14 files changed, 371 insertions, 157 deletions

diff --git a/sci-mathematics/rstudio/ChangeLog b/sci-mathematics/rstudio/ChangeLog
index e1d519c340dc..9a7872ac23a3 100644
--- a/sci-mathematics/rstudio/ChangeLog
+++ b/sci-mathematics/rstudio/ChangeLog
@@ -1,6 +1,28 @@
 # ChangeLog for sci-mathematics/rstudio
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/rstudio/ChangeLog,v 1.17 2014/11/29 11:31:36 gienah Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/rstudio/ChangeLog,v 1.18 2014/12/06 12:32:01 gienah Exp $
+
+*rstudio-0.98.1091 (06 Dec 2014)
+
+  06 Dec 2014; Mark Wright <gienah@gentoo.org> +files/rsession.conf,
+  +files/rstudio-0.98.1091-pandoc.patch, +files/rstudio-server.conf,
+  +files/rstudio-server.initd, +rstudio-0.98.1091.ebuild,
+  -files/rstudio-rserver.initd, -rstudio-0.97.318.ebuild,
+  rstudio-0.97.336.ebuild, rstudio-0.97.551.ebuild, rstudio-0.98.1028.ebuild,
+  rstudio-0.98.490-r1.ebuild, rstudio-0.98.490.ebuild, rstudio-0.98.932.ebuild,
+  rstudio-0.98.953.ebuild:
+  Bump rstudio to 0.98.1091. Fix Bug 519290 sci-mathematics/rstudio-0.98.490 -
+  rstudio-server start: /usr/bin/rstudio-server: 1: eval: /etc/init.d/rstudio-
+  server: not found, thanks to Franz Fellner for reporting, Adam Tygart and
+  Franz Fellner for suggesting the fix, Silvio for testing. Fix Bug 522196 -
+  sci-mathematics/rstudio lack of server part and two more conf files, thanks to
+  Silvio for reporting and providing the conf files. Fix Bug 523296 - sci-
+  mathematics/rstudio-0.98-1028 with dev-libs/boost-1.56.0 -
+  .../work/rstudio-0.98.1028/src/cpp/core/Assert.cpp:40:10: error:
+  boost::core::log has not been declared. paxmark m rstudio for Gentoo Hardened.
+  Add missing dependencies app-text/pandoc and dev-haskell/pandoc-citeproc to
+  rstudio-0.98.1028.ebuild. Remove obsolete rstudio-0.97.318.ebuild, as the this
+  failed to build in my tests.
 
   29 Nov 2014; Mark Wright <gienah@gentoo.org> metadata.xml:
   Set the maintainer.
diff --git a/sci-mathematics/rstudio/files/rsession.conf b/sci-mathematics/rstudio/files/rsession.conf
new file mode 100644
index 000000000000..645bfa46b208
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rsession.conf
@@ -0,0 +1,26 @@
+######rsession.conf############
+# Session Timeouts
+# By default if a user hasn't issued a command for 2 hours 
+# RStudio will suspend that user's R session to disk so 
+# they are no longer consuming server resources (the next 
+# time the user attempts to access the server their session 
+# will be restored). You can change the timeout (including 
+# disabling it by specifying a value of 0) using the 
+# session-timeout-minutes setting
+#session-timeout-minutes=30
+
+# By default RStudio sets the R_LIBS_USER environment 
+# variable to ~/R/library. This ensures that packages 
+# installed by end users do not have R version numbers 
+# encoded in the path (which is the default behavior). 
+# This in turn enables administrators to upgrade the version 
+# of R on the server without reseting users installed packages
+# (which would occur if the installed packages were in an 
+# R-version derived directory).
+# If you wish to override this behavior you can do so using 
+# the r-libs-user settings
+#r-libs-user=~/R/packages
+
+# You can set the default CRAN repository for the server 
+# using the r-cran-repos setting
+#r-cran-repos=http://cran.case.edu/
diff --git a/sci-mathematics/rstudio/files/rstudio-0.98.1091-pandoc.patch b/sci-mathematics/rstudio/files/rstudio-0.98.1091-pandoc.patch
new file mode 100644
index 000000000000..3df8d1a986a3
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-0.98.1091-pandoc.patch
@@ -0,0 +1,26 @@
+--- rstudio-0.98.1091-orig/src/cpp/session/CMakeLists.txt	2014-11-06 23:15:47.000000000 +1100
++++ rstudio-0.98.1091/src/cpp/session/CMakeLists.txt	2014-11-26 17:12:42.699712510 +1100
+@@ -25,9 +25,6 @@
+ if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-23")
+   message(FATAL_ERROR "Mathjax 2.3 not found (re-run install-dependencies script to install)")
+ endif()
+-if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc")
+-  message(FATAL_ERROR "pandoc not found (re-run install-dependencies script to install)")
+-endif()
+ if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/rmarkdown")
+   message(FATAL_ERROR "rmarkdown package not found (re-run install-dependencies script to install)")
+ endif()
+@@ -343,13 +340,6 @@
+    install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-23"
+            DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources")
+ 
+-   # install pandoc
+-   set(PANDOC_BIN "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc/1.12.4.2")
+-   file(GLOB PANDOC_FILES "${PANDOC_BIN}/pandoc*")
+-   install(FILES ${PANDOC_FILES}
+-           PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
+-           DESTINATION  ${RSTUDIO_INSTALL_BIN}/pandoc)
+-
+    # install rmarkdown package
+    file(GLOB RMARKDOWN_PACKAGE "${RSTUDIO_DEPENDENCIES_DIR}/common/rmarkdown*.tar.gz")
+    install(FILES ${RMARKDOWN_PACKAGE}
diff --git a/sci-mathematics/rstudio/files/rstudio-server.conf b/sci-mathematics/rstudio/files/rstudio-server.conf
new file mode 100644
index 000000000000..ebf1a1649169
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-server.conf
@@ -0,0 +1,35 @@
+###########rstudio-server.conf#############
+
+# www-port entry corresponding to the port you want RStudio to listen on
+#www-port=80
+
+
+# By default RStudio binds to address 0.0.0.0 (accepting connections 
+# from any remote IP). You can modify this behavior using the 
+# www-address entry.
+#www-address=127.0.0.1
+
+
+# You can add elements to the default LD_LIBRARY_PATH for R 
+# sessions (as determined by the R ldpaths script) by adding 
+# an rsession-ld-library-path entry to the server config file. 
+# This might be useful for ensuring that packages can 
+# locate external library dependencies that aren't installed 
+# in the system standard library paths
+#rsession-ld-library-path=/opt/local/lib:/opt/local/someapp/lib
+
+
+#By default RStudio Server runs against the version of R which 
+# is found on the system PATH (using which R). You can override 
+# which version of R is used via the rsession-which-r setting 
+# in the server config file. For example, if you have two 
+# versions of R installed on the server and want to make sure 
+# the one at /usr/local/bin/R is used by RStudio then you would use:
+rsession-which-r=/usr/bin/R
+
+########ADDITIONALAL#########
+
+# To limit the users who can login to RStudio to the members 
+# of a specific group, you use the auth-required-user-group 
+# setting
+auth-required-user-group=rstudio_users
diff --git a/sci-mathematics/rstudio/files/rstudio-rserver.initd b/sci-mathematics/rstudio/files/rstudio-server.initd
index 37a684cdd76f..e6ca6b942bb9 100644
--- a/sci-mathematics/rstudio/files/rstudio-rserver.initd
+++ b/sci-mathematics/rstudio/files/rstudio-server.initd
@@ -1,5 +1,5 @@
 #!/sbin/runscript
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 start() {
diff --git a/sci-mathematics/rstudio/rstudio-0.97.318.ebuild b/sci-mathematics/rstudio/rstudio-0.97.318.ebuild
deleted file mode 100644
index 6030fb1a8dc0..000000000000
--- a/sci-mathematics/rstudio/rstudio-0.97.318.ebuild
+++ /dev/null
@@ -1,134 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/rstudio/rstudio-0.97.318.ebuild,v 1.2 2013/03/02 23:25:58 hwoarang Exp $
-
-EAPI=5
-
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-# * fix the about/help/menu and get rid of license
-
-GWTVER=2.5.0.rc1
-GINVER=1.5
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="http://www.rstudio.org"
-SRC_URI="https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GINVER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWTVER}.zip
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated server"
-
-QTVER=4.8
-QTSLOT=4
-RDEPEND=">=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.50
-	dev-libs/mathjax
-	dev-libs/openssl
-	>=virtual/jre-1.5
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QTVER}:${QTSLOT}
-		>=dev-qt/qtdbus-${QTVER}:${QTSLOT}
-		>=dev-qt/qtgui-${QTVER}:${QTSLOT}
-		>=dev-qt/qtwebkit-${QTVER}:${QTSLOT}
-		>=dev-qt/qtxmlpatterns-${QTVER}:${QTSLOT}
-		server? ( virtual/pam )
-	)
-	dedicated? ( virtual/pam )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.5
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWTVER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} dependencies/common/dictionaries || die
-	mv ../gwt-${GWTVER} src/gwt/lib/gwt/${GWTVER} || die
-	unzip -qd src/gwt/lib/gin/${GINVER} "${DISTDIR}"/gin-${GINVER}.zip || die
-	unzip -qd dependencies/common/dictionaries "${DISTDIR}"/core-dictionaries.zip || die
-}
-
-src_prepare() {
-	java-pkg-2_src_prepare
-
-	find . -name .gitignore -delete || die
-
-	epatch "${FILESDIR}"/${P}-prefs.patch \
-		"${FILESDIR}"/${P}-paths.patch \
-		"${FILESDIR}"/${P}-linker_flags.patch
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		$(cmake-utils_use !dedicated RSTUDIO_INSTALL_FREEDESKTOP)
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "All" "Desktop")")
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile
-}
-
-src_install() {
-	cmake-utils_src_install
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-rserver.initd rstudio-rserver
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-}
diff --git a/sci-mathematics/rstudio/rstudio-0.97.336.ebuild b/sci-mathematics/rstudio/rstudio-0.97.336.ebuild
index 1e9f90a5153a..b49cb580cf9b 100644
--- a/sci-mathematics/rstudio/rstudio-0.97.336.ebuild
+++ b/sci-mathematics/rstudio/rstudio-0.97.336.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/rstudio/rstudio-0.97.336.ebuild,v 1.2 2013/07/15 15:21:58 hasufell Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/rstudio/rstudio-0.97.336.ebuild,v 1.3 2014/12/06 12:32:01 gienah Exp $
 
 EAPI=5
 
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2
+inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils
 
 # TODO
 # * package gin and gwt
@@ -84,6 +84,11 @@ src_prepare() {
 	sed -i \
 		-e "s:/usr:${EPREFIX}/usr:g" \
 		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
+
+	# specify that namespace core the is in the global namespace and not
+	# relative to some other namespace (like its ::core not ::boost::core)
+	find . \( -name *.cpp -or -name *.hpp \) -exec sed \
+		-e 's@<core::@< ::core::@g' -e 's@\([^:]\)core::@\1::core::@g' -i {} \;
 }
 
 src_configure() {
@@ -106,9 +111,10 @@ src_compile() {
 
 src_install() {
 	cmake-utils_src_install
+	pax-mark m "${ED}usr/bin/rstudio"
 	if use dedicated || use server; then
 		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-rserver.initd rstudio-rserver
+		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
 	fi
 }
 
diff --git a/sci-mathematics/rstudio/rstudio-0.97.551.ebuild b/sci-mathematics/rstudio/rstudio-0.97.551.ebuild
index 6de5d19c5753..79d871e7889d 100644
--- a/sci-mathematics/rstudio/rstudio-0.97.551.ebuild
+++ b/sci-mathematics/rstudio/rstudio-0.97.551.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/rstudio/rstudio-0.97.551.ebuild,v 1.1 2013/07/16 11:39:28 hasufell Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/rstudio/rstudio-0.97.551.ebuild,v 1.2 2014/12/06 12:32:01 gienah Exp $
 
 EAPI=5
 
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2
+inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils
 
 # TODO
 # * package gin and gwt
@@ -84,6 +84,11 @@ src_prepare() {
 	sed -i \
 		-e "s:/usr:${EPREFIX}/usr:g" \
 		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
+
+	# specify that namespace core the is in the global namespace and not
+	# relative to some other namespace (like its ::core not ::boost::core)
+	find . \( -name *.cpp -or -name *.hpp \) -exec sed \
+		-e 's@<core::@< ::core::@g' -e 's@\([^:]\)core::@\1::core::@g' -i {} \;
 }
 
 src_configure() {
@@ -106,9 +111,10 @@ src_compile() {
 
 src_install() {
 	cmake-utils_src_install
+	pax-mark m "${ED}usr/bin/rstudio"
 	if use dedicated || use server; then
 		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-rserver.initd rstudio-rserver
+		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
 	fi
 }
 
diff --git a/sci-mathematics/rstudio/rstudio-0.98.1028.ebuild b/sci-mathematics/rstudio/rstudio-0.98.1028.ebuild
index 086d714b60b5..f21ff18c4864 100644
--- a/sci-mathematics/rstudio/rstudio-0.98.1028.ebuild
+++ b/sci-mathematics/rstudio/rstudio-0.98.1028.ebuild
@@ -1,10 +1,10 @@
 # Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/rstudio/rstudio-0.98.1028.ebuild,v 1.1 2014/08/27 15:51:02 hasufell Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/rstudio/rstudio-0.98.1028.ebuild,v 1.2 2014/12/06 12:32:01 gienah Exp $
 
 EAPI=5
 
-inherit eutils cmake-utils gnome2-utils versionator fdo-mime java-pkg-2
+inherit eutils cmake-utils gnome2-utils versionator fdo-mime java-pkg-2 pax-utils
 
 # TODO
 # * package gin and gwt
@@ -41,6 +41,8 @@ IUSE=""
 QTVER=4.8
 QTSLOT=4
 RDEPEND="
+	app-text/pandoc
+	dev-haskell/pandoc-citeproc
 	>=dev-lang/R-2.11.1
 	>=dev-libs/boost-1.50
 	dev-libs/mathjax
@@ -112,6 +114,11 @@ src_prepare() {
 	sed -i \
 		-e "s:/usr:${EPREFIX}/usr:g" \
 		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
+
+	# specify that namespace core the is in the global namespace and not
+	# relative to some other namespace (like its ::core not ::boost::core)
+	find . \( -name *.cpp -or -name *.hpp \) -exec sed \
+		-e 's@<core::@< ::core::@g' -e 's@\([^:]\)core::@\1::core::@g' -i {} \;
 }
 
 src_configure() {
@@ -134,6 +141,7 @@ src_compile() {
 
 src_install() {
 	cmake-utils_src_install
+	pax-mark m "${ED}usr/bin/rstudio"
 }
 
 pkg_preinst() {
diff --git a/sci-mathematics/rstudio/rstudio-0.98.1091.ebuild b/sci-mathematics/rstudio/rstudio-0.98.1091.ebuild
new file mode 100644
index 000000000000..a59098b1adbc
--- /dev/null
+++ b/sci-mathematics/rstudio/rstudio-0.98.1091.ebuild
@@ -0,0 +1,195 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/rstudio/rstudio-0.98.1091.ebuild,v 1.1 2014/12/06 12:32:01 gienah Exp $
+
+EAPI=5
+
+inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils
+
+# TODO
+# * package gin and gwt
+# * use dict from tree, linguas
+# * do src_test (use junit from tree?)
+
+# update from scripts in dependencies/common
+GWTVER=2.6.0
+GINVER=1.5
+SELENIUMVER=2.37.0
+CHROMEDRIVER_VER=2.7
+PANDOC_VER=1.12.4.2
+PACKRAT_VER=0.98.1000
+RMARKDOWN_VER=0.98.1000
+SHINYAPPS_VER=0.98.1000
+
+DESCRIPTION="IDE for the R language"
+HOMEPAGE="http://www.rstudio.org
+	https://github.com/rstudio/rstudio/"
+SRC_URI="https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
+	https://s3.amazonaws.com/rstudio-buildtools/gin-${GINVER}.zip
+	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWTVER}.zip
+	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUMVER}.zip
+	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUMVER}.jar
+	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
+	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
+	http://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
+	http://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
+	http://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz"
+
+LICENSE="AGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="dedicated server"
+
+QTVER=4.8
+QTSLOT=4
+RDEPEND="
+	app-text/pandoc
+	dev-haskell/pandoc-citeproc
+	>=dev-lang/R-2.11.1
+	>=dev-libs/boost-1.50:=
+	>=dev-libs/mathjax-2.3
+	dev-libs/openssl:0
+	sys-apps/util-linux
+	sys-libs/zlib
+	>=virtual/jre-1.5
+	x11-libs/pango
+	!dedicated? (
+		>=dev-qt/qtcore-${QTVER}:${QTSLOT}
+		>=dev-qt/qtdbus-${QTVER}:${QTSLOT}
+		>=dev-qt/qtgui-${QTVER}:${QTSLOT}
+		>=dev-qt/qtwebkit-${QTVER}:${QTSLOT}
+		>=dev-qt/qtxmlpatterns-${QTVER}:${QTSLOT}
+		server? ( virtual/pam )
+	)
+	dedicated? ( virtual/pam )"
+DEPEND="${RDEPEND}
+	app-arch/unzip
+	dev-java/ant-core
+	>=virtual/jdk-1.5
+	virtual/pkgconfig"
+#	test? ( dev-java/junit:4 )
+
+src_unpack() {
+	unpack ${P}.tar.gz gwt-${GWTVER}.zip
+	cd "${S}" || die
+	mkdir -p src/gwt/lib/{gin,gwt} \
+		dependencies/common/dictionaries \
+		src/gwt/lib/selenium/${SELENIUMVER} \
+		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
+	mv ../gwt-${GWTVER} src/gwt/lib/gwt/${GWTVER} || die
+	unzip -qd src/gwt/lib/gin/${GINVER} \
+		"${DISTDIR}"/gin-${GINVER}.zip || die
+	unzip -qd dependencies/common/dictionaries \
+		"${DISTDIR}"/core-dictionaries.zip || die
+	unzip -qd src/gwt/lib/selenium/${SELENIUMVER} \
+		"${DISTDIR}"/selenium-java-${SELENIUMVER}.zip || die
+	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUMVER}.jar \
+		src/gwt/lib/selenium/${SELENIUMVER}/ || die
+	cp "${DISTDIR}"/chromedriver-linux \
+		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
+	cd dependencies/common || die
+	unpack packrat-${PACKRAT_VER}.tar.gz
+	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
+	unpack shinyapps-${RMARKDOWN_VER}.tar.gz
+	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
+		. || die
+	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
+		. || die
+	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
+		. || die
+}
+
+src_prepare() {
+	java-pkg-2_src_prepare
+
+	find . -name .gitignore -delete || die
+
+	epatch "${FILESDIR}"/${PN}-0.98.490-prefs.patch \
+		"${FILESDIR}"/${PN}-0.98.932-paths.patch \
+		"${FILESDIR}"/${PN}-0.98.1091-pandoc.patch \
+		"${FILESDIR}"/${PN}-0.98.490-linker_flags.patch
+
+	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
+	# this sed hack for now. ~RMH
+	sed -i \
+		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
+		src/cpp/server/ServerOptions.cpp \
+		src/cpp/session/SessionOptions.cpp || die
+
+	# use mathjax from system
+	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-23 || die
+
+	# make sure icons and mime stuff are with prefix
+	sed -i \
+		-e "s:/usr:${EPREFIX}/usr:g" \
+		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
+
+	# specify that namespace core the is in the global namespace and not
+	# relative to some other namespace (like its ::core not ::boost::core)
+	find . \( -name *.cpp -or -name *.hpp \) -exec sed \
+		 -e 's@<core::@< ::core::@g' -e 's@\([^:]\)core::@\1::core::@g' -i {} \;
+
+	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
+	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}etc/conf.d/rstudio-server.conf@" \
+		-i src/cpp/server/ServerOptions.cpp \
+		|| die
+
+	# Set the rsession.conf file location for Gentoo prefix
+	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}etc/rstudio/rsession.conf@" \
+		-i src/cpp/session/SessionOptions.cpp \
+		|| die
+}
+
+src_configure() {
+	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
+	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
+	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
+
+	local mycmakeargs=(
+		-DDISTRO_SHARE=share/${PN}
+		$(cmake-utils_use !dedicated RSTUDIO_INSTALL_FREEDESKTOP)
+		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
+		)
+
+	cmake-utils_src_configure
+}
+
+src_compile() {
+	cmake-utils_src_compile
+}
+
+src_install() {
+	cmake-utils_src_install
+	pax-mark m "${ED}usr/bin/rstudio"
+	doconfd "${FILESDIR}"/rstudio-server.conf
+	dodir /etc/rstudio
+	insinto /etc/rstudio
+	doins "${FILESDIR}"/rsession.conf
+	dosym /etc/conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
+	if use dedicated || use server; then
+		dopamd src/cpp/server/extras/pam/rstudio
+		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
+	fi
+}
+
+pkg_preinst() {
+	use dedicated || gnome2_icon_savelist
+	java-pkg-2_pkg_preinst
+}
+
+pkg_postinst() {
+	use dedicated || { fdo-mime_desktop_database_update
+		fdo-mime_mime_database_update
+		gnome2_icon_cache_update ;}
+
+	if use dedicated || use server; then
+		enewgroup rstudio-server
+		enewuser rstudio-server -1 -1 -1 rstudio-server
+	fi
+}
+
+pkg_postrm() {
+	use dedicated || { fdo-mime_desktop_database_update
+		fdo-mime_mime_database_update
+		gnome2_icon_cache_update ;}
+}
diff --git a/sci-mathematics/rstudio/rstudio-0.98.490-r1.ebuild b/sci-mathematics/rstudio/rstudio-0.98.490-r1.ebuild
index 4de7ad2e3e68..f2624bad47e1 100644
--- a/sci-mathematics/rstudio/rstudio-0.98.490-r1.ebuild
+++ b/sci-mathematics/rstudio/rstudio-0.98.490-r1.ebuild
@@ -1,10 +1,10 @@
 # Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/rstudio/rstudio-0.98.490-r1.ebuild,v 1.2 2014/08/30 15:46:38 nimiux Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/rstudio/rstudio-0.98.490-r1.ebuild,v 1.3 2014/12/06 12:32:01 gienah Exp $
 
 EAPI=5
 
-inherit eutils cmake-utils gnome2-utils versionator fdo-mime java-pkg-2
+inherit eutils cmake-utils gnome2-utils versionator fdo-mime java-pkg-2 pax-utils
 
 # TODO
 # * package gin and gwt
@@ -79,6 +79,11 @@ src_prepare() {
 	sed -i \
 		-e "s:/usr:${EPREFIX}/usr:g" \
 		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
+
+	# specify that namespace core the is in the global namespace and not
+	# relative to some other namespace (like its ::core not ::boost::core)
+	find . \( -name *.cpp -or -name *.hpp \) -exec sed \
+		-e 's@<core::@< ::core::@g' -e 's@\([^:]\)core::@\1::core::@g' -i {} \;
 }
 
 src_configure() {
@@ -101,6 +106,7 @@ src_compile() {
 
 src_install() {
 	cmake-utils_src_install
+	pax-mark m "${ED}usr/bin/rstudio"
 }
 
 pkg_preinst() {
diff --git a/sci-mathematics/rstudio/rstudio-0.98.490.ebuild b/sci-mathematics/rstudio/rstudio-0.98.490.ebuild
index 8247d4c7d32f..43ef5c39a7e9 100644
--- a/sci-mathematics/rstudio/rstudio-0.98.490.ebuild
+++ b/sci-mathematics/rstudio/rstudio-0.98.490.ebuild
@@ -1,10 +1,10 @@
 # Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/rstudio/rstudio-0.98.490.ebuild,v 1.3 2014/07/27 11:33:09 phajdan.jr Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/rstudio/rstudio-0.98.490.ebuild,v 1.4 2014/12/06 12:32:01 gienah Exp $
 
 EAPI=5
 
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2
+inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils
 
 # TODO
 # * package gin and gwt
@@ -83,6 +83,11 @@ src_prepare() {
 	sed -i \
 		-e "s:/usr:${EPREFIX}/usr:g" \
 		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
+
+	# specify that namespace core the is in the global namespace and not
+	# relative to some other namespace (like its ::core not ::boost::core)
+	find . \( -name *.cpp -or -name *.hpp \) -exec sed \
+		-e 's@<core::@< ::core::@g' -e 's@\([^:]\)core::@\1::core::@g' -i {} \;
 }
 
 src_configure() {
@@ -105,9 +110,10 @@ src_compile() {
 
 src_install() {
 	cmake-utils_src_install
+	pax-mark m "${ED}usr/bin/rstudio"
 	if use dedicated || use server; then
 		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-rserver.initd rstudio-rserver
+		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
 	fi
 }
 
diff --git a/sci-mathematics/rstudio/rstudio-0.98.932.ebuild b/sci-mathematics/rstudio/rstudio-0.98.932.ebuild
index 54c8065a81a0..5ab66202c31f 100644
--- a/sci-mathematics/rstudio/rstudio-0.98.932.ebuild
+++ b/sci-mathematics/rstudio/rstudio-0.98.932.ebuild
@@ -1,10 +1,10 @@
 # Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/rstudio/rstudio-0.98.932.ebuild,v 1.1 2014/07/04 13:53:22 hasufell Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/rstudio/rstudio-0.98.932.ebuild,v 1.2 2014/12/06 12:32:01 gienah Exp $
 
 EAPI=5
 
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2
+inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils
 
 # TODO
 # * package gin and gwt
@@ -115,6 +115,11 @@ src_prepare() {
 	sed -i \
 		-e "s:/usr:${EPREFIX}/usr:g" \
 		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
+
+	# specify that namespace core the is in the global namespace and not
+	# relative to some other namespace (like its ::core not ::boost::core)
+	find . \( -name *.cpp -or -name *.hpp \) -exec sed \
+		-e 's@<core::@< ::core::@g' -e 's@\([^:]\)core::@\1::core::@g' -i {} \;
 }
 
 src_configure() {
@@ -137,9 +142,10 @@ src_compile() {
 
 src_install() {
 	cmake-utils_src_install
+	pax-mark m "${ED}usr/bin/rstudio"
 	if use dedicated || use server; then
 		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-rserver.initd rstudio-rserver
+		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
 	fi
 }
 
diff --git a/sci-mathematics/rstudio/rstudio-0.98.953.ebuild b/sci-mathematics/rstudio/rstudio-0.98.953.ebuild
index 9a3b3d5a7d51..8e87354cb264 100644
--- a/sci-mathematics/rstudio/rstudio-0.98.953.ebuild
+++ b/sci-mathematics/rstudio/rstudio-0.98.953.ebuild
@@ -1,10 +1,10 @@
 # Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/rstudio/rstudio-0.98.953.ebuild,v 1.1 2014/07/04 14:08:16 hasufell Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/rstudio/rstudio-0.98.953.ebuild,v 1.2 2014/12/06 12:32:01 gienah Exp $
 
 EAPI=5
 
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2
+inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils
 
 # TODO
 # * package gin and gwt
@@ -116,6 +116,11 @@ src_prepare() {
 	sed -i \
 		-e "s:/usr:${EPREFIX}/usr:g" \
 		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
+
+	# specify that namespace core the is in the global namespace and not
+	# relative to some other namespace (like its ::core not ::boost::core)
+	find . \( -name *.cpp -or -name *.hpp \) -exec sed \
+		-e 's@<core::@< ::core::@g' -e 's@\([^:]\)core::@\1::core::@g' -i {} \;
 }
 
 src_configure() {
@@ -138,9 +143,10 @@ src_compile() {
 
 src_install() {
 	cmake-utils_src_install
+	pax-mark m "${ED}usr/bin/rstudio"
 	if use dedicated || use server; then
 		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-rserver.initd rstudio-rserver
+		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
 	fi
 }