+
+  02 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +jellyfish-2.1.3.ebuild, +metadata.xml:
+  sci-biology/jellyfish: new package, works
diff --git a/sci-biology/jellyfish/Manifest b/sci-biology/jellyfish/Manifest
new file mode 100644
index 000000000..b5035d2e6
--- /dev/null
+++ b/sci-biology/jellyfish/Manifest
@@ -0,0 +1,2 @@
+DIST JellyfishUserGuide.pdf 142367 SHA256 6f4365f1839b0370fff50fcd25ffcf2dad4192c2ff5b8540fd929d73a8cf85c3 SHA512 a9d65be7591d4b9b275b9f76ab79806d31bf7ef36b297b67b1802a302687aa8d49d4c491c3bb9201aec58268bcfc8c703940c72991b9080bbd1bde95bbda5b8a WHIRLPOOL 1c57b1596ccfff2159bb86359f9dafac1f994b33ab38dc334827d74b8c7541728c6c8b400df54d756bfa0b98ae023fae020ccbebbb24e3eb51baccac5024a6e6
+DIST jellyfish-2.1.3.tar.gz 955773 SHA256 00530abd01c1253646f29fa4554e96fd31148ed92402940e6f357bd5cab38e9b SHA512 2b6fea6c2686de7b568988543d5a9466676eb17252ecce3243b0dc7e3c833aed02ae6570749df58c2921289db0167b39848ccd80eb3cc568cdbaa0045114b702 WHIRLPOOL 4a1e6568932db0cc4773e89e4b8f049e96ed929723ffd518ce7e0ed12bd29041d0774fba1069251a336e448dd75703a350917ffc3db5a35f2cfac828572da566
diff --git a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
new file mode 100644
index 000000000..4ac06b224
--- /dev/null
+++ b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="k-mer counter withing reads for assemblies"
+HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
+SRC_URI="ftp://ftp.genome.umd.edu/pub/jellyfish/jellyfish-2.1.3.tar.gz
+	ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
diff --git a/sci-biology/jellyfish/metadata.xml b/sci-biology/jellyfish/metadata.xml
new file mode 100644
index 000000000..2bc893037
--- /dev/null
+++ b/sci-biology/jellyfish/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/tablet-bin/ChangeLog b/sci-biology/tablet-bin/ChangeLog
index d48473ae8..8b3878105 100644
--- a/sci-biology/tablet-bin/ChangeLog
+++ b/sci-biology/tablet-bin/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*tablet-bin-1.14.04.10 (02 Jul 2014)
+
+  02 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +tablet-bin-1.14.04.10.ebuild:
+  sci-biology/tablet-bin: version bump; updated the license
+
 *tablet-bin-1.13.12.17 (20 Jan 2014)
 
   20 Jan 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/tablet-bin/Manifest b/sci-biology/tablet-bin/Manifest
index ae1e4a6af..7c1877c79 100644
--- a/sci-biology/tablet-bin/Manifest
+++ b/sci-biology/tablet-bin/Manifest
@@ -1,2 +1,3 @@
 DIST coveragestats.py 4800 SHA256 358b686d00fd75d2cc9af490b0e7d635f74cbb1c0b153df22d8ff879884d47bc SHA512 d5688832c13dc9c2e2e015df0b5c50113f72e2eeae076d479c43b65a4b028f8dcfa5f0fb833b4341d76d3956ea27707c55a51389b73a2efed6abd2b96ccdc3cd WHIRLPOOL 0b1eb20189b343d6014097748c053f35f8ad162400312cfbde16bac7fee52f24ac8b0055e991c823dcb64d7a20df3fbb88d8cd6119f838d4e9a5f26e82604664
 DIST tablet-bin-1.13.12.17.sh 34395356 SHA256 fab481dd2a19e1c25142c41e75c483eeac36cc6793921a2643d9472f0aecbd2b SHA512 6fee28fd68ac4dde777dc7b873735e165d19bec47997a49185f21eecaaf2f38ca019b5af30ff18177ed69ad01eb8a797ef8b892631780ad548bf8fdf3ceb2f0b WHIRLPOOL 274e3849096179707af5ad36001ba060b5c5be068350454553997a120ec5c5f33b347ea26f3f9bd356bb7191b1c1e07199a6f6c0073e5b7edb7bf953d46c0974
+DIST tablet-bin-1.14.04.10.sh 36267340 SHA256 d716eab1c4f8f7de099bed6b10a7346fcc2340cf69e527e5af33f521fad00b97 SHA512 9ef7f3332171f66bee6cfceb46dae56170fc744709bc34ebcd6abf201b8d4dd9f6a3e21b61ec341297b66c1b2527970cd15715d1b87f9b864ac97aae4f994ac9 WHIRLPOOL 0369d8bd46ce3ce5bd4da66f23d21a47dcdb74bfa54ff7748fd1ae28180c3ec300eb1e02caeeb8f7090e908fe3984bd14845d9a4e5c099e76bd67ee562759124
diff --git a/sci-biology/tablet-bin/tablet-bin-1.14.04.10.ebuild b/sci-biology/tablet-bin/tablet-bin-1.14.04.10.ebuild
new file mode 100644
index 000000000..1a0fdf12d
--- /dev/null
+++ b/sci-biology/tablet-bin/tablet-bin-1.14.04.10.ebuild
@@ -0,0 +1,97 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit java-pkg-2 python-r1
+
+DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
+HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
+SRC_URI="
+	x86? ( http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators _).sh -> ${P}.sh )
+	amd64? ( http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x64_$(replace_all_version_separators _).sh -> ${P}.sh )
+	http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py"
+
+# Upstream says regarding source code unavailability:
+# Tablet uses a modified version of the BSD License which has been edited to
+# remove references to distribution and use in source forms. This means that
+# we are happy for you to distribute and use Tablet however you please, but we
+# do not (yet) want to make the source code publicly available.
+
+# The licence file itself is in the installer, and ends up on disk after
+# installation at /opt/Tablet/docs/tablet.html
+# The original BSD licence was modified to remove references to distribution
+# and use in source forms, because we cannot make the source code available
+# for Tablet.
+
+LICENSE="Tablet"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="${PYTHON_DEPS}"
+RDEPEND="${DEPEND}
+		virtual/jre"
+
+S="${WORKDIR}"
+
+src_unpack() {
+	local file
+	for file in ${A}; do
+		cp "${DISTDIR}"/${file} "${WORKDIR}" || die
+	done
+}
+
+src_install() {
+	# In theory it seems this binary package could be installed through ant
+	# instead of the install4j package which is not easy to be forced
+	# non-interactive. The below approach via install4j is not ideal but works.
+	sed "s#\"\${D}\"#\"${D}\"#g" "${FILESDIR}"/response.varfile > "${WORKDIR}"/response.varfile || die "sed failed"
+
+	# the intallation script somehow does not pickup
+	# -varfile="${DISTDIR}"/response.varfile from the commandline and therefore
+	# we place the file rather directly into the place where it should reside.
+	# In the file you can read details how the variables were mangled. For
+	# example, the trick with sys.symlinkDir in the response.varfile is to
+	# disable the installation process to symlink from /usr/local/bin/table to
+	# /opt/Tablet/tablet. That was logged in that file with the following line:
+	#
+	# /var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log:
+	#	Variable changed: sys.symlinkDir=/usr/local/bin[class java.lang.String]
+	#
+	# The file is then left on the installed system in "${D}"/opt/Tablet/.install4j/response.varfile
+	dodir /opt/Tablet/.install4j
+	cat "${WORKDIR}"/response.varfile > "${ED}"/opt/Tablet/.install4j/response.varfile || die
+
+	# make sure we force java to point a to $HOME which is inside our sanbox
+	# directory area. We force -Duser.home . It seems also -Dinstall4j.userHome
+	# could be done based on the figure shown at http://resources.ej-technologies.com/install4j/help/doc/
+	sed \
+		-e "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${TMPDIR}" -Dinstall4j.jvmDir#" \
+		-i "${WORKDIR}"/${P}.sh || die
+	sh \
+		"${WORKDIR}"/${P}.sh \
+		-q -overwrite \
+		-varfile="${DISTDIR}"/response.varfile \
+		--destination="${ED}"/opt/Tablet \
+		-dir "${ED}"/opt/Tablet || die
+
+	rm -rf "${ED}"/opt/Tablet/jre || die
+
+    # this dies with tablet-bin-1.14.04.10 with
+	#  * python2_7: running python_doscript /mnt/1TB/var/tmp/portage/sci-biology/tablet-bin-1.14.04.10/work/coveragestats.py
+	#  * The file has incompatible shebang:
+	#  *   file: /usr/lib/python-exec/python2.7/coveragestats.py
+	#  *   current shebang: #!/usr/bin/env python
+	#  *   requested impl: python2.7
+	#
+	# python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py
+
+	echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
+	doenvd 99Tablet || die
+}
diff --git a/sci-biology/tablet/ChangeLog b/sci-biology/tablet/ChangeLog
index 0080ef21c..0cca8d837 100644
--- a/sci-biology/tablet/ChangeLog
+++ b/sci-biology/tablet/ChangeLog
@@ -2,6 +2,14 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*tablet-1.14.04.10 (02 Jul 2014)
+
+  02 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +tablet-1.14.04.10.ebuild, -Manifest, tablet-1.13.12.17.ebuild,
+  tablet-9999.ebuild:
+  sci-biology/tablet: cleaned up the ebuilds, they compile and install but the
+  bundled samtools-*.jar is not found
+
 *tablet-1.13.12.17 (28 Mar 2014)
 *tablet-9999 (28 Mar 2014)
 
diff --git a/sci-biology/tablet/Manifest b/sci-biology/tablet/Manifest
deleted file mode 100644
index 05da7e849..000000000
--- a/sci-biology/tablet/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST coveragestats.py 4800 SHA256 358b686d00fd75d2cc9af490b0e7d635f74cbb1c0b153df22d8ff879884d47bc SHA512 d5688832c13dc9c2e2e015df0b5c50113f72e2eeae076d479c43b65a4b028f8dcfa5f0fb833b4341d76d3956ea27707c55a51389b73a2efed6abd2b96ccdc3cd WHIRLPOOL 0b1eb20189b343d6014097748c053f35f8ad162400312cfbde16bac7fee52f24ac8b0055e991c823dcb64d7a20df3fbb88d8cd6119f838d4e9a5f26e82604664
-DIST tablet-1.13.12.17.sh 34395356 SHA256 fab481dd2a19e1c25142c41e75c483eeac36cc6793921a2643d9472f0aecbd2b SHA512 6fee28fd68ac4dde777dc7b873735e165d19bec47997a49185f21eecaaf2f38ca019b5af30ff18177ed69ad01eb8a797ef8b892631780ad548bf8fdf3ceb2f0b WHIRLPOOL 274e3849096179707af5ad36001ba060b5c5be068350454553997a120ec5c5f33b347ea26f3f9bd356bb7191b1c1e07199a6f6c0073e5b7edb7bf953d46c0974
diff --git a/sci-biology/tablet/tablet-1.13.12.17.ebuild b/sci-biology/tablet/tablet-1.13.12.17.ebuild
index 112709b08..1940cb9c7 100644
--- a/sci-biology/tablet/tablet-1.13.12.17.ebuild
+++ b/sci-biology/tablet/tablet-1.13.12.17.ebuild
@@ -6,84 +6,45 @@ EAPI=5
 
 PYTHON_COMPAT=( python{2_6,2_7} )
 
-inherit java-pkg-2 python-r1
+inherit java-pkg-2 java-ant-2 python-r1
+
+# [ "$PV" == "9999" ] && inherit subversion
+inherit subversion
 
 DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
 HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
-SRC_URI="
-	x86? ( http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators _).sh -> ${P}.sh )
-	amd64? ( http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x64_$(replace_all_version_separators _).sh -> ${P}.sh )
-	http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py"
-
-# Upstream says regarding source code unavailability:
-# Tablet uses a modified version of the BSD License which has been edited to
-# remove references to distribution and use in source forms. This means that
-# we are happy for you to distribute and use Tablet however you please, but we
-# do not (yet) want to make the source code publicly available.
-
-# The licence file itself is in the installer, and ends up on disk after
-# installation at /opt/Tablet/docs/tablet.html
-# The original BSD licence was modified to remove references to distribution
-# and use in source forms, because we cannot make the source code available
-# for Tablet.
+if [ "$PV" == "9999" ]; then
+	ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/"
+	KEYWORDS=""
+else
+	ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV}"
+	KEYWORDS=""
+fi
 
 LICENSE="Tablet"
 SLOT="0"
-KEYWORDS=""
 IUSE=""
 
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
-DEPEND="${PYTHON_DEPS}"
+DEPEND="${PYTHON_DEPS}
+	>=virtual/jdk-1.7"
 RDEPEND="${DEPEND}
-		virtual/jre"
+	>=virtual/jre-1.7
+	sci-biology/samtools
+	sci-biology/picard
+	dev-db/sqlite"
 
 S="${WORKDIR}"
 
-src_unpack() {
-	local file
-	for file in ${A}; do
-		cp "${DISTDIR}"/${file} "${WORKDIR}" || die
-	done
-}
-
 src_install() {
-	# In theory it seems this binary package could be installed through ant
-	# instead of the install4j package which is not easy to be forced
-	# non-interactive. The below approach via install4j is not ideal but works.
-	sed "s#\"\${D}\"#\"${D}\"#g" "${FILESDIR}"/response.varfile > "${WORKDIR}"/response.varfile || die "sed failed"
-
-	# the intallation script somehow does not pickup
-	# -varfile="${DISTDIR}"/response.varfile from the commandline and therefore
-	# we place the file rather directly into the place where it should reside.
-	# In the file you can read details how the variables were mangled. For
-	# example, the trick with sys.symlinkDir in the response.varfile is to
-	# disable the installation process to symlink from /usr/local/bin/table to
-	# /opt/Tablet/tablet. That was logged in that file with the following line:
-	#
-	# /var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log:
-	#	Variable changed: sys.symlinkDir=/usr/local/bin[class java.lang.String]
-	#
-	# The file is then left on the installed system in "${D}"/opt/Tablet/.install4j/response.varfile
-	dodir /opt/Tablet/.install4j
-	cat "${WORKDIR}"/response.varfile > "${ED}"/opt/Tablet/.install4j/response.varfile || die
-
-	# make sure we force java to point a to $HOME which is inside our sanbox
-	# directory area. We force -Duser.home . It seems also -Dinstall4j.userHome
-	# could be done based on the figure shown at http://resources.ej-technologies.com/install4j/help/doc/
-	sed \
-		-e "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${TMPDIR}" -Dinstall4j.jvmDir#" \
-		-i "${WORKDIR}"/${P}.sh || die
-	sh \
-		"${WORKDIR}"/${P}.sh \
-		-q -overwrite \
-		-varfile="${DISTDIR}"/response.varfile \
-		--destination="${ED}"/opt/Tablet \
-		-dir "${ED}"/opt/Tablet || die
-
-	rm -rf "${ED}"/opt/Tablet/jre || die
+	java-pkg_dojar lib/tablet-resources.jar || die
+	java-pkg_dojar lib/tablet.jar || die
+	java-pkg_dojar lib/flamingo.jar || die
+	java-pkg_dojar lib/scri-commons.jar || die
+	java-pkg_dojar lib/samtools*.jar || die
 
-	python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py
+	dobin www/additional/coveragestats.py
 
 	echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
 	doenvd 99Tablet || die
diff --git a/sci-biology/tablet/tablet-1.14.04.10.ebuild b/sci-biology/tablet/tablet-1.14.04.10.ebuild
new file mode 100644
index 000000000..1940cb9c7
--- /dev/null
+++ b/sci-biology/tablet/tablet-1.14.04.10.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit java-pkg-2 java-ant-2 python-r1
+
+# [ "$PV" == "9999" ] && inherit subversion
+inherit subversion
+
+DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
+HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
+if [ "$PV" == "9999" ]; then
+	ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/"
+	KEYWORDS=""
+else
+	ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV}"
+	KEYWORDS=""
+fi
+
+LICENSE="Tablet"
+SLOT="0"
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="${PYTHON_DEPS}
+	>=virtual/jdk-1.7"
+RDEPEND="${DEPEND}
+	>=virtual/jre-1.7
+	sci-biology/samtools
+	sci-biology/picard
+	dev-db/sqlite"
+
+S="${WORKDIR}"
+
+src_install() {
+	java-pkg_dojar lib/tablet-resources.jar || die
+	java-pkg_dojar lib/tablet.jar || die
+	java-pkg_dojar lib/flamingo.jar || die
+	java-pkg_dojar lib/scri-commons.jar || die
+	java-pkg_dojar lib/samtools*.jar || die
+
+	dobin www/additional/coveragestats.py
+
+	echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
+	doenvd 99Tablet || die
+}
diff --git a/sci-biology/tablet/tablet-9999.ebuild b/sci-biology/tablet/tablet-9999.ebuild
index 40472c753..1940cb9c7 100644
--- a/sci-biology/tablet/tablet-9999.ebuild
+++ b/sci-biology/tablet/tablet-9999.ebuild
@@ -6,9 +6,10 @@ EAPI=5
 
 PYTHON_COMPAT=( python{2_6,2_7} )
 
-inherit java-pkg-2 java-ant-2 python-r1 eutils
+inherit java-pkg-2 java-ant-2 python-r1
 
-[ "$PV" == "9999" ] && inherit subversion
+# [ "$PV" == "9999" ] && inherit subversion
+inherit subversion
 
 DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
 HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
@@ -20,23 +21,6 @@ else
 	KEYWORDS=""
 fi
 
-#SRC_URI="
-#	x86? ( http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators _).sh -> ${P}.sh )
-#	amd64? ( http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x64_$(replace_all_version_separators _).sh -> ${P}.sh )
-#	http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py"
-
-# Upstream says regarding source code unavailability:
-# Tablet uses a modified version of the BSD License which has been edited to
-# remove references to distribution and use in source forms. This means that
-# we are happy for you to distribute and use Tablet however you please, but we
-# do not (yet) want to make the source code publicly available.
-
-# The licence file itself is in the installer, and ends up on disk after
-# installation at /opt/Tablet/docs/tablet.html
-# The original BSD licence was modified to remove references to distribution
-# and use in source forms, because we cannot make the source code available
-# for Tablet.
-
 LICENSE="Tablet"
 SLOT="0"
 IUSE=""
@@ -44,56 +28,23 @@ IUSE=""
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 DEPEND="${PYTHON_DEPS}
-	virtual/jdk"
+	>=virtual/jdk-1.7"
 RDEPEND="${DEPEND}
-		virtual/jre"
+	>=virtual/jre-1.7
+	sci-biology/samtools
+	sci-biology/picard
+	dev-db/sqlite"
 
 S="${WORKDIR}"
 
-src_unpack() {
-	local file
-	for file in ${A}; do
-		cp "${DISTDIR}"/${file} "${WORKDIR}" || die
-	done
-}
-
 src_install() {
-	# In theory it seems this binary package could be installed through ant
-	# instead of the install4j package which is not easy to be forced
-	# non-interactive. The below approach via install4j is not ideal but works.
-	sed "s#\"\${D}\"#\"${D}\"#g" "${FILESDIR}"/response.varfile > "${WORKDIR}"/response.varfile || die "sed failed"
-
-	# the intallation script somehow does not pickup
-	# -varfile="${DISTDIR}"/response.varfile from the commandline and therefore
-	# we place the file rather directly into the place where it should reside.
-	# In the file you can read details how the variables were mangled. For
-	# example, the trick with sys.symlinkDir in the response.varfile is to
-	# disable the installation process to symlink from /usr/local/bin/table to
-	# /opt/Tablet/tablet. That was logged in that file with the following line:
-	#
-	# /var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log:
-	#	Variable changed: sys.symlinkDir=/usr/local/bin[class java.lang.String]
-	#
-	# The file is then left on the installed system in "${D}"/opt/Tablet/.install4j/response.varfile
-	dodir /opt/Tablet/.install4j
-	cat "${WORKDIR}"/response.varfile > "${ED}"/opt/Tablet/.install4j/response.varfile || die
-
-	# make sure we force java to point a to $HOME which is inside our sanbox
-	# directory area. We force -Duser.home . It seems also -Dinstall4j.userHome
-	# could be done based on the figure shown at http://resources.ej-technologies.com/install4j/help/doc/
-	sed \
-		-e "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${TMPDIR}" -Dinstall4j.jvmDir#" \
-		-i "${WORKDIR}"/${P}.sh || die
-	sh \
-		"${WORKDIR}"/${P}.sh \
-		-q -overwrite \
-		-varfile="${DISTDIR}"/response.varfile \
-		--destination="${ED}"/opt/Tablet \
-		-dir "${ED}"/opt/Tablet || die
-
-	rm -rf "${ED}"/opt/Tablet/jre || die
+	java-pkg_dojar lib/tablet-resources.jar || die
+	java-pkg_dojar lib/tablet.jar || die
+	java-pkg_dojar lib/flamingo.jar || die
+	java-pkg_dojar lib/scri-commons.jar || die
+	java-pkg_dojar lib/samtools*.jar || die
 
-	python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py
+	dobin www/additional/coveragestats.py
 
 	echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
 	doenvd 99Tablet || die
diff --git a/sci-chemistry/cpmgfit/ChangeLog b/sci-chemistry/cpmgfit/ChangeLog
new file mode 100644
index 000000000..7eb5da667
--- /dev/null
+++ b/sci-chemistry/cpmgfit/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-chemistry/cpmgfit
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*cpmgfit-1.43 (03 Jul 2014)
+
+  03 Jul 2014; Justin Lecher <jlec@gentoo.org> +cpmgfit-1.43.ebuild,
+  +metadata.xml:
+  New package written by me
+
diff --git a/sci-chemistry/cpmgfit/Manifest b/sci-chemistry/cpmgfit/Manifest
new file mode 100644
index 000000000..ba3c56168
--- /dev/null
+++ b/sci-chemistry/cpmgfit/Manifest
@@ -0,0 +1 @@
+DIST cpmgfit-1.43.tar.gz 89002 SHA256 b96c356c9783d95ee1fe14f2fdc66fa80d2f1839d538f9417747829527befc2a SHA512 ad10ec8cde4eb13dd21f99ebca5552ec844b89785a0485df287e8fad7b63a2f99cd713d281904d2f83cc9485c5fc0a0b3f963d23af8785f0277cb1f7418051a3 WHIRLPOOL c8368f69ed2e3c17da84397f014a590cc83ce69ca33e8f798efc84e22538dab4b0c3917737cb4c497bac78847404afb02cba61cb7d3aa73a836cf5b51e66e624
diff --git a/sci-chemistry/cpmgfit/cpmgfit-1.43.ebuild b/sci-chemistry/cpmgfit/cpmgfit-1.43.ebuild
new file mode 100644
index 000000000..37c657edd
--- /dev/null
+++ b/sci-chemistry/cpmgfit/cpmgfit-1.43.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit fortran-2 multilib
+
+DESCRIPTION="non-linear least squares fitting of CPMG relaxation dispersion curves"
+HOMEPAGE="http://biochemistry.hs.columbia.edu/labs/palmer/software/cpmgfit.html"
+SRC_URI="http://biochemistry.hs.columbia.edu/labs/palmer/software/cpmgfit.linux.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples"
+
+RDEPEND="
+	sci-libs/blas-reference
+	sys-devel/gcc:4.1"
+DEPEND="dev-util/patchelf"
+
+S="${WORKDIR}"/linux
+
+QA_PREBUILT="opt/bin/.*"
+
+src_install() {
+	local _exe
+
+	exeinto /opt/bin
+	if use x86; then
+		_exe=./linux_32/${PN}
+	elif use amd64; then
+		_exe=./linux_64/${PN}
+	fi
+
+	patchelf --set-rpath "${EPREFIX}/opt/${PN}:${EPREFIX}/usr/$(get_libdir)/gcc/x86_64-pc-linux-gnu/4.1.2/" ${_exe}
+
+	doexe ${_exe}
+
+	dosym ../../usr/$(get_libdir)/librefblas.so /opt/${PN}/libblas.so.3
+
+	dohtml ${PN}_manual.html
+
+	if use examples; then
+		insinto /usr/share/${PN}/examples/
+		doins sample*
+	fi
+}
diff --git a/sci-chemistry/cpmgfit/metadata.xml b/sci-chemistry/cpmgfit/metadata.xml
new file mode 100644
index 000000000..51fdedab1
--- /dev/null
+++ b/sci-chemistry/cpmgfit/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-chemistry</herd>
+</pkgmetadata>
diff --git a/sci-chemistry/direx/ChangeLog b/sci-chemistry/direx/ChangeLog
deleted file mode 100644
index 6cb0c581d..000000000
--- a/sci-chemistry/direx/ChangeLog
+++ /dev/null
@@ -1,16 +0,0 @@
-# ChangeLog for sci-chemistry/direx
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-*direx-0.2 (08 May 2009)
-
-  08 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> direx-0.2.ebuild:
-  renamed ebuild
-  unmasked
-
-*direx-0.2-r92 (07 May 2009)
-
-  07 May 2009; Alexey Shvetsov <alexxy@gentoo.org> +direx-0.2-r92.ebuild,
-  -direx-0.2_r92.ebuild:
-  rename ebuild
-
diff --git a/sci-chemistry/direx/Manifest b/sci-chemistry/direx/Manifest
deleted file mode 100644
index e7dcabfd8..000000000
--- a/sci-chemistry/direx/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST direx-0.2-rev92-linux.tgz 1096211 SHA256 567741da0d94db38ca0576b73498c3e5667e8d5bb8b7241d9dc5664eca91a23b
diff --git a/sci-chemistry/direx/direx-0.2.ebuild b/sci-chemistry/direx/direx-0.2.ebuild
deleted file mode 100644
index fb8b7642a..000000000
--- a/sci-chemistry/direx/direx-0.2.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-# inherit
-
-MY_REV="92"
-
-DESCRIPTION="Low Resolution Structure Refinement"
-HOMEPAGE="https://simtk.org/home/direx"
-SRC_URI="${P}-rev${MY_REV}-linux.tgz"
-
-LICENSE="direx"
-SLOT="0"
-KEYWORDS="-* ~amd64 ~x86"
-IUSE=""
-
-RDEPEND="amd64? ( app-emulation/emul-linux-x86-compat )"
-DEPEND="${RDEPEND}"
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
-	einfo "Go to ${HOMEPAGE} and download ${A}"
-	einfo "into ${DISTDIR}"
-}
-
-src_install() {
-	exeinto /opt/${PN}/bin
-	doexe ${PN} || die
-
-	cat >> "${T}"/20${PN} <<- EOF
-	PATH="/opt/${PN}/bin"
-	EOF
-
-	doenvd "${T}"/20${PN}
-
-	insinto /usr/share/${PN}
-	doins -r tutorial || die
-	dohtml doc/* || die
-	dodoc README || die
-}
diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index e98a9ec6a..fa5fa261f 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  07 Jul 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-5.0.9999.ebuild:
+  sync with gx86, fix FEATURES=test
+
   26 Jun 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
   live ebuild update
 
diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 37018bad2..286583313 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -4,8 +4,8 @@
 
 EAPI=5
 
-TEST_PV="4.6.2"
-MANUAL_PV="4.6.2"
+TEST_PV="4.6.6"
+MANUAL_PV="4.6.6"
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
@@ -17,7 +17,7 @@ if [[ $PV = *9999* ]]; then
 		git://github.com/gromacs/gromacs.git
 		http://repo.or.cz/r/gromacs.git"
 	EGIT_BRANCH="release-4-6"
-	inherit git-2
+	inherit git-r3
 	LIVE_DEPEND="doc? (
 		app-doc/doxygen
 		dev-texlive/texlive-latex
@@ -25,11 +25,13 @@ if [[ $PV = *9999* ]]; then
 		media-gfx/imagemagick
 		sys-apps/coreutils
 	)"
+	KEYWORDS=""
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
 		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf )
-		test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"
+		test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )"
 	LIVE_DEPEND=""
+	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
 fi
 
 ACCE_IUSE="sse2 sse4_1 avx128fma avx256"
@@ -42,7 +44,6 @@ HOMEPAGE="http://www.gromacs.org/"
 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
-KEYWORDS=""
 IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
 
 CDEPEND="
@@ -87,18 +88,18 @@ src_unpack() {
 	if [[ ${PV} != *9999 ]]; then
 		default
 	else
-		git-2_src_unpack
+		git-r3_src_unpack
 		if use doc; then
 			EGIT_REPO_URI="git://git.gromacs.org/manual.git" \
-			EGIT_BRANCH="release-4-6" EGIT_NOUNPACK="yes" EGIT_COMMIT="release-4-6" \
-			EGIT_SOURCEDIR="${WORKDIR}/manual"\
-				git-2_src_unpack
+			EGIT_BRANCH="release-4-6" EGIT_COMMIT="release-4-6" \
+			EGIT_CHECKOUT_DIR="${WORKDIR}/manual"\
+				git-r3_src_unpack
 		fi
 		if use test; then
 			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="release-4-6" \
-			EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\
-				git-2_src_unpack
+			EGIT_BRANCH="release-4-6" EGIT_COMMIT="release-4-6" \
+			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
+				git-r3_src_unpack
 		fi
 	fi
 }
diff --git a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
index 6488bd5f5..88169b2f1 100644
--- a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
@@ -17,9 +17,11 @@ if [[ $PV = *9999* ]]; then
 		http://repo.or.cz/r/gromacs.git"
 	EGIT_BRANCH="release-5-0"
 	inherit git-r3
+	KEYWORDS=""
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
 		test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )"
+	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
 fi
 
 ACCE_IUSE="sse2 sse4_1 avx_128_fma avx_256 avx2_256"
@@ -32,7 +34,6 @@ HOMEPAGE="http://www.gromacs.org/"
 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
-KEYWORDS=""
 IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
 
 CDEPEND="
@@ -83,8 +84,8 @@ src_unpack() {
 		git-r3_src_unpack
 		if use test; then
 			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \
-			EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\
+			EGIT_BRANCH="master" EGIT_COMMIT="master" \
+			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
 				git-r3_src_unpack
 		fi
 	fi
diff --git a/sci-chemistry/hydronmr/ChangeLog b/sci-chemistry/hydronmr/ChangeLog
index 128ca1a8a..359e0ed0a 100644
--- a/sci-chemistry/hydronmr/ChangeLog
+++ b/sci-chemistry/hydronmr/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  04 Jul 2014; Justin Lecher <jlec@gentoo.org> hydronmr-7c.ebuild:
+  Fix emul-linux deps for modern multilib
+
   06 Jan 2014; Justin Lecher <jlec@gentoo.org> hydronmr-7c.ebuild:
   Fix emul dep
 
diff --git a/sci-chemistry/hydronmr/hydronmr-7c.ebuild b/sci-chemistry/hydronmr/hydronmr-7c.ebuild
index 5a7dfdba1..b360c8cb8 100644
--- a/sci-chemistry/hydronmr/hydronmr-7c.ebuild
+++ b/sci-chemistry/hydronmr/hydronmr-7c.ebuild
@@ -28,9 +28,6 @@ LICENSE="all-rights-reserved"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="examples"
 
-DEPEND=""
-RDEPEND="amd64? ( app-emulation/emul-linux-x86-baselibs )"
-
 QA_PREBUILT="opt/bin/.*"
 
 src_unpack() {
diff --git a/sci-chemistry/nmrpipe/ChangeLog b/sci-chemistry/nmrpipe/ChangeLog
index 3af5fe517..630fe3b88 100644
--- a/sci-chemistry/nmrpipe/ChangeLog
+++ b/sci-chemistry/nmrpipe/ChangeLog
@@ -1,7 +1,15 @@
 # ChangeLog for sci-chemistry/nmrpipe
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  04 Jul 2014; Justin Lecher <jlec@gentoo.org>
+  nmrpipe-8.1.2013.218.23.09-r1.ebuild:
+  Fix emul-linux deps for modern multilib
+
+  04 Jul 2014; Justin Lecher <jlec@gentoo.org>
+  nmrpipe-8.1.2013.218.23.09-r1.ebuild:
+  Fix emul-linux deps for modern multilib
+
   28 Oct 2013; Justin Lecher <jlec@gentoo.org>
   -nmrpipe-8.1.2013.218.23.09.ebuild, +nmrpipe-8.1.2013.218.23.09-r1.ebuild,
   +files/extract.M:
diff --git a/sci-chemistry/nmrpipe/nmrpipe-8.1.2013.218.23.09-r1.ebuild b/sci-chemistry/nmrpipe/nmrpipe-8.1.2013.218.23.09-r1.ebuild
index 4be5ae22e..7602935c0 100644
--- a/sci-chemistry/nmrpipe/nmrpipe-8.1.2013.218.23.09-r1.ebuild
+++ b/sci-chemistry/nmrpipe/nmrpipe-8.1.2013.218.23.09-r1.ebuild
@@ -46,11 +46,14 @@ RDEPEND="${DEPEND}
 	!sci-chemistry/talos+
 	sys-libs/ncurses
 	x11-apps/xset
-	x11-libs/libX11
 	|| ( x11-libs/xview x11-libs/xview-bin )
-	amd64? (
-		app-emulation/emul-linux-x86-baselibs
-		app-emulation/emul-linux-x86-xlibs
+	|| (
+		(
+			x11-libs/libX11[abi_x86_32(-)]
+		)
+		(
+			app-emulation/emul-linux-x86-xlibs[-abi_x86_32(-)]
+		)
 	)
 	prefix? ( dev-util/patchelf )"
 
diff --git a/sci-chemistry/unio/ChangeLog b/sci-chemistry/unio/ChangeLog
index 05ca5142c..98fac3e4e 100644
--- a/sci-chemistry/unio/ChangeLog
+++ b/sci-chemistry/unio/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  04 Jul 2014; Justin Lecher <jlec@gentoo.org> unio-2.0.3-r1.ebuild:
+  Fix emul-linux deps for modern multilib
+
 *unio-2.0.3-r1 (21 Mar 2014)
 
   21 Mar 2014; Justin Lecher <jlec@gentoo.org> +unio-2.0.3-r1.ebuild:
diff --git a/sci-chemistry/unio/unio-2.0.3-r1.ebuild b/sci-chemistry/unio/unio-2.0.3-r1.ebuild
index 8ca4d34db..91c2693c1 100644
--- a/sci-chemistry/unio/unio-2.0.3-r1.ebuild
+++ b/sci-chemistry/unio/unio-2.0.3-r1.ebuild
@@ -20,10 +20,10 @@ RDEPEND="
 	app-shells/ksh
 	|| (
 		(
-			x11-libs/libX11[abi_x86_32]
-			x11-libs/libXext[abi_x86_32]
+			x11-libs/libX11[abi_x86_32(-)]
+			x11-libs/libXext[abi_x86_32(-)]
 		)
-		app-emulation/emul-linux-x86-xlibs
+		app-emulation/emul-linux-x86-xlibs[-abi_x86_32(-)]
 		)"
 DEPEND=""
 
diff --git a/sci-libs/cblas-reference/ChangeLog b/sci-libs/cblas-reference/ChangeLog
index a48b811ad..b998a4a77 100644
--- a/sci-libs/cblas-reference/ChangeLog
+++ b/sci-libs/cblas-reference/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/sci-libs/cblas-reference/ChangeLog,v 1.33 2010/03/07 19:14:51 jlec Exp $
 
+  02 Jul 2014; François Bissey <francois.bissey@canterbury.ac.nz>
+  cblas-reference-20110218.ebuild:
+  More fix for macos. We need to create the link for both linux and macos.
+
   30 Jun 2014; François Bissey <francois.bissey@canterbury.ac.nz>
   cblas-reference-20110218.ebuild:
   Tweak src_install for OS X support. Added documentation in the ebuild itself.
diff --git a/sci-libs/cblas-reference/cblas-reference-20110218.ebuild b/sci-libs/cblas-reference/cblas-reference-20110218.ebuild
index 52fa8c817..cec9dae28 100644
--- a/sci-libs/cblas-reference/cblas-reference-20110218.ebuild
+++ b/sci-libs/cblas-reference/cblas-reference-20110218.ebuild
@@ -46,8 +46,8 @@ static_to_shared() {
 		if [[ $(get_version_component_count) -gt 1 ]]; then
 			ln -s ${soname} ${libdir}/${libname}$(get_libname $(get_major_version)) || die
 		fi
-		ln -s ${soname} ${libdir}/${libname}$(get_libname) || die
 	fi
+	ln -s ${soname} ${libdir}/${libname}$(get_libname) || die
 }
 
 src_prepare() {
diff --git a/sci-libs/fftw/ChangeLog b/sci-libs/fftw/ChangeLog
index c22b85c8b..cedc57e84 100644
--- a/sci-libs/fftw/ChangeLog
+++ b/sci-libs/fftw/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  04 Jul 2014; Justin Lecher <jlec@gentoo.org> fftw-9999.ebuild:
+  Drop reference to app-emulation/emul-linux-x86-soundlibs
+
   06 Jan 2014; Justin Lecher <jlec@gentoo.org> fftw-9999.ebuild:
   Switch from git-2 to git-r3
 
diff --git a/sci-libs/fftw/fftw-9999.ebuild b/sci-libs/fftw/fftw-9999.ebuild
index 891b6a192..1b02b6299 100644
--- a/sci-libs/fftw/fftw-9999.ebuild
+++ b/sci-libs/fftw/fftw-9999.ebuild
@@ -26,10 +26,7 @@ LICENSE="GPL-2"
 SLOT="3.0"
 IUSE="altivec avx doc fma fortran mpi neon openmp quad sse sse2 static-libs test threads zbus"
 
-RDEPEND="
-	mpi? ( virtual/mpi )
-	abi_x86_32? ( !<=app-emulation/emul-linux-x86-soundlibs-20130224-r2
-					!app-emulation/emul-linux-x86-soundlibs[-abi_x86_32(-)] )"
+RDEPEND="mpi? ( virtual/mpi )"
 DEPEND="${RDEPEND}
 	test? ( dev-lang/perl )"
 
diff --git a/sci-libs/gsl/ChangeLog b/sci-libs/gsl/ChangeLog
index f35223d33..81ecb25b5 100644
--- a/sci-libs/gsl/ChangeLog
+++ b/sci-libs/gsl/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-libs/gsl
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/sci-libs/gsl/ChangeLog,v 1.77 2010/08/09 09:32:55 xarthisius Exp $
 
+  02 Jul 2014; François Bissey <francois.bissey@canterbury.ac.nz>
+  gsl-1.16-r1.ebuild:
+  Tested on x64-macos, keywording.
+
 *gsl-1.16-r1 (19 Aug 2013)
 
   19 Aug 2013; Sébastien Fabbro <bicatali@gentoo.org>
diff --git a/sci-libs/gsl/gsl-1.16-r1.ebuild b/sci-libs/gsl/gsl-1.16-r1.ebuild
index c1fd0e551..f19bba153 100644
--- a/sci-libs/gsl/gsl-1.16-r1.ebuild
+++ b/sci-libs/gsl/gsl-1.16-r1.ebuild
@@ -14,7 +14,7 @@ SRC_URI="mirror://gnu/${PN}/${P}.tar.gz"
 
 LICENSE="GPL-3"
 SLOT="0"
-KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~x86-fbsd ~x86-interix ~amd64-linux ~x86-linux ~x86-macos ~sparc-solaris ~x86-solaris"
+KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~x86-fbsd ~x86-interix ~amd64-linux ~x86-linux ~x86-macos ~x64-macos ~sparc-solaris ~x86-solaris"
 IUSE="cblas-external static-libs"
 
 RDEPEND="cblas-external? ( virtual/cblas )"
diff --git a/sci-libs/libcerf/ChangeLog b/sci-libs/libcerf/ChangeLog
new file mode 100644
index 000000000..798151cbe
--- /dev/null
+++ b/sci-libs/libcerf/ChangeLog
@@ -0,0 +1,13 @@
+# ChangeLog for sci-libs/libcerf
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  14 Jul 2014; Christoph Junghans <ottxor@gentoo.org>
+  +files/libcerf-1.3-autotools.patch, libcerf-1.3.ebuild:
+  fix make install/check
+
+*libcerf-1.3 (14 Jul 2014)
+
+  14 Jul 2014; Christoph Junghans <ottxor@gentoo.org> +libcerf-1.3.ebuild,
+  +metadata.xml:
+  initial commit
diff --git a/sci-libs/libcerf/Manifest b/sci-libs/libcerf/Manifest
new file mode 100644
index 000000000..90cdcc9c2
--- /dev/null
+++ b/sci-libs/libcerf/Manifest
@@ -0,0 +1 @@
+DIST libcerf-1.3.tgz 385600 SHA256 d7059e923d3f370c89fb4d19ed4f827d381bc3f0e36da5595a04aeaaf3e6a859 SHA512 274fa7f3b149bb27582a54a39fe76b478cd5acc6716dd0588a2f637b77c87a6bbc4f467b52bb067ebad2d1ba18750211cc71c6a6feef75fa08d01ac1dbf5dc56 WHIRLPOOL 6f003e26aa76458da620dc4261cfc3b9ec77882a62e5f1a42ffa83c252ae39399e1244c16ad101ff98469ed59970be04b5f901a418e9681f7657adc76e0698f2
diff --git a/sci-libs/libcerf/files/libcerf-1.3-autotools.patch b/sci-libs/libcerf/files/libcerf-1.3-autotools.patch
new file mode 100644
index 000000000..bd22e3196
--- /dev/null
+++ b/sci-libs/libcerf/files/libcerf-1.3-autotools.patch
@@ -0,0 +1,48 @@
+diff -Naur libcerf-1.3.orig/libcerf.pc.in libcerf-1.3/libcerf.pc.in
+--- libcerf-1.3.orig/libcerf.pc.in	2013-07-17 03:51:59.000000000 -0600
++++ libcerf-1.3/libcerf.pc.in	2014-07-14 11:18:01.646512503 -0600
+@@ -7,4 +7,5 @@
+ Description: Complex error function library
+ Version: @PACKAGE_VERSION@
+ Libs: -L${libdir} -lcerf
++Libs.private: -lm
+ Cflags: -I${includedir}
+diff -Naur libcerf-1.3.orig/man/Makefile.am libcerf-1.3/man/Makefile.am
+--- libcerf-1.3.orig/man/Makefile.am	2013-02-01 02:00:14.000000000 -0700
++++ libcerf-1.3/man/Makefile.am	2014-07-14 11:17:36.266182267 -0600
+@@ -19,9 +19,8 @@
+ # Website:
+ #   http://apps.jcns.fz-juelich.de/libcerf
+ 
+-man_MANS = w_of_z.3 im_w_of_x.3 dawson.3 cdawson.3 cerf.3 cerfc.3 erfcx.3 cerfcx.3 erfi.3 cerfi.3 voigt.3 
+-auxdir = $(datadir)/man/html
+-aux_DATA = w_of_z.html voigt.html dawson.html cerf.html erfcx.html erfi.html
++man_MANS = w_of_z.3 im_w_of_x.3 dawson.3 cdawson.3 libcerf-cerf.3 cerfc.3 erfcx.3 cerfcx.3 erfi.3 cerfi.3 voigt.3 
++html_DATA = w_of_z.html voigt.html dawson.html cerf.html erfcx.html erfi.html
+ 
+ w_of_z.3 : w_of_z.pod
+ 	pod2man -s 3 -c "libcerf manual" $< > $@
+@@ -35,7 +34,7 @@
+ cdawson.3 : dawson.pod
+ 	pod2man -s 3 -c "libcerf manual" $< > $@
+ 
+-cerf.3 : cerf.pod
++libcerf-cerf.3 : cerf.pod
+ 	pod2man -s 3 -c "libcerf manual" $< > $@
+ 
+ cerfc.3 : cerf.pod
+diff -Naur libcerf-1.3.orig/test/Makefile.am libcerf-1.3/test/Makefile.am
+--- libcerf-1.3.orig/test/Makefile.am	2013-07-17 01:45:37.000000000 -0600
++++ libcerf-1.3/test/Makefile.am	2014-07-14 11:16:00.204932368 -0600
+@@ -20,8 +20,10 @@
+ #   http://apps.jcns.fz-juelich.de/libcerf
+ 
+ AM_CFLAGS += -I$(srcdir)/../lib
+-noinst_PROGRAMS = test_libcerf_1 runvoigt run_w_of_z
++noinst_PROGRAMS = runvoigt run_w_of_z
+ test_libcerf_1_SOURCES = test1.c
+ runvoigt_SOURCES = runvoigt.c
+ run_w_of_z_SOURCES = run_w_of_z.c
+ AM_LDFLAGS = -lm -L../lib -lcerf
++check_PROGRAMS = test_libcerf_1
++TESTS = test_libcerf_1
diff --git a/sci-libs/libcerf/libcerf-1.3.ebuild b/sci-libs/libcerf/libcerf-1.3.ebuild
new file mode 100644
index 000000000..2a61e84bd
--- /dev/null
+++ b/sci-libs/libcerf/libcerf-1.3.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit autotools-utils multilib
+
+DESCRIPTION="library that provides an efficient and accurate implementation of complex error functions"
+HOMEPAGE="http://apps.jcns.fz-juelich.de/doku/sc/libcerf"
+SRC_URI="http://apps.jcns.fz-juelich.de/src/${PN}/${P}.tgz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc static-libs test"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+PATCHES=( "${FILESDIR}/${P}-autotools.patch" )
+AUTOTOOLS_AUTORECONF=1
diff --git a/sci-chemistry/direx/metadata.xml b/sci-libs/libcerf/metadata.xml
index 9ac9ffdb3..897aa2e6b 100644
--- a/sci-chemistry/direx/metadata.xml
+++ b/sci-libs/libcerf/metadata.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-chemistry</herd>
+  <herd>sci</herd>
 </pkgmetadata>
diff --git a/sci-mathematics/scilab/files/scilab-5.5.0-accessviolation.patch b/sci-mathematics/scilab/files/scilab-5.5.0-accessviolation.patch
index 39b4302a8..a84de9a2b 100644
--- a/sci-mathematics/scilab/files/scilab-5.5.0-accessviolation.patch
+++ b/sci-mathematics/scilab/files/scilab-5.5.0-accessviolation.patch
@@ -1,21 +1,21 @@
---- bin/scilab.orig	2013-10-28 01:08:06.623143085 -0400
-+++ bin/scilab	2013-10-30 22:57:00.781289235 -0400
-@@ -650,11 +650,13 @@
- # libEGL may be partially supported by the closed-source NVIDIA driver.
- # Until they release an EGL driver, we force the egl_glx driver.
- # http://bugzilla.scilab.org/show_bug.cgi?id=12940
+diff -urN scilab-5.5.0-orig/bin/scilab scilab-5.5.0/bin/scilab
+--- scilab-5.5.0-orig/bin/scilab	2014-07-12 15:24:17.105686656 -0400
++++ scilab-5.5.0/bin/scilab	2014-07-12 15:25:29.307725409 -0400
+@@ -647,17 +647,6 @@
+ GTK_MODULES=$(echo $GTK_MODULES | sed s/gnomebreakpad//g)
+ export GTK_MODULES
+ 
+-# libEGL may be partially supported by the closed-source NVIDIA driver.
+-# Until they release an EGL driver, we force the egl_glx driver.
+-# http://bugzilla.scilab.org/show_bug.cgi?id=12940
 -if test -x /usr/bin/glxinfo; then
 -    NVIDIA_GLX_VENDOR=$(/usr/bin/glxinfo |grep "NVIDIA Corporation")
 -    if test ! -z "$NVIDIA_GLX_VENDOR"; then
 -        EGL_DRIVER=egl_glx
 -        export EGL_DRIVER
-+if test $SCILAB_MODE != "nw"; then
-+    if test -x /usr/bin/glxinfo; then
-+    	NVIDIA_GLX_VENDOR=$(/usr/bin/glxinfo |grep "NVIDIA Corporation")
-+    	if test ! -z "$NVIDIA_GLX_VENDOR"; then
-+            EGL_DRIVER=egl_glx
-+            export EGL_DRIVER
-+    	fi
-     fi
- fi
- 
+-    fi
+-fi
+-
+ if test $SCIVERBOSE -ne 0; then
+     echo "SCI : $SCI"
+     echo "SCIBIN : $SCIBIN"
diff --git a/sci-mathematics/scilab/scilab-5.5.0.ebuild b/sci-mathematics/scilab/scilab-5.5.0.ebuild
index 38ad3e4f3..3fe7558b5 100644
--- a/sci-mathematics/scilab/scilab-5.5.0.ebuild
+++ b/sci-mathematics/scilab/scilab-5.5.0.ebuild
@@ -241,6 +241,10 @@ src_install() {
 
 pkg_postinst() {
 	fdo-mime_mime_database_update
+	einfo "If you are using the NVIDIA binary drivers, and run into graphics"
+	einfo "crashes, you may try to run scilab as follows:"
+	einfo "EGL_DRIVER=egl_glx scilab"
+	einfo "See upstream http://bugzilla.scilab.org/show_bug.cgi?id=12940"
 }
 
 pkg_postrm() {
diff --git a/sci-mathematics/ufc/ChangeLog b/sci-mathematics/ufc/ChangeLog
index cbba8f5a0..3e9549b60 100644
--- a/sci-mathematics/ufc/ChangeLog
+++ b/sci-mathematics/ufc/ChangeLog
@@ -1,7 +1,15 @@
 # ChangeLog for sci-mathematics/ufc
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jul 2014; Andrew Reisner <andrew@reisner.co> ufc-2.3.0.ebuild:
+  added keyword
+
+*ufc-2.3.0 (15 Jul 2014)
+
+  15 Jul 2014; Andrew Reisner <andrew@reisner.co> +ufc-2.3.0.ebuild:
+  version bump
+
   02 Jul 2013; Christoph Junghans <ottxor@gentoo.org> ufc-1.4.2.ebuild:
   bumped to EAPI=5
 
diff --git a/sci-mathematics/ufc/Manifest b/sci-mathematics/ufc/Manifest
index 9a54f63c4..5ea515bee 100644
--- a/sci-mathematics/ufc/Manifest
+++ b/sci-mathematics/ufc/Manifest
@@ -1 +1,2 @@
-DIST ufc-1.4.2.tar.gz 560547 SHA256 7f67e67c1e51753cbc0755db4122e2ece585af53a7869ddb670ee6aae7f2ff91
+DIST ufc-1.4.2.tar.gz 560547 SHA256 7f67e67c1e51753cbc0755db4122e2ece585af53a7869ddb670ee6aae7f2ff91 SHA512 6737e2125d7551d893c2034ad0fb5e623c51524510b072f3ad11c1851313d6c67c71bef14426f0a29ca3e92f821b9b320f1dbe7d98ba936a393b29a98ee89ece WHIRLPOOL d5fa9db8f07108b7345c8435915779ec6a5d8535c30f5b28b4173254fe1fbe9824a422d56eb21f33a513fa84b784c72854186b3149c8a70d55ab62971505c211
+DIST ufc-2.3.0.tar.gz 93771 SHA256 e58c0033c2f4977613ab8597c6eb900fde793c22e60621cf9444d38447ee2e89 SHA512 b60a7641fcd694466e0388989e8405ebb1cb2e15320dede45c1edc1fb80ea320e5177bdbed826b3a54c8e7fcd68180bc13fb18f458b2e3fca8af9f4994b51ad6 WHIRLPOOL 295920ee84515a1eec3a78105cfb2f7377575d3ff75f01c032059f01d1a2f975c993d8cf17761ba25b9973cbe0f2b17f241d2c3c4f29dc3ee2deaafb7d806e78
diff --git a/sci-mathematics/ufc/ufc-2.3.0.ebuild b/sci-mathematics/ufc/ufc-2.3.0.ebuild
new file mode 100644
index 000000000..9d0b1568c
--- /dev/null
+++ b/sci-mathematics/ufc/ufc-2.3.0.ebuild
@@ -0,0 +1,19 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit cmake-utils
+
+DESCRIPTION="Unified framework for finite element assembly"
+HOMEPAGE="https://bitbucket.org/fenics-project/${PN}-deprecated/"
+SRC_URI="https://bitbucket.org/fenics-project/${PN}-deprecated/downloads/${P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
diff --git a/sci-physics/abinit/ChangeLog b/sci-physics/abinit/ChangeLog
index 11dd22a11..7c785b663 100644
--- a/sci-physics/abinit/ChangeLog
+++ b/sci-physics/abinit/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  10 Jul 2014; Honza Macháček <Hloupy.Honza@centrum.cz>
+  +files/7.6.3-libabinit_options.patch:
+  Added forgotten patch file 7.6.3-libabinit_options.patch for sci-
+  physics/abinit
+
 *abinit-7.6.4 (27 Jun 2014)
 
   27 Jun 2014; Honza Macháček <Hloupy.Honza@centrum.cz> +abinit-7.6.4.ebuild,
diff --git a/sci-physics/abinit/files/7.6.3-libabinit_options.patch b/sci-physics/abinit/files/7.6.3-libabinit_options.patch
new file mode 100644
index 000000000..d97d2daef
--- /dev/null
+++ b/sci-physics/abinit/files/7.6.3-libabinit_options.patch
@@ -0,0 +1,80 @@
+diff -Naurp abinit-7.6.3.orig/Makefile.am abinit-7.6.3/Makefile.am
+--- abinit-7.6.3.orig/Makefile.am	2014-04-06 20:33:21.000000000 +0000
++++ abinit-7.6.3/Makefile.am	2014-05-02 10:33:49.836301391 +0000
+@@ -1622,7 +1622,9 @@ libabinit.a:
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/11_qespresso_ext/lib11_qespresso_ext.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/12_hide_mpi/lib12_hide_mpi.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/14_hidewrite/lib14_hidewrite.a
++if DO_BUILD_15_GPU_TOOLBOX
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/15_gpu_toolbox/lib15_gpu_toolbox.a
++endif
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/16_hideleave/lib16_hideleave.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/18_timing/lib18_timing.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/21_psiesta_noabirule/lib21_psiesta_noabirule.a
+@@ -1642,7 +1644,9 @@ libabinit.a:
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/49_gw_toolbox_oop/lib49_gw_toolbox_oop.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/51_manage_mpi/lib51_manage_mpi.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_fft_mpi_noabirule/lib52_fft_mpi_noabirule.a
++if DO_BUILD_52_MANAGE_CUDA
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_manage_cuda/lib52_manage_cuda.a
++endif
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_abiutil/lib53_abiutil.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_ffts/lib53_ffts.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_spacepar/lib53_spacepar.a
+@@ -1661,14 +1665,18 @@ libabinit.a:
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/62_wvl_wfs/lib62_wvl_wfs.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/63_bader/lib63_bader.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/64_atompaw/lib64_atompaw.a
++if DO_BUILD_65_LOTF_BASE
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_lotf_base/lib65_lotf_base.a
++endif
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_nonlocal/lib65_nonlocal.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_psp/lib65_psp.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/66_paw/lib66_paw.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/66_wfs/lib66_wfs.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/67_common/lib67_common.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_dmft/lib68_dmft.a
++if DO_BUILD_68_LOTF
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_lotf/lib68_lotf.a
++endif
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_recursion/lib68_recursion.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_rsprc/lib68_rsprc.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/69_wfdesc/lib69_wfdesc.a
+diff -Naurp abinit-7.6.3.orig/Makefile.in abinit-7.6.3/Makefile.in
+--- abinit-7.6.3.orig/Makefile.in	2014-04-06 20:33:32.000000000 +0000
++++ abinit-7.6.3/Makefile.in	2014-05-02 11:25:34.961648440 +0000
+@@ -2746,7 +2746,7 @@ libabinit.a:
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/11_qespresso_ext/lib11_qespresso_ext.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/12_hide_mpi/lib12_hide_mpi.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/14_hidewrite/lib14_hidewrite.a
+-	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/15_gpu_toolbox/lib15_gpu_toolbox.a
++@DO_BUILD_15_GPU_TOOLBOX_TRUE@	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/15_gpu_toolbox/lib15_gpu_toolbox.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/16_hideleave/lib16_hideleave.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/18_timing/lib18_timing.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/21_psiesta_noabirule/lib21_psiesta_noabirule.a
+@@ -2766,7 +2766,7 @@ libabinit.a:
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/49_gw_toolbox_oop/lib49_gw_toolbox_oop.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/51_manage_mpi/lib51_manage_mpi.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_fft_mpi_noabirule/lib52_fft_mpi_noabirule.a
+-	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_manage_cuda/lib52_manage_cuda.a
++@DO_BUILD_52_MANAGE_CUDA_TRUE@	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_manage_cuda/lib52_manage_cuda.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_abiutil/lib53_abiutil.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_ffts/lib53_ffts.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_spacepar/lib53_spacepar.a
+@@ -2785,14 +2785,14 @@ libabinit.a:
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/62_wvl_wfs/lib62_wvl_wfs.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/63_bader/lib63_bader.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/64_atompaw/lib64_atompaw.a
+-	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_lotf_base/lib65_lotf_base.a
++@DO_BUILD_65_LOTF_BASE_TRUE@	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_lotf_base/lib65_lotf_base.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_nonlocal/lib65_nonlocal.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_psp/lib65_psp.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/66_paw/lib66_paw.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/66_wfs/lib66_wfs.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/67_common/lib67_common.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_dmft/lib68_dmft.a
+-	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_lotf/lib68_lotf.a
++@DO_BUILD_68_LOTF_TRUE@	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_lotf/lib68_lotf.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_recursion/lib68_recursion.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_rsprc/lib68_rsprc.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/69_wfdesc/lib69_wfdesc.a
diff --git a/sci-physics/espresso++/ChangeLog b/sci-physics/espresso++/ChangeLog
index ff742e1d5..ea6f0050e 100644
--- a/sci-physics/espresso++/ChangeLog
+++ b/sci-physics/espresso++/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  02 Jul 2014; Christoph Junghans <ottxor@gentoo.org> espresso++-9999.ebuild:
+  use ninja
+
   21 Jun 2014; Christoph Junghans <ottxor@gentoo.org> espresso++-9999.ebuild:
   added missing deps (bug #514084)
 
diff --git a/sci-physics/espresso++/espresso++-9999.ebuild b/sci-physics/espresso++/espresso++-9999.ebuild
index 66425269b..43c4297a0 100644
--- a/sci-physics/espresso++/espresso++-9999.ebuild
+++ b/sci-physics/espresso++/espresso++-9999.ebuild
@@ -5,6 +5,7 @@
 EAPI=5
 
 PYTHON_COMPAT=( python{2_6,2_7} )
+CMAKE_MAKEFILE_GENERATOR="ninja"
 
 inherit cmake-utils multilib python-single-r1
 
diff --git a/sci-physics/geant-vmc/ChangeLog b/sci-physics/geant-vmc/ChangeLog
index 353b8417e..807b464c9 100644
--- a/sci-physics/geant-vmc/ChangeLog
+++ b/sci-physics/geant-vmc/ChangeLog
@@ -2,6 +2,14 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*geant-vmc-9999 (06 Jul 2014)
+
+  06 Jul 2014; Oliver Freyermuth <o.freyermuth@googlemail.com>
+  +geant-vmc-9999.ebuild, metadata.xml:
+  New live ebuild, using cmake-buildsystem (upstream switches to cmake for next
+  release), add flags for g4root and mtroot. Adapt to upstream's fixes
+  concerning install paths, we don't need to do manually installation anymore.
+
   31 Mar 2014; Oliver Freyermuth <o.freyermuth@googlemail.com>
   geant-vmc-3.1.15a.ebuild:
   Fix syntax bug in dependency atom
diff --git a/sci-physics/geant-vmc/geant-vmc-9999.ebuild b/sci-physics/geant-vmc/geant-vmc-9999.ebuild
new file mode 100644
index 000000000..fa8fa5592
--- /dev/null
+++ b/sci-physics/geant-vmc/geant-vmc-9999.ebuild
@@ -0,0 +1,79 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit cmake-utils versionator git-r3
+
+if [[ ${PV} == *9999* ]]; then
+	EGIT_REPO_URI=" http://root.cern.ch/git/geant4_vmc.git"
+	KEYWORDS=""
+else
+	MPV=$(get_version_component_range 2-)
+	SRC_URI="ftp://root.cern.ch/root/vmc/geant4_vmc.${MPV}.tar.gz"
+	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+DESCRIPTION="Virtual Monte Carlo Geant4 implementation"
+HOMEPAGE="http://root.cern.ch/root/vmc/VirtualMC.html"
+
+LICENSE="GPL-2"
+SLOT="4"
+IUSE="doc examples geant3 +g4root +mtroot vgm"
+
+RDEPEND="
+	sci-physics/root:=
+	>=sci-physics/geant-4.9.6[opengl,geant3?]
+	vgm? ( >=sci-physics/vgm-4.00 )"
+DEPEND="${RDEPEND}
+	doc? ( app-doc/doxygen )"
+
+src_configure() {
+	local mycmakeargs=(
+			$(cmake-utils_use vgm Geant4VMC_USE_VGM)
+			$(cmake-utils_use geant3 Geant4VMC_USE_GEANT4_G3TOG4)
+			$(cmake-utils_use g4root Geant4VMC_USE_G4Root)
+			$(cmake-utils_use mtroot Geant4VMC_USE_MTRoot)
+			$(cmake-utils_use examples Geant4VMC_INSTALL_EXAMPLES)
+			)
+	cmake-utils_src_configure
+}
+
+src_compile() {
+	cmake-utils_src_compile
+	local dirs="g4root mtroot source"
+	use g4root && dirs+=" g4root "
+	use mtroot && dirs+=" mtroot "
+	use examples && dirs+=" examples "
+	local d
+	for d in ${dirs}; do
+		pushd ${d} > /dev/null || die
+		if use doc; then
+			doxygen || die
+		fi
+		popd > /dev/null
+	done
+}
+
+src_test() {
+	cd examples || die
+	local origDir=${CMAKE_USE_DIR}
+	CMAKE_USE_DIR=${CMAKE_USE_DIR}/examples
+	CMAKE_IN_SOURCE_BUILD=1
+	CMAKE_MODULE_PATH=../cmake
+	local mycmakeargs=(
+			-DCMAKE_MODULE_PATH=${origDir}/cmake
+			)
+	cmake-utils_src_configure
+	cmake-utils_src_compile
+	./run_suite.sh || die
+	CMAKE_IN_SOURCE_BUILD=0
+	CMAKE_USE_DIR=$origDir
+}
+
+src_install() {
+	cmake-utils_src_install
+	dodoc README history version_number
+	use doc && dohtml -r Geant4VMC.html doc/*
+}
diff --git a/sci-physics/geant-vmc/metadata.xml b/sci-physics/geant-vmc/metadata.xml
index 1bbc127a3..828e0454c 100644
--- a/sci-physics/geant-vmc/metadata.xml
+++ b/sci-physics/geant-vmc/metadata.xml
@@ -15,5 +15,8 @@
 </longdescription>
   <use>
     <flag name="vgm">Enable the Virtual Geometry Model (<pkg>sci-physics/vgm</pkg>)</flag>
+    <flag name="g4root">Build G4Root (interface for GEANT4 simulation with a ROOT geometry)</flag>
+    <flag name="geant3">Build with Geant4 G3toG4 library</flag>
+    <flag name="mtroot">Build MTRoot (provides ROOT IO manager classes with multi-threading support)</flag>
   </use>
 </pkgmetadata>
diff --git a/sci-physics/root/ChangeLog b/sci-physics/root/ChangeLog
index 678d6210c..e2b9be70f 100644
--- a/sci-physics/root/ChangeLog
+++ b/sci-physics/root/ChangeLog
@@ -2,6 +2,44 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/sci-physics/root/ChangeLog,v 1.96 2012/03/29 18:21:49 bicatali Exp $
 
+*root-5.34.18-r2 (06 Jul 2014)
+
+  06 Jul 2014; Andrew Savchenko <bircoph@gmail.com> +root-5.34.18-r2.ebuild,
+  +files/root-5.32.00-dotfont.patch, +files/root-5.32.00-prop-flags.patch,
+  +files/root-5.34.05-nobyte-compile.patch,
+  +files/root-5.34.18-tutorials-path.patch, metadata.xml:
+  Backport fixes for .credits, .demos, .license from ROOT-6 branch.
+
+  06 Jul 2014; Andrew Savchenko <bircoph@gmail.com> root-6.00.01-r1.ebuild,
+  root-6.00.02.ebuild, root-9999.ebuild:
+  Update LICENSE: GPL-2 code is not used during compilation.
+
+*root-6.00.02 (05 Jul 2014)
+
+  05 Jul 2014; Andrew Savchenko <bircoph@gmail.com> +root-6.00.02.ebuild:
+  Version bump. Cling fixes.
+
+  03 Jul 2014; Andrew Savchenko <bircoph@gmail.com> root-9999.ebuild:
+  Tutorial-dirs patch is accepted upstream.
+
+  02 Jul 2014; Andrew Savchenko <bircoph@gmail.com> root-6.00.01-r1.ebuild,
+  root-9999.ebuild, files/root-6.00.01-tutorials-path.patch:
+  Do not compress files required for .credits, .demo, .license
+  commands. Fix tutorials patch.
+
+  02 Jul 2014; Andrew Savchenko <bircoph@gmail.com> root-6.00.01-r1.ebuild,
+  +files/root-6.00.01-tutorials-path.patch:
+  Honor --tutdir from .demos CLI command.
+  Install files for .license and .credits commands to work.
+  Disable compression for files needed by commands above.
+
+*root-6.00.01-r1 (02 Jul 2014)
+
+  02 Jul 2014; Andrew Savchenko <bircoph@gmail.com> -root-6.00.01.ebuild,
+  +root-6.00.01-r1.ebuild, +files/root-6.00.01-cling.patch:
+  Fix Cling when prefix setup is used (see bug ROOT-6410).
+  Remove warning message because with bug fixed it is meaningless.
+
 *root-6.00.01 (29 Jun 2014)
 
   29 Jun 2014; Andrew Savchenko <bircoph@gmail.com> +root-6.00.01.ebuild,
diff --git a/sci-physics/root/Manifest b/sci-physics/root/Manifest
index 923e7cbde..9b2800970 100644
--- a/sci-physics/root/Manifest
+++ b/sci-physics/root/Manifest
@@ -1 +1,3 @@
+DIST root_v5.34.18.source.tar.gz 74218396 SHA256 9196dce7d76b31e5bcabd985bd31bc4d9b7c8c4d0c7ce84f730efa4ef82a3567 SHA512 7c659d1a92e6ad1b901956cf0a04aacc391c936eb2881528d105f61373128e5fd4caad6e76988050a8a8bc69a8ba0b53055974b4c618800345127ae2e6dd7a14 WHIRLPOOL 15221bbdabd5abd50dc87e3cc8fa3de24c5888e3ac0a75535983c8ec0718433c84c2400da59d27f3b83b687c7c5f5d60bf769c8a1eefce45dd7d39cbc002a6b7
 DIST root_v6.00.01.source.tar.gz 97783289 SHA256 245c75fd6b53b84cae6251f950e259311439da678b2cdebb9578d51561a6b61f SHA512 e5f56750a0637aa884ea2d9d2ebf7b677cd1fac1819042948ba3530a25366cb7d853dba6fa7127764e3ae7cec23f89ed60d8913c0ff10ce2664bcc87df1620cf WHIRLPOOL 92f34c13ee0161d556b54b1bdd971774b2637c5cd57916ee75f0572a30713df820df3bb07f276d16ca31d11fda7e762de673c943b8bffda9db501d2ee8848654
+DIST root_v6.00.02.source.tar.gz 97811067 SHA256 db92818781f842c33b8b583f1f9be02b51cedbf5f2943df986cbbd0c0006a06f SHA512 bd72eb43d2a4ace27738ba2dc509f6d81ec3555e59454426d28c2c5522b4b19d2678ed515b84efaf953146c1f50c65e304532456d76076d03598bda67c69e8a5 WHIRLPOOL 12b87e9b1612ea3625f7ea0970b733887051b5173b728b5f13a032eb103eeda22de8a4c18417e02a92fe02f29b9acd9114fa1420fac42bea31bde07c7a0ce697
diff --git a/sci-physics/root/files/root-5.32.00-dotfont.patch b/sci-physics/root/files/root-5.32.00-dotfont.patch
new file mode 100644
index 000000000..85d6dea76
--- /dev/null
+++ b/sci-physics/root/files/root-5.32.00-dotfont.patch
@@ -0,0 +1,58 @@
+--- root/html/src/TClassDocOutput.cxx.orig	2012-05-25 16:18:10.000000000 +0400
++++ root/html/src/TClassDocOutput.cxx	2012-05-29 21:36:53.813593012 +0400
+@@ -625,7 +625,7 @@
+       << "size=\"8,10\";" << endl
+       << "ratio=auto;" << endl
+       << "margin=0;" << endl
+-      << "node [shape=plaintext,fontsize=40,width=4,height=0.75];" << endl
++      << "node [shape=plaintext,fontsize=40,width=4,height=0.75,fontname=\"DejaVu Serif\"];" << endl
+       << "\"" << fCurrentClass->GetName() << "\" [shape=ellipse];" << endl;
+ 
+    std::stringstream ssDep;
+@@ -704,7 +704,7 @@
+             outdot << ";" << endl;
+          } else if (writeAndMoreFor) {
+                outdot << "  \"...andmore" << writeAndMoreFor->GetName()
+-                      << "\" [label=\"...and more\",fontname=\"Times-Italic\",fillcolor=lightgrey,style=filled];" << endl;
++                      << "\" [label=\"...and more\",fontname=\"DejaVu Serif Italic\",fillcolor=lightgrey,style=filled];" << endl;
+          }
+       }
+       if (!levelExists) break;
+@@ -733,7 +733,7 @@
+       << "ranksep=0.1;" << endl
+       << "nodesep=0;" << endl
+       << "margin=0;" << endl;
+-   outdot << "  node [style=filled,width=0.7,height=0.15,fixedsize=true,shape=plaintext,fontsize=10];" << endl;
++   outdot << "  node [style=filled,width=0.7,height=0.15,fixedsize=true,shape=plaintext,fontsize=10,fontname=\"DejaVu Serif\"];" << endl;
+ 
+    std::stringstream ssDep;
+    const int numColumns = 3;
+@@ -939,7 +939,7 @@
+       << "ranksep=0;" << endl
+       << "nodesep=0;" << endl
+       << "size=\"8,10\";" << endl
+-      << "node [fontsize=20,shape=plaintext];" << endl;
++      << "node [fontsize=20,shape=plaintext,fontname=\"DejaVu Serif\"];" << endl;
+ 
+    for (std::list<std::string>::iterator iFile = listFilesToParse.begin();
+       iFile != listFilesToParse.end(); ++iFile) {
+@@ -999,7 +999,8 @@
+       << "ranksep=0.7;" << endl
+       << "nodesep=0.3;" << endl
+       << "size=\"8,8\";" << endl
+-      << "ratio=compress;" << endl;
++      << "ratio=compress;" << endl
++      << "node [fontname=\"DejaVu Serif\"];" << endl;
+ 
+    TString libs(fCurrentClass->GetSharedLibs());
+    outdot << "\"All Libraries\" [URL=\"LibraryDependencies.html\",shape=box,rank=max,fillcolor=lightgray,style=filled];" << endl;
+@@ -1109,7 +1110,8 @@
+ 
+    dotout << "digraph G {" << endl
+           << "ratio=auto;" << endl
+-          << "rankdir=RL;" << endl;
++          << "rankdir=RL;" << endl
++          << "node [fontname=\"DejaVu Serif\"];" << endl;
+ 
+    // loop on all classes
+    TClassDocInfo* cdi = 0;
diff --git a/sci-physics/root/files/root-5.32.00-prop-flags.patch b/sci-physics/root/files/root-5.32.00-prop-flags.patch
new file mode 100644
index 000000000..7dfeb1cc3
--- /dev/null
+++ b/sci-physics/root/files/root-5.32.00-prop-flags.patch
@@ -0,0 +1,15 @@
+--- root/config/Makefile.in.orig	2013-01-21 22:04:43.011452938 +0400
++++ root/config/Makefile.in	2013-01-21 22:04:18.027352209 +0400
+@@ -25,9 +25,9 @@
+ USECONFIG      := @useconfig@
+ MKLIBOPTIONS   := @mkliboption@
+ 
+-EXTRA_CFLAGS   := -Iinclude @cflags@
+-EXTRA_CXXFLAGS := -Iinclude @cflags@
+-EXTRA_LDFLAGS  := @ldflags@
++EXTRA_CFLAGS   := -Iinclude @cflags@ $(CFLAGS)
++EXTRA_CXXFLAGS := -Iinclude @cflags@ $(CXXFLAGS)
++EXTRA_LDFLAGS  := @ldflags@ $(LDFLAGS)
+ WINRTDEBUG     := @winrtdebug@
+ 
+ GLBPATCHFLAGS  := @glbpatchcflags@
diff --git a/sci-physics/root/files/root-5.34.05-nobyte-compile.patch b/sci-physics/root/files/root-5.34.05-nobyte-compile.patch
new file mode 100644
index 000000000..ec67a1588
--- /dev/null
+++ b/sci-physics/root/files/root-5.34.05-nobyte-compile.patch
@@ -0,0 +1,137 @@
+diff -Naur root.as-needed/Makefile root/Makefile
+--- a/Makefile.orig	2013-02-15 02:27:56.000000000 +0400
++++ b/Makefile	2013-02-23 02:22:14.556465852 +0400
+@@ -1258,10 +1258,7 @@
+ 	   for lib in $(RFLX_GRFLXPY); do \
+ 	      rm -f $(DESTDIR)$(LIBDIR)/$${lib#lib/}; \
+ 	   done; \
+-	   for lib in $(RFLX_GRFLXPYC); do \
+-	      rm -f $(DESTDIR)$(LIBDIR)/$${lib#lib/}; \
+-	   done; \
+-	   if test "x$(RFLX_GRFLXPY)$(RFLX_GRFLXPYC)" != "x"; then \
++	   if test "x$(RFLX_GRFLXPY)" != "x"; then \
+ 	      dir=$(subst lib/,,$(RFLX_GRFLXDD)); \
+ 	      while test "x$${dir}" != "x" && \
+ 	         test -d $(DESTDIR)$(LIBDIR)/$${dir} && \
+diff -Naur root.as-needed/bindings/pyroot/Module.mk root/bindings/pyroot/Module.mk
+--- root.as-needed/bindings/pyroot/Module.mk	2011-07-10 10:42:48.991561304 +0400
++++ root/bindings/pyroot/Module.mk	2011-07-10 10:43:21.493339703 +0400
+@@ -48,8 +48,6 @@
+ ROOTPY       := $(subst $(MODDIR),$(LPATH),$(ROOTPYS))
+ $(LPATH)/%.py: $(MODDIR)/%.py; cp $< $@
+ endif
+-ROOTPYC      := $(ROOTPY:.py=.pyc)
+-ROOTPYO      := $(ROOTPY:.py=.pyo)
+ 
+ # used in the main Makefile
+ ALLHDRS      += $(patsubst $(MODDIRI)/%.h,include/%.h,$(PYROOTH))
+@@ -68,10 +66,8 @@
+ include/%.h:    $(PYROOTDIRI)/%.h
+ 		cp $< $@
+ 
+-%.pyc: %.py;    python -c 'import py_compile; py_compile.compile( "$<" )'
+-%.pyo: %.py;    python -O -c 'import py_compile; py_compile.compile( "$<" )'
+ 
+-$(PYROOTLIB):   $(PYROOTO) $(PYROOTDO) $(ROOTPY) $(ROOTPYC) $(ROOTPYO) \
++$(PYROOTLIB):   $(PYROOTO) $(PYROOTDO) $(ROOTPY) \
+                 $(ROOTLIBSDEP) $(PYTHONLIBDEP)
+ 		@$(MAKELIB) $(PLATFORM) $(LD) "$(LDFLAGS)" \
+ 		  "$(SOFLAGS)" libPyROOT.$(SOEXT) $@ \
+@@ -113,7 +109,7 @@
+ 
+ distclean-$(MODNAME): clean-$(MODNAME)
+ 		@rm -f $(PYROOTDEP) $(PYROOTDS) $(PYROOTDH) $(PYROOTLIB) \
+-		   $(ROOTPY) $(ROOTPYC) $(ROOTPYO) $(PYROOTMAP) \
++		   $(ROOTPY) $(PYROOTMAP) \
+ 		   $(PYROOTPYD) $(PYTHON64DEP) $(PYTHON64)
+ 
+ distclean::     distclean-$(MODNAME)
+diff -Naur root.as-needed/build/package/debian/rules root/build/package/debian/rules
+--- root.as-needed/build/package/debian/rules	2011-07-10 10:42:49.241549346 +0400
++++ root/build/package/debian/rules	2011-07-10 10:48:06.989670589 +0400
+@@ -691,10 +691,6 @@
+ 		-X$(SYSCONFDIR)/root/system.rootauthrc			\
+ 		-X$(SYSCONFDIR)/root/system.rootdaemonrc		\
+ 		-X$(PREFIX)/lib/root/$(SOVERS)/libAfterImage.a		\
+-		-X$(PREFIX)/lib/root/$(SOVERS)/PyCintex.pyc		\
+-		-X$(PREFIX)/lib/root/$(SOVERS)/PyCintex.pyo		\
+-		-X$(PREFIX)/lib/root/$(SOVERS)/ROOT.pyc			\
+-		-X$(PREFIX)/lib/root/$(SOVERS)/ROOT.pyo			\
+ 		-X$(PREFIX)/lib/root/$(SOVERS)/cint7			\
+ 		-X$(PREFIX)/include/root/Minuit2
+ #		$(foreach i, \
+diff -Naur root.as-needed/cint/cintex/Module.mk root/cint/cintex/Module.mk
+--- root.as-needed/cint/cintex/Module.mk	2011-07-10 10:42:49.104889217 +0400
++++ root/cint/cintex/Module.mk	2011-07-10 10:43:21.496672876 +0400
+@@ -31,10 +31,6 @@
+ CINTEXPY     := $(subst $(MODDIR)/python,$(LPATH),$(CINTEXPYS))
+ $(LPATH)/%.py: $(MODDIR)/python/%.py; cp $< $@
+ endif
+-ifneq ($(BUILDPYTHON),no)
+-CINTEXPYC    := $(CINTEXPY:.py=.pyc)
+-CINTEXPYO    := $(CINTEXPY:.py=.pyo)
+-endif
+ 
+ # used in the main Makefile
+ ALLHDRS      += $(patsubst $(MODDIRI)/Cintex/%.h,include/Cintex/%.h,$(CINTEXH))
+@@ -86,8 +82,6 @@
+ 		fi)
+ 		cp $< $@
+ 
+-%.pyc: %.py;    python -c 'import py_compile; py_compile.compile( "$<" )'
+-%.pyo: %.py;    python -O -c 'import py_compile; py_compile.compile( "$<" )'
+ 
+ $(CINTEXLIB):   $(CINTEXO) $(CINTEXPY) $(CINTEXPYC) $(CINTEXPYO) \
+                 $(ORDER_) $(subst $(CINTEXLIB),,$(MAINLIBS)) $(CINTEXLIBDEP)
+diff -Naur root.as-needed/cint/reflex/Module.mk root/cint/reflex/Module.mk
+--- root.as-needed/cint/reflex/Module.mk	2011-07-10 10:42:49.074890651 +0400
++++ root/cint/reflex/Module.mk	2011-07-10 10:43:21.496672876 +0400
+@@ -48,9 +48,6 @@
+ RFLX_GRFLXS   := $(wildcard $(RFLX_GRFLXSD)/*.py)
+ RFLX_GRFLXPY  := $(patsubst $(RFLX_GRFLXSD)/%.py,$(RFLX_GRFLXDD)/%.py,$(RFLX_GRFLXS))
+ RFLX_GRFLXPY  += $(RFLX_GCCXMLPATHPY)
+-ifneq ($(BUILDPYTHON),no)
+-RFLX_GRFLXPYC := $(subst .py,.pyc,$(RFLX_GRFLXPY))
+-endif
+ 
+ RFLX_LIBDIR = $(LIBDIR)
+ 
+@@ -92,7 +89,7 @@
+ 
+ ALLEXECS += $(RFLX_GENMAPX)
+ 
+-POSTBIN  += $(RFLX_GRFLXPYC) $(RFLX_GRFLXPY)
++POSTBIN  += $(RFLX_GRFLXPY)
+ 
+ ##### local rules #####
+ .PHONY:         all-$(MODNAME) clean-$(MODNAME) distclean-$(MODNAME) \
+@@ -122,8 +119,6 @@
+ 		  mkdir -p lib/python/genreflex; fi )
+ 		cp $< $@
+ 
+-$(RFLX_GRFLXDD)/%.pyc: $(RFLX_GRFLXDD)/%.py
+-		@python -c 'import py_compile; py_compile.compile( "$<" )'
+ 
+ $(RFLX_GENMAPO) : CXXFLAGS += -I$(REFLEXDIRS)/genmap
+ 
+@@ -149,7 +144,7 @@
+ 		$(RLIBMAP) -o $@ -l $(REFLEXDICTLIB) \
+ 		   -d $(REFLEXDICTLIBDEPM) -c $(REFLEXL)
+ 
+-all-$(MODNAME): $(REFLEXLIB) $(REFLEXDICTLIB) $(REFLEXDICTMAP) $(RFLX_GRFLXPYC) $(RFLX_GRFLXPY)
++all-$(MODNAME): $(REFLEXLIB) $(REFLEXDICTLIB) $(REFLEXDICTMAP) $(RFLX_GRFLXPY)
+ 
+ clean-genreflex:
+ 		@rm -rf lib/python/genreflex
+diff -Naur root.as-needed/cint/reflex/python/CMakeLists.txt root/cint/reflex/python/CMakeLists.txt
+--- root.as-needed/cint/reflex/python/CMakeLists.txt	2011-07-10 10:42:49.074890651 +0400
++++ root/cint/reflex/python/CMakeLists.txt	2011-07-10 10:43:21.496672876 +0400
+@@ -15,7 +15,7 @@
+ #####################   sources   ####################
+ 
+ FILE(GLOB_RECURSE GENREFLEX_SRCS RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} genreflex/*.py)
+-SET(GENREFLEX_SCRIPT ${CMAKE_CURRENT_BINARY_DIR}/genreflex/genreflex.pyc PARENT_SCOPE)
++SET(GENREFLEX_SCRIPT PARENT_SCOPE)
+ 
+ #####################  gccxmlpath ####################
+ 
diff --git a/sci-physics/root/files/root-5.34.18-tutorials-path.patch b/sci-physics/root/files/root-5.34.18-tutorials-path.patch
new file mode 100644
index 000000000..8bf88594d
--- /dev/null
+++ b/sci-physics/root/files/root-5.34.18-tutorials-path.patch
@@ -0,0 +1,94 @@
+diff --git a/config/RConfigure.in b/config/RConfigure.in
+index 5950401..e4fbfbf 100644
+--- a/config/RConfigure.in
++++ b/config/RConfigure.in
+@@ -11,6 +11,7 @@
+ #define ROOTDATADIR   "@datadir@"
+ #define ROOTDOCDIR    "@docdir@"
+ #define ROOTMACRODIR  "@macrodir@"
++#define ROOTTUTDIR    "@tutdir@"
+ #define ROOTSRCDIR    "@srcdir@"
+ #define ROOTICONPATH  "@iconpath@"
+ #define EXTRAICONPATH "@extraiconpath@"
+diff --git a/configure b/configure
+index 131df92..2c8ea95 100755
+--- a/configure
++++ b/configure
+@@ -7537,6 +7537,7 @@ sed \
+     -e "s|@prefix@|$prefix|"               \
+     -e "s|@srcdir@|$srcdir|"               \
+     -e "s|@ttffontdir@|$fontdir|"          \
++    -e "s|@tutdir@|$tutdir|"               \
+     -e "s|@setresuid@|$setresuid|"         \
+     -e "s|@hasmathmore@|$hasmathmore|"     \
+     -e "s|@haspthread@|$haspthread|"       \
+diff --git a/core/base/src/TApplication.cxx b/core/base/src/TApplication.cxx
+index 95fb1e5..3830955 100644
+--- a/core/base/src/TApplication.cxx
++++ b/core/base/src/TApplication.cxx
+@@ -794,6 +794,22 @@ Long_t TApplication::ProcessRemote(const char *line, Int_t *)
+    return 1;
+ }
+ 
++namespace {
++   static int PrintFile(const char* filename) {
++      TString sFileName(filename);
++      gSystem->ExpandPathName(sFileName);
++      if (gSystem->AccessPathName(sFileName)) {
++         Error("ProcessLine()", "Cannot find file %s", filename);
++         return 1;
++      }
++      std::ifstream instr(sFileName);
++      TString content;
++      content.ReadFile(instr);
++      Printf("%s", content.Data());
++      return 0;
++   }
++}
++
+ //______________________________________________________________________________
+ Long_t TApplication::ProcessLine(const char *line, Bool_t sync, Int_t *err)
+ {
+@@ -827,11 +843,41 @@ Long_t TApplication::ProcessLine(const char *line, Bool_t sync, Int_t *err)
+       return 0;
+    }
+ 
+-   if (!strncmp(line, "?", 1)) {
++   if (!strncmp(line, "?", 1) || !strncmp(line, ".help", 5)) {
+       Help(line);
+       return 1;
+    }
+ 
++   if (!strncmp(line, ".demo", 5)) {
++      if (gROOT->IsBatch()) {
++         Error("ProcessLine", "Cannot show demos in batch mode!");
++         return 1;
++      }
++#ifdef ROOTTUTDIR
++      ProcessLine(".x " ROOTTUTDIR "/demos.C");
++#else
++      ProcessLine(".x $(ROOTSYS)/tutorials/demos.C");
++#endif
++      return 0;
++   }
++
++   if (!strncmp(line, ".license", 8)) {
++#ifdef ROOTDOCDIR
++      return PrintFile(ROOTDOCDIR "/LICENSE");
++#else
++      return PrintFile("$(ROOTSYS)/LICENSE");
++#endif
++   }
++
++   if (!strncmp(line, ".credits", 8)) {
++#ifdef ROOTDOCDIR
++      return PrintFile(ROOTDOCDIR "/CREDITS");
++#else
++      return PrintFile("$(ROOTSYS)/README/CREDITS");
++#endif
++     
++   }
++
+    if (!strncmp(line, ".pwd", 4)) {
+       if (gDirectory)
+          Printf("Current directory: %s", gDirectory->GetPath());
diff --git a/sci-physics/root/files/root-6.00.01-cling.patch b/sci-physics/root/files/root-6.00.01-cling.patch
new file mode 100644
index 000000000..146e89fde
--- /dev/null
+++ b/sci-physics/root/files/root-6.00.01-cling.patch
@@ -0,0 +1,19 @@
+commit eea9517c17bd86beda895a5a8b3ffe59af18596f
+Author: Axel Naumann <Axel.Naumann@cern.ch>
+Date:   Tue Jul 1 17:45:20 2014 +0200
+
+    From Pere: go via TSystem to use prefix if defined (ROOT-6410).
+
+diff --git a/core/meta/src/TCling.cxx b/core/meta/src/TCling.cxx
+index baec571..4976d4e 100644
+--- a/core/meta/src/TCling.cxx
++++ b/core/meta/src/TCling.cxx
+@@ -4703,7 +4703,7 @@ void* TCling::LazyFunctionCreatorAutoload(const std::string& mangled_name) {
+    TString lib;
+    Ssiz_t posLib = 0;
+    while (libs.Tokenize(lib, posLib)) {
+-      if (Load(lib, kFALSE /*system*/) < 0) {
++      if (gSystem->Load(lib, "", kFALSE /*system*/) < 0) {
+          // The library load failed, all done.
+          //fprintf(stderr, "load failed: %s\n", errmsg.c_str());
+          return 0;
diff --git a/sci-physics/root/files/root-6.00.01-tutorials-path.patch b/sci-physics/root/files/root-6.00.01-tutorials-path.patch
new file mode 100644
index 000000000..cb6861554
--- /dev/null
+++ b/sci-physics/root/files/root-6.00.01-tutorials-path.patch
@@ -0,0 +1,39 @@
+diff --git a/config/RConfigure.in b/config/RConfigure.in
+index 5950401..e4fbfbf 100644
+--- a/config/RConfigure.in
++++ b/config/RConfigure.in
+@@ -11,6 +11,7 @@
+ #define ROOTDATADIR   "@datadir@"
+ #define ROOTDOCDIR    "@docdir@"
+ #define ROOTMACRODIR  "@macrodir@"
++#define ROOTTUTDIR    "@tutdir@"
+ #define ROOTSRCDIR    "@srcdir@"
+ #define ROOTICONPATH  "@iconpath@"
+ #define EXTRAICONPATH "@extraiconpath@"
+diff --git a/configure b/configure
+index 131df92..2c8ea95 100755
+--- a/configure
++++ b/configure
+@@ -7537,6 +7537,7 @@ sed \
+     -e "s|@prefix@|$prefix|"               \
+     -e "s|@srcdir@|$srcdir|"               \
+     -e "s|@ttffontdir@|$fontdir|"          \
++    -e "s|@tutdir@|$tutdir|"               \
+     -e "s|@setresuid@|$setresuid|"         \
+     -e "s|@hasmathmore@|$hasmathmore|"     \
+     -e "s|@haspthread@|$haspthread|"       \
+diff --git a/core/base/src/TApplication.cxx b/core/base/src/TApplication.cxx
+index 1c1809a..7d7ed37 100644
+--- a/core/base/src/TApplication.cxx
++++ b/core/base/src/TApplication.cxx
+@@ -866,8 +866,8 @@ Long_t TApplication::ProcessLine(const char *line, Bool_t sync, Int_t *err)
+          Error("ProcessLine", "Cannot show demos in batch mode!");
+          return 1;
+       }
+-#ifdef ROOTDOCDIR
+-      ProcessLine(".x " ROOTDOCDIR "/tutorials/demos.C");
++#ifdef ROOTTUTDIR
++      ProcessLine(".x " ROOTTUTDIR "/demos.C");
+ #else
+       ProcessLine(".x $(ROOTSYS)/tutorials/demos.C");
+ #endif
diff --git a/sci-physics/root/metadata.xml b/sci-physics/root/metadata.xml
index 2a666cfdc..622d99ad4 100644
--- a/sci-physics/root/metadata.xml
+++ b/sci-physics/root/metadata.xml
@@ -17,12 +17,14 @@
   GUI toolkit, and a complete visualization framework.
 </longdescription>
 <use>
+  <flag name="c++0x"> Build ROOT using the C++11 standard. Not supported, requires <pkg>sys-devel/gcc</pkg>&gt;=4.7.0</flag>
   <flag name="fits">Support for images and data from FITS files with <pkg>sci-libs/cfitsio</pkg></flag>
   <flag name="geocad">Enable ROOT-CAD interface using <pkg>sci-libs/opencascade</pkg></flag>
   <flag name="http">Enable http server support including but not limited to fastcgi support</flag>
   <flag name="math">Build all math related libraries plugins, needs <pkg>sci-libs/gsl</pkg> </flag>
   <flag name="pythia6">Build the interface for <pkg>sci-physics/pythia</pkg> version 6.x </flag>
   <flag name="pythia8">Build the interface for <pkg>sci-physics/pythia</pkg> version 8.x </flag>
+  <flag name="reflex">Build the reflection database for the C++ interpreter</flag>
   <flag name="xrootd">Build the interface for <pkg>net-libs/xrootd</pkg> </flag>
 </use>
 </pkgmetadata>
diff --git a/sci-physics/root/root-5.34.18-r2.ebuild b/sci-physics/root/root-5.34.18-r2.ebuild
new file mode 100644
index 000000000..072b81d9c
--- /dev/null
+++ b/sci-physics/root/root-5.34.18-r2.ebuild
@@ -0,0 +1,387 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-physics/root/root-5.34.18-r1.ebuild,v 1.3 2014/03/27 18:51:54 bicatali Exp $
+
+EAPI=5
+
+if [[ ${PV} == "9999" ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="http://root.cern.ch/git/root.git"
+	SRC_URI=""
+	KEYWORDS=""
+else
+	SRC_URI="ftp://root.cern.ch/${PN}/${PN}_v${PV}.source.tar.gz"
+	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+PYTHON_COMPAT=( python2_{6,7} )
+
+inherit elisp-common eutils fdo-mime fortran-2 multilib python-single-r1 \
+	toolchain-funcs user versionator
+
+DESCRIPTION="C++ data analysis framework and interpreter from CERN"
+HOMEPAGE="http://root.cern.ch/"
+DOC_URI="ftp://root.cern.ch/${PN}/doc"
+
+SLOT="0/$(get_version_component_range 1-3 ${PV})"
+LICENSE="LGPL-2.1 freedist MSttfEULA LGPL-3 libpng UoI-NCSA"
+IUSE="+X afs avahi c++0x doc emacs examples fits fftw graphviz
+	kerberos ldap +math minimal mpi mysql odbc +opengl openmp
+	oracle postgres	prefix pythia6 pythia8 python qt4 +reflex
+	ruby sqlite	ssl xinetd xml xrootd"
+
+REQUIRED_USE="
+	!X? ( !opengl !qt4 )
+	mpi? ( math !openmp )
+	openmp? ( math !mpi )
+	python? ( ${PYTHON_REQUIRED_USE} )"
+
+CDEPEND="
+	app-arch/xz-utils:0=
+	>=dev-lang/cfortran-4.4-r2
+	dev-libs/libpcre:3=
+	media-fonts/dejavu
+	media-libs/freetype:2=
+	media-libs/giflib:0=
+	media-libs/libpng:0=
+	media-libs/tiff:0=
+	sys-libs/zlib:0=
+	virtual/jpeg:0
+	virtual/shadow
+	X? (
+		media-libs/ftgl:0=
+		media-libs/glew:0=
+		x11-libs/libX11:0=
+		x11-libs/libXext:0=
+		x11-libs/libXpm:0=
+		!minimal? (
+			|| (
+				media-libs/libafterimage:0=[gif,jpeg,png,tiff]
+				>=x11-wm/afterstep-2.2.11:0=[gif,jpeg,png,tiff]
+			)
+			opengl? ( virtual/opengl virtual/glu x11-libs/gl2ps:0= )
+			qt4? (
+				dev-qt/qtgui:4=
+				dev-qt/qtopengl:4=
+				dev-qt/qt3support:4=
+				dev-qt/qtsvg:4=
+				dev-qt/qtwebkit:4=
+				dev-qt/qtxmlpatterns:4=
+			)
+			x11-libs/libXft:0=
+		)
+	)
+	!minimal? (
+		afs? ( net-fs/openafs )
+		avahi? ( net-dns/avahi:0= )
+		emacs? ( virtual/emacs )
+		fits? ( sci-libs/cfitsio:0= )
+		fftw? ( sci-libs/fftw:3.0= )
+		graphviz? ( media-gfx/graphviz:0= )
+		kerberos? ( virtual/krb5 )
+		ldap? ( net-nds/openldap:0= )
+		math? (
+			sci-libs/gsl:0=
+			sci-mathematics/unuran:0=
+			mpi? ( virtual/mpi )
+		)
+		mysql? ( virtual/mysql )
+		odbc? ( || ( dev-db/libiodbc:0= dev-db/unixODBC:0= ) )
+		oracle? ( dev-db/oracle-instantclient-basic:0= )
+		postgres? ( dev-db/postgresql-base:= )
+		pythia6? ( sci-physics/pythia:6= )
+		pythia8? ( >=sci-physics/pythia-8.1.80:8= )
+		python? ( ${PYTHON_DEPS} )
+		ruby? (
+			dev-lang/ruby
+			dev-ruby/rubygems
+		)
+		sqlite? ( dev-db/sqlite:3= )
+		ssl? ( dev-libs/openssl:0= )
+		xml? ( dev-libs/libxml2:2= )
+		xrootd? ( >=net-libs/xrootd-3.3.5:0= )
+	)"
+
+DEPEND="${CDEPEND}
+	virtual/pkgconfig"
+
+RDEPEND="${CDEPEND}
+	reflex? ( dev-cpp/gccxml )
+	xinetd? ( sys-apps/xinetd )"
+
+PDEPEND="doc? ( ~app-doc/root-docs-${PV}[math=] )"
+
+S="${WORKDIR}/${PN}"
+
+# install stuff in ${P} and not ${PF} for easier tracking in root-docs
+DOC_DIR="/usr/share/doc/${P}"
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	use python && python-single-r1_pkg_setup
+	echo
+	elog "There are extra options on packages not yet in Gentoo:"
+	elog "Afdsmgrd, AliEn, castor, Chirp, dCache, gfal, Globus, gLite,"
+	elog "HDFS, Monalisa, MaxDB/SapDB, SRP."
+	elog "You can use the env variable EXTRA_ECONF variable for this."
+	elog "For example, for SRP, you would set: "
+	elog "EXTRA_ECONF=\"--enable-srp --with-srp-libdir=${EROOT%/}/usr/$(get_libdir)\""
+	echo
+
+	enewgroup rootd
+	enewuser rootd -1 -1 /var/spool/rootd rootd
+
+	use minimal && return
+
+	if use math; then
+		if use openmp; then
+			if [[ $(tc-getCXX)$ == *g++* ]] && ! tc-has-openmp; then
+				ewarn "You are using a g++ without OpenMP capabilities"
+				die "Need an OpenMP capable compiler"
+			else
+				export USE_OPENMP=1 USE_PARALLEL_MINUIT2=1
+			fi
+		elif use mpi; then
+			export USE_MPI=1 USE_PARALLEL_MINUIT2=1
+		fi
+	fi
+	if use c++0x && [[ $(tc-getCXX) == *g++* ]] && \
+		! version_is_at_least "4.7" "$(gcc-version)"; then
+		eerror "You are using a g++ without C++0x capabilities"
+		die "Need an C++0x capable compiler"
+	fi
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PN}-5.28.00b-glibc212.patch \
+		"${FILESDIR}"/${PN}-5.32.00-prop-flags.patch \
+		"${FILESDIR}"/${PN}-5.32.00-afs.patch \
+		"${FILESDIR}"/${PN}-5.32.00-cfitsio.patch \
+		"${FILESDIR}"/${PN}-5.32.00-chklib64.patch \
+		"${FILESDIR}"/${PN}-5.32.00-dotfont.patch \
+		"${FILESDIR}"/${PN}-5.34.05-nobyte-compile.patch \
+		"${FILESDIR}"/${PN}-5.34.13-unuran.patch \
+		"${FILESDIR}"/${PN}-5.34.13-desktop.patch \
+		"${FILESDIR}"/${PN}-5.34.18-tutorials-path.patch
+
+	# make sure we use system libs and headers
+	rm montecarlo/eg/inc/cfortran.h README/cfortran.doc || die
+	rm -r graf2d/asimage/src/libAfterImage || die
+	rm -r graf3d/ftgl/{inc,src} || die
+	rm -r graf2d/freetype/src || die
+	rm -r graf3d/glew/{inc,src} || die
+	rm -r core/pcre/src || die
+	rm -r math/unuran/src/unuran-*.tar.gz || die
+	LANG=C LC_ALL=C find core/zip -type f -name "[a-z]*" -print0 | \
+		xargs -0 rm || die
+	rm -r core/lzma/src/*.tar.gz || die
+	rm graf3d/gl/{inc,src}/gl2ps.* || die
+	sed -i -e 's/^GLLIBS *:= .* $(OPENGLLIB)/& -lgl2ps/' \
+		graf3d/gl/Module.mk || die
+
+	# In Gentoo, libPythia6 is called libpythia6
+	# iodbc is in /usr/include/iodbc
+	# pg_config.h is checked instead of libpq-fe.h
+	sed -i \
+		-e 's:libPythia6:libpythia6:g' \
+		-e 's:$ODBCINCDIR:$ODBCINCDIR /usr/include/iodbc:' \
+		-e 's:libpq-fe.h:pg_config.h:' \
+		configure || die "adjusting configure for Gentoo failed"
+
+	# prefixify the configure script
+	sed -i \
+		-e 's:/usr:${EPREFIX}/usr:g' \
+		configure || die "prefixify configure failed"
+
+	# fix reflex path (bug #497280)
+	sed -i -e 's|${ROOTSYS}/lib|@libdir@|' config/genreflex.in || die
+
+	# QTDIR only used for qt3 in gentoo, and configure looks for it.
+	unset QTDIR
+}
+
+src_configure() {
+
+	# the configure script is not the standard autotools
+	local myconf=(
+		--prefix="${EPREFIX}/usr"
+		--etcdir="${EPREFIX}/etc/root"
+		--libdir="${EPREFIX}/usr/$(get_libdir)/${PN}"
+		--docdir="${EPREFIX}${DOC_DIR}"
+		--tutdir="${EPREFIX}${DOC_DIR}/examples/tutorials"
+		--testdir="${EPREFIX}${DOC_DIR}/examples/tests"
+		--with-cc="$(tc-getCC)"
+		--with-cxx="$(tc-getCXX)"
+		--with-f77="$(tc-getFC)"
+		--with-ld="$(tc-getCXX)"
+		--nohowto
+	)
+
+	if use minimal; then
+		myconf+=( $(usex X --gminimal --minimal) )
+	else
+		myconf+=(
+			--with-afs-shared=yes
+			--with-sys-iconpath="${EPREFIX}/usr/share/pixmaps"
+			--disable-builtin-afterimage
+			--disable-builtin-ftgl
+			--disable-builtin-freetype
+			--disable-builtin-glew
+			--disable-builtin-pcre
+			--disable-builtin-zlib
+			--disable-builtin-lzma
+			--disable-cling
+			--enable-astiff
+			--enable-explicitlink
+			--enable-gdml
+			--enable-memstat
+			--enable-shadowpw
+			--enable-shared
+			--enable-soversion
+			--enable-table
+			--fail-on-missing
+			$(use_enable X x11)
+			$(use_enable X asimage)
+			$(use_enable X xft)
+			$(use_enable afs)
+			$(use_enable avahi bonjour)
+			$(use_enable c++0x cxx11)
+			$(use_enable fits fitsio)
+			$(use_enable fftw fftw3)
+			$(use_enable graphviz gviz)
+			$(use_enable kerberos krb5)
+			$(use_enable ldap)
+			$(use_enable math gsl-shared)
+			$(use_enable math genvector)
+			$(use_enable math mathmore)
+			$(use_enable math minuit2)
+			$(use_enable math roofit)
+			$(use_enable math tmva)
+			$(use_enable math unuran)
+			$(use_enable mysql)
+			$(use_enable odbc)
+			$(use_enable opengl)
+			$(use_enable oracle)
+			$(use_enable postgres pgsql)
+			$(usex postgres \
+				"--with-pgsql-incdir=$(pg_config --includedir)" "")
+			$(use_enable prefix rpath)
+			$(use_enable pythia6)
+			$(use_enable pythia8)
+			$(use_enable python)
+			$(use_enable qt4 qt)
+			$(use_enable qt4 qtgsi)
+			$(use_enable reflex cintex)
+			$(use_enable reflex)
+			$(use_enable ruby)
+			$(use_enable sqlite)
+			$(use_enable ssl)
+			$(use_enable xml)
+			$(use_enable xrootd)
+			${EXTRA_ECONF}
+		)
+	fi
+
+	./configure ${myconf[@]} || die "configure failed"
+}
+
+src_compile() {
+	emake \
+		OPT="${CXXFLAGS}" \
+		F77OPT="${FFLAGS}" \
+		ROOTSYS="${S}" \
+		LD_LIBRARY_PATH="${S}/lib"
+	use emacs && ! use minimal && elisp-compile build/misc/*.el
+}
+
+daemon_install() {
+	local daemons="rootd proofd"
+	dodir /var/spool/rootd
+	fowners rootd:rootd /var/spool/rootd
+	dodir /var/spool/rootd/{pub,tmp}
+	fperms 1777 /var/spool/rootd/{pub,tmp}
+
+	for i in ${daemons}; do
+		newinitd "${FILESDIR}"/${i}.initd ${i}
+		newconfd "${FILESDIR}"/${i}.confd ${i}
+	done
+	if use xinetd; then
+		insinto /etc/xinetd
+		doins "${S}"/etc/daemons/{rootd,proofd}.xinetd
+	fi
+}
+
+desktop_install() {
+	cd "${S}"
+	echo "Icon=root-system-bin" >> etc/root.desktop
+	domenu etc/root.desktop
+	doicon build/package/debian/root-system-bin.png
+
+	insinto /usr/share/icons/hicolor/48x48/mimetypes
+	doins build/package/debian/application-x-root.png
+
+	insinto /usr/share/icons/hicolor/48x48/apps
+	doicon build/package/debian/root-system-bin.xpm
+}
+
+cleanup_install() {
+	# Cleanup of files either already distributed or unused on Gentoo
+	pushd "${ED}" > /dev/null
+	rm usr/share/root/fonts/LICENSE || die
+	rm etc/root/proof/*.sample || die
+	rm -r etc/root/daemons || die
+	# these should be in PATH
+	mv etc/root/proof/utils/pq2/pq2* usr/bin/ || die
+	rm ${DOC_DIR#/}/{INSTALL,LICENSE,COPYING.CINT} || die
+	use examples || rm -r ${DOC_DIR#/}/examples || die
+	cd usr/$(get_libdir)/root/cint/cint
+	rm lib/posix/mktypes lib/dll_stl/setup lib/G__* || die
+	rm lib/dll_stl/G__* lib/dll_stl/rootcint_* lib/posix/exten.o || die
+	rm include/makehpib || die
+	popd > /dev/null
+}
+
+src_install() {
+	emake DESTDIR="${D}" install
+
+	echo "LDPATH=${EPREFIX%/}/usr/$(get_libdir)/root" > 99root
+
+	if ! use minimal; then
+		use pythia8 && echo "PYTHIA8=${EPREFIX%/}/usr" >> 99root
+		if use python; then
+			echo "PYTHONPATH=${EPREFIX%/}/usr/$(get_libdir)/root" >> 99root
+			python_optimize "${D}/usr/$(get_libdir)/root"
+		fi
+		use ruby && \
+			echo "RUBYLIB=${EPREFIX%/}/usr/$(get_libdir)/root" >> 99root
+		use emacs && elisp-install ${PN} build/misc/*.{el,elc}
+		if use examples; then
+			# these should really be taken care of by the root make install
+			insinto ${DOC_DIR}/examples/tutorials/tmva
+			doins -r tmva/test
+		fi
+	fi
+	doenvd 99root
+
+	# The build system installs Emacs support unconditionally in the wrong
+	# directory. Remove it and call elisp-install in case of USE=emacs.
+	rm -r "${ED}"/usr/share/emacs || die
+
+	daemon_install
+	desktop_install
+	cleanup_install
+
+	# do not copress files used by ROOT's CLI (.credit, .demo, .license)
+	docompress -x "${DOC_DIR}"/{CREDITS,LICENSE,examples/tutorials}
+	# needed for .license command to work
+	dosym "${ED}"usr/portage/licenses/LGPL-2.1 "${DOC_DIR}/LICENSE"
+}
+
+pkg_postinst() {
+	fdo-mime_desktop_database_update
+}
+
+pkg_postrm() {
+	fdo-mime_desktop_database_update
+}
diff --git a/sci-physics/root/root-6.00.01.ebuild b/sci-physics/root/root-6.00.01-r1.ebuild
index 440bd32b7..ebc10e1ed 100644
--- a/sci-physics/root/root-6.00.01.ebuild
+++ b/sci-physics/root/root-6.00.01-r1.ebuild
@@ -24,7 +24,7 @@ HOMEPAGE="http://root.cern.ch/"
 DOC_URI="ftp://root.cern.ch/${PN}/doc"
 
 SLOT="0/$(get_version_component_range 1-3 ${PV})"
-LICENSE="LGPL-2.1 freedist GPL-2 MSttfEULA LGPL-3 libpng UoI-NCSA"
+LICENSE="LGPL-2.1 freedist MSttfEULA LGPL-3 libpng UoI-NCSA"
 IUSE="+X afs avahi doc emacs examples fits fftw geocad graphviz
 	http kerberos ldap +math minimal mpi mysql odbc +opengl openmp
 	oracle postgres	prefix pythia6 pythia8 python qt4 sqlite ssl
@@ -200,7 +200,9 @@ src_prepare() {
 		"${FILESDIR}"/${PN}-6.00.01-nobyte-compile.patch \
 		"${FILESDIR}"/${PN}-6.00.01-prop-flags.patch \
 		"${FILESDIR}"/${PN}-6.00.01-llvm.patch \
-		"${FILESDIR}"/${PN}-6.00.01-geocad.patch
+		"${FILESDIR}"/${PN}-6.00.01-geocad.patch \
+		"${FILESDIR}"/${PN}-6.00.01-cling.patch \
+		"${FILESDIR}"/${PN}-6.00.01-tutorials-path.patch
 
 	# make sure we use system libs and headers
 	rm montecarlo/eg/inc/cfortran.h README/cfortran.doc || die
@@ -422,17 +424,15 @@ src_install() {
 	daemon_install
 	desktop_install
 	cleanup_install
+
+	# do not copress files used by ROOT's CLI (.credit, .demo, .license)
+	docompress -x "${DOC_DIR}"/{CREDITS,LICENSE,examples/tutorials}
+	# needed for .license command to work
+	dosym "${ED}"usr/portage/licenses/LGPL-2.1 "${DOC_DIR}/LICENSE"
 }
 
 pkg_postinst() {
 	fdo-mime_desktop_database_update
-	if [[ -z ${REPLACING_VERSIONS} ||
-		$(get_major_version ${REPLACING_VERSIONS}) -lt 6 ]]; then
-		ewarn "ROOT-6 uses Cling instead of CINT. Cling follows the C++ standard much more"
-		ewarn "strictly than CINT, in particular in requires headers to be included and"
-		ewarn "libraries to be properly loaded. Please carefully follow a migration guide:"
-		ewarn "http://root.cern.ch/root/htmldoc/notes/release-notes.html#cling-vs-cint"
-	fi
 }
 
 pkg_postrm() {
diff --git a/sci-physics/root/root-6.00.02.ebuild b/sci-physics/root/root-6.00.02.ebuild
new file mode 100644
index 000000000..01d4eda5a
--- /dev/null
+++ b/sci-physics/root/root-6.00.02.ebuild
@@ -0,0 +1,439 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-physics/root/root-5.34.18-r1.ebuild,v 1.3 2014/03/27 18:51:54 bicatali Exp $
+
+EAPI=5
+
+if [[ ${PV} == "9999" ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="http://root.cern.ch/git/root.git"
+	KEYWORDS=""
+else
+	SRC_URI="ftp://root.cern.ch/${PN}/${PN}_v${PV}.source.tar.gz"
+	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+	S="${WORKDIR}/${PN}"
+fi
+
+PYTHON_COMPAT=( python2_{6,7} )
+
+inherit elisp-common eutils fdo-mime fortran-2 multilib python-single-r1 \
+	toolchain-funcs user versionator
+
+DESCRIPTION="C++ data analysis framework and interpreter from CERN"
+HOMEPAGE="http://root.cern.ch/"
+DOC_URI="ftp://root.cern.ch/${PN}/doc"
+
+SLOT="0/$(get_version_component_range 1-3 ${PV})"
+LICENSE="LGPL-2.1 freedist MSttfEULA LGPL-3 libpng UoI-NCSA"
+IUSE="+X afs avahi doc emacs examples fits fftw geocad graphviz
+	http kerberos ldap +math minimal mpi mysql odbc +opengl openmp
+	oracle postgres	prefix pythia6 pythia8 python qt4 sqlite ssl
+	xinetd xml xrootd"
+
+# TODO: add support for: davix
+# TODO: ROOT-6 supports x32 ABI, but half of its dependencies doesn't
+# TODO: unbundle: cling, vdt
+
+REQUIRED_USE="
+	mpi? ( math !openmp )
+	opengl? ( X )
+	openmp? ( math !mpi )
+	python? ( ${PYTHON_REQUIRED_USE} )
+	qt4? ( X )
+"
+
+CDEPEND="
+	app-arch/xz-utils:0=
+	>=dev-lang/cfortran-4.4-r2
+	dev-libs/libpcre:3=
+	media-fonts/dejavu
+	media-libs/freetype:2=
+	media-libs/giflib:0=
+	media-libs/libpng:0=
+	media-libs/tiff:0=
+	>=sys-devel/clang-3.4
+	sys-libs/zlib:0=
+	virtual/jpeg:0
+	virtual/shadow
+	X? (
+		media-libs/ftgl:0=
+		media-libs/glew:0=
+		x11-libs/libX11:0=
+		x11-libs/libXext:0=
+		x11-libs/libXpm:0=
+		!minimal? (
+			opengl? ( virtual/opengl virtual/glu x11-libs/gl2ps:0= )
+			qt4? (
+				dev-qt/qtgui:4=
+				dev-qt/qtopengl:4=
+				dev-qt/qt3support:4=
+				dev-qt/qtsvg:4=
+				dev-qt/qtwebkit:4=
+				dev-qt/qtxmlpatterns:4=
+			)
+			x11-libs/libXft:0=
+		)
+	)
+	!minimal? (
+		afs? ( net-fs/openafs )
+		avahi? ( net-dns/avahi:0= )
+		emacs? ( virtual/emacs )
+		fits? ( sci-libs/cfitsio:0= )
+		fftw? ( sci-libs/fftw:3.0= )
+		geocad? ( sci-libs/opencascade:= )
+		graphviz? ( media-gfx/graphviz:0= )
+		http? ( dev-libs/fcgi:0= )
+		kerberos? ( virtual/krb5 )
+		ldap? ( net-nds/openldap:0= )
+		math? (
+			sci-libs/gsl:0=
+			sci-mathematics/unuran:0=
+			mpi? ( virtual/mpi )
+		)
+		mysql? ( virtual/mysql )
+		odbc? ( || ( dev-db/libiodbc:0= dev-db/unixODBC:0= ) )
+		oracle? ( dev-db/oracle-instantclient-basic:0= )
+		postgres? ( dev-db/postgresql-base:= )
+		pythia6? ( sci-physics/pythia:6= )
+		pythia8? ( >=sci-physics/pythia-8.1.80:8= )
+		python? ( ${PYTHON_DEPS} )
+		sqlite? ( dev-db/sqlite:3= )
+		ssl? ( dev-libs/openssl:0= )
+		xml? ( dev-libs/libxml2:2= )
+		xrootd? ( >=net-libs/xrootd-3.3.5:0= )
+	)"
+
+# TODO: ruby is not yet ported to ROOT-6, reenable when (if?) ready
+#		ruby? (
+#			dev-lang/ruby
+#			dev-ruby/rubygems
+#		)
+#
+# TODO: root-6.00.01 crashes with system libafterimage
+#			|| (
+#				media-libs/libafterimage:0=[gif,jpeg,png,tiff]
+#				>=x11-wm/afterstep-2.2.11:0=[gif,jpeg,png,tiff]
+#			)
+#			--disable-builtin-afterimage
+
+DEPEND="${CDEPEND}
+	virtual/pkgconfig"
+
+RDEPEND="${CDEPEND}
+	xinetd? ( sys-apps/xinetd )"
+
+PDEPEND="doc? ( ~app-doc/root-docs-${PV}[http=,math=] )"
+
+# install stuff in ${P} and not ${PF} for easier tracking in root-docs
+DOC_DIR="/usr/share/doc/${P}"
+
+die_compiler() {
+	die "Need one of the following C++11 capable compilers:"
+	die "    >=sys-devel/gcc[cxx]-4.8"
+	die "    >=sys-devel/clang-3.4"
+	die "    >=dev-lang/icc-13"
+}
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	use python && python-single-r1_pkg_setup
+	echo
+	elog "There are extra options on packages not yet in Gentoo:"
+	elog "Afdsmgrd, AliEn, castor, Chirp, dCache, gfal, Globus, gLite,"
+	elog "HDFS, Monalisa, MaxDB/SapDB, SRP."
+	elog "You can use the env variable EXTRA_ECONF variable for this."
+	elog "For example, for SRP, you would set: "
+	elog "EXTRA_ECONF=\"--enable-srp --with-srp-libdir=${EROOT%/}/usr/$(get_libdir)\""
+	echo
+
+	enewgroup rootd
+	enewuser rootd -1 -1 /var/spool/rootd rootd
+
+	use minimal && return
+
+	if use math; then
+		if use openmp; then
+			if [[ $(tc-getCXX)$ == *g++* ]] && ! tc-has-openmp; then
+				ewarn "You are using a g++ without OpenMP capabilities"
+				die "Need an OpenMP capable compiler"
+			else
+				export USE_OPENMP=1 USE_PARALLEL_MINUIT2=1
+			fi
+		elif use mpi; then
+			export USE_MPI=1 USE_PARALLEL_MINUIT2=1
+		fi
+	fi
+
+	# check for supported compilers
+	case $(tc-getCXX) in
+		*g++*)
+			if ! version_is_at_least "4.8" "$(gcc-version)"; then
+				eerror "You are using a g++ without C++11 capabilities"
+				die_compiler
+			fi
+		;;
+		*clang++*)
+			# >=clang-3.4 is already in DEPEND
+		;;
+		*icc*|*icpc*)
+			if ! version_is_at_least "13" "$(has_version dev-lang/icc)"; then
+				eerror "You are using an icc without C++11 capabilities"
+				die_compiler
+			fi
+		;;
+		*)
+			ewarn "You are using an unsupported compiler."
+			ewarn "Please report any issues upstream."
+		;;
+	esac
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PN}-5.28.00b-glibc212.patch \
+		"${FILESDIR}"/${PN}-5.32.00-afs.patch \
+		"${FILESDIR}"/${PN}-5.32.00-cfitsio.patch \
+		"${FILESDIR}"/${PN}-5.32.00-chklib64.patch \
+		"${FILESDIR}"/${PN}-5.34.13-unuran.patch \
+		"${FILESDIR}"/${PN}-5.34.13-desktop.patch \
+		"${FILESDIR}"/${PN}-6.00.01-dotfont.patch \
+		"${FILESDIR}"/${PN}-6.00.01-nobyte-compile.patch \
+		"${FILESDIR}"/${PN}-6.00.01-prop-flags.patch \
+		"${FILESDIR}"/${PN}-6.00.01-llvm.patch \
+		"${FILESDIR}"/${PN}-6.00.01-geocad.patch \
+		"${FILESDIR}"/${PN}-6.00.01-tutorials-path.patch
+
+	# make sure we use system libs and headers
+	rm montecarlo/eg/inc/cfortran.h README/cfortran.doc || die
+	#rm -r graf2d/asimage/src/libAfterImage || die
+	rm -r graf3d/ftgl/{inc,src} || die
+	rm -r graf2d/freetype/src || die
+	rm -r graf3d/glew/{inc,src} || die
+	rm -r core/pcre/src || die
+	rm -r math/unuran/src/unuran-*.tar.gz || die
+	LANG=C LC_ALL=C find core/zip -type f -name "[a-z]*" -print0 | \
+		xargs -0 rm || die
+	rm -r core/lzma/src/*.tar.gz || die
+	rm graf3d/gl/{inc,src}/gl2ps.* || die
+	sed -i -e 's/^GLLIBS *:= .* $(OPENGLLIB)/& -lgl2ps/' \
+		graf3d/gl/Module.mk || die
+
+	# In Gentoo, libPythia6 is called libpythia6
+	# iodbc is in /usr/include/iodbc
+	# pg_config.h is checked instead of libpq-fe.h
+	sed -i \
+		-e 's:libPythia6:libpythia6:g' \
+		-e 's:$ODBCINCDIR:$ODBCINCDIR /usr/include/iodbc:' \
+		-e 's:libpq-fe.h:pg_config.h:' \
+		configure || die "adjusting configure for Gentoo failed"
+
+	# prefixify the configure script
+	sed -i \
+		-e 's:/usr:${EPREFIX}/usr:g' \
+		configure || die "prefixify configure failed"
+
+	# CSS should use local images
+	sed -i -e 's,http://.*/images/,,' etc/html/ROOT.css || die "html sed failed"
+}
+
+# NB: ROOT uses bundled LLVM, because it is patched and API-incompatible with
+# system LLVM.
+# NB: As of 6.00.0.1 cmake is not ready as it can't fully replace configure,
+# e.g. for afs and geocad.
+
+src_configure() {
+	local -a myconf
+	# Some compilers need special care
+	case $(tc-getCXX) in
+		*clang++*)
+			myconf=(
+				--with-clang
+				--with-f77="$(tc-getFC)"
+			)
+		;;
+		*icc*|*icpc*)
+			# For icc we need to provide architecture manually
+			# and not to tamper with tc-get*
+			use x86 && myconf=( linuxicc )
+			use amd64 && myconf=( linuxx8664icc )
+		;;
+		*)	# gcc goes here too
+			myconf=(
+				--with-cc="$(tc-getCC)"
+				--with-cxx="$(tc-getCXX)"
+				--with-f77="$(tc-getFC)"
+				--with-ld="$(tc-getCXX)"
+			)
+		;;
+	esac
+
+	# the configure script is not the standard autotools
+	myconf+=(
+		--prefix="${EPREFIX}/usr"
+		--etcdir="${EPREFIX}/etc/root"
+		--libdir="${EPREFIX}/usr/$(get_libdir)/${PN}"
+		--docdir="${EPREFIX}${DOC_DIR}"
+		--tutdir="${EPREFIX}${DOC_DIR}/examples/tutorials"
+		--testdir="${EPREFIX}${DOC_DIR}/examples/tests"
+		--disable-werror
+		--nohowto
+	)
+
+	if use minimal; then
+		myconf+=( $(usex X --gminimal --minimal) )
+	else
+		myconf+=(
+			--with-afs-shared=yes
+			--with-sys-iconpath="${EPREFIX}/usr/share/pixmaps"
+			--disable-builtin-ftgl
+			--disable-builtin-freetype
+			--disable-builtin-glew
+			--disable-builtin-pcre
+			--disable-builtin-zlib
+			--disable-builtin-lzma
+			--enable-astiff
+			--enable-explicitlink
+			--enable-gdml
+			--enable-memstat
+			--enable-shadowpw
+			--enable-shared
+			--enable-soversion
+			--enable-table
+			--fail-on-missing
+			$(use_enable X x11)
+			$(use_enable X asimage)
+			$(use_enable X xft)
+			$(use_enable afs)
+			$(use_enable avahi bonjour)
+			$(use_enable fits fitsio)
+			$(use_enable fftw fftw3)
+			$(use_enable geocad)
+			$(use_enable graphviz gviz)
+			$(use_enable kerberos krb5)
+			$(use_enable ldap)
+			$(use_enable math genvector)
+			$(use_enable math gsl-shared)
+			$(use_enable math mathmore)
+			$(use_enable math minuit2)
+			$(use_enable math roofit)
+			$(use_enable math tmva)
+			$(use_enable math vc)
+			$(use_enable math vdt)
+			$(use_enable math unuran)
+			$(use_enable mysql)
+			$(use_enable odbc)
+			$(use_enable opengl)
+			$(use_enable oracle)
+			$(use_enable postgres pgsql)
+			$(usex postgres \
+				"--with-pgsql-incdir=$(pg_config --includedir)" "")
+			$(use_enable prefix rpath)
+			$(use_enable pythia6)
+			$(use_enable pythia8)
+			$(use_enable python)
+			$(use_enable qt4 qt)
+			$(use_enable qt4 qtgsi)
+			$(use_enable sqlite)
+			$(use_enable ssl)
+			$(use_enable xml)
+			$(use_enable xrootd)
+			${EXTRA_ECONF}
+		)
+	fi
+
+	./configure ${myconf[@]} || die "configure failed"
+}
+
+src_compile() {
+	emake \
+		OPT="${CXXFLAGS}" \
+		F77OPT="${FFLAGS}" \
+		ROOTSYS="${S}" \
+		LD_LIBRARY_PATH="${S}/lib"
+	use emacs && ! use minimal && elisp-compile build/misc/*.el
+}
+
+daemon_install() {
+	local daemons="rootd proofd"
+	dodir /var/spool/rootd
+	fowners rootd:rootd /var/spool/rootd
+	dodir /var/spool/rootd/{pub,tmp}
+	fperms 1777 /var/spool/rootd/{pub,tmp}
+
+	for i in ${daemons}; do
+		newinitd "${FILESDIR}"/${i}.initd ${i}
+		newconfd "${FILESDIR}"/${i}.confd ${i}
+	done
+	if use xinetd; then
+		insinto /etc/xinetd
+		doins "${S}"/etc/daemons/{rootd,proofd}.xinetd
+	fi
+}
+
+desktop_install() {
+	cd "${S}"
+	echo "Icon=root-system-bin" >> etc/root.desktop
+	domenu etc/root.desktop
+	doicon build/package/debian/root-system-bin.png
+
+	insinto /usr/share/icons/hicolor/48x48/mimetypes
+	doins build/package/debian/application-x-root.png
+
+	insinto /usr/share/icons/hicolor/48x48/apps
+	doicon build/package/debian/root-system-bin.xpm
+}
+
+cleanup_install() {
+	# Cleanup of files either already distributed or unused on Gentoo
+	pushd "${ED}" > /dev/null
+	rm usr/share/root/fonts/LICENSE || die
+	rm etc/root/proof/*.sample || die
+	rm -r etc/root/daemons || die
+	# these should be in PATH
+	mv etc/root/proof/utils/pq2/pq2* usr/bin/ || die
+	rm ${DOC_DIR#/}/{INSTALL,LICENSE} || die
+	use examples || rm -r ${DOC_DIR#/}/examples || die
+}
+
+src_install() {
+	emake DESTDIR="${D}" install
+	dodoc README.md
+
+	echo "LDPATH=${EPREFIX%/}/usr/$(get_libdir)/root" > 99root
+
+	if ! use minimal; then
+		use pythia8 && echo "PYTHIA8=${EPREFIX%/}/usr" >> 99root
+		if use python; then
+			echo "PYTHONPATH=${EPREFIX%/}/usr/$(get_libdir)/root" >> 99root
+			python_optimize "${D}/usr/$(get_libdir)/root"
+		fi
+		use emacs && elisp-install ${PN} build/misc/*.{el,elc}
+		if use examples; then
+			# these should really be taken care of by the root make install
+			insinto ${DOC_DIR}/examples/tutorials/tmva
+			doins -r tmva/test
+		fi
+	fi
+	doenvd 99root
+
+	# The build system installs Emacs support unconditionally in the wrong
+	# directory. Remove it and call elisp-install in case of USE=emacs.
+	rm -r "${ED}"/usr/share/emacs || die
+
+	daemon_install
+	desktop_install
+	cleanup_install
+
+	# do not copress files used by ROOT's CLI (.credit, .demo, .license)
+	docompress -x "${DOC_DIR}"/{CREDITS,LICENSE,examples/tutorials}
+	# needed for .license command to work
+	dosym "${ED}"usr/portage/licenses/LGPL-2.1 "${DOC_DIR}/LICENSE"
+}
+
+pkg_postinst() {
+	fdo-mime_desktop_database_update
+}
+
+pkg_postrm() {
+	fdo-mime_desktop_database_update
+}
diff --git a/sci-physics/root/root-9999.ebuild b/sci-physics/root/root-9999.ebuild
index b46789a5e..b2074ac3f 120000..100644
--- a/sci-physics/root/root-9999.ebuild
+++ b/sci-physics/root/root-9999.ebuild
@@ -1 +1,438 @@
-root-6.00.01.ebuild
-\ No newline at end of file
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-physics/root/root-5.34.18-r1.ebuild,v 1.3 2014/03/27 18:51:54 bicatali Exp $
+
+EAPI=5
+
+if [[ ${PV} == "9999" ]] ; then
+	inherit git-r3
+	EGIT_REPO_URI="http://root.cern.ch/git/root.git"
+	KEYWORDS=""
+else
+	SRC_URI="ftp://root.cern.ch/${PN}/${PN}_v${PV}.source.tar.gz"
+	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+	S="${WORKDIR}/${PN}"
+fi
+
+PYTHON_COMPAT=( python2_{6,7} )
+
+inherit elisp-common eutils fdo-mime fortran-2 multilib python-single-r1 \
+	toolchain-funcs user versionator
+
+DESCRIPTION="C++ data analysis framework and interpreter from CERN"
+HOMEPAGE="http://root.cern.ch/"
+DOC_URI="ftp://root.cern.ch/${PN}/doc"
+
+SLOT="0/$(get_version_component_range 1-3 ${PV})"
+LICENSE="LGPL-2.1 freedist MSttfEULA LGPL-3 libpng UoI-NCSA"
+IUSE="+X afs avahi doc emacs examples fits fftw geocad graphviz
+	http kerberos ldap +math minimal mpi mysql odbc +opengl openmp
+	oracle postgres	prefix pythia6 pythia8 python qt4 sqlite ssl
+	xinetd xml xrootd"
+
+# TODO: add support for: davix
+# TODO: ROOT-6 supports x32 ABI, but half of its dependencies doesn't
+# TODO: unbundle: cling, vdt
+
+REQUIRED_USE="
+	mpi? ( math !openmp )
+	opengl? ( X )
+	openmp? ( math !mpi )
+	python? ( ${PYTHON_REQUIRED_USE} )
+	qt4? ( X )
+"
+
+CDEPEND="
+	app-arch/xz-utils:0=
+	>=dev-lang/cfortran-4.4-r2
+	dev-libs/libpcre:3=
+	media-fonts/dejavu
+	media-libs/freetype:2=
+	media-libs/giflib:0=
+	media-libs/libpng:0=
+	media-libs/tiff:0=
+	>=sys-devel/clang-3.4
+	sys-libs/zlib:0=
+	virtual/jpeg:0
+	virtual/shadow
+	X? (
+		media-libs/ftgl:0=
+		media-libs/glew:0=
+		x11-libs/libX11:0=
+		x11-libs/libXext:0=
+		x11-libs/libXpm:0=
+		!minimal? (
+			opengl? ( virtual/opengl virtual/glu x11-libs/gl2ps:0= )
+			qt4? (
+				dev-qt/qtgui:4=
+				dev-qt/qtopengl:4=
+				dev-qt/qt3support:4=
+				dev-qt/qtsvg:4=
+				dev-qt/qtwebkit:4=
+				dev-qt/qtxmlpatterns:4=
+			)
+			x11-libs/libXft:0=
+		)
+	)
+	!minimal? (
+		afs? ( net-fs/openafs )
+		avahi? ( net-dns/avahi:0= )
+		emacs? ( virtual/emacs )
+		fits? ( sci-libs/cfitsio:0= )
+		fftw? ( sci-libs/fftw:3.0= )
+		geocad? ( sci-libs/opencascade:= )
+		graphviz? ( media-gfx/graphviz:0= )
+		http? ( dev-libs/fcgi:0= )
+		kerberos? ( virtual/krb5 )
+		ldap? ( net-nds/openldap:0= )
+		math? (
+			sci-libs/gsl:0=
+			sci-mathematics/unuran:0=
+			mpi? ( virtual/mpi )
+		)
+		mysql? ( virtual/mysql )
+		odbc? ( || ( dev-db/libiodbc:0= dev-db/unixODBC:0= ) )
+		oracle? ( dev-db/oracle-instantclient-basic:0= )
+		postgres? ( dev-db/postgresql-base:= )
+		pythia6? ( sci-physics/pythia:6= )
+		pythia8? ( >=sci-physics/pythia-8.1.80:8= )
+		python? ( ${PYTHON_DEPS} )
+		sqlite? ( dev-db/sqlite:3= )
+		ssl? ( dev-libs/openssl:0= )
+		xml? ( dev-libs/libxml2:2= )
+		xrootd? ( >=net-libs/xrootd-3.3.5:0= )
+	)"
+
+# TODO: ruby is not yet ported to ROOT-6, reenable when (if?) ready
+#		ruby? (
+#			dev-lang/ruby
+#			dev-ruby/rubygems
+#		)
+#
+# TODO: root-6.00.01 crashes with system libafterimage
+#			|| (
+#				media-libs/libafterimage:0=[gif,jpeg,png,tiff]
+#				>=x11-wm/afterstep-2.2.11:0=[gif,jpeg,png,tiff]
+#			)
+#			--disable-builtin-afterimage
+
+DEPEND="${CDEPEND}
+	virtual/pkgconfig"
+
+RDEPEND="${CDEPEND}
+	xinetd? ( sys-apps/xinetd )"
+
+PDEPEND="doc? ( ~app-doc/root-docs-${PV}[http=,math=] )"
+
+# install stuff in ${P} and not ${PF} for easier tracking in root-docs
+DOC_DIR="/usr/share/doc/${P}"
+
+die_compiler() {
+	die "Need one of the following C++11 capable compilers:"
+	die "    >=sys-devel/gcc[cxx]-4.8"
+	die "    >=sys-devel/clang-3.4"
+	die "    >=dev-lang/icc-13"
+}
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	use python && python-single-r1_pkg_setup
+	echo
+	elog "There are extra options on packages not yet in Gentoo:"
+	elog "Afdsmgrd, AliEn, castor, Chirp, dCache, gfal, Globus, gLite,"
+	elog "HDFS, Monalisa, MaxDB/SapDB, SRP."
+	elog "You can use the env variable EXTRA_ECONF variable for this."
+	elog "For example, for SRP, you would set: "
+	elog "EXTRA_ECONF=\"--enable-srp --with-srp-libdir=${EROOT%/}/usr/$(get_libdir)\""
+	echo
+
+	enewgroup rootd
+	enewuser rootd -1 -1 /var/spool/rootd rootd
+
+	use minimal && return
+
+	if use math; then
+		if use openmp; then
+			if [[ $(tc-getCXX)$ == *g++* ]] && ! tc-has-openmp; then
+				ewarn "You are using a g++ without OpenMP capabilities"
+				die "Need an OpenMP capable compiler"
+			else
+				export USE_OPENMP=1 USE_PARALLEL_MINUIT2=1
+			fi
+		elif use mpi; then
+			export USE_MPI=1 USE_PARALLEL_MINUIT2=1
+		fi
+	fi
+
+	# check for supported compilers
+	case $(tc-getCXX) in
+		*g++*)
+			if ! version_is_at_least "4.8" "$(gcc-version)"; then
+				eerror "You are using a g++ without C++11 capabilities"
+				die_compiler
+			fi
+		;;
+		*clang++*)
+			# >=clang-3.4 is already in DEPEND
+		;;
+		*icc*|*icpc*)
+			if ! version_is_at_least "13" "$(has_version dev-lang/icc)"; then
+				eerror "You are using an icc without C++11 capabilities"
+				die_compiler
+			fi
+		;;
+		*)
+			ewarn "You are using an unsupported compiler."
+			ewarn "Please report any issues upstream."
+		;;
+	esac
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PN}-5.28.00b-glibc212.patch \
+		"${FILESDIR}"/${PN}-5.32.00-afs.patch \
+		"${FILESDIR}"/${PN}-5.32.00-cfitsio.patch \
+		"${FILESDIR}"/${PN}-5.32.00-chklib64.patch \
+		"${FILESDIR}"/${PN}-5.34.13-unuran.patch \
+		"${FILESDIR}"/${PN}-5.34.13-desktop.patch \
+		"${FILESDIR}"/${PN}-6.00.01-dotfont.patch \
+		"${FILESDIR}"/${PN}-6.00.01-nobyte-compile.patch \
+		"${FILESDIR}"/${PN}-6.00.01-prop-flags.patch \
+		"${FILESDIR}"/${PN}-6.00.01-llvm.patch \
+		"${FILESDIR}"/${PN}-6.00.01-geocad.patch
+
+	# make sure we use system libs and headers
+	rm montecarlo/eg/inc/cfortran.h README/cfortran.doc || die
+	#rm -r graf2d/asimage/src/libAfterImage || die
+	rm -r graf3d/ftgl/{inc,src} || die
+	rm -r graf2d/freetype/src || die
+	rm -r graf3d/glew/{inc,src} || die
+	rm -r core/pcre/src || die
+	rm -r math/unuran/src/unuran-*.tar.gz || die
+	LANG=C LC_ALL=C find core/zip -type f -name "[a-z]*" -print0 | \
+		xargs -0 rm || die
+	rm -r core/lzma/src/*.tar.gz || die
+	rm graf3d/gl/{inc,src}/gl2ps.* || die
+	sed -i -e 's/^GLLIBS *:= .* $(OPENGLLIB)/& -lgl2ps/' \
+		graf3d/gl/Module.mk || die
+
+	# In Gentoo, libPythia6 is called libpythia6
+	# iodbc is in /usr/include/iodbc
+	# pg_config.h is checked instead of libpq-fe.h
+	sed -i \
+		-e 's:libPythia6:libpythia6:g' \
+		-e 's:$ODBCINCDIR:$ODBCINCDIR /usr/include/iodbc:' \
+		-e 's:libpq-fe.h:pg_config.h:' \
+		configure || die "adjusting configure for Gentoo failed"
+
+	# prefixify the configure script
+	sed -i \
+		-e 's:/usr:${EPREFIX}/usr:g' \
+		configure || die "prefixify configure failed"
+
+	# CSS should use local images
+	sed -i -e 's,http://.*/images/,,' etc/html/ROOT.css || die "html sed failed"
+}
+
+# NB: ROOT uses bundled LLVM, because it is patched and API-incompatible with
+# system LLVM.
+# NB: As of 6.00.0.1 cmake is not ready as it can't fully replace configure,
+# e.g. for afs and geocad.
+
+src_configure() {
+	local -a myconf
+	# Some compilers need special care
+	case $(tc-getCXX) in
+		*clang++*)
+			myconf=(
+				--with-clang
+				--with-f77="$(tc-getFC)"
+			)
+		;;
+		*icc*|*icpc*)
+			# For icc we need to provide architecture manually
+			# and not to tamper with tc-get*
+			use x86 && myconf=( linuxicc )
+			use amd64 && myconf=( linuxx8664icc )
+		;;
+		*)	# gcc goes here too
+			myconf=(
+				--with-cc="$(tc-getCC)"
+				--with-cxx="$(tc-getCXX)"
+				--with-f77="$(tc-getFC)"
+				--with-ld="$(tc-getCXX)"
+			)
+		;;
+	esac
+
+	# the configure script is not the standard autotools
+	myconf+=(
+		--prefix="${EPREFIX}/usr"
+		--etcdir="${EPREFIX}/etc/root"
+		--libdir="${EPREFIX}/usr/$(get_libdir)/${PN}"
+		--docdir="${EPREFIX}${DOC_DIR}"
+		--tutdir="${EPREFIX}${DOC_DIR}/examples/tutorials"
+		--testdir="${EPREFIX}${DOC_DIR}/examples/tests"
+		--disable-werror
+		--nohowto
+	)
+
+	if use minimal; then
+		myconf+=( $(usex X --gminimal --minimal) )
+	else
+		myconf+=(
+			--with-afs-shared=yes
+			--with-sys-iconpath="${EPREFIX}/usr/share/pixmaps"
+			--disable-builtin-ftgl
+			--disable-builtin-freetype
+			--disable-builtin-glew
+			--disable-builtin-pcre
+			--disable-builtin-zlib
+			--disable-builtin-lzma
+			--enable-astiff
+			--enable-explicitlink
+			--enable-gdml
+			--enable-memstat
+			--enable-shadowpw
+			--enable-shared
+			--enable-soversion
+			--enable-table
+			--fail-on-missing
+			$(use_enable X x11)
+			$(use_enable X asimage)
+			$(use_enable X xft)
+			$(use_enable afs)
+			$(use_enable avahi bonjour)
+			$(use_enable fits fitsio)
+			$(use_enable fftw fftw3)
+			$(use_enable geocad)
+			$(use_enable graphviz gviz)
+			$(use_enable kerberos krb5)
+			$(use_enable ldap)
+			$(use_enable math genvector)
+			$(use_enable math gsl-shared)
+			$(use_enable math mathmore)
+			$(use_enable math minuit2)
+			$(use_enable math roofit)
+			$(use_enable math tmva)
+			$(use_enable math vc)
+			$(use_enable math vdt)
+			$(use_enable math unuran)
+			$(use_enable mysql)
+			$(use_enable odbc)
+			$(use_enable opengl)
+			$(use_enable oracle)
+			$(use_enable postgres pgsql)
+			$(usex postgres \
+				"--with-pgsql-incdir=$(pg_config --includedir)" "")
+			$(use_enable prefix rpath)
+			$(use_enable pythia6)
+			$(use_enable pythia8)
+			$(use_enable python)
+			$(use_enable qt4 qt)
+			$(use_enable qt4 qtgsi)
+			$(use_enable sqlite)
+			$(use_enable ssl)
+			$(use_enable xml)
+			$(use_enable xrootd)
+			${EXTRA_ECONF}
+		)
+	fi
+
+	./configure ${myconf[@]} || die "configure failed"
+}
+
+src_compile() {
+	emake \
+		OPT="${CXXFLAGS}" \
+		F77OPT="${FFLAGS}" \
+		ROOTSYS="${S}" \
+		LD_LIBRARY_PATH="${S}/lib"
+	use emacs && ! use minimal && elisp-compile build/misc/*.el
+}
+
+daemon_install() {
+	local daemons="rootd proofd"
+	dodir /var/spool/rootd
+	fowners rootd:rootd /var/spool/rootd
+	dodir /var/spool/rootd/{pub,tmp}
+	fperms 1777 /var/spool/rootd/{pub,tmp}
+
+	for i in ${daemons}; do
+		newinitd "${FILESDIR}"/${i}.initd ${i}
+		newconfd "${FILESDIR}"/${i}.confd ${i}
+	done
+	if use xinetd; then
+		insinto /etc/xinetd
+		doins "${S}"/etc/daemons/{rootd,proofd}.xinetd
+	fi
+}
+
+desktop_install() {
+	cd "${S}"
+	echo "Icon=root-system-bin" >> etc/root.desktop
+	domenu etc/root.desktop
+	doicon build/package/debian/root-system-bin.png
+
+	insinto /usr/share/icons/hicolor/48x48/mimetypes
+	doins build/package/debian/application-x-root.png
+
+	insinto /usr/share/icons/hicolor/48x48/apps
+	doicon build/package/debian/root-system-bin.xpm
+}
+
+cleanup_install() {
+	# Cleanup of files either already distributed or unused on Gentoo
+	pushd "${ED}" > /dev/null
+	rm usr/share/root/fonts/LICENSE || die
+	rm etc/root/proof/*.sample || die
+	rm -r etc/root/daemons || die
+	# these should be in PATH
+	mv etc/root/proof/utils/pq2/pq2* usr/bin/ || die
+	rm ${DOC_DIR#/}/{INSTALL,LICENSE} || die
+	use examples || rm -r ${DOC_DIR#/}/examples || die
+}
+
+src_install() {
+	emake DESTDIR="${D}" install
+	dodoc README.md
+
+	echo "LDPATH=${EPREFIX%/}/usr/$(get_libdir)/root" > 99root
+
+	if ! use minimal; then
+		use pythia8 && echo "PYTHIA8=${EPREFIX%/}/usr" >> 99root
+		if use python; then
+			echo "PYTHONPATH=${EPREFIX%/}/usr/$(get_libdir)/root" >> 99root
+			python_optimize "${D}/usr/$(get_libdir)/root"
+		fi
+		use emacs && elisp-install ${PN} build/misc/*.{el,elc}
+		if use examples; then
+			# these should really be taken care of by the root make install
+			insinto ${DOC_DIR}/examples/tutorials/tmva
+			doins -r tmva/test
+		fi
+	fi
+	doenvd 99root
+
+	# The build system installs Emacs support unconditionally in the wrong
+	# directory. Remove it and call elisp-install in case of USE=emacs.
+	rm -r "${ED}"/usr/share/emacs || die
+
+	daemon_install
+	desktop_install
+	cleanup_install
+
+	# do not copress files used by ROOT's CLI (.credit, .demo, .license)
+	docompress -x "${DOC_DIR}"/{CREDITS,LICENSE,examples/tutorials}
+	# needed for .license command to work
+	dosym "${ED}"usr/portage/licenses/LGPL-2.1 "${DOC_DIR}/LICENSE"
+}
+
+pkg_postinst() {
+	fdo-mime_desktop_database_update
+}
+
+pkg_postrm() {
+	fdo-mime_desktop_database_update
+}
diff --git a/sci-physics/vgm/ChangeLog b/sci-physics/vgm/ChangeLog
index 78f7e21fc..5b5dce520 100644
--- a/sci-physics/vgm/ChangeLog
+++ b/sci-physics/vgm/ChangeLog
@@ -2,6 +2,16 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  06 Jul 2014; Oliver Freyermuth <o.freyermuth@googlemail.com> vgm-3.06.ebuild:
+  Add subslot dependency on clhep, we need to rebuild for each clhep subslot
+  change.
+
+*vgm-9999 (06 Jul 2014)
+
+  06 Jul 2014; Oliver Freyermuth <o.freyermuth@googlemail.com> +vgm-9999.ebuild:
+  New live ebuild for VGM, adapting to fixes for cmake install paths in upstream
+  (no need to manually install in ebuild anymore).
+
   03 Apr 2014; Oliver Freyermuth <o.freyermuth@googlemail.com> vgm-3.06.ebuild:
   Use zip-snapshot mirrored by jlec, sourceforge cannot automatically recreate
   them and changes CRC each time
diff --git a/sci-physics/vgm/vgm-3.06.ebuild b/sci-physics/vgm/vgm-3.06.ebuild
index ccdc5a3d2..bd650c6e2 100644
--- a/sci-physics/vgm/vgm-3.06.ebuild
+++ b/sci-physics/vgm/vgm-3.06.ebuild
@@ -24,7 +24,7 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="doc examples +geant4 +root test xml"
 
 RDEPEND="
-	sci-physics/clhep
+	sci-physics/clhep:=
 	root? ( sci-physics/root:= )
 	geant4? ( >=sci-physics/geant-4.9.6[examples?] )
 	xml? ( dev-libs/xerces-c )"
diff --git a/sci-physics/vgm/vgm-9999.ebuild b/sci-physics/vgm/vgm-9999.ebuild
new file mode 100644
index 000000000..ddadd9970
--- /dev/null
+++ b/sci-physics/vgm/vgm-9999.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit cmake-utils versionator subversion
+
+if [[ ${PV} == *9999* ]]; then
+	ESVN_REPO_URI="svn://svn.code.sf.net/p/vgm/code/trunk/vgm"
+	KEYWORDS=""
+else
+	# .zip-snapshot can be recreated by visiting
+	# http://sourceforge.net/p/${PN}/code/${COMMIT}/tarball?path=/tags/v$(replace_all_version_separators '-')
+	TAG_VER="${PN}-code-731-tags-v$(replace_all_version_separators '-')"
+	SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${TAG_VER}.zip"
+	S=${WORKDIR}/${TAG_VER}/${PN}
+	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+DESCRIPTION="Virtual Geometry Model for High Energy Physics Experiments"
+HOMEPAGE="http://ivana.home.cern.ch/ivana/VGM.html"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="doc examples +geant4 +root test xml"
+
+RDEPEND="
+	sci-physics/clhep:=
+	root? ( sci-physics/root:= )
+	geant4? ( >=sci-physics/geant-4.9.6 )
+	xml? ( dev-libs/xerces-c )"
+DEPEND="${RDEPEND}
+	doc? ( app-doc/doxygen[dot] )
+	test? ( geant4? ( xml? ( >=sci-physics/geant-4.9.6[gdml] ) ) )"
+
+src_configure() {
+	local mycmakeargs=(
+		-DCLHEP_DIR="${EROOT}usr"
+		$(cmake-utils_use_with examples)
+		$(cmake-utils_use examples VGM_INSTALL_EXAMPLES)
+		$(cmake-utils_use_with geant4)
+		$(cmake-utils_use_with root)
+		$(cmake-utils_use_with test)
+		$(cmake-utils_use_with xml xercesc)
+	)
+	cmake-utils_src_configure
+}
+
+src_compile() {
+	cmake-utils_src_compile
+	if use doc; then
+		cd packages
+		doxygen || die
+	fi
+}
+
+src_test() {
+	cd "${BUILD_DIR}"/test
+	./test_suite.sh || die
+}
+
+src_install() {
+	cmake-utils_src_install
+	cd doc || die
+	dodoc README todo.txt VGMhistory.txt VGM.html VGMversions.html
+	use doc && dohtml -r html/*
+}
diff --git a/sci-visualization/gnuplot/ChangeLog b/sci-visualization/gnuplot/ChangeLog
index a0839262a..595435908 100644
--- a/sci-visualization/gnuplot/ChangeLog
+++ b/sci-visualization/gnuplot/ChangeLog
@@ -2,6 +2,15 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  14 Jul 2014; Christoph Junghans <ottxor@gentoo.org> gnuplot-5.0.9999.ebuild:
+  added support for libcerf
+
+*gnuplot-5.0.9999 (13 Jul 2014)
+
+  13 Jul 2014; Christoph Junghans <ottxor@gentoo.org> +gnuplot-5.0.9999.ebuild,
+  -gnuplot-4.7.9999.ebuild:
+  version bump
+
   22 Mar 2014; Ulrich Müller <ulm@gentoo.org> gnuplot-4.7.9999.ebuild:
   Add libcaca USE flag, thanks to James Cloos <cloos@jhcloos.com>, bug 504354.
   Remove thin-splines USE flag and configure option.
diff --git a/sci-visualization/gnuplot/gnuplot-4.7.9999.ebuild b/sci-visualization/gnuplot/gnuplot-5.0.9999.ebuild
index fbbe71048..071e763fb 100644
--- a/sci-visualization/gnuplot/gnuplot-4.7.9999.ebuild
+++ b/sci-visualization/gnuplot/gnuplot-5.0.9999.ebuild
@@ -45,6 +45,7 @@ RDEPEND="
 		>=dev-qt/qtgui-4.5:4
 		>=dev-qt/qtsvg-4.5:4 )
 	readline? ( sys-libs/readline )
+	sci-libs/libcerf
 	svga? ( media-libs/svgalib )
 	wxwidgets? (
 		x11-libs/wxGTK:2.8[X]
author	Andreas Schäfer <gentryx@gmx.de>	2014-07-21 17:06:10 +0200
committer	Andreas Schäfer <gentryx@gmx.de>	2014-07-21 17:06:10 +0200
commit	a2a4f4884319c4ce9b539716ed17951c4abcd3d4 (patch)
tree	2e4d90db21fa8aff4ca74c75057a5695eb7a92bc
parent	HPX live ebuild now reflects changes in trunk (diff)
parent	fixed dependency issue (diff)
download	sci-a2a4f4884319c4ce9b539716ed17951c4abcd3d4.tar.gz sci-a2a4f4884319c4ce9b539716ed17951c4abcd3d4.tar.bz2 sci-a2a4f4884319c4ce9b539716ed17951c4abcd3d4.zip